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Merge branch 'master' into gnome-team

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Change-Id: I62da840b7600f2d3d8541e666d09e2f2a1b7d8c4
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Liliana Marie Prikler 2023-11-19 10:02:15 +01:00
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9
Makefile.am
View file

@ -13,11 +13,12 @@
# Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
# Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
# Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
# Copyright © 2019 Efraim Flashner <efraim@flashner.co.il>
# Copyright © 2019, 2023 Efraim Flashner <efraim@flashner.co.il>
# Copyright © 2020, 2021, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
# Copyright © 2021 Chris Marusich <cmmarusich@gmail.com>
# Copyright © 2021 Andrew Tropin <andrew@trop.in>
# Copyright © 2023 Clément Lassieur <clement@lassieur.org>
# Copyright © 2023 Wilko Meyer <w@wmeyer.eu>
#
# This file is part of GNU Guix.
#
@ -185,6 +186,7 @@ MODULES = \
guix/build-system/texlive.scm \
guix/build-system/tree-sitter.scm \
guix/build-system/trivial.scm \
guix/build-system/vim.scm \
guix/build-system/zig.scm \
guix/ftp-client.scm \
guix/http-client.scm \
@ -243,6 +245,7 @@ MODULES = \
guix/build/scons-build-system.scm \
guix/build/texlive-build-system.scm \
guix/build/tree-sitter-build-system.scm \
guix/build/vim-build-system.scm \
guix/build/waf-build-system.scm \
guix/build/haskell-build-system.scm \
guix/build/julia-build-system.scm \
@ -413,6 +416,10 @@ AUX_FILES = \
gnu/packages/aux-files/chromium/master-preferences.json \
gnu/packages/aux-files/emacs/guix-emacs.el \
gnu/packages/aux-files/guix.vim \
gnu/packages/aux-files/linux-libre/6.6-arm.conf \
gnu/packages/aux-files/linux-libre/6.6-arm64.conf \
gnu/packages/aux-files/linux-libre/6.6-i686.conf \
gnu/packages/aux-files/linux-libre/6.6-x86_64.conf \
gnu/packages/aux-files/linux-libre/6.5-arm.conf \
gnu/packages/aux-files/linux-libre/6.5-arm64.conf \
gnu/packages/aux-files/linux-libre/6.5-i686.conf \

141
doc/contributing.texi
View file

@ -29,6 +29,7 @@ choice.
* Submitting Patches:: Share your work.
* Tracking Bugs and Changes:: Keeping it all organized.
* Commit Access:: Pushing to the official repository.
* Reviewing the Work of Others:: Some guidelines for sharing reviews.
* Updating the Guix Package:: Updating the Guix package definition.
* Writing Documentation:: Improving documentation in GNU Guix.
* Translating Guix:: Make Guix speak your native language.
@ -190,7 +191,7 @@ After updating the repository, @command{make} might fail with an error
similar to the following example:
@example
error: failed to load 'gnu/packages/dunst.scm':
error: failed to load 'gnu/packages/linux.scm':
ice-9/eval.scm:293:34: In procedure abi-check: #<record-type <origin>>: record ABI mismatch; recompilation needed
@end example
@ -385,6 +386,7 @@ copyright-update}. If you want to do it automatically after each buffer
save then add @code{(add-hook 'after-save-hook 'copyright-update)} in
Emacs.
@node Viewing Bugs within Emacs
@subsection Viewing Bugs within Emacs
Emacs has a nice minor mode called @code{bug-reference}, which, when
@ -452,6 +454,13 @@ configuration file:
(group (zero-or-one "cgi/bugreport.cgi?bug="))
(group-n 3 (one-or-more digit))
line-end))
;; Reduce the number of prompts with 'M-x debbugs-gnu'.
(setq debbugs-gnu-default-packages '("guix" "guix-patches"))
;; Show feature requests.
(setq debbugs-gnu-default-severities
'("serious" "important" "normal" "minor" "wishlist"))
@end lisp
For more information, refer to @ref{Bug Reference,,, emacs, The GNU
@ -1279,11 +1288,16 @@ implement low-level concepts, such as the @code{memoize} procedure.
@node Modules
@subsection Modules
@cindex build-side modules
@cindex host-side modules
Guile modules that are meant to be used on the builder side must live in
the @code{(guix build @dots{})} name space. They must not refer to
other Guix or GNU modules. However, it is OK for a ``host-side'' module
to use a build-side module.
to use a build-side module. As an example, the @code{(guix
search-paths)} module should not be imported and used by a package since
it isn't meant to be used as a ``build-side'' module. It would also
couple the module with the package's dependency graph, which is
undesirable.
Modules that deal with the broader GNU system should be in the
@code{(gnu @dots{})} name space rather than @code{(guix @dots{})}.
@ -1862,7 +1876,7 @@ browse issues:
interface@footnote{The web interface at
@url{https://issues.guix.gnu.org} is powered by Mumi, a nice piece of
software written in Guile, and you can help! See
@url{https://git.elephly.net/gitweb.cgi?p=software/mumi.git}.} to browse
@url{https://git.savannah.gnu.org/cgit/guix/mumi.git}.} to browse
bug reports and patches, and to participate in discussions;
@item
@url{https://bugs.gnu.org/guix} lists bug reports;
@ -1969,6 +1983,15 @@ For example, to list all open issues on @code{guix-patches}, hit:
@kbd{C-u} @kbd{M-x} debbugs-gnu @kbd{RET} @kbd{RET} guix-patches @kbd{RET} n y
@end example
For a more convenient (shorter) way to access both the bugs and patches
submissions, you may want to configure the
@code{debbugs-gnu-default-packages} and
@code{debbugs-gnu-default-severities} Emacs variables (@pxref{Viewing
Bugs within Emacs}).
To search for bugs, @samp{@kbd{M-x} debbugs-gnu-guix-search} can be
used.
@xref{Top,,, debbugs-ug, Debbugs User Guide}, for more information on
this nifty tool!
@ -1981,7 +2004,12 @@ Debbugs provides a feature called @dfn{usertags} that allows any user to
tag any bug with an arbitrary label. Bugs can be searched by usertag,
so this is a handy way to organize bugs@footnote{The list of usertags is
public information, and anyone can modify any user's list of usertags,
so keep that in mind if you choose to use this feature.}.
so keep that in mind if you choose to use this feature.}. If you use
Emacs Debbugs, the entry-point to consult existing usertags is the
@samp{C-u M-x debbugs-gnu-usertags} procedure. To set a usertag, press
@samp{C} while consulting a bug within the *Guix-Patches* buffer opened
with @samp{C-u M-x debbugs-gnu-bugs} buffer, then select @code{usertag}
and follow the instructions.
For example, to view all the bug reports (or patches, in the case of
@code{guix-patches}) tagged with the usertag @code{powerpc64le-linux}
@ -1994,9 +2022,9 @@ documentation for Debbugs or the documentation for whatever tool you use
to interact with Debbugs.
In Guix, we are experimenting with usertags to keep track of
architecture-specific issues. To facilitate collaboration, all our
usertags are associated with the single user @code{guix}. The following
usertags currently exist for that user:
architecture-specific issues, as well as reviewed ones. To facilitate
collaboration, all our usertags are associated with the single user
@code{guix}. The following usertags currently exist for that user:
@table @code
@ -2014,6 +2042,9 @@ For issues related to reproducibility. For example, it would be
appropriate to assign this usertag to a bug report for a package that
fails to build reproducibly.
@item reviewed-looks-good
You have reviewed the series and it looks good to you (LGTM).
@end table
If you're a committer and you want to add a usertag, just start using it
@ -2283,6 +2314,100 @@ only push their own awesome changes, but also offer some of their time
you're welcome to use your expertise and commit rights to help other
contributors, too!
@node Reviewing the Work of Others
@section Reviewing the Work of Others
Perhaps the biggest action you can do to help GNU Guix grow as a project
is to review the work contributed by others. You do not need to be a
committer to do so; applying, reading the source, building, linting and
running other people's series and sharing your comments about your
experience will give some confidence to committers. Basically, you gmust
ensure the check list found in the @ref{Submitting Patches} section has
been correctly followed. A reviewed patch series should give the best
chances for the proposed change to be merged faster, so if a change you
would like to see merged hasn't yet been reviewed, this is the most
appropriate thing to do!
@cindex reviewing, guidelines
Review comments should be unambiguous; be as clear and explicit as you
can about what you think should be changed, ensuring the author can take
action on it. Please try to keep the following guidelines in mind
during review:
@enumerate
@item
@emph{Be clear and explicit about changes you are suggesting}, ensuring
the author can take action on it. In particular, it is a good idea to
explicitly ask for new revisions when you want it.
@item
@emph{Remain focused: do not change the scope of the work being
reviewed.} For example, if the contribution touches code that follows a
pattern deemed unwieldy, it would be unfair to ask the submitter to fix
all occurrences of that pattern in the code; to put it simply, if a
problem unrelated to the patch at hand was already there, do not ask the
submitter to fix it.
@item
@emph{Ensure progress.} As they respond to review, submitters may
submit new revisions of their changes; avoid requesting changes that you
did not request in the previous round of comments. Overall, the
submitter should get a clear sense of progress; the number of items open
for discussion should clearly decrease over time.
@item
@emph{Aim for finalization.} Reviewing code is time-consuming. Your
goal as a reviewer is to put the process on a clear path towards
integration, possibly with agreed-upon changes, or rejection, with a
clear and mutually-understood reasoning. Avoid leaving the review
process in a lingering state with no clear way out.
@item
@emph{Review is a discussion.} The submitter's and reviewer's views on
how to achieve a particular change may not always be aligned. To lead
the discussion, remain focused, ensure progress and aim for
finalization, spending time proportional to the stakes@footnote{The
tendency to discuss minute details at length is often referred to as
``bikeshedding'', where much time is spent discussing each one's
preference for the color of the shed at the expense of progress made on
the project to keep bikes dry.}. As a reviewer, try hard to explain the
rationale for suggestions you make, and to understand and take into
account the submitter's motivation for doing things in a certain way.
@end enumerate
@cindex LGTM, Looks Good To Me
@cindex review tags
@cindex Reviewed-by, git trailer
When you deem the proposed change adequate and ready for inclusion
within Guix, the following well understood/codified
@samp{Reviewed-by:@tie{}Your@tie{}Name<your-email@@example.com>}
@footnote{The @samp{Reviewed-by} Git trailer is used by other projects
such as Linux, and is understood by third-party tools such as the
@samp{b4 am} sub-command, which is able to retrieve the complete
submission email thread from a public-inbox instance and add the Git
trailers found in replies to the commit patches.} line should be used to
sign off as a reviewer, meaning you have reviewed the change and that it
looks good to you:
@itemize
@item
If the @emph{whole} series (containing multiple commits) looks good to
you, reply with @samp{Reviewed-by:@tie{}Your@tie{}Name<your-email@@example.com>}
to the cover page if it has one, or to the last patch of the series
otherwise, adding another @samp{(for the whole series)} comment on the
line below to explicit this fact.
@item
If you instead want to mark a @emph{single commit} as reviewed (but not
the whole series), simply reply with
@samp{Reviewed-by:@tie{}Your@tie{}Name<your-email@@example.com>} to that
commit message.
@end itemize
If you are not a committer, you can help others find a @emph{series} you
have reviewed more easily by adding a @code{reviewed-looks-good} usertag
for the @code{guix} user (@pxref{Debbugs Usertags}).
@node Updating the Guix Package
@section Updating the Guix Package

76
doc/guix.texi
View file

@ -8375,6 +8375,13 @@ hash @var{hash} of type @var{hash-algo} (a symbol). Use @var{name} as
the file name, or a generic name if @code{#f}.
@end deffn
@deffn {Procedure} git-fetch/lfs ref hash-algo hash
This is a variant of the @code{git-fetch} procedure that supports the
Git @acronym{LFS, Large File Storage} extension. This may be useful to
pull some binary test data to run the test suite of a package, for
example.
@end deffn
@deftp {Data Type} git-reference
This data type represents a Git reference for @code{git-fetch} to
retrieve.
@ -9441,6 +9448,41 @@ e.g., install @file{foo/sub/file} to @file{share/my-app/sub/file}.
@end itemize
@end defvar
@defvar vim-build-system
This variable is exported by @code{(guix build-system vim)}. It is an
extension of the @code{copy-build-system}, installing Vim and Neovim plugins
into locations where these two text editors know to find their plugins, using
their packpaths.
Packages which are prefixed with @code{vim-} will be installed in Vim's
packpath, while those prefixed with @code{neovim-} will be installed in
Neovim's packpath. If there is a @code{doc} directory with the plugin then
helptags will be generated automatically.
There are a couple of keywords added with the @code{vim-build-system}:
@itemize
@item With @code{plugin-name} it is possible to set the name of the plugin.
While by default this is set to the name and version of the package, it is
often more helpful to set this to name which the upstream author calls their
plugin. This is the name used for @command{:packadd} from inside Vim.
@item With @code{install-plan} it is possible to augment the built-in
install-plan of the @code{vim-build-system}. This is particularly helpful if
you have files which should be installed in other locations. For more
information about using the @code{install-plan}, see the
@code{copy-build-system} (@pxref{Build Systems, @code{copy-build-system}}).
@item With @code{#:vim} it is possible to add this package to Vim's packpath,
in addition to if it is added automatically because of the @code{vim-} prefix
in the package's name.
@item With @code{#:neovim} it is possible to add this package to Neovim's
packpath, in addition to if it is added automatically because of the
@code{neovim-} prefix in the package's name.
@item With @code{#:mode} it is possible to adjust the path which the plugin is
installed into. By default the plugin is installed into @code{start} and other
options are available, including @code{opt}. Adding a plugin into @code{opt}
will mean you will need to run, for example, @command{:packadd foo} to load the
@code{foo} plugin from inside of Vim.
@end itemize
@end defvar
@cindex Clojure (programming language)
@cindex simple Clojure build system
@ -44510,6 +44552,40 @@ The @code{(gnu home services desktop)} module provides services that you
may find useful on ``desktop'' systems running a graphical user
environment such as Xorg.
@cindex X Window, for Guix Home services
@cindex X11, in Guix Home
@defvar home-x11-service-type
This is the service type representing the X Window graphical display
server (also referred to as ``X11'').
X Window is necessarily started by a system service; on Guix System,
starting it is the responsibility of @code{gdm-service-type} and similar
services (@pxref{X Window}). At the level of Guix Home, as an
unprivileged user, we cannot start X Window; all we can do is check
whether it is running. This is what this service does.
As a user, you probably don't need to worry or explicitly instantiate
@code{home-x11-service-type}. Services that require an X Window
graphical display, such as @code{home-redshift-service-type} below,
instantiate it and depend on its corresponding @code{x11-display}
Shepherd service (@pxref{Shepherd Home Service}).
When X Window is running, the @code{x11-display} Shepherd service starts
and sets the @env{DISPLAY} environment variable of the
@command{shepherd} process, using its original value if it was already
set; otherwise, it fails to start.
The service can also be forced to use a given value for @env{DISPLAY},
like so:
@example
herd start x11-display :3
@end example
In the example above, @code{x11-display} is instructed to set
@env{DISPLAY} to @code{:3}.
@end defvar
@defvar home-redshift-service-type
This is the service type for @uref{https://github.com/jonls/redshift,
Redshift}, a program that adjusts the display color temperature

4
etc/completion/fish/guix.fish
View file

@ -298,7 +298,7 @@ complete -f -c guix -n '__fish_guix_using_command publish' -l repl -d '[=PORT] s
#### lint
set -l remotecommands checkers list-checkers
complete -f -c guix -n '__fish_guix_needs_command' -a lint -d 'Run a set of checkers on the specificied package.'
complete -f -c guix -n '__fish_guix_needs_command' -a lint -d 'Run a set of checkers on the specified package.'
complete -f -c guix -n '__fish_guix_using_command lint' -l list-checkers -d 'Display the list of available lint checkers.'
complete -f -c guix -n '__fish_guix_using_command lint' -l checkers -d 'Only run the specified checkers.'
complete -f -c guix -n '__fish_guix_using_command lint' -l description -d 'Validate package descriptions.'
@ -327,7 +327,7 @@ complete -f -c guix -n '__fish_guix_using_command import; and not __fish_seen_su
##### import cpan
complete -f -c guix -n '__fish_guix_using_command import; and not __fish_seen_subcommand_from $remotecommands' -a cpan -d 'Import and convert the CPAN package for PACKAGE-NAME.'
##### import hackage
complete -f -c guix -n '__fish_guix_using_command import; and not __fish_seen_subcommand_from $remotecommands' -a hackage -d 'Import and convert the Hackage package for PACKAGE-NAME. If PACKAGE-NAME includes a suffix constituted by a at-sign followed by a numerical version (as used with Guix packages), then a definition for the specified version of the package will be generated. If no version suffix is pecified, then the generated package definition will correspond to the latest available version.'
complete -f -c guix -n '__fish_guix_using_command import; and not __fish_seen_subcommand_from $remotecommands' -a hackage -d 'Import and convert the Hackage package for PACKAGE-NAME. If PACKAGE-NAME includes a suffix constituted by a at-sign followed by a numerical version (as used with Guix packages), then a definition for the specified version of the package will be generated. If no version suffix is specified, then the generated package definition will correspond to the latest available version.'
complete -f -c guix -n '__fish_guix_using_command import; and __fish_seen_subcommand_from hackage' -s e -d 'ALIST specify environment for Cabal evaluation.'
complete -f -c guix -n '__fish_guix_using_command import; and __fish_seen_subcommand_from hackage' -a "--cabal-environment=" -d 'ALIST specify environment for Cabal evaluation.'
complete -f -c guix -n '__fish_guix_using_command import; and __fish_seen_subcommand_from hackage' -s s -l stdin -d 'Read from standard input.'

7
etc/git/gitconfig
View file

@ -16,3 +16,10 @@
to = guix-patches@gnu.org
headerCmd = etc/teams.scm cc-members-header-cmd
thread = no
[b4]
attestation-check-dkim = off
attestation-policy = off
linkmask = https://yhetil.org/guix/%s
linktrailermask = https://yhetil.org/guix/%s
midmask = https://yhetil.org/guix/%s

13
etc/teams.scm
View file

@ -529,6 +529,15 @@ (define-team audio
#:description "Audio related packages."
#:scope (list "gnu/packages/audio.scm")))
(define-team zig
(team 'zig
#:name "Zig team"
#:description "Zig, Zig packages, and the zig-build system"
#:scope (list "gnu/packages/zig.scm"
"gnu/packages/zig-xyz.scm"
"guix/build/zig-build-system.scm"
"guix/build-system/zig.scm")))
(define-member (person "Eric Bavier"
"bavier@posteo.net")
@ -662,6 +671,10 @@ (define-member (person "Gabriel Wicki"
"gabriel@erlikon.ch")
audio)
(define-member (person "Ekaitz Zarraga"
"ekaitz@elenq.tech")
bootstrap zig)
(define (find-team name)
(or (hash-ref %teams (string->symbol name))

109
gnu/home/services/desktop.scm
View file

@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2022 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2022-2023 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2022 ( <paren@disroot.org>
;;; Copyright © 2023 conses <contact@conses.eu>
;;; Copyright © 2023 Janneke Nieuwenhuizen <janneke@gnu.org>
@ -30,7 +30,9 @@ (define-module (gnu home services desktop)
#:use-module (guix gexp)
#:use-module (srfi srfi-1)
#:use-module (ice-9 match)
#:export (home-redshift-configuration
#:export (home-x11-service-type
home-redshift-configuration
home-redshift-configuration?
home-redshift-service-type
@ -43,6 +45,79 @@ (define-module (gnu home services desktop)
home-xmodmap-configuration
home-xmodmap-service-type))
;;;
;;; Waiting for X11.
;;;
(define (x11-shepherd-service delay)
(list (shepherd-service
(provision '(x11-display))
(modules '((ice-9 ftw)
(ice-9 match)
(srfi srfi-1)))
(start
#~(lambda* (#:optional (display (getenv "DISPLAY")))
(define x11-directory
"/tmp/.X11-unix")
(define (find-display delay)
;; Wait for an accessible socket to show up in X11-DIRECTORY,
;; up to DELAY seconds.
(let loop ((attempts delay))
(define socket
(find (match-lambda
((or "." "..") #f)
(name
(let ((name (in-vicinity x11-directory
name)))
(access? name O_RDWR))))
(or (scandir x11-directory) '())))
(if (and socket (string-prefix? "X" socket))
(let ((display (string-append
":" (string-drop socket 1))))
(format #t "X11 display server found at ~s.~%"
display)
display)
(if (zero? attempts)
(begin
(format (current-error-port)
"X11 display server did not show up; \
giving up.\n")
#f)
(begin
(sleep 1)
(loop (- attempts 1)))))))
(let ((display (or display (find-display #$delay))))
(when display
;; Note: 'make-forkexec-constructor' calls take their
;; default #:environment-variables value before this service
;; is started and are thus unaffected by the 'setenv' call
;; below. Users of this service have to explicitly query
;; its value.
(setenv "DISPLAY" display))
display)))
(stop #~(lambda (_)
(unsetenv "DISPLAY")
#f))
(respawn? #f))))
(define home-x11-service-type
(service-type
(name 'home-x11-display)
(extensions (list (service-extension home-shepherd-service-type
x11-shepherd-service)))
(default-value 10)
(description
"Create a @code{x11-display} Shepherd service that waits for the X
Window (or ``X11'') graphical display server to be up and running, up to a
configurable delay, and sets the @code{DISPLAY} environment variable of
@command{shepherd} itself accordingly. If no accessible X11 server shows up
during that time, the @code{x11-display} service is marked as failing to
start.")))
;;;
;;; Redshift.
@ -169,11 +244,25 @@ (define config-file
(list (shepherd-service
(documentation "Redshift program.")
(provision '(redshift))
;; FIXME: This fails to start if Home is first activated from a
;; non-X11 session.
(start #~(make-forkexec-constructor
(list #$(file-append (home-redshift-configuration-redshift config) "/bin/redshift")
"-c" #$config-file)))
;; Depend on 'x11-display', which sets 'DISPLAY' if an X11 server is
;; available, and fails to start otherwise.
(requirement '(x11-display))
(modules '((srfi srfi-1)
(srfi srfi-26)))
(start #~(lambda _
(fork+exec-command
(list #$(file-append
(home-redshift-configuration-redshift config)
"/bin/redshift")
"-c" #$config-file)
;; Inherit the 'DISPLAY' variable set by 'x11-display'.
#:environment-variables
(cons (string-append "DISPLAY=" (getenv "DISPLAY"))
(remove (cut string-prefix? "DISPLAY=" <>)
(default-environment-variables))))))
(stop #~(make-kill-destructor))
(actions (list (shepherd-configuration-action config-file))))))
@ -181,7 +270,11 @@ (define home-redshift-service-type
(service-type
(name 'home-redshift)
(extensions (list (service-extension home-shepherd-service-type
redshift-shepherd-service)))
redshift-shepherd-service)
;; Ensure 'home-x11-service-type' is instantiated so we
;; can depend on the Shepherd 'x11-display' service.
(service-extension home-x11-service-type
(const #t))))
(default-value (home-redshift-configuration))
(description
"Run Redshift, a program that adjusts the color temperature of display

6
gnu/local.mk
View file

@ -235,7 +235,6 @@ GNU_SYSTEM_MODULES = \
%D%/packages/docbook.scm \
%D%/packages/docker.scm \
%D%/packages/documentation.scm \
%D%/packages/dunst.scm \
%D%/packages/dvtm.scm \
%D%/packages/easyrpg.scm \
%D%/packages/ebook.scm \
@ -901,7 +900,9 @@ dist_patch_DATA = \
%D%/packages/patches/aegisub-make43.patch \
%D%/packages/patches/agda-categories-remove-incompatible-flags.patch \
%D%/packages/patches/agda-categories-use-find.patch \
%D%/packages/patches/agda-categories-use-stdlib-1.7.3.patch \
%D%/packages/patches/agda-libdirs-env-variable.patch \
%D%/packages/patches/agda-use-sphinx-5.patch \
%D%/packages/patches/agda-stdlib-use-runhaskell.patch \
%D%/packages/patches/agg-am_c_prototype.patch \
%D%/packages/patches/agg-2.5-gcc8.patch \
@ -1020,6 +1021,8 @@ dist_patch_DATA = \
%D%/packages/patches/clang-13.0-libc-search-path.patch \
%D%/packages/patches/clang-14.0-libc-search-path.patch \
%D%/packages/patches/clang-15.0-libc-search-path.patch \
%D%/packages/patches/clang-16.0-libc-search-path.patch \
%D%/packages/patches/clang-17.0-libc-search-path.patch \
%D%/packages/patches/clang-runtime-asan-build-fixes.patch \
%D%/packages/patches/clang-runtime-esan-build-fixes.patch \
%D%/packages/patches/clang-runtime-9-libsanitizer-mode-field.patch \
@ -1102,7 +1105,6 @@ dist_patch_DATA = \
%D%/packages/patches/elm-reactor-static-files.patch \
%D%/packages/patches/elogind-fix-rpath.patch \
%D%/packages/patches/emacs-all-the-icons-remove-duplicate-rs.patch \
%D%/packages/patches/emacs-debbugs-keep-patch-subject.patch \
%D%/packages/patches/emacs-deferred-fix-number-of-arguments.patch \
%D%/packages/patches/emacs-elpy-dup-test-name.patch \
%D%/packages/patches/emacs-exec-path.patch \

18
gnu/packages/admin.scm
View file

@ -4432,6 +4432,9 @@ (define-public launchmon
" *lmonpl = '\\0'"))
#t))))
(build-system gnu-build-system)
(arguments
;; GCC 11 defaults to c++17 but this package needs something older.
(list #:configure-flags #~'("CXXFLAGS=-std=c++14 -O2 -g")))
(inputs
(list openmpi
munge
@ -4439,7 +4442,7 @@ (define-public launchmon
libelf
libgcrypt
libgpg-error))
(synopsis "Infrastructue for large scale tool daemon launching")
(synopsis "Infrastructure for large-scale tool daemon launching")
(description
"LaunchMON is a software infrastructure that enables HPC run-time
tools to co-locate tool daemons with a parallel job. Its API allows a
@ -4452,7 +4455,7 @@ (define-public launchmon
(define-public spindle
(package
(name "spindle")
(version "0.10")
(version "0.13")
(source (origin
;; We use git checkout to avoid github auto-generated tarballs
(method git-fetch)
@ -4462,16 +4465,15 @@ (define-public spindle
(file-name (git-file-name name version))
(sha256
(base32
"15n3ay0qq81r5v7fif61q1vdjcq44pp2nynkh3fvbzc9fj3c39wd"))))
"1z594nhash1him9v00qmyqv9jvikzrs4wxqy1cvnfwqwnrrkp707"))))
(build-system gnu-build-system)
(arguments '(#:configure-flags '("--enable-sec-launchmon"
"--enable-sec-munge"
"--enable-sec-none")))
"--enable-sec-none"
;; Fails to build as c++17.
"CXXFLAGS=-std=c++14 -O2 -g")))
(inputs
`(("mpi" ,openmpi)
("munge" ,munge)
("launchmon" ,launchmon)
("libgcrypt" ,libgcrypt)))
(list openmpi munge launchmon libgcrypt))
(synopsis "Scalable library loading in HPC environments")
(description
"Spindle is a tool for improving the performance of dynamic library and

37
gnu/packages/agda.scm
View file

@ -44,7 +44,7 @@ (define-module (gnu packages agda)
(define-public agda
(package
(name "agda")
(version "2.6.3")
(version "2.6.4")
(source
(origin
(method git-fetch)
@ -53,12 +53,14 @@ (define-public agda
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1s7zd01i8pmvi90ywx497kc07z50nah7h0fc2dn6jzb132k5sh1q"))
(patches (search-patches "agda-libdirs-env-variable.patch"))))
(base32 "0n4avd58j45rdcmnwgrmz5s0ril0z4n2z711mwwbahl50f7359ky"))
(patches (search-patches "agda-libdirs-env-variable.patch"
"agda-use-sphinx-5.patch"))))
(build-system haskell-build-system)
(inputs
(list ghc-aeson
ghc-alex
ghc-ansi-terminal
ghc-async
ghc-blaze-html
ghc-boxes
@ -73,9 +75,11 @@ (define-public agda
ghc-monad-control
ghc-murmur-hash
ghc-parallel
ghc-peano
ghc-regex-tdfa
ghc-split
ghc-strict
ghc-text-icu
ghc-unordered-containers
ghc-uri-encode
ghc-vector-hashtables
@ -91,6 +95,7 @@ (define-public agda
(guix build utils)
(srfi srfi-26)
(ice-9 match))
#:configure-flags #~(list "-foptimise-heavily" "-fenable-cluster-counting")
#:phases
#~(modify-phases %standard-phases
;; This allows us to call the 'agda' binary before installing.
@ -194,7 +199,7 @@ (define-public agda-ial
(define-public agda-stdlib
(package
(name "agda-stdlib")
(version "1.7.2")
(version "1.7.3")
(source (origin
(method git-fetch)
(uri (git-reference
@ -203,7 +208,7 @@ (define-public agda-stdlib
(file-name (git-file-name name version))
(sha256
(base32
"065hf24xjpciwdrvk4isslgcgi01q0k93ql0y1sjqqvy5ryg5xmy"))))
"0y6rns64rrkh8hw7mamcf6797329pi4ravpak5zijpnkzdagmlmy"))))
(build-system agda-build-system)
(arguments
(list
@ -241,7 +246,8 @@ (define-public agda-categories
(base32
"0xwgm2mfl2pxipsv31bin8p14y1yhd9n27lv3clvsxd4z9yc034m"))
(patches (search-patches "agda-categories-remove-incompatible-flags.patch"
"agda-categories-use-find.patch"))))
"agda-categories-use-find.patch"
"agda-categories-use-stdlib-1.7.3.patch"))))
(build-system agda-build-system)
(arguments
(list
@ -259,12 +265,9 @@ (define-public agda-categories
(license license:expat)))
(define-public agda-cubical
;; Upstream's HEAD follows the latest Agda release, but they don't release
;; until a newer Agda release comes up, so their releases are always one
;; version late.
(package
(name "agda-cubical")
(version "0.5")
(version "0.6")
(source (origin
(method git-fetch)
(uri (git-reference
@ -273,7 +276,7 @@ (define-public agda-cubical
(file-name (git-file-name name version))
(sha256
(base32
"0yfg7gr55n08ly1qgzpcp16s15k1abycppbcdi9lzg1hjryqxcg3"))))
"0zq0z328zcjmm43mrv2ks27i1dnbylcf8mhzja2hd4gvz1kq1ays"))))
(build-system agda-build-system)
(arguments
(list
@ -290,10 +293,10 @@ (define-public agda-cubical
(license license:expat)))
(define-public agda-1lab
;; Upstream doesn't do releases (yet). Use a commit that builds with 2.6.3,
;; Upstream doesn't do releases (yet). Use a commit that builds with 2.6.4,
;; since they use Agda HEAD.
(let* ((revision "1")
(commit "47ca1d23640a6f49a3abe3c2fe27738bcc10c9c6"))
(let* ((revision "2")
(commit "549fdb1c948a975e90e70f871993a4a4239aa280"))
(package
(name "agda-1lab")
(version (git-version "0.0" revision commit))
@ -306,10 +309,12 @@ (define-public agda-1lab
(file-name (git-file-name name version))
(sha256
(base32
"0j7mp6c0xd0849skdxzncklkxynxnyfrbpcjv4qp5p1xfn0dnfqx"))))
"1k4zj8dibyplakpxaw4a8hpsaqhakynjb83dqxrva4h4ssj6gkqj"))))
(build-system agda-build-system)
(arguments
(list #:plan '(("src/index\\.lagda\\.md$"))))
;; Check files individually first, to avoid running out of heap :(
(list #:plan '(("src/.+/.+\\.lagda\\.md$")
("src/index\\.lagda\\.md$"))))
(synopsis "Reference resource for mathematics done in Homotopy Type Theory")
(description "A formalised, cross-linked reference resource for
mathematics done in Homotopy Type Theory. Unlike the HoTT book, the 1lab is

407
gnu/packages/astronomy.scm
View file

@ -589,13 +589,13 @@ (define-public python-astroml
(define-public python-fitsio
(package
(name "python-fitsio")
(version "1.2.0")
(version "1.2.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "fitsio" version))
(sha256
(base32 "04fbg1ffj7qrlzw50xzzkfnlk6qjjqq96j0im7phprmwb1rbvzzh"))
(base32 "19him5rcpjyz14ghkmifnd1xl3ivlyy84h45k6j2pyr5ixc60ky6"))
(modules '((guix build utils)))
(snippet
;; Remove the bundled cfitsio. When update the package check the
@ -703,7 +703,7 @@ (define-public qfits
(define-public erfa
(package
(name "erfa")
(version "2.0.0")
(version "2.0.1")
(source
(origin
(method git-fetch)
@ -712,7 +712,7 @@ (define-public erfa
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0s9dpj0jdkqcg552f00jhd722czji4pffabmpys5pgi6djckq4f4"))))
(base32 "1hxjbcvdlq4871r17fphbaf3bd8dsjagp1rdb3j8v6kr4f1dil9n"))))
(build-system gnu-build-system)
(native-inputs
(list automake autoconf libtool pkg-config))
@ -923,7 +923,7 @@ (define-public glnemo2
libtirpc
qtbase-5
zlib))
(home-page "https://projets.lam.fr/projects/unsio/wiki")
(home-page "https://projets.lam.fr/projects/glnemo2/wiki/Wiki")
(synopsis "3D interactive visualization program for n-body like particles")
(description
"GLNEMO2 is an interactive 3D visualization program which displays
@ -1121,7 +1121,7 @@ (define-public siril
(define-public splash
(package
(name "splash")
(version "3.8.4")
(version "3.9.0")
(source (origin
(method git-fetch)
(uri (git-reference
@ -1129,7 +1129,7 @@ (define-public splash
(commit (string-append "v" version))))
(sha256
(base32
"1l18sqz5mpab9wb5hlbfy18wfwq6fpijc3p9wa5bv6lrcymvpirp"))
"19r5j4jrxhp3gf865ns59vvfnn5a303dqgmb8y2kgcsx26fci1hs"))
(file-name (git-file-name name version))))
(build-system gnu-build-system)
(arguments
@ -1385,7 +1385,7 @@ (define-public swarp
(define-public celestia
(package
(name "celestia")
(version "1.6.3")
(version "1.6.4")
(source
(origin
(method git-fetch)
@ -1394,7 +1394,7 @@ (define-public celestia
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "0dzci5n7gcnm1vq916gsn9zddkhbzhbsakqxrpnmvzibsqznn6c8"))))
(base32 "0nz9k5nd2zmrbwj1qhsfwmvqymqk8c4yjxpybck44isrild2ah9j"))))
(build-system gnu-build-system)
(arguments
(list
@ -1466,13 +1466,13 @@ (define-public celestia-gtk
(define-public python-astropy
(package
(name "python-astropy")
(version "5.3.3")
(version "5.3.4")
(source
(origin
(method url-fetch)
(uri (pypi-uri "astropy" version))
(sha256
(base32 "1fwk7x4q1hgdf9m8q613c6q7045sam1g934vgqv588ksbngxyc03"))
(base32 "1n7iwvjari4xv37094cpiapmjhhm57b04hi4r40wqb5czbigg46l"))
(modules '((guix build utils)))
(snippet
'(begin
@ -1527,7 +1527,9 @@ (define-public python-astropy
"not remote_data"
;; XXX: Check why this tests failing.
" and not test_ignore_sigint"
" and not test_parquet_filter"))))))))
" and not test_parquet_filter"
;; See https://github.com/astropy/astropy/issues/15537
" and not test_pvstar"))))))))
(native-inputs
(list pkg-config
python-colorlog
@ -1612,19 +1614,27 @@ (define-public python-astroquery
(uri (pypi-uri "astroquery" version))
(sha256
(base32 "1vhkzsqlgn3ji5by2rdf2gwklhbyzvpzb1iglalhqjkkrdaaaz1h"))))
(build-system python-build-system)
(build-system pyproject-build-system)
(arguments
(list #:phases
#~(modify-phases %standard-phases
(add-before 'check 'writable-home
(lambda _ ; some tests need a writable home
(setenv "HOME" (getcwd))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "python" "-m" "pytest" "--pyargs" "astroquery"
;; Skip tests that require online data.
"-m" "not remote_data")))))))
(list
#:test-flags
#~(list "--pyargs" "astroquery"
"-m" "not remote_data")
#:phases
#~(modify-phases %standard-phases
(add-before 'check 'prepare-test-environment
(lambda _
(setenv "HOME" (getcwd)) ; some tests need a writable home
;; To solve pytest/conftest issue. Pytest tries to load all
;; files with word 'test' in them.
;;
;; ImportError while loading conftest ...
;; _pytest.pathlib.ImportPathMismatchError: ...
;;
(call-with-output-file "pytest.ini"
(lambda (port)
(format port "[pytest]
python_files = test_*.py"))))))))
(propagated-inputs
(list python-astropy
python-beautifulsoup4
@ -1634,12 +1644,13 @@ (define-public python-astroquery
python-pyvo
python-requests))
(native-inputs
(list python-flask
python-jinja2
(list python-astropy-healpix
python-matplotlib
;; python-mocpy : Not packed yet, optional
python-pytest-astropy
python-pytest-dependency))
(home-page "https://www.astropy.org/astroquery/")
python-pytest-dependency
python-regions))
(home-page "https://astroquery.readthedocs.io/en/latest/index.html")
(synopsis "Access online astronomical data resources")
(description "Astroquery is a package that contains a collection of tools
to access online Astronomical data. Each web service has its own sub-package.")
@ -1724,13 +1735,13 @@ (define-public python-bayesicfitting
(define-public python-casa-formats-io
(package
(name "python-casa-formats-io")
(version "0.2.1")
(version "0.2.2")
(source (origin
(method url-fetch)
(uri (pypi-uri "casa-formats-io" version))
(sha256
(base32
"07cchih2ws6jf6q1a4xhkv0jk96s3w08kzxx9l1911wzqk0pw9pj"))))
"16qwr6yq86qgdb0lvnmfm5mn6g2d29b1vrmfv26v77kxm6szxr8h"))))
(build-system pyproject-build-system)
(arguments
(list
@ -1784,7 +1795,7 @@ (define-public python-ccdproc
(define-public python-cdflib
(package
(name "python-cdflib")
(version "1.2.1")
(version "1.2.3")
(source
(origin
(method git-fetch) ; no tests in pypi archive
@ -1793,7 +1804,7 @@ (define-public python-cdflib
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "0v73fl69pxbk52ilhj2593zmn3qhqy4hrrwby8m9z2sq3fd5xk0v"))))
(base32 "0vpgcbc9pmx0qqfia1frnwq3jkgfp8y3ikqdnzs5bs1sr13p9p3w"))))
(build-system pyproject-build-system)
(arguments
(list #:phases
@ -1833,13 +1844,13 @@ (define-public python-cdflib
(define-public python-crds
(package
(name "python-crds")
(version "11.17.6")
(version "11.17.9")
(source (origin
(method url-fetch)
(uri (pypi-uri "crds" version))
(sha256
(base32
"1sbfl45rx21g622vm8baqv0ydcdixf1jdjgydn07sxl7kn15fa4g"))))
"0ha7ibs5lmqs9pcr546jyxzgrmx1xyqps7fsp220rvlsbsisdgm0"))))
(build-system pyproject-build-system)
(arguments
(list
@ -1922,18 +1933,7 @@ (define-public python-drms
(uri (pypi-uri "drms" version))
(sha256
(base32 "0mkrmr55fgca441z7hvsyri6x9cjsh0sfas3hrj0k1k10k8vszbw"))))
(build-system python-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(replace 'check
(lambda* (#:key inputs outputs tests?
#:allow-other-keys)
(when tests?
(add-installed-pythonpath inputs outputs)
(setenv "JSOC_EMAIL" "jsoc@sunpy.org")
(invoke "python" "-m" "pytest" "-vv")))))))
(build-system pyproject-build-system)
(native-inputs
(list python-astropy
python-pytest-astropy
@ -1994,13 +1994,13 @@ (define-public python-drizzle
(define-public python-ephem
(package
(name "python-ephem")
(version "4.1.4")
(version "4.1.5")
(source (origin
(method url-fetch)
(uri (pypi-uri "ephem" version))
(sha256
(base32
"0q67z79lgwdylxagbsjm42xvsmk5jmgvghy36m2n5lb2446rz9bk"))))
"0ainqbnvw320pc61q5b6ad6f2mhn1pvrlnq489cwfx0m82mahr0c"))))
(build-system python-build-system)
(native-inputs (list tzdata))
(home-page "https://rhodesmill.org/pyephem/")
@ -2118,27 +2118,22 @@ (define-public python-poliastro
(build-system pyproject-build-system)
(arguments
(list
#:test-flags
#~(list "-m" "not remote_data"
;; TODO: Review failing tests later when any upstream
;; suggestions are provided:
;; https://github.com/poliastro/poliastro/issues/1618
"-k" (string-append "not test_czml_add_trajectory"
" and not test_czml_custom_packet"
" and not test_czml_ground_station"
" and not test_czml_groundtrack"
" and not test_czml_preamble"))
#:phases
#~(modify-phases %standard-phases
;; NOTE: Tests take about 7-10 minutes to pass.
(add-before 'check 'prepare-test-environment
(lambda _
(setenv "HOME" "/tmp")
;; TODO: Review failing tests later when any upstream
;; suggestions are provided:
;; https://github.com/poliastro/poliastro/issues/1618
(substitute* "tests/test_czml.py"
(("def test_czml_add_trajectory") "def __off_test_czml_add_trajectory")
(("def test_czml_custom_packet") "def __off_test_czml_custom_packet")
(("def test_czml_ground_station") "def __off_test_czml_ground_station")
(("def test_czml_groundtrack") "def __off_test_czml_groundtrack")
(("def test_czml_preamble") "def __off_test_czml_preamble"))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "python" "-m" "pytest"
;; Skip tests that need remote data.
"-m" "not remote_data")))))))
(setenv "HOME" "/tmp"))))))
(native-inputs
(list python-coverage
python-hypothesis
@ -2371,13 +2366,13 @@ (define-public python-reproject
(define-public python-sgp4
(package
(name "python-sgp4")
(version "2.22")
(version "2.23")
(source
(origin
(method url-fetch)
(uri (pypi-uri "sgp4" version))
(sha256
(base32 "1yc6gcbhz80i875j0wf6ikx7rzs0m7m1qp72dmdhdjidmpma5w0p"))))
(base32 "0aalbmldks6ykgkcxwkvnp04q0avhv903m5zwvg8i7zvl99xrbfq"))))
(build-system python-build-system)
(propagated-inputs
(list python-numpy))
@ -2601,24 +2596,22 @@ (define-public python-spherical-geometry
(file-name (git-file-name name version))
(sha256
(base32 "0kzcncqir4v7nhk9lxj9gxr32p3krkaqa58y2i4kksgxxy24qw4z"))))
(build-system python-build-system)
(build-system pyproject-build-system)
(arguments
(list
;; NOTE: (Sharlatan-20220523T231348+0100): Tests depends on old Python2
;; libarry `sphere'
#:tests? #f
;; XXX: Disable one failing test
;; See https://github.com/spacetelescope/spherical_geometry/issues/252
#:test-flags #~(list "-k" "not test_overlap")
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'preparations
(lambda _
;; Fixing: setuptools-scm was unable to detect version for ...
(substitute* "setup.py"
(("use_scm_version=True")
(format #f "version=~s" #$version))
(("setup_requires=\\['setuptools_scm'\\],.*")
""))
(setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)
;; Use our own libraries in place of bundles.
(setenv "USE_SYSTEM_QD" "1"))))))
(setenv "USE_SYSTEM_QD" "1")))
(add-before 'check 'build-extensions
(lambda _
(invoke "python" "setup.py" "build_ext" "--inplace"))))))
(native-inputs
(list python-pytest
python-setuptools-scm))
@ -2674,7 +2667,7 @@ (define-public python-stsci-imagestats
(sha256
(base32
"14457izlbnks84dyza75ib3nvx2w8nhlqm9vc1zb7hbhknb5gjvw"))))
(build-system python-build-system)
(build-system pyproject-build-system)
(arguments
(list #:tests? #f)) ;No tests
(propagated-inputs (list python-numpy))
@ -2702,11 +2695,23 @@ (define-public python-stsci-stimage
(build-system pyproject-build-system)
(arguments
(list
;; XXX: Fix failing tests. There are errors to load test files.
#:tests? #f))
#:phases
#~(modify-phases %standard-phases
;; Test steps are taken from GitHub Actions.
;; See https://github.com/spacetelescope/stsci.stimage/issues/27
(replace 'check
(lambda _
(copy-file (string-append
#$(this-package-native-input "python-waf") "/bin/waf")
"waf")
(invoke "python" "waf" "configure" "build" "do_tests"))))))
(propagated-inputs (list python-numpy))
(native-inputs (list python-codecov python-pytest python-pytest-cov
python-setuptools-scm))
(native-inputs
(list python-codecov
python-pytest
python-pytest-cov
python-setuptools-scm
python-waf))
(home-page "https://stscistimage.readthedocs.io/en/latest/")
(synopsis "STScI image processing")
(description "This package provides an astronomical Python package with
@ -2974,44 +2979,40 @@ (define-public libskry
(license license:gpl3+)))
(define-public libpasastro
;; NOTE: (Sharlatan-20210122T215921+0000): the version tag has a build
;; error on spice which is resolved with the latest commit.
(let ((commit "e3c218d1502a18cae858c83a9a8812ab197fcb60")
(revision "1"))
(package
(name "libpasastro")
(version (git-version "1.4.0" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/pchev/libpasastro")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"0asp2sn34nds5va2ghppwc41vb6j3d1mf049j949rgrll817kx47"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f
#:make-flags
(list
,(match (or (%current-target-system) (%current-system))
((or "aarch64-linux" "armhf-linux" "i686-linux" "x86_64-linux")
"OS_TARGET=linux")
(_ #f))
,(match (or (%current-target-system) (%current-system))
("i686-linux" "CPU_TARGET=i386")
("x86_64-linux" "CPU_TARGET=x86_64")
((or "armhf-linux" "aarch64-linux") "CPU_TARGET=armv7l")
(_ #f))
(string-append "PREFIX=" (assoc-ref %outputs "out")))
#:phases
(modify-phases %standard-phases
(delete 'configure))))
(home-page "https://github.com/pchev/libpasastro")
(synopsis "Interface to astronomy library for use from Pascal program")
(description
"This package provides shared libraries to interface Pascal program with
(package
(name "libpasastro")
(version "1.4.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/pchev/libpasastro")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1h92p9ph3zi4w8krny1azd9wgwna2nf07ims983jcky1chkfm0is"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f
#:make-flags
(list
,(match (or (%current-target-system) (%current-system))
((or "aarch64-linux" "armhf-linux" "i686-linux" "x86_64-linux")
"OS_TARGET=linux")
(_ #f))
,(match (or (%current-target-system) (%current-system))
("i686-linux" "CPU_TARGET=i386")
("x86_64-linux" "CPU_TARGET=x86_64")
((or "armhf-linux" "aarch64-linux") "CPU_TARGET=armv7l")
(_ #f))
(string-append "PREFIX=" (assoc-ref %outputs "out")))
#:phases
(modify-phases %standard-phases
(delete 'configure))))
(home-page "https://github.com/pchev/libpasastro")
(synopsis "Interface to astronomy library for use from Pascal program")
(description
"This package provides shared libraries to interface Pascal program with
standard astronomy libraries:
@itemize
@ -3020,12 +3021,12 @@ (define-public libpasastro
@item @code{libpaswcs.so}: Interface with libwcs to work with FITS WCS.
@item @code{libpasspice.so}: To work with NAIF/SPICE kernel.
@end itemize\n")
(license license:gpl2+))))
(license license:gpl2+)))
(define-public libxisf
(package
(name "libxisf")
(version "0.2.9")
(version "0.2.10")
(source
(origin
(method git-fetch)
@ -3034,7 +3035,7 @@ (define-public libxisf
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "02cxv86h0ng4kmvyjkf7cr2ak2i3vpf0q0ik7jg4nmqjsidcs796"))))
(base32 "0q5qipn8887yhrk9pmi4fksxxmqas3w2aw2p194yhzkjapxk2k9h"))))
(build-system cmake-build-system)
(arguments
(list #:configure-flags #~(list "-DUSE_BUNDLED_LIBS=OFF")))
@ -3153,23 +3154,21 @@ (define-public gpredict
(sha256
(base32 "0hwf97kng1zy8rxyglw04x89p0bg07zq30hgghm20yxiw2xc8ng7"))))
(build-system gnu-build-system)
(arguments
(list
#:configure-flags #~(list "CFLAGS=-O2 -g -fcommon")
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'fix-tests
(lambda _
;; Remove reference to non-existent file.
(substitute* "po/POTFILES.in"
(("src/gtk-sat-tree\\.c") "")))))))
(native-inputs
`(("intltool" ,intltool)
("gettext" ,gettext-minimal)
("pkg-config" ,pkg-config)))
(list gettext-minimal intltool pkg-config))
(inputs
(list curl glib goocanvas gtk+))
(arguments
`(#:configure-flags '("CFLAGS=-O2 -g -fcommon")
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-tests
(lambda _
;; Remove reference to non-existent file.
(substitute* "po/POTFILES.in"
(("src/gtk-sat-tree\\.c")
""))
#t)))))
(home-page "http://gpredict.oz9aec.net/index.php")
(synopsis "Satellite tracking and orbit prediction application")
(description
"Gpredict is a real-time satellite tracking and orbit prediction
@ -3177,7 +3176,6 @@ (define-public gpredict
position and other data in lists, tables, maps, and polar plots (radar view).
Gpredict can also predict the time of future passes for a satellite, and
provide you with detailed information about each pass.")
(home-page "http://gpredict.oz9aec.net/index.php")
(license license:gpl2+)))
(define-public sgp4
@ -3231,19 +3229,8 @@ (define-public imppg
(base32 "0a6wb1a9adwd01dmy0r03xxp8iz9y7mvh30088ajilhj4lf90vxa"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f ;no test provided
#:phases
(modify-phases %standard-phases
(replace 'configure
(lambda* (#:key outputs #:allow-other-keys)
(mkdir-p "build")
(chdir "build")
(invoke
"cmake"
"-G" "Unix Makefiles"
"-DCMAKE_BUILD_TYPE=Release"
(string-append "-DCMAKE_INSTALL_PREFIX=" (assoc-ref outputs "out"))
".."))))))
(list ;; No test provided
#:tests? #f))
(native-inputs
(list boost pkg-config))
(inputs
@ -3404,13 +3391,13 @@ (define-public sunclock
(define-public python-jplephem
(package
(name "python-jplephem")
(version "2.19")
(version "2.20")
(source
(origin
(method url-fetch)
(uri (pypi-uri "jplephem" version))
(sha256
(base32 "1kvdzwyh0invinvcnwfr14r9zbqzcwkdh0cpzw1m4vkdcm64aqn1"))))
(base32 "1yp1l3n07849411099f976ps0pyv8jk8k5l9da9nhv54ir86v65v"))))
(build-system pyproject-build-system)
(arguments
(list
@ -3435,13 +3422,13 @@ (define-public python-jplephem
(define-public python-jwst
(package
(name "python-jwst")
(version "1.12.3")
(version "1.12.5")
(source (origin
(method url-fetch)
(uri (pypi-uri "jwst" version))
(sha256
(base32
"0bw7i0pmpdgk2zf47d57g45hm3yb4wbrf1p19z9vg555qv4f4kr5"))))
"0blrl00lz1snhcnr7j59nh05rnpqxdnfp8hhgagkr50h85q4smrn"))))
(build-system pyproject-build-system)
(arguments
(list
@ -3502,13 +3489,13 @@ (define-public python-jwst
(define-public python-pyerfa
(package
(name "python-pyerfa")
(version "2.0.0.3")
(version "2.0.1.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pyerfa" version))
(sha256
(base32 "0f8zykzxjsiwv5ibdn5asla2ng2xl0xdkrcrrd61j31mb3xbnzyp"))
(base32 "0swsdkipnk73iflsa7qbaw89wahbnfyvplqaxwi0yfrxippp9b6v"))
(modules '((guix build utils)))
(snippet
#~(begin
@ -3519,6 +3506,7 @@ (define-public python-pyerfa
(list
;; Disable only one failing test:
;; AttributeError: __warningregistry__
;; See https://github.com/liberfa/pyerfa/issues/126
#:test-flags #~(list "-k" "not test_errwarn_reporting")
#:phases
#~(modify-phases %standard-phases
@ -3547,13 +3535,21 @@ (define-public python-pyerfa
(define-public python-pynbody
(package
(name "python-pynbody")
(version "1.3.1")
(version "1.4.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pynbody" version))
(method git-fetch) ;PyPi doesn't have not prebuit version.
(uri (git-reference
(url "https://github.com/pynbody/pynbody")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1yp7ja66zqmbnh7bbwbyimxq1nkrmjrcif2rzfm1hswm0fp2fbga"))))
(base32 "1lwjs8vf3pc4a64c93fa5k6r276g1c60722swns2r10ig1s4wk0a"))
(modules '((guix build utils)))
(snippet
;; Symlink goes to not existing directory.
#~(for-each delete-file '("docs/testdata"
"docs/tutorials/example_code/testdata")))))
(build-system pyproject-build-system)
(arguments
(list #:test-flags #~(list
@ -3584,7 +3580,12 @@ (define-public python-pynbody
"--ignore=tests/sph_smooth_test.py"
"--ignore=tests/subfind_test.py"
"--ignore=tests/subfindhdf_gadget4_test.py"
"--ignore=tests/tipsy_test.py")))
"--ignore=tests/tipsy_test.py")
#:phases
#~(modify-phases %standard-phases
(add-before 'build 'set-compiler
(lambda _
(setenv "CC" #$(cc-for-target)))))))
(native-inputs
(list python-cython
python-pandas
@ -3723,9 +3724,21 @@ (define-public python-synphot
(build-system pyproject-build-system)
(arguments
(list
;; XXX: Test needs more love to pass.
;; ERROR collecting synphot/tests/test_utils.py
#:tests? #f))
#:phases
#~(modify-phases %standard-phases
(add-before 'check 'prepare-test-environment
(lambda _
(invoke "python" "setup.py" "build_ext" "--inplace")
;; To solve pytest/conftest issue. Pytest tries to load all
;; files with word 'test' in them.
;;
;; ImportError while loading conftest ...
;; _pytest.pathlib.ImportPathMismatchError: ...
;;
(call-with-output-file "pytest.ini"
(lambda (port)
(format port "[pytest]
python_files = test_*.py"))))))))
(propagated-inputs (list python-astropy python-numpy python-scipy))
(native-inputs (list python-pytest python-pytest-astropy
python-setuptools-scm))
@ -3771,32 +3784,23 @@ (define-public python-tweakwcs
@code{FITS WCS} and @code{JWST gWCS} are supported.")
(license license:bsd-3)))
(define-public python-asdf
(define-public python-asdf-3.0
(package
(name "python-asdf")
(version "2.15.0")
(version "3.0.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "asdf" version))
(sha256
(base32 "11s56797l5330kkhppkyz0bsvms016knmyswj4gx91zrxf8iqvv8"))))
(base32 "1jsk7b4mx04l0a08j832vnl309dba3gjnha9mbd61dzs9ridrfna"))))
(build-system pyproject-build-system)
(arguments
(list #:test-flags
#~(list "-k" (string-append
"not test_overwrite"
" and not test_tagging_scalars"
" and not test_info_command"
" and not test_array_inline_threshold_recursive"))))
(native-inputs
(list python-astropy
python-fsspec
(list python-fsspec
python-packaging
python-psutil
python-pytest
python-pytest-doctestplus
python-pytest-openfiles
python-pytest-remotedata
python-semantic-version
python-setuptools-scm))
@ -3804,10 +3808,9 @@ (define-public python-asdf
(list python-asdf-standard
python-asdf-transform-schemas
python-asdf-unit-schemas
python-attrs ;; for vendorized jsonschema
python-importlib-metadata
python-importlib-resources
python-jmespath
python-jsonschema
python-lz4
python-numpy
python-pyyaml))
@ -3819,6 +3822,34 @@ (define-public python-asdf
implementation of the ASDF Standard.")
(license license:bsd-3)))
(define-public python-asdf-2.15
(package
(inherit python-asdf-3.0)
(version "2.15.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "asdf" version))
(sha256
(base32 "11s56797l5330kkhppkyz0bsvms016knmyswj4gx91zrxf8iqvv8"))))
(arguments
(list #:test-flags
#~(list "-k" (string-append
"not test_overwrite"
" and not test_tagging_scalars"
" and not test_info_command"
" and not test_array_inline_threshold_recursive"))))
(native-inputs
(modify-inputs (package-native-inputs python-asdf-3.0)
(prepend python-astropy python-pytest-openfiles)))
(propagated-inputs
(modify-inputs (package-propagated-inputs python-asdf-3.0)
(prepend python-jsonschema python-importlib-resources)))))
(define-public python-asdf
;; Default version of ASDF..
python-asdf-2.15)
(define-public python-asdf-standard
(package
(name "python-asdf-standard")
@ -4101,13 +4132,13 @@ (define-public python-gwcs
(define-public python-rad
(package
(name "python-rad")
(version "0.17.1")
(version "0.18.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "rad" version))
(sha256
(base32
"11jhh3qmd00g8sn6hcfshbpb2qy1rfj0xkxn30pd63lqazg4ra3p"))))
"1wgnbhldgq0j55yzg33y11vd5k5nzwckiccxywvmq518qh19pky5"))))
(build-system pyproject-build-system)
(arguments
(list
@ -4163,13 +4194,13 @@ (define-public python-radio-beam
(define-public python-roman-datamodels
(package
(name "python-roman-datamodels")
(version "0.17.1")
(version "0.18.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "roman_datamodels" version))
(sha256
(base32
"1y12cp8172i4a314gmhpi86jw6pfylz1adh0rzr5zqmvd3mrjqlj"))))
"0crlmd99p2nyqmrbykdqqng7v8zb4sibm8j9aqrq3ppak3r3r7q1"))))
(build-system pyproject-build-system)
(arguments
(list
@ -4207,7 +4238,7 @@ (define-public python-roman-datamodels
(define-public python-astroalign
(package
(name "python-astroalign")
(version "2.4.2")
(version "2.5.1")
(source
(origin
;; There are no tests in the PyPI tarball.
@ -4217,7 +4248,7 @@ (define-public python-astroalign
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0hly20a65540hr3l1lsd1i4d90a0vdrbwnn6zx3z8s89ha9lq3pb"))))
(base32 "1kr5cszcxvrdbksy7mvv3ps1h1jzrn4yamfr6x7whkbi6bpqf7xp"))))
(build-system pyproject-build-system)
(native-inputs
(list python-astropy
@ -4265,13 +4296,13 @@ (define-public python-skyfield
(define-public python-wiimatch
(package
(name "python-wiimatch")
(version "0.3.1")
(version "0.3.2")
(source (origin
(method url-fetch)
(uri (pypi-uri "wiimatch" version))
(sha256
(base32
"0x6p5z6a2cqinckwlpinjxagvmswl149s1jn6ihmdxk4k0h8rrz0"))))
"15kq7z30m9i286ncs9xvpaq3dq1p5fa47jz21prq146qwr7j6dm8"))))
(build-system pyproject-build-system)
(propagated-inputs (list python-numpy python-scipy))
(native-inputs (list python-codecov python-pytest python-pytest-cov

11
gnu/packages/aux-files/guix.vim
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@ -1,13 +1,8 @@
" This appends all of the vim plugins to the end of Vim's runtimepath.
" This appends all applicable vim paths to the end of packagepath. Once we
" have told vim the packagepath vim will add it to the runtimepath for us.
for directory in ["/run/current-system/profile", $HOME . "/.guix-profile", $HOME ."/.guix-home/profile", $GUIX_PROFILE, $GUIX_ENVIRONMENT]
let vimplugins = directory . "/share/vim/vimfiles"
if isdirectory(vimplugins)
let &rtp = join([&rtp,vimplugins], ',')
let &pp = join([&pp,vimplugins], ',')
endif
endfor
" Unconditionally add */after directories last, as intended by upstream
" TODO: Remove duplicate */after directories
for directory in [$VIM . "/vimfiles", $HOME ."/.vim"]
let vimplugins = directory . "/after"
let &rtp = join([&rtp,vimplugins], ',')
endfor

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gnu/packages/benchmark.scm
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@ -137,7 +137,7 @@ (define-public fio
(define-public intel-mpi-benchmarks/openmpi
(package
(name "intel-mpi-benchmarks")
(version "2019.6")
(version "2021.3")
(source (origin
(method git-fetch)
(uri (git-reference
@ -146,7 +146,7 @@ (define-public intel-mpi-benchmarks/openmpi
(file-name (git-file-name name version))
(sha256
(base32
"02hxbk9g9nl59bk5qcfl3djj7b58vsqys340m1xdbyqwcrbnahh9"))
"04kczch2hlfzbgk929vcxx480kc6raba8rbz246j7d26k1z1zh8h"))
(modules '((guix build utils)))
(snippet
'(begin

535
gnu/packages/bioconductor.scm
View file

@ -68,6 +68,42 @@ (define-module (gnu packages bioconductor)
;;; Annotations
(define-public r-bsgenome-hsapiens-ucsc-hg38-masked
(package
(name "r-bsgenome-hsapiens-ucsc-hg38-masked")
(version "1.4.5")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38.masked" version
'annotation))
(sha256
(base32 "0j71hdxqvvc0s8mc6jp6zk502mrf095qazj95yzzb4rm6sjvd20m"))))
(properties `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38.masked")))
(build-system r-build-system)
(propagated-inputs (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg38
r-genomeinfodb))
(home-page
"https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38.masked")
(synopsis
"Full masked genomic sequences for Homo sapiens (UCSC version hg38)")
(description
"This package provides the complete genome sequences for Homo sapiens as
provided by UCSC (genome hg38, based on assembly GRCh38.p14 since 2023/01/31).
The sequences are the same as in BSgenome.Hsapiens.UCSC.hg38, except that each
of them has the 4 following masks on top:
@enumerate
@item the mask of assembly gaps (AGAPS mask);
@item the mask of intra-contig ambiguities (AMB mask);
@item the mask of repeats from @code{RepeatMasker} (RM mask);
@item the mask of repeats from Tandem Repeats Finder (TRF mask).
@end enumerate
Only the AGAPS and AMB masks are \"active\" by default. The sequences are stored
in @code{MaskedDNAString} objects.")
(license license:artistic2.0)))
(define-public r-hpo-db
(package
(name "r-hpo-db")
@ -507,6 +543,28 @@ (define-public r-bsgenome-drerio-ucsc-danrer11
as provided by UCSC (danRer11, May 2017) and stored in Biostrings objects.")
(license license:artistic2.0)))
(define-public r-bsgenome-ecoli-ncbi-20080805
(package
(name "r-bsgenome-ecoli-ncbi-20080805")
(version "1.3.1000")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BSgenome.Ecoli.NCBI.20080805" version
'annotation))
(sha256
(base32 "1l7mjyys1kaq4mbia9jamyw6sd0ij1wypwxvwy8aksan3gcfnh27"))))
(properties `((upstream-name . "BSgenome.Ecoli.NCBI.20080805")))
(build-system r-build-system)
(propagated-inputs (list r-bsgenome))
(home-page
"https://bioconductor.org/packages/BSgenome.Ecoli.NCBI.20080805")
(synopsis "Escherichia coli full genomes")
(description
"This package provides Escherichia coli full genomes for several strains
as provided by NCBI on 2008/08/05 and stored in Biostrings objects.")
(license license:artistic2.0)))
(define-public r-bsgenome-hsapiens-1000genomes-hs37d5
(package
(name "r-bsgenome-hsapiens-1000genomes-hs37d5")
@ -1575,6 +1633,26 @@ (define-public r-breakpointrdata
demonstrate functionalities of the @code{breakpointR} package.")
(license license:expat)))
(define-public r-breastcancervdx
(package
(name "r-breastcancervdx")
(version "1.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "breastCancerVDX" version
'experiment))
(sha256
(base32 "12r8zql30ssr0cxy8v1qawwsky54321c737ny19n2yrl7sm08gf0"))))
(properties `((upstream-name . "breastCancerVDX")))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/breastCancerVDX")
(synopsis "Gene expression datasets")
(description
"This package is a collection of gene expression data from a breast
cancer study published in Wang et al. 2005 and Minn et al 2007.")
(license license:artistic2.0)))
(define-public r-celldex
(package
(name "r-celldex")
@ -4165,6 +4243,27 @@ (define-public r-baalchip
alleles, a known phenotypical feature of cancer samples.")
(license license:artistic2.0)))
(define-public r-bags
(package
(name "r-bags")
(version "2.42.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BAGS" version))
(sha256
(base32 "0356ragpcldr48yycqj91sn3bcqvvfp5spv2z02r8g6hs0dndwdh"))))
(properties `((upstream-name . "BAGS")))
(build-system r-build-system)
(propagated-inputs (list r-biobase r-breastcancervdx))
(home-page "https://bioconductor.org/packages/BAGS")
(synopsis "Bayesian approach for geneset selection")
(description
"This R package is providing functions to perform geneset significance
analysis over simple cross-sectional data between 2 and 5 phenotypes of
interest.")
(license license:artistic2.0)))
(define-public r-basespacer
(package
(name "r-basespacer")
@ -8133,6 +8232,42 @@ (define-public r-rhtslib
of other R packages who wish to make use of HTSlib.")
(license license:lgpl2.0+)))
(define-public r-rnbeads
(package
(name "r-rnbeads")
(version "2.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RnBeads" version))
(sha256
(base32 "15z7l4nmpy01xm19717l27nwf3rfsn6wjv211fn2y4ls40mz75qp"))))
(properties `((upstream-name . "RnBeads")))
(build-system r-build-system)
(propagated-inputs
(list r-biocgenerics
r-cluster
r-ff
r-fields
r-genomicranges
r-ggplot2
r-gplots
r-gridextra
r-illuminaio
r-iranges
r-limma
r-mass
r-matrixstats
r-methylumi
r-plyr
r-s4vectors))
(home-page "https://bioconductor.org/packages/RnBeads")
(synopsis "RnBeads")
(description
"@code{RnBeads} facilitates comprehensive analysis of various types of DNA
methylation data at the genome scale.")
(license license:gpl3)))
(define-public r-impute
(package
(name "r-impute")
@ -8637,6 +8772,44 @@ (define-public r-metaneighbor
profiles than cells of different types.")
(license license:expat)))
(define-public r-methylaid
(package
(name "r-methylaid")
(version "1.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MethylAid" version))
(sha256
(base32 "0mzml9j6f7yycf9747ikkpfvxnwji07h8jhwa9a54ix2d0wyxk3d"))))
(properties `((upstream-name . "MethylAid")))
(build-system r-build-system)
(propagated-inputs
(list r-biobase
r-biocgenerics
r-biocparallel
r-ggplot2
r-gridbase
r-hexbin
r-matrixstats
r-minfi
r-rcolorbrewer
r-shiny
r-summarizedexperiment))
(native-inputs (list r-knitr))
(home-page "https://git.bioconductor.org/packages/MethylAid")
(synopsis
"Quality control of large Illumina DNA Methylation array data sets")
(description
"This package provides a visual and interactive web application using
RStudio's shiny package. Bad quality samples are detected using sample-dependent
and sample-independent controls present on the array and user adjustable
thresholds. In depth exploration of bad quality samples can be performed using
several interactive diagnostic plots of the quality control probes present on
the array. Furthermore, the impact of any batch effect provided by the user can
be explored.")
(license license:gpl2+)))
(define-public r-methylkit
(package
(name "r-methylkit")
@ -9419,6 +9592,37 @@ (define-public r-piano
set analyses.")
(license license:gpl2+)))
(define-public r-powertcr
(package
(name "r-powertcr")
(version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "powerTCR" version))
(sha256
(base32 "06fmphdq95pjbbvm8m8h1wajbp3vhl0zj7ddbzks9fy7ankp1n3i"))))
(properties `((upstream-name . "powerTCR")))
(build-system r-build-system)
(propagated-inputs
(list r-cubature
r-doparallel
r-evmix
r-foreach
r-magrittr
r-purrr
r-truncdist
r-vegan
r-vgam))
(native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/powerTCR")
(synopsis "Model-based comparative analysis of the TCR repertoire")
(description
"This package provides a model for the clone size distribution of the
@acronym{TCR, T-cell receptor} repertoire. Further, it permits comparative
analysis of TCR repertoire libraries based on theoretical model fits.")
(license license:artistic2.0)))
;; This is a CRAN package, but it depends on a Bioconductor package:
;; r-aroma-light, r-dnacopy..
(define-public r-pscbs
@ -10150,6 +10354,49 @@ (define-public r-scmap
different experiment.")
(license license:gpl3)))
(define-public r-screpertoire
(package
(name "r-screpertoire")
(version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "scRepertoire" version))
(sha256
(base32 "1wgs8dv5zl82iciy86w5ws1gq8v2piklcifbw7gmbw60kijyr2l1"))))
(properties `((upstream-name . "scRepertoire")))
(build-system r-build-system)
(propagated-inputs
(list r-doparallel
r-dplyr
r-ggalluvial
r-ggplot2
r-ggraph
r-igraph
r-plyr
r-powertcr
r-reshape2
r-rlang
r-seuratobject
r-singlecellexperiment
r-stringdist
r-stringr
r-summarizedexperiment
r-tidygraph
r-vegan))
(native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/scRepertoire")
(synopsis "Toolkit for single-cell immune receptor profiling")
(description
"The scRepertoire package was built to process data derived from the 10x
Genomics Chromium Immune Profiling for both @acronym{TCR, T-cell receptor} and
@acronym{Ig, immunoglobulin} enrichment workflows and subsequently interacts with
the popular Seurat and SingleCellExperiment R packages. It also allows for
general analysis of single-cell clonotype information without the use of
expression information. The package functions as a wrapper for Startrac and
powerTCR R packages.")
(license license:gpl2)))
(define-public r-scry
(package
(name "r-scry")
@ -11956,13 +12203,13 @@ (define-public r-ggtreeextra
(define-public r-ggpicrust2
(package
(name "r-ggpicrust2")
(version "1.7.2")
(version "1.7.3")
(source (origin
(method url-fetch)
(uri (cran-uri "ggpicrust2" version))
(sha256
(base32
"0yk62cc0vmv6dyfiwvvbgpsqlvp1cw61db60153xvzmcdvd077cl"))))
"0zjlsvzl2f74fvqw4ijnai23qwhlcpgd5p8z9dclnwnsgdbm6hcq"))))
(properties `((upstream-name . "ggpicrust2")))
(build-system r-build-system)
(propagated-inputs (list r-aldex2
@ -18780,14 +19027,14 @@ (define-public r-activedriverwgs
(define-public r-activepathways
(package
(name "r-activepathways")
(version "2.0.2")
(version "2.0.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "ActivePathways" version))
(sha256
(base32
"1h0ih87pf6b5mdhmh65frv3nqx7v5adqv37wn2p3gkpszd6hwc79"))))
"0mgvxpqaq0jncr1kzmwhqkv3pajx2fz6vwhv5arw7fgla6w09p9h"))))
(properties
`((upstream-name . "ActivePathways")))
(build-system r-build-system)
@ -21782,14 +22029,14 @@ (define-public r-ldheatmap
(define-public r-abn
(package
(name "r-abn")
(version "3.0.2")
(version "3.0.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "abn" version))
(sha256
(base32
"06n69cbkdqpwpxks8276h43132c9v57n4hg33vsjjyxjifwbwxwh"))))
"1yh9nhfphalxh77132r0fkpp71mqsfhb8jk11is4d5nvlvr5316z"))))
(build-system r-build-system)
(inputs
(list gsl))
@ -22344,6 +22591,122 @@ (define-public r-dir-expiry
eliminating obsolete caches generated by old versions of packages.")
(license license:gpl3)))
(define-public r-basic4cseq
(package
(name "r-basic4cseq")
(version "1.38.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Basic4Cseq" version))
(sha256
(base32 "1vlrrkg885w77w34m2q8hngr95hhh5bkw9hrzyhnp39igjkcwqx4"))))
(properties `((upstream-name . "Basic4Cseq")))
(build-system r-build-system)
(propagated-inputs
(list r-biostrings
r-bsgenome-ecoli-ncbi-20080805
r-catools
r-genomicalignments
r-genomicranges
r-rcircos))
(home-page "https://bioconductor.org/packages/Basic4Cseq")
(synopsis "Analyzing 4C-seq data")
(description
"Basic4Cseq is an R package for basic filtering, analysis and subsequent
visualization of @acronym{4C-seq, circular chromosome conformation capture
sequencing} data. Virtual fragment libraries can be created for any BSGenome
package, and filter functions for both reads and fragments and basic quality
controls are included. Fragment data in the vicinity of the experiment's
viewpoint can be visualized as a coverage plot based on a running median
approach and a multi-scale contact profile.")
(license license:lgpl3)))
(define-public r-basics
(package
(name "r-basics")
(version "2.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BASiCS" version))
(sha256
(base32 "0kf215n151sxphc5w9h4i2xsk7lmysi4abwcpyz4slbwhpki3ac8"))))
(properties `((upstream-name . "BASiCS")))
(build-system r-build-system)
(propagated-inputs
(list r-assertthat
r-biobase
r-biocgenerics
r-biocparallel
r-coda
r-cowplot
r-ggextra
r-ggplot2
r-hexbin
r-mass
r-matrix
r-matrixstats
r-posterior
r-rcpp
r-rcpparmadillo
r-reshape2
r-s4vectors
r-scran
r-scuttle
r-singlecellexperiment
r-summarizedexperiment
r-viridis))
(native-inputs (list r-knitr))
(home-page "https://github.com/catavallejos/BASiCS")
(synopsis "Bayesian analysis of single-cell sequencing data")
(description
"@acronym{BASiCS, Bayesian analysis of single-cell sequencing data} is an
integrated Bayesian hierarchical model to perform statistical analyses of
single-cell RNA sequencing datasets in the context of supervised experiments
(where the groups of cells of interest are known a priori. BASiCS performs
built-in data normalisation (global scaling) and technical noise quantification
(based on spike-in genes). BASiCS provides an intuitive detection criterion
for highly (or lowly) variable genes within a single group of cells.
Additionally, BASiCS can compare gene expression patterns between two or more
pre-specified groups of cells.")
(license license:gpl3)))
(define-public r-basicstarrseq
(package
(name "r-basicstarrseq")
(version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BasicSTARRseq" version))
(sha256
(base32 "1dw6bv1qk2bn0l3m458sqgvm3s1karh4n3431pl7r0jj2r3mr6xa"))))
(properties `((upstream-name . "BasicSTARRseq")))
(build-system r-build-system)
(propagated-inputs
(list r-genomeinfodb
r-genomicalignments
r-genomicranges
r-iranges
r-s4vectors))
(native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/BasicSTARRseq")
(synopsis "Basic peak calling on STARR-seq data")
(description
"This package implements a method that aims to identify enhancers on
large scale. The STARR-seq data consists of two sequencing datasets of the
same targets in a specifc genome. The input sequences show which regions
where tested for enhancers. Significant enriched peaks i.e. a lot more
sequences in one region than in the input where enhancers in the genomic DNA
are, can be identified. So the approach pursued is to call peak every region
in which there is a lot more
(significant in a binomial model) STARR-seq signal than input signal and
propose an enhancer at that very same position. Enhancers then are called
weak or strong dependent of there degree of enrichment in comparison to
input.")
(license license:lgpl3)))
(define-public r-basilisk-utils
(package
(name "r-basilisk-utils")
@ -22394,6 +22757,166 @@ (define-public r-basilisk
Python environments in a single R session.")
(license license:gpl3)))
(define-public r-bayesknockdown
(package
(name "r-bayesknockdown")
(version "1.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BayesKnockdown" version))
(sha256
(base32 "1argd4gfld2yb0vvpgb5k7m6agmi58712f6g5dj4gnb7kg4rp1l8"))))
(properties `((upstream-name . "BayesKnockdown")))
(build-system r-build-system)
(propagated-inputs (list r-biobase))
(home-page "https://bioconductor.org/packages/BayesKnockdown")
(synopsis "Posterior probabilities for edges from knockdown data")
(description
"This package provides a simple, fast Bayesian method for computing
posterior probabilities for relationships between a single predictor variable
and multiple potential outcome variables, incorporating prior probabilities of
relationships. In the context of knockdown experiments, the predictor
variable is the knocked-down gene, while the other genes are potential
targets. It can also be used for differential expression/2-class data.")
(license license:gpl3)))
(define-public r-bayesspace
(package
(name "r-bayesspace")
(version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BayesSpace" version))
(sha256
(base32 "1mqgsylnrvf197cin5zzihjv31bm2q0m5a612ncbglys6n1jd105"))))
(properties `((upstream-name . "BayesSpace")))
(build-system r-build-system)
(propagated-inputs
(list r-assertthat
r-biocfilecache
r-biocsingular
r-coda
r-dirichletreg
r-ggplot2
r-matrix
r-mclust
r-purrr
r-rcpp
r-rcpparmadillo
r-rcppdist
r-rcppprogress
r-rcurl
r-rhdf5
r-s4vectors
r-scales
r-scater
r-scran
r-singlecellexperiment
r-summarizedexperiment
r-xgboost))
(native-inputs (list r-knitr))
(home-page "https://www.ezstatconsulting.com/BayesSpace/")
(synopsis "Clustering and resolution enhancement of spatial transcriptomes")
(description
"This package provides tools for clustering and enhancing the resolution
of spatial gene expression experiments. BayesSpace clusters a low-dimensional
representation of the gene expression matrix, incorporating a spatial prior to
encourage neighboring spots to cluster together. The method can enhance the
resolution of the low-dimensional representation into \"sub-spots\", for which
features such as gene expression or cell type composition can be imputed.")
(license license:expat)))
(define-public r-baynorm
(package
(name "r-baynorm")
(version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bayNorm" version))
(sha256
(base32 "01lv4w1x43x3f9sdrqikhsr1gdvkgqzrgcd9wnjj76qsljn57ifq"))))
(properties `((upstream-name . "bayNorm")))
(build-system r-build-system)
(propagated-inputs
(list r-bb
r-biocparallel
r-dosnow
r-fitdistrplus
r-foreach
r-iterators
r-locfit
r-mass
r-matrix
r-rcpp
r-rcpparmadillo
r-rcppprogress
r-singlecellexperiment
r-summarizedexperiment))
(native-inputs (list r-knitr))
(home-page "https://github.com/WT215/bayNorm")
(synopsis "Single-cell RNA sequencing data normalization")
(description
"The bayNorm package is used for normalizing single-cell RNA-seq data.
The main function is @code{bayNorm}, which is a wrapper function for gene
specific prior parameter estimation and normalization. The input is a matrix
of scRNA-seq data with rows different genes and coloums different cells. The
output is either point estimates from posterior (2D array) or samples from
posterior (3D array).")
(license license:gpl2+)))
(define-public r-bbcanalyzer
(package
(name "r-bbcanalyzer")
(version "1.32.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BBCAnalyzer" version))
(sha256
(base32 "108jcgsf5hyj348y17hcw8m3zcfjgzpx8nz4n5jgxp2lgxjyizy1"))))
(properties `((upstream-name . "BBCAnalyzer")))
(build-system r-build-system)
(propagated-inputs
(list r-biostrings
r-genomicranges
r-iranges
r-rsamtools
r-summarizedexperiment
r-variantannotation))
(home-page "https://bioconductor.org/packages/BBCAnalyzer")
(synopsis "Visualizing base counts")
(description
"BBCAnalyzer is a package for visualizing the relative or absolute number
of bases, deletions and insertions at defined positions in sequence alignment
data available as bam files in comparison to the reference bases. Markers for
the relative base frequencies, the mean quality of the detected bases, known
mutations or polymorphisms and variants called in the data may additionally be
included in the plots.")
(license license:lgpl3)))
(define-public r-bcrank
(package
(name "r-bcrank")
(version "1.64.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BCRANK" version))
(sha256
(base32 "1m1ccacryf8wjzp0d37n9n1kpa6734ddb8nvv1sy0sz5gplrars9"))))
(properties `((upstream-name . "BCRANK")))
(build-system r-build-system)
(propagated-inputs (list r-biostrings))
(home-page "https://bioconductor.org/packages/BCRANK")
(synopsis "Predicting binding site consensus from ranked DNA sequences")
(description
"This package provides functions and classes for de novo prediction of
transcription factor binding consensus by heuristic search.")
(license license:gpl2)))
(define-public r-biocthis
(package
(name "r-biocthis")

112
gnu/packages/bioinformatics.scm
View file

@ -876,6 +876,38 @@ (define-public r-conqur
simultaneously considered.")
(license license:gpl3))))
(define-public r-ewastools
(let ((commit "f7646cacd73266708479b3fea5d625054d179f95")
(revision "1"))
(package
(name "r-ewastools")
(version (git-version "1.7.2" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/hhhh5/ewastools/")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "0irarlnxfnasa755adxsn67rxsy01zwhjhw18g4cag08cqiyyw41"))))
(properties `((upstream-name . "ewastools")))
(build-system r-build-system)
(propagated-inputs
(list r-data-table
r-igraph
r-illuminaio
r-mblm
r-quadprog))
(native-inputs (list r-knitr))
(home-page "https://github.com/hhhh5/ewastools/")
(synopsis
"Quality control toolset for the Illumina Infinium DNA methylation")
(description
"This package provides a collection of useful functions for working
with DNA methylation micro-array data.")
(license license:unlicense))))
(define-public r-numbat
(let ((commit "4ab7752e7d267a3f443756675728521a9b0a7295")
(revision "1"))
@ -9891,6 +9923,51 @@ (define-public r-chromunity
Pore-C concatemers.")
(license license:gpl3))))
(define-public r-dnamcrosshyb
;; There aren't any releases.
(let ((commit "fe8acb33667e81f00dcb84e0fa75c87ab2db5d8f")
(revision "1"))
(package
(name "r-dnamcrosshyb")
(version (git-version "0.0.0.9000" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/pjhop/DNAmCrosshyb")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "12j1xsiqpvny5rp23z1az0k4cj5ajbcwkg65z00s16vywi2rx6nb"))))
(properties `((upstream-name . "DNAmCrosshyb")))
(build-system r-build-system)
(propagated-inputs
(list r-biocgenerics
r-biocparallel
r-biostrings
r-bsgenome-hsapiens-ucsc-hg19-masked
r-bsgenome-hsapiens-ucsc-hg38-masked
r-dplyr
r-genomicranges
r-ggplot2
r-iranges
r-magrittr
r-minfi
r-purrr
r-s4vectors
r-shiny
r-stringi
r-stringr
r-tibble
r-tidyr
r-watermelon))
(home-page "https://github.com/pjhop/DNAmCrosshyb")
(synopsis "DNAmCrosshyb")
(description
"This package provides helper functions to detect cross-hybridization
on Illumina DNAm arrays.")
(license license:gpl3))))
(define-public r-doubletcollection
(let ((commit "c0d62f1853942ee6a087eaf7b000d9e4261e2dfd")
(revision "1"))
@ -15580,6 +15657,41 @@ (define-public r-giotto
spatial single-cell expression data.")
(license license:expat))))
;; Variant of r-illuminahumanmethylationepicmanifest in the
;; (gnu packages bioconductor) module.
(define-public r-illuminahumanmethylationepicmanifest-latest
(let ((commit "a9ffbad36f5e496ece6c4c37b80e2f4f7e02d0c3")
(revision "1"))
(package
(name "r-illuminahumanmethylationepicmanifest")
(version (git-version "1.0.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url
"https://github.com/achilleasNP/IlluminaHumanMethylationEPICmanifest")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "0v8f0hl0v8gwi61vgqw56rn5j09h95hj54rb8pzbn0znm162n4fc"))))
(properties `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
(build-system r-build-system)
(home-page
"https://github.com/achilleasNP/IlluminaHumanMethylationEPICmanifest")
(synopsis "Illumina Human Methylation Manifest 1.0 B5 for R and minfi")
(description
"This is a drop-in replacement for the
@code{IlluminaHumanMethylationEPIC} package. It utilizes a Manifest based on
1.0B5 annotation. As of version 0.3.0, the
@code{IlluminaHumanMethylationEPIC} package still employs the 1.0B2 annotation
manifest. A corresponding annotation package,
@code{IlluminaHumanMethylationEPICanno.ilm10b5.hg38}, is available to ensure
proper annotation. The decision to maintain the same name is due to
complications in downstream processing caused by array name lookup in certain
preprocessing options.")
(license license:artistic2.0))))
(define-public r-illuminahumanmethylationepicanno-ilm10b5-hg38
(let ((commit "3db06910e27f626e0cc8b335ff45cf9a4050a36a")
(revision "1"))

20
gnu/packages/boost.scm
View file

@ -8,7 +8,7 @@
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2018, 2019, 2021 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2018, 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2018, 2020, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2018, 2020 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2019 Mathieu Othacehe <m.othacehe@gmail.com>
;;; Copyright © 2019, 2020 Giacomo Leidi <goodoldpaul@autistici.org>
@ -44,6 +44,7 @@ (define-module (gnu packages boost)
#:use-module (guix build-system gnu)
#:use-module (guix build-system trivial)
#:use-module (gnu packages)
#:use-module (gnu packages autotools)
#:use-module (gnu packages compression)
#:use-module (gnu packages icu4c)
#:use-module (gnu packages llvm)
@ -445,15 +446,18 @@ (define-public boost-mpi
(define-public mdds
(package
(name "mdds")
(version "2.0.3")
(version "2.1.1")
(source (origin
(method url-fetch)
(uri (string-append "https://kohei.us/files/mdds/src/mdds-"
version ".tar.xz"))
(sha256
(base32
"1r68kxqppmhfg0dhz54d0hqzs5882cqrv1x6wpg7lak6gyyws0bc"))))
(method git-fetch)
(uri (git-reference
(url "https://gitlab.com/mdds/mdds")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"0866020brc1kmiryh7dmhjamnywlsd56ks649hy87283k0p7d3bb"))))
(build-system gnu-build-system)
(native-inputs (list autoconf automake))
(propagated-inputs
(list boost)) ; inclusion of header files
(home-page "https://gitlab.com/mdds/mdds")

16
gnu/packages/browser-extensions.scm
View file

@ -57,8 +57,8 @@ (define ublock-main-assets
;; Arbitrary commit of branch master,
;; Update when updating uBlockOrigin.
(let* ((name "ublock-main-assets")
(commit "c8783488f377723165e3661062bd124ae6d57165")
(revision "0")
(commit "d93605b8584df8cd47bcc91b3d932feecd9e3a2a")
(revision "1")
(version (git-version "0" revision commit)))
(origin
(method git-fetch)
@ -67,14 +67,14 @@ (define ublock-main-assets
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "1b6a1m6s060r49vg563f32rsy057af6i4jcyprym4sdci3z90nls")))))
(base32 "1bbwxmb5rb1afh6i5a7m1ysaw0022wi5g091vpahi4h805p1s7a2")))))
(define ublock-prod-assets
;; Arbitrary commit of branch gh-pages,
;; Update when updating uBlockOrigin.
(let* ((name "ublock-prod-assets")
(commit "fbcfe9229ab6b865ef349c01a4eac73943be8418")
(revision "0")
(commit "1d3df32ef6672763f44b27a95fd5cb3b5770d5e2")
(revision "1")
(version (git-version "0" revision commit)))
(origin
(method git-fetch)
@ -83,12 +83,12 @@ (define ublock-prod-assets
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "0s5rvaz8lc9lk44yfc8463vah8yppy1ybmag0dpd4m1hyj6165h0")))))
(base32 "1cbx7w1nzdcjq0z4z7j9nr8922i27nslprrw5dy03xcdqwc3x4l6")))))
(define ublock-origin
(package
(name "ublock-origin")
(version "1.51.0")
(version "1.53.2")
(home-page "https://github.com/gorhill/uBlock")
(source (origin
(method git-fetch)
@ -98,7 +98,7 @@ (define ublock-origin
(file-name (git-file-name name version))
(sha256
(base32
"1i8rnij3sbwg6vj6znprrsca0n5xjzhmhppaa8v6jyxg6wrrfch1"))))
"0mz1k5ghyc25v51md02qx7chrbg4cxagvqi18bcbs4agq8ix6sp7"))))
(build-system gnu-build-system)
(outputs '("xpi" "firefox" "chromium"))
(properties '((addon-id . "uBlock0@raymondhill.net")))

11
gnu/packages/c.scm
View file

@ -3,7 +3,7 @@
;;; Copyright © 2016, 2017, 2018, 2019, 2021 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2018, 2020–2022 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018, 2019 Pierre Neidhardt <mail@ambrevar.xyz>
;;; Copyright © 2019, 2020, 2022 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2019, 2020, 2022, 2023 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2019, 2021 Guillaume Le Vaillant <glv@posteo.net>
;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
@ -1198,7 +1198,7 @@ (define-public aws-c-mqtt
(define-public mimalloc
(package
(name "mimalloc")
(version "2.0.9")
(version "2.1.2")
(source (origin
(method git-fetch)
(uri (git-reference
@ -1207,10 +1207,13 @@ (define-public mimalloc
(file-name (git-file-name name version))
(sha256
(base32
"19w0i28p6knjd192rrcw1ayc3x0qp6rcm48cwkls4kwn8fng81fj"))))
"1pyf05snc1ib7zjjm9kspvbmynd8lmxqw72qcpz8lcyzyywmz24i"))))
(build-system cmake-build-system)
(arguments
`(#:build-type "Release"))
`(#:build-type "Release"
,@(if (target-ppc32?)
`(#:configure-flags '("-DMI_USE_LIBATOMIC=ON"))
'())))
(synopsis "General purpose memory allocator")
(description "@code{mimalloc} is a drop-in replacement for @code{malloc}.")
(home-page "https://microsoft.github.io/mimalloc/")

8
gnu/packages/ccache.scm
View file

@ -1,6 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014, 2015, 2016, 2018 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016, 2017, 2023 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2018–2021 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2021, 2022 Greg Hogan <code@greghogan.com>
;;; Copyright © 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
@ -62,7 +62,11 @@ (define-public ccache
;; Tests require a writable HOME.
(lambda _
(setenv "HOME" (getenv "TMPDIR")))))))
(native-inputs (list perl ruby-asciidoctor which))
(native-inputs
(append (list perl which)
(if (supported-package? ruby-asciidoctor)
(list ruby-asciidoctor)
'())))
(inputs (list zlib `(,zstd "lib")))
(home-page "https://ccache.dev/")
(synopsis "Compiler cache")

33
gnu/packages/check.scm
View file

@ -2551,7 +2551,7 @@ (define-public python-pytest-pep8
(define-public python-pytest-perf
(package
(name "python-pytest-perf")
(version "0.12.0")
(version "0.13.1")
(source (origin
(method git-fetch)
(uri (git-reference
@ -2560,26 +2560,21 @@ (define-public python-pytest-perf
(file-name (git-file-name name version))
(sha256
(base32
"05mgknvrmyz1kmkgw8jzvisavc68wz1g2wxv69i6xvzgqxf17m9f"))))
(build-system python-build-system)
"1hrccvrbccqwba04pqj749hdzn4sgldmbpg74nf3fzz7wyg6jxqk"))))
(build-system pyproject-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "pytest" "-k"
(string-append
;; Do not test the myproject.toml build as it tries to pull
;; dependencies from the internet.
"not project "
;; The benchmark test attempts to install the
;; package, failing to pull its dependencies from the
;; network.
"and not BenchmarkRunner "
;; The upstream_url test requires networking.
"and not upstream_url"))))))))
#:test-flags '(list "-k"
(string-append
;; Do not test the myproject.toml build as it tries to pull
;; dependencies from the internet.
"not project "
;; The benchmark test attempts to install the
;; package, failing to pull its dependencies from the
;; network.
"and not BenchmarkRunner "
;; The upstream_url test requires networking.
"and not upstream_url"))))
(native-inputs
(list python-pytest
python-pytest-black

43
gnu/packages/cluster.scm
View file

@ -4,6 +4,7 @@
;;; Copyright © 2019 Andrew Miloradovsky <andrew@interpretmath.pw>
;;; Copyright © 2020, 2022 Marius Bakke <marius@gnu.org>
;;; Copyright © 2021 Dion Mendel <guix@dm9.info>
;;; Copyright © 2023 Efraim Flashner <efraim@flashner.co.il>
;;;
;;; This file is part of GNU Guix.
;;;
@ -74,14 +75,18 @@ (define-public drbd-utils
(arguments
(list
#:configure-flags
#~(list "--sysconfdir=/etc"
"--localstatedir=/var"
;; Do not install sysv or systemd init scripts.
"--with-initscripttype=none"
;; Disable support for DRBD 8.3 as it is only for
;; Linux-Libre versions < 3.8. 8.4 is the latest
;; kernel driver as of Linux 5.18.
"--without-83support")
#~(append
(list "--sysconfdir=/etc"
"--localstatedir=/var"
;; Do not install sysv or systemd init scripts.
"--with-initscripttype=none"
;; Disable support for DRBD 8.3 as it is only for
;; Linux-Libre versions < 3.8. 8.4 is the latest
;; kernel driver as of Linux 5.18.
"--without-83support")
#$(if (this-package-native-input "ruby-asciidoctor")
#~'()
#~(list "--without-manual")))
#:test-target "test"
#:make-flags #~(list "WANT_DRBD_REPRODUCIBLE_BUILD=yesplease")
#:phases
@ -126,16 +131,18 @@ (define-public drbd-utils
(("\\$\\(DESTDIR\\)\\$\\(DRBD_LIB_DIR\\)")
"$(DESTDIR)$(prefix)$(DRBD_LIB_DIR)")))))))
(native-inputs
(list clitest
eudev ;just to satisfy a configure check
flex
;; For the documentation.
docbook-xml
docbook-xml-4.4 ;used by documentation/ra2refentry.xsl
docbook-xsl
libxml2 ;for XML_CATALOG_FILES
libxslt ;for xsltproc
ruby-asciidoctor))
(append (list clitest
eudev ;just to satisfy a configure check
flex)
;; For the documentation.
(if (supported-package? ruby-asciidoctor)
(list docbook-xml
docbook-xml-4.4 ;used by documentation/ra2refentry.xsl
docbook-xsl
libxml2 ;for XML_CATALOG_FILES
libxslt ;for xsltproc
ruby-asciidoctor)
'())))
(home-page "https://www.linbit.com/drbd/")
(synopsis "Replicate block devices between machines")
(description

5
gnu/packages/code.scm
View file

@ -237,8 +237,9 @@ (define-public global ; a global variable
(lambda _
;; Install the plugin files in the right place.
(let* ((data (string-append #$output "/share/gtags"))
(vim (string-append #$output
"/share/vim/vimfiles/plugin"))
(vim (string-append
#$output
"/share/vim/vimfiles/pack/guix/start/global/plugin"))
(lisp (string-append #$output "/share/emacs/site-lisp/"
#$(package-name this-package) "-"
#$(package-version this-package))))

43
gnu/packages/cpp.scm
View file

@ -31,7 +31,7 @@
;;; Copyright © 2022 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2022, 2023 David Elsing <david.elsing@posteo.net>
;;; Copyright © 2022, 2023 Zheng Junjie <873216071@qq.com>
;;; Copyright © 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2022 Antero Mejr <antero@mailbox.org>
;;; Copyright © 2023 Sughosha <Sughosha@proton.me>
;;; Copyright © 2023 Artyom V. Poptsov <poptsov.artyom@gmail.com>
@ -609,6 +609,47 @@ (define-public fifo-map
as ordering relation.")
(license license:expat)))
(define-public frozen
;; The test suite fails to compile with the latest 1.1.1 release; use a
;; newer commit (see:
;; https://github.com/serge-sans-paille/frozen/issues/163).
(let ((commit "dd1f58c5f6c97fbf0832cc4e84676663839b913e")
(revision "0"))
(package
(name "frozen")
(version (git-version "1.1.1" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/serge-sans-paille/frozen")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"06i307a7v6alxfy24d47b1sjkz5f4mrqwl2vb4j8zx7wlgnrf08b"))))
(build-system cmake-build-system)
(home-page "https://github.com/serge-sans-paille/frozen")
(synopsis "C++ constexpr alternative header-only library")
(description "@code{frozen} is a header-only library that provides zero
cost initialization for immutable containers, fixed-size containers, and
various algorithms. It provides features such as:
@itemize
@item
immutable (also known as frozen), @code{constexpr}-compatible versions of
{std::set}, {std::unordered_set}, {std::map} and {std::unordered_map}
@item
fixed-capacity, @code{constinit}-compatible versions of @code{std::map} and
@code{std::unordered_map} with immutable, compile-time selected keys mapped to
mutable values.
@item
zero cost initialization version of @code{std::search} for frozen needles
using Boyer-Moore or Knuth-Morris-Pratt algorithms.
@end itemize
The @code{unordered_*} containers are guaranteed perfect (no hash
collision) and the extra storage is linear with respect to the number of
keys.")
(license license:asl2.0))))
(define-public json-dto
(package
(name "json-dto")

336
gnu/packages/cran.scm
View file

@ -147,13 +147,13 @@ (define-public r-aer
(define-public r-afpt
(package
(name "r-afpt")
(version "1.1.0.3")
(version "1.1.0.4")
(source (origin
(method url-fetch)
(uri (cran-uri "afpt" version))
(sha256
(base32
"18izncbr3ljckil97xx2w1y0y7qjykp06wm0ap8ismahqvia3xz3"))))
"15pa4p78p6r478l05481lzx6z4ahswj728s1sb3xp3pvn6rv4jfj"))))
(properties `((upstream-name . "afpt")))
(build-system r-build-system)
(native-inputs (list r-knitr))
@ -391,13 +391,13 @@ (define-public r-consort
(define-public r-collapse
(package
(name "r-collapse")
(version "2.0.3")
(version "2.0.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "collapse" version))
(sha256
(base32 "16y4qxqr4k04690xn8s6c9fr3igpk34pgxygxkc41gc1na0ym37v"))))
(base32 "0azyl6667dzwns9knp3fplv6f9nav36wsrv42qzv90p5kzcaa872"))))
(properties `((upstream-name . "collapse")))
(build-system r-build-system)
(propagated-inputs (list r-rcpp))
@ -1490,14 +1490,14 @@ (define-public r-ruv
(define-public r-waldo
(package
(name "r-waldo")
(version "0.5.1")
(version "0.5.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "waldo" version))
(sha256
(base32
"0inzdwna22axhjw0jdrk800g7zbkpcs7g1cmdi83r7j4zxn0ggs5"))))
"019fvypq36kwvr2znlr0fd9f2ihb08rgigf6ypdybry5n8daxkc2"))))
(properties `((upstream-name . "waldo")))
(build-system r-build-system)
(propagated-inputs
@ -2201,14 +2201,14 @@ (define-public r-ggalluvial
(define-public r-ggpp
(package
(name "r-ggpp")
(version "0.5.4")
(version "0.5.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggpp" version))
(sha256
(base32
"05w74003jp7kprxxbni0plr7ydzyc5hzw8g39kn0qd4p7dksjpwr"))))
"0nysan87vgy0pbcks3bychm84zcwx9pf4p250b45ghimhvxh5cvm"))))
(properties `((upstream-name . "ggpp")))
(build-system r-build-system)
(propagated-inputs
@ -3223,6 +3223,27 @@ (define-public r-matrix-utils
objects.")
(license license:gpl3)))
(define-public r-mblm
(package
(name "r-mblm")
(version "0.12.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "mblm" version))
(sha256
(base32 "1fipb3bryaimr30lcxsxrn0ymv24z39swca7s4z7p9xcfg3ban1b"))))
(properties `((upstream-name . "mblm")))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/mblm/index.html")
(synopsis "Median-based linear models")
(description
"This package provides linear models based on Theil-Sen single median and
Siegel repeated medians. They are very robust (29 or 50 percent breakdown
point, respectively), and if no outliers are present, the estimators are very
similar to OLS.")
(license license:gpl2+)))
(define-public r-mboost
(package
(name "r-mboost")
@ -4059,24 +4080,26 @@ (define-public r-httpuv
(define-public r-httr2
(package
(name "r-httr2")
(version "0.2.3")
(version "1.0.0")
(source (origin
(method url-fetch)
(uri (cran-uri "httr2" version))
(sha256
(base32
"0gabjyv2699p7fb4225jsr2kkbarx1w01kha8ipqzwhjjl13481m"))))
"0jaajfr1hr6bzb1vz2nw2csl2l09kbq619vsq5yrlchcarpjv1fb"))))
(properties `((upstream-name . "httr2")))
(build-system r-build-system)
(propagated-inputs
(list r-cli
r-curl
r-glue
r-lifecycle
r-magrittr
r-openssl
r-r6
r-rappdirs
r-rlang
r-vctrs
r-withr))
(native-inputs (list r-knitr))
(home-page "https://httr2.r-lib.org")
@ -4206,13 +4229,13 @@ (define-public r-howmany
(define-public r-htmltools
(package
(name "r-htmltools")
(version "0.5.6.1")
(version "0.5.7")
(source (origin
(method url-fetch)
(uri (cran-uri "htmltools" version))
(sha256
(base32
"0km08kvg0j2h1d0v6wpxf09yjadhp2srjjnmqwcahfyh37w4xf09"))))
"11mkk26pjck6r2w2nv6niy90c6l13g64zi01s3j4jgq634kdic7c"))))
(build-system r-build-system)
(propagated-inputs
(list r-base64enc r-digest r-ellipsis r-fastmap r-rlang))
@ -5202,14 +5225,14 @@ (define-public r-sankeyd3
(define-public r-wesanderson
(package
(name "r-wesanderson")
(version "0.3.6")
(version "0.3.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "wesanderson" version))
(sha256
(base32
"09mr6p2jmqdjq27cz974w5hyxgn929zp9z3inhxqmmh1582fmdi2"))))
"0kjyz5mrkrirg2glf57b0rhxj2fdp1m6q8zx947y0jg1w425cbn9"))))
(properties `((upstream-name . "wesanderson")))
(build-system r-build-system)
(home-page "https://github.com/karthik/wesanderson")
@ -5541,14 +5564,14 @@ (define-public r-mapdata
(define-public r-maps
(package
(name "r-maps")
(version "3.4.1")
(version "3.4.1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "maps" version))
(sha256
(base32
"0034114pdakxcx480b45qy9j4vq1v5ss961ssy92w4nqiqhsb4z6"))))
"06l58919kgks9adwzgfir44q6gnx46j3c7ah9c6d4dn36xsld7fk"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/maps")
(synopsis "Draw geographical maps")
@ -5580,18 +5603,18 @@ (define-public r-mapproj
(define-public r-rgooglemaps
(package
(name "r-rgooglemaps")
(version "1.4.5.3")
(version "1.5.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "RgoogleMaps" version))
(sha256
(base32
"02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
"197q5i2sky824dwq0x4hhrpkrsd1b6f9qg06mjlwb89mv4vnrzhl"))))
(properties `((upstream-name . "RgoogleMaps")))
(build-system r-build-system)
(propagated-inputs
(list r-png r-sp))
(list r-png))
(home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
(synopsis "Use Google Maps in R")
(description "This package serves two purposes:
@ -6185,6 +6208,30 @@ (define-public r-rcppde
performs global optimization by differential evolution.")
(license license:gpl2+)))
(define-public r-rcppdist
(package
(name "r-rcppdist")
(version "0.1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "RcppDist" version))
(sha256
(base32 "02g57xwfipdcljv06krhm02dbqn9kfyj2km6rdg0a7vq9prwdz1x"))))
(properties `((upstream-name . "RcppDist")))
(build-system r-build-system)
(propagated-inputs (list r-rcpp r-rcpparmadillo))
(native-inputs (list r-knitr))
(home-page "https://github.com/duckmayr/RcppDist")
(synopsis "Integration of additional probability distributions")
(description
"RcppDist provides a header-only C++ library with functions for
additional statistical distributions that can be called from C++ when writing
code using Rcpp or RcppArmadillo. Functions are available that return a
@code{NumericVector} as well as doubles, and for multivariate or matrix
distributions, Armadillo vectors and matrices.")
(license license:gpl2+)))
(define-public r-rcppml
(package
(name "r-rcppml")
@ -6295,6 +6342,27 @@ (define-public r-rcppxptrutils
components.")
(license license:expat)))
(define-public r-bb
(package
(name "r-bb")
(version "2019.10-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "BB" version))
(sha256
(base32 "0kf9sfsm3n036a8a8gjfpc9qdryvadb019kqjh80n1szdv7bdl04"))))
(properties `((upstream-name . "BB")))
(build-system r-build-system)
(propagated-inputs (list r-quadprog))
(home-page "https://publichealth.jhu.edu/")
(synopsis "Solving and optimizing large-scale nonlinear systems")
(description
"This package implements Barzilai-Borwein spectral methods for solving
nonlinear system of equations, and for optimizing nonlinear objective
functions subject to simple constraints.")
(license license:gpl3)))
(define-public r-bindr
(package
(name "r-bindr")
@ -7122,13 +7190,13 @@ (define-public r-rmpi
(define-public r-rmumps
(package
(name "r-rmumps")
(version "5.2.1-23")
(version "5.2.1-25")
(source
(origin
(method url-fetch)
(uri (cran-uri "rmumps" version))
(sha256
(base32 "1mypmf9j9fzaldpv56bqng5yhyxfc55hvzd98d1dk6w1m1sncn09"))))
(base32 "15yn5i6v3xz90gimvaqgvp805cfpvr439y9wpckyvwn1iwp2745y"))))
(properties `((upstream-name . "rmumps")))
(build-system r-build-system)
(inputs (list zlib))
@ -7210,6 +7278,57 @@ (define-public r-etrunct
which should be seen for details.")
(license license:expat)))
(define-public r-evd
(package
(name "r-evd")
(version "2.3-6.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "evd" version))
(sha256
(base32 "0wc95hfj0gwkyghipdrhwd3s6q2agh9x2wy6y7dr6mjw7wnmjb36"))))
(properties `((upstream-name . "evd")))
(build-system r-build-system)
(home-page "https://cran.r-project.org/package=evd")
(synopsis "Functions for extreme value distributions")
(description
"This package extends simulation, distribution, quantile and density
functions to univariate and multivariate parametric extreme value distributions,
and provides fitting functions which calculate maximum likelihood estimates for
univariate and bivariate maxima models, and for univariate and bivariate
threshold models.")
(license license:gpl3)))
(define-public r-evmix
(package
(name "r-evmix")
(version "2.12")
(source
(origin
(method url-fetch)
(uri (cran-uri "evmix" version))
(sha256
(base32 "02rabc9snci00s1x7h0svfr66lmw1wjcdg0149wc52mnccsdaivf"))))
(properties `((upstream-name . "evmix")))
(build-system r-build-system)
(propagated-inputs
(list r-gsl
r-mass
r-sparsem))
(home-page "http://www.math.canterbury.ac.nz/~c.scarrott/evmix.shtml")
(synopsis
"Extreme value threshold estimation and uncertainty quantification")
(description
"This package provides the usual distribution functions, maximum likelihood
inference and model diagnostics for univariate stationary extreme value mixture
models. Also, there are provided kernel density estimation including various
boundary corrected kernel density estimation methods and a wide choice of kernels,
with cross-validation likelihood based bandwidth estimator. Reasonable
consistency with the base functions in the evd package is provided, so that users
can safely interchange most code.")
(license license:gpl3)))
(define-public r-excelr
(package
(name "r-excelr")
@ -7825,14 +7944,14 @@ (define-public r-progressr
(define-public r-lava
(package
(name "r-lava")
(version "1.7.2.1")
(version "1.7.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "lava" version))
(sha256
(base32
"0bpg75w0ri1mkf7cw9gbw1fjpy4mh9h48k019y772xjfgrf1yayl"))))
"023av1mz4hr1lqv8cpbx0j1y3c7ljyns35rm838c618b6pqps22f"))))
(build-system r-build-system)
(propagated-inputs
(list r-future-apply r-numderiv r-progressr r-squarem r-survival))
@ -8932,6 +9051,30 @@ (define-public r-truncnorm
functions, as well as a random generation function.")
(license license:gpl2)))
(define-public r-truncdist
(package
(name "r-truncdist")
(version "1.0-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "truncdist" version))
(sha256
(base32 "02ihw4ixhadwr3sqm6r264i8vpcaz8pn69vkzabd8fwqvn5vcj5q"))))
(properties `((upstream-name . "truncdist")))
(build-system r-build-system)
(propagated-inputs (list r-evd))
(home-page "https://cran.r-project.org/package=truncdist")
(synopsis "Truncated random variables")
(description
"This package provides a collection of tools to evaluate probability density
functions, cumulative distribution functions, quantile functions and random
numbers for truncated random variables. These functions are provided to also
compute the expected value and variance. @acronym{Q-Q, quantile–quantile} plots
can be produced. All the probability functions in the stats, stats4 and evd
packages are automatically available for truncation.")
(license license:gpl2+)))
(define-public r-rsolnp
(package
(name "r-rsolnp")
@ -9785,13 +9928,13 @@ (define-public r-seriation
(define-public r-xfun
(package
(name "r-xfun")
(version "0.40")
(version "0.41")
(source
(origin
(method url-fetch)
(uri (cran-uri "xfun" version))
(sha256
(base32 "1xvngh0kbd87cl39bzmjx5i57pmxik9gw50li8dh42j438cnma8y"))))
(base32 "00ivgr557ja8l33lvawrivfhgj1xbjmdi4dj07zybwa1y6wc6x13"))))
(build-system r-build-system)
(properties
;; knitr itself depends on xfun
@ -10353,13 +10496,13 @@ (define-public r-leaflet-providers
(define-public r-leaflet
(package
(name "r-leaflet")
(version "2.2.0")
(version "2.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "leaflet" version))
(sha256
(base32 "0k0zplbhmvld6q1id17s827z1230kvnz16c4hlvp6jn9g26yy0dq"))
(base32 "1gfsf7bsmp418zv4gpk5i1xg5vvgqwpdkznnvj5x0mk4rcqk1i81"))
(snippet
'(for-each
delete-file
@ -10750,13 +10893,13 @@ (define-public r-extradistr
(define-public r-fbasics
(package
(name "r-fbasics")
(version "4031.95")
(version "4032.96")
(source (origin
(method url-fetch)
(uri (cran-uri "fBasics" version))
(sha256
(base32
"1d1pbyidng68fcc6vrm98ybklz6yzrinqc2dhg8q6f1pg3kkx6bj"))))
"14461d6ac8hcn1x3srh45a4s5imafqb0xy8bn5l6d0qwhw4njmg1"))))
(properties `((upstream-name . "fBasics")))
(build-system r-build-system)
(propagated-inputs
@ -12487,20 +12630,20 @@ (define-public r-rgexf
(define-public r-data-tree
(package
(name "r-data-tree")
(version "1.0.0")
(version "1.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "data.tree" version))
(sha256
(base32
"0pizmx2312zsym4m42b97q2184bg3hibvbdrblcga05xln84qrs0"))))
"0qxd1g159phc6f18iddjljdg96sh09w63xqawjwbwyhg4blm9ddh"))))
(properties `((upstream-name . "data.tree")))
(build-system r-build-system)
(propagated-inputs
(list r-r6 r-stringi))
(native-inputs
(list r-knitr))
(list r-knitr r-rmarkdown))
(home-page "https://github.com/gluc/data.tree")
(synopsis "General purpose hierarchical data structure")
(description
@ -12547,14 +12690,14 @@ (define-public r-dtplyr
(define-public r-collapsibletree
(package
(name "r-collapsibletree")
(version "0.1.7")
(version "0.1.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "collapsibleTree" version))
(sha256
(base32
"0b65pbp1wnpsrayqi630ds4r98jvcvynnlp6wxdqrnnr9nzw5343"))
"1i5nmw5w7m8xdgxzim8z8n4w321f42isxbvvajl8ii59pg7drilq"))
(snippet
'(begin
;; Delete minified JavaScript file
@ -12640,14 +12783,14 @@ (define-public r-rappdirs
(define-public r-rastervis
(package
(name "r-rastervis")
(version "0.51.5")
(version "0.51.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "rasterVis" version))
(sha256
(base32
"18bsrw629p4pkyhrpjmiyhq73w882bhgpwmkih0gjnw3ywwgx7rs"))))
"12cl201gwah0bn14ji4nbygayd77w5fck9zkcikhrda5s0chvgb1"))))
(properties `((upstream-name . "rasterVis")))
(build-system r-build-system)
(propagated-inputs
@ -13477,14 +13620,14 @@ (define-public r-rbibutils
(define-public r-rdpack
(package
(name "r-rdpack")
(version "2.5")
(version "2.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "Rdpack" version))
(sha256
(base32
"0xy8w3law1dn53f1gv4jd637pwssr928pvgchpbrpsqz8ghv4kad"))))
"02i21i85pb5aim529byjwhmyyz9jd82mi4j26a3kay0pcn6djxba"))))
(properties `((upstream-name . "Rdpack")))
(build-system r-build-system)
(propagated-inputs
@ -14219,14 +14362,14 @@ (define-public r-deriv
(define-public r-doby
(package
(name "r-doby")
(version "4.6.19")
(version "4.6.20")
(source
(origin
(method url-fetch)
(uri (cran-uri "doBy" version))
(sha256
(base32
"14hvbhf9zamqkjhr9jd8zjpm9xlc8hwqj04gy6ln32n2hzqqqr6v"))))
"08nsl9xzyi2k7xkwa9mn91fn77ji0z9z5lm388pfdmydbfmpy2ks"))))
(properties `((upstream-name . "doBy")))
(build-system r-build-system)
(propagated-inputs
@ -14328,14 +14471,14 @@ (define-public r-blockfest
(define-public r-proc
(package
(name "r-proc")
(version "1.18.4")
(version "1.18.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "pROC" version))
(sha256
(base32
"0lqar1lbm461in4jb9rkdnpccl8lshrhig2qxr892m91mdxym46m"))))
"129cnh3kh9sr42nc7n9f14kr9svi3501834x40njynnzlr0wi4sm"))))
(properties `((upstream-name . "pROC")))
(build-system r-build-system)
(propagated-inputs
@ -15002,13 +15145,13 @@ (define-public r-qualv
(define-public r-mosaiccore
(package
(name "r-mosaiccore")
(version "0.9.2.1")
(version "0.9.4.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "mosaicCore" version))
(sha256
(base32 "1yns15yxr6215xf9qsxfvl24a9zvh1chw49n31dql7fy1zr1dkmp"))))
(base32 "0v3xhv6yfk1hc6a40jjgp6vvq102qa1l4n787pfywx6jhzbhamp2"))))
(properties `((upstream-name . "mosaicCore")))
(build-system r-build-system)
(propagated-inputs
@ -15053,21 +15196,18 @@ (define-public r-labelled
(define-public r-ggformula
(package
(name "r-ggformula")
(version "0.10.4")
(version "0.12.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggformula" version))
(sha256
(base32 "07d9sq0dqi0g5x9h58icfk1f4hgg1xz4mhbp2z2rxg9qgs74fvdj"))))
(base32 "0vbpivyxms46px3wqkbl1wq199mqdxq94gsiplv4i7lz0lzghsfm"))))
(build-system r-build-system)
(propagated-inputs
(list r-ggforce
r-ggplot2
(list r-ggplot2
r-ggridges
r-ggstance
r-labelled
r-magrittr
r-mosaiccore
r-rlang
r-scales
@ -15087,13 +15227,13 @@ (define-public r-ggformula
(define-public r-mosaicdata
(package
(name "r-mosaicdata")
(version "0.20.3")
(version "0.20.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "mosaicData" version))
(sha256
(base32 "1s97yq24z7yhzmx0dpspfadpd8hndyhn7aiw0nslwrhvilhwa409"))))
(base32 "0y6ii234paknak0p8cm5wcjia4s4wh7iixjbbvdgp0w17c05dckh"))))
(properties `((upstream-name . "mosaicData")))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/mosaicData/")
@ -15128,13 +15268,13 @@ (define-public r-raster
(define-public r-mosaic
(package
(name "r-mosaic")
(version "1.8.4.2")
(version "1.9.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "mosaic" version))
(sha256
(base32 "12kpkb7vm54na9hjjkvzw6gm5plx0m6i0l9kihz2r30zanfx5jca"))))
(base32 "1dydqawljv5l9lmhdrhmr7wh3q1c2mnc61gc99jr0jbb1bmls327"))))
(build-system r-build-system)
(propagated-inputs
(list r-dplyr
@ -15147,6 +15287,7 @@ (define-public r-mosaic
r-mosaicdata
r-purrr
r-rlang
r-tibble
r-tidyr))
(native-inputs
(list r-knitr))
@ -21838,14 +21979,14 @@ (define-public r-zim
(define-public r-nor1mix
(package
(name "r-nor1mix")
(version "1.3-0")
(version "1.3-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "nor1mix" version))
(sha256
(base32
"1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
"0252kqhdsp374isc59pm1c6dmsb16jibpnsp1bpyh4k5mg73cdj6"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/nor1mix/")
(synopsis "Normal (1-d) mixture models")
@ -22149,14 +22290,14 @@ (define-public r-reinforcelearn
(define-public r-lemon
(package
(name "r-lemon")
(version "0.4.6")
(version "0.4.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "lemon" version))
(sha256
(base32
"0v1kbyk64yzsk92h6yq03kp9alc9632qprznsws61r8firiskim5"))))
"1r33n7bkfhjpyi23j7gsi387qvyazcy9b912dsd3vg2yqir8s26p"))))
(build-system r-build-system)
(propagated-inputs
(list r-ggplot2
@ -24968,14 +25109,14 @@ (define-public r-rsparse
(define-public r-text2vec
(package
(name "r-text2vec")
(version "0.6.3")
(version "0.6.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "text2vec" version))
(sha256
(base32
"1hi7ydb7xkgbff4lwnnz1biyl8m90w16hn3x5rrzvscvm53sj4y7"))))
"0sjlvp4zhzwc0ai7626fpw3ws8xv0xhl8gv8mrk24lrpk5nhin2h"))))
(properties `((upstream-name . "text2vec")))
(build-system r-build-system)
(propagated-inputs
@ -25077,14 +25218,14 @@ (define-public r-cyclocomp
(define-public r-lintr
(package
(name "r-lintr")
(version "3.1.0")
(version "3.1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "lintr" version))
(sha256
(base32
"1kb3jrzh1vn1fpj6phm2ni542yjgbbjmzgkn8w7khmh1sd9mj7pp"))))
"07c7h30nh1529wba8xkyg2sapj6r7jjckrxyzhrg2ssfwzs4dwdw"))))
(properties `((upstream-name . "lintr")))
(build-system r-build-system)
(propagated-inputs
@ -26348,13 +26489,13 @@ (define-public r-harmony
(define-public r-covr
(package
(name "r-covr")
(version "3.6.3")
(version "3.6.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "covr" version))
(sha256
(base32 "17m2zzgfghr7gzcdgim21vsl12nd4714867dcp9xfb6ili31ikn0"))
(base32 "0al6n4gnnvgxk968skqnajpqpqyl6kpam3fmn782kihhcl1h8qib"))
(modules '((guix build utils)))
;; TODO: still need to replace highlight.js/highlight.pack.js
(snippet
@ -26475,14 +26616,14 @@ (define-public r-systemfonts
(define-public r-graphlayouts
(package
(name "r-graphlayouts")
(version "1.0.1")
(version "1.0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "graphlayouts" version))
(sha256
(base32
"0x777ixw2vvj1z3dams0zmyk25v7cdm4sx8v6knlb2mfkkg2gcyk"))))
"1mg0j9kcjp8dbpd8fy9vr5f35pz41v18vxc7q4pyl986pj859jam"))))
(properties `((upstream-name . "graphlayouts")))
(build-system r-build-system)
(propagated-inputs
@ -26626,14 +26767,14 @@ (define-public r-assertr
(define-public r-parameters
(package
(name "r-parameters")
(version "0.21.2")
(version "0.21.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "parameters" version))
(sha256
(base32
"05ryyyibnm69hq1xa84r9n2gr1s1ifds70z4awmib2ch62098m43"))))
"091zpyq37v7xjicj4h4r4fqhrrc7d3hicgbdznsjn85sw4d7q595"))))
(properties `((upstream-name . "parameters")))
(build-system r-build-system)
(propagated-inputs
@ -26711,14 +26852,14 @@ (define-public r-insol
(define-public r-lifecycle
(package
(name "r-lifecycle")
(version "1.0.3")
(version "1.0.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "lifecycle" version))
(sha256
(base32
"1hk9mblhap429fk77qpgc4hv0j91q5wpahi0y76w118m471zsnb4"))))
"1k4ibf2x90xgmzaq47vf9wrsh6a2fp2lg1l8bq89632bx33x795d"))))
(build-system r-build-system)
(propagated-inputs
(list r-cli r-glue r-rlang))
@ -26849,12 +26990,12 @@ (define-public r-pmcmrplus
(define-public r-pracma
(package
(name "r-pracma")
(version "2.4.2")
(version "2.4.4")
(source (origin
(method url-fetch)
(uri (cran-uri "pracma" version))
(sha256
(base32 "05lwx2yx7f45cr5amzbjv3b2p6ibspjxl0aglq2dga6rvxzk6l0x"))))
(base32 "0zxsqr7f4pcr1nmbbzliihyldv091ykzajv1mbdrkycp46pz6khs"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/pracma/")
(synopsis "Practical numerical math functions")
@ -28856,14 +28997,14 @@ (define-public r-gdina
(define-public r-actcd
(package
(name "r-actcd")
(version "1.2-0")
(version "1.3-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ACTCD" version))
(sha256
(base32
"0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
"1a0gsznca5fv7i29xpcns4rkas5q88wv01rxvd4j66n64gw0ri4j"))))
(properties `((upstream-name . "ACTCD")))
(build-system r-build-system)
(propagated-inputs
@ -29262,14 +29403,14 @@ (define-public r-expint
(define-public r-actuar
(package
(name "r-actuar")
(version "3.3-3")
(version "3.3-4")
(source
(origin
(method url-fetch)
(uri (cran-uri "actuar" version))
(sha256
(base32
"0ji5p19vqnr3i3vfrql2qndhzcjnr57jrh0szil6gaz6bm56afc4"))))
"06693w4cwcchi0z64vgg7khc4k4209nw6m2x441nwix4x6rk1zjs"))))
(properties `((upstream-name . "actuar")))
(build-system r-build-system)
(propagated-inputs (list r-expint))
@ -31191,14 +31332,14 @@ (define-public r-rpf
(define-public r-openmx
(package
(name "r-openmx")
(version "2.21.8")
(version "2.21.10")
(source
(origin
(method url-fetch)
(uri (cran-uri "OpenMx" version))
(sha256
(base32
"1vvlb9q3w6i6g7kf0r5jnrlmdxskh3rbfss90icand046rl37qdz"))))
"1kll5iim5l71dxkjd8y9ma1494818j369gp92qdsy3x6lxy244ym"))))
(properties `((upstream-name . "OpenMx")))
(build-system r-build-system)
(propagated-inputs
@ -31391,14 +31532,14 @@ (define-public r-d3network
(define-public r-qgraph
(package
(name "r-qgraph")
(version "1.9.5")
(version "1.9.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "qgraph" version))
(sha256
(base32
"1mi19bjx83zb42wmgb716a3l4gvwch3rmybdqmm8k3dl8xr2qnjc"))))
"1m019j5nxc0184p0r2zgdn457g555nxsp2s08maa053nydj1va0l"))))
(properties `((upstream-name . "qgraph")))
(build-system r-build-system)
(propagated-inputs
@ -34115,14 +34256,14 @@ (define-public r-rcppziggurat
(define-public r-rfast
(package
(name "r-rfast")
(version "2.0.9")
(version "2.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "Rfast" version))
(sha256
(base32
"12jl5kqjn571zcqh4n351d7nx86b3jh46ds8krqz92f0z6fjmkzz"))))
"1zqq4k85i0nbzndkh0iiq3k83ly0mpl3pn4wkka6qxfvk6n6rr7r"))))
(properties `((upstream-name . "Rfast")))
(build-system r-build-system)
(propagated-inputs
@ -35006,14 +35147,14 @@ (define-public r-yardstick
(define-public r-warp
(package
(name "r-warp")
(version "0.2.0")
(version "0.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "warp" version))
(sha256
(base32
"0s0acddc5h14245hi1faycxp0fyvw6nlgaz2df7da4fpyd2f638f"))))
"1gj65kgs7x63f6y2vnv13k293b52k4afbmdlcam635h9vs8da2h2"))))
(properties `((upstream-name . "warp")))
(build-system r-build-system)
(native-inputs (list r-knitr))
@ -36067,21 +36208,23 @@ (define-public r-seurat5object
(define-public r-seurat
(package
(name "r-seurat")
(version "4.4.0")
(version "5.0.0")
(source (origin
(method url-fetch)
(uri (cran-uri "Seurat" version))
(sha256
(base32
"1pdlvjh5xs1fyj2zic98sfz9zazbb45qywfqnhfzqb34jyaxy5qg"))))
"1hvqxfskwpw06dxc9hc9zvxqb73wr7qjxgrqgyjklxaq1xhr335v"))))
(properties `((upstream-name . "Seurat")))
(build-system r-build-system)
(propagated-inputs
(list r-cluster
r-cowplot
r-fastdummies
r-fitdistrplus
r-future
r-future-apply
r-generics
r-ggplot2
r-ggrepel
r-ggridges
@ -36092,6 +36235,7 @@ (define-public r-seurat
r-jsonlite
r-kernsmooth
r-leiden
r-lifecycle
r-lmtest
r-mass
r-matrix
@ -36108,10 +36252,12 @@ (define-public r-seurat
r-rcpp
r-rcppannoy
r-rcppeigen
r-rcpphnsw
r-rcppprogress
r-reticulate
r-rlang
r-rocr
r-rspectra
r-rtsne
r-scales
r-scattermore
@ -36867,14 +37013,14 @@ (define-public r-mlr3learners
(define-public r-bbotk
(package
(name "r-bbotk")
(version "0.7.2")
(version "0.7.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "bbotk" version))
(sha256
(base32
"1gw0rkbiv93ifl9110r9sr0p9g4vg7qc11mznmmjq0a5vzmqgpm9"))))
"1ddr5w7n68d3imcrm0ipgk1waml8zj4szi566dmmiqvlpzpgdr3p"))))
(properties `((upstream-name . "bbotk")))
(build-system r-build-system)
(propagated-inputs
@ -37128,14 +37274,14 @@ (define-public r-highlight
(define-public r-clustree
(package
(name "r-clustree")
(version "0.5.0")
(version "0.5.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "clustree" version))
(sha256
(base32
"1haam13aifak8fladyxwa0gz56anj1zfczfjgs07gbw90kf6azx8"))))
"05yizn8hcf4nsibypxahp2mz64sy10vli776mi0d2gvfb5p4kwmm"))))
(properties `((upstream-name . "clustree")))
(build-system r-build-system)
(propagated-inputs
@ -39205,14 +39351,14 @@ (define-public r-zoon
(define-public r-paws-common
(package
(name "r-paws-common")
(version "0.6.2")
(version "0.6.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "paws.common" version))
(sha256
(base32
"1jgls5fks9s8m616qs6b7hvv0wf7nhzajyds15hnlasqwg387h3d"))))
"1pzgwljrk3maxcbmiy3yiccijm6c2ach8f9kzpqr7w5k5vkyhpvx"))))
(properties `((upstream-name . "paws.common")))
(build-system r-build-system)
(propagated-inputs
@ -40269,17 +40415,17 @@ (define-public r-logger
(define-public r-fasterize
(package
(name "r-fasterize")
(version "1.0.4")
(version "1.0.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "fasterize" version))
(sha256
(base32 "1ckxi2iyxdahhgbliblcrkzziblfagzr54srjk27yp1lcgivvvs4"))))
(base32 "1d63q77hfbn2ly8cwsik4gaavdhidpi7idf7qj2y5bi9xhd10kyl"))))
(properties `((upstream-name . "fasterize")))
(build-system r-build-system)
(propagated-inputs
(list r-raster r-rcpp r-rcpparmadillo r-sp))
(list r-raster r-rcpp r-rcpparmadillo r-wk))
(native-inputs (list r-knitr))
(home-page "https://github.com/ecohealthalliance/fasterize")
(synopsis "Fast Polygon to Raster Conversion")

39
gnu/packages/crates-io.scm
View file

@ -8645,8 +8645,32 @@ (define-public rust-bitvec-0.19
("rust-serde-test" ,rust-serde-test-1)
("rust-static-assertions" ,rust-static-assertions-1))))))
(define-public rust-blake2-0.10
(package
(name "rust-blake2")
(version "0.10.6")
(source
(origin
(method url-fetch)
(uri (crate-uri "blake2" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32 "1zlf7w7gql12v61d9jcbbswa3dw8qxsjglylsiljp9f9b3a2ll26"))))
(build-system cargo-build-system)
(arguments
`(#:cargo-inputs
(("rust-digest" ,rust-digest-0.10))
#:cargo-development-inputs
(("rust-digest" ,rust-digest-0.10)
("rust-hex-literal" ,rust-hex-literal-0.2))))
(home-page "https://github.com/RustCrypto/hashes")
(synopsis "BLAKE2 hash functions")
(description "This package provides BLAKE2 hash functions in Rust.")
(license (list license:expat license:asl2.0))))
(define-public rust-blake2-0.9
(package
(inherit rust-blake2-0.10)
(name "rust-blake2")
(version "0.9.2")
(source
@ -8656,7 +8680,6 @@ (define-public rust-blake2-0.9
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32 "0x7i67c0hn3bzcwny08rgjrrnarqnqw10qpmh2blbx9hd78kfkha"))))
(build-system cargo-build-system)
(arguments
`(#:cargo-inputs
(("rust-crypto-mac" ,rust-crypto-mac-0.8)
@ -8665,14 +8688,11 @@ (define-public rust-blake2-0.9
#:cargo-development-inputs
(("rust-crypto-mac" ,rust-crypto-mac-0.8)
("rust-digest" ,rust-digest-0.9)
("rust-hex-literal" ,rust-hex-literal-0.2))))
(home-page "https://github.com/RustCrypto/hashes")
(synopsis "BLAKE2 hash functions")
(description "This package provides BLAKE2 hash functions in Rust.")
(license (list license:expat license:asl2.0))))
("rust-hex-literal" ,rust-hex-literal-0.2))))))
(define-public rust-blake2-0.8
(package
(inherit rust-blake2-0.10)
(name "rust-blake2")
(version "0.8.1")
(source
@ -8684,7 +8704,6 @@ (define-public rust-blake2-0.8
(sha256
(base32
"0c4k11j04kqhkci6i9b7lz6p13kpcv228pdqixgrawvavaq0gjwl"))))
(build-system cargo-build-system)
(arguments
`(#:cargo-inputs
(("rust-byte-tools" ,rust-byte-tools-0.3)
@ -8694,11 +8713,7 @@ (define-public rust-blake2-0.8
#:cargo-development-inputs
(("rust-crypto-mac" ,rust-crypto-mac-0.7)
("rust-digest" ,rust-digest-0.8)
("rust-hex-literal" ,rust-hex-literal-0.1))))
(home-page "https://github.com/RustCrypto/hashes")
(synopsis "BLAKE2 hash functions")
(description "This package provides BLAKE2 hash functions in Rust.")
(license (list license:expat license:asl2.0))))
("rust-hex-literal" ,rust-hex-literal-0.1))))))
(define-public rust-blake2b-simd-1
(package

4
gnu/packages/databases.scm
View file

@ -5001,7 +5001,9 @@ (define-public soci
`(#:configure-flags
;; C++11 (-DSOCI_CXX11) is OFF by default. hyperledger-iroha needs it.
(list "-DCMAKE_CXX_STANDARD=17"
"-DSOCI_LIBDIR=lib")
"-DSOCI_LIBDIR=lib"
;; This is for relocation when linking statically
"-DCMAKE_CXX_FLAGS=-fPIE")
#:tests? #f)) ; may require running database management systems
(synopsis "C++ Database Access Library")
(description

4
gnu/packages/dezyne.scm
View file

@ -32,14 +32,14 @@ (define-module (gnu packages dezyne)
(define-public dezyne
(package
(name "dezyne")
(version "2.17.7")
(version "2.17.8")
(source
(origin
(method url-fetch)
(uri (string-append "https://dezyne.org/download/dezyne/"
name "-" version ".tar.gz"))
(sha256
(base32 "09w2rl2ghm8z6fv3iflxnikcj2q98119imvlgvkmkhch5cplx7ny"))))
(base32 "0m5cnymcyg7k1jhp4xjpvpay7ia72xdzyjnjg0spsr4p7fy7yql4"))))
(inputs (list bash-minimal
guile-3.0-latest
guile-json-4

89
gnu/packages/dunst.scm
View file

@ -1,89 +0,0 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015, 2017, 2018 Alex Kost <alezost@gmail.com>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019, 2023 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2020 Brice Waegeneire <brice@waegenei.re>
;;; Copyright © 2021 Alexandru-Sergiu Marton <brown121407@posteo.ro>
;;; Copyright © 2021 Guillaume Le Vaillant <glv@posteo.net>
;;; Copyright © 2022 Jai Vetrivelan <jaivetrivelan@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (gnu packages dunst)
#:use-module (guix packages)
#:use-module (guix git-download)
#:use-module (guix build-system gnu)
#:use-module (guix utils)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (gnu packages)
#:use-module (gnu packages base)
#:use-module (gnu packages freedesktop)
#:use-module (gnu packages glib)
#:use-module (gnu packages gnome)
#:use-module (gnu packages gtk)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages xorg))
(define-public dunst
(package
(name "dunst")
(version "1.9.0")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/dunst-project/dunst")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1nfxf2rahngxpy606yrizrz16d0pswl5sa9jfzpv7h19x6xy24vx"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no check target
#:make-flags (list (string-append "CC=" ,(cc-for-target))
(string-append "PREFIX=" %output)
(string-append "SYSCONFDIR=" %output "/etc")
;; Otherwise it tries to install service file
;; to "dbus" store directory.
(string-append "SERVICEDIR_DBUS=" %output
"/share/dbus-1/services")
"dunstify")
#:phases (modify-phases %standard-phases
(delete 'configure))))
(native-inputs
(list pkg-config perl ; for pod2man
which))
(inputs
(list dbus
(librsvg-for-system) ; for svg support
glib
cairo
pango
libnotify ; for dunstify
libx11
libxscrnsaver
libxinerama
libxrandr
libxdg-basedir
wayland)) ; for wayland support
(home-page "https://dunst-project.org/")
(synopsis "Customizable and lightweight notification daemon")
(description
"Dunst is a highly configurable and minimalistic notification daemon.
It provides @code{org.freedesktop.Notifications} D-Bus service, so it is
started automatically on the first call via D-Bus.")
(license license:bsd-3)))

434
gnu/packages/emacs-xyz.scm
View file

File diff suppressed because it is too large Load diff

12
gnu/packages/engineering.scm
View file

@ -1092,7 +1092,7 @@ (define-public inspekt3d
(define-public kicad
(package
(name "kicad")
(version "7.0.8")
(version "7.0.9")
(source (origin
(method git-fetch)
(uri (git-reference
@ -1100,7 +1100,7 @@ (define-public kicad
(commit version)))
(sha256
(base32
"1gaj833hm3avyb7gyjnl4jk9cckcmj8084y6q45ysjvh283rxsy4"))
"1hq9rba1gcks14zwbr8nbicpsil4imslgfch6ll33fhizbks3fq4"))
(file-name (git-file-name name version))))
(build-system cmake-build-system)
(arguments
@ -1200,7 +1200,7 @@ (define-public kicad-doc
(file-name (git-file-name name version))
(sha256
(base32
"1ya9kwcbsh8cqbinjr1hr14sd0g6rls1awmvw8hwd7715f97x8fg"))))
"14dg99fvl6av9sn6gig6d6k1sdcf2svxy4fipqcz994z2khhz1sj"))))
(build-system cmake-build-system)
(arguments
`(#:configure-flags (list "-DBUILD_FORMATS=html")
@ -1234,7 +1234,7 @@ (define-public kicad-symbols
(file-name (git-file-name name version))
(sha256
(base32
"176zb7df25vz3wbhs94plmpabcgzxsnzbqmpdyssqr7m2wb2424a"))))
"0ynsnjq3z126cjkgm1fjbjvdvpc0walnr42ya9dv46l27kxy2j77"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f)) ; no tests exist
@ -1263,7 +1263,7 @@ (define-public kicad-footprints
(file-name (git-file-name name version))
(sha256
(base32
"1560m5mwwq0jrjhr8zdh2xrm1w7pgr250p81xzhdc4wj7zsb0rrp"))))
"16a4c2xs4i8wbm01a901yxabxk0qdsjkzlccfawddv82bkh4b87h"))))
(synopsis "Official KiCad footprint libraries")
(description "This package contains the official KiCad footprint libraries.")))
@ -1280,7 +1280,7 @@ (define-public kicad-packages3d
(file-name (git-file-name name version))
(sha256
(base32
"1ypy2nzs1x8i98jr5kmlxfd6y592qs22aq73yl8nq0s6640fc4kk"))))
"1cly28vc07i54v487zbb8d1h70nrd3naxvq146b0xnbrjwnd2q28"))))
(synopsis "Official KiCad 3D model libraries")
(description "This package contains the official KiCad 3D model libraries.")))

34
gnu/packages/fabric-management.scm
View file

@ -46,7 +46,7 @@ (define-module (gnu packages fabric-management)
(define-public opensm
(package
(name "opensm")
(version "3.3.22")
(version "3.3.24")
(source
(origin
(method url-fetch)
@ -54,7 +54,7 @@ (define-public opensm
(string-append "https://github.com/linux-rdma/opensm/releases/download/"
version "/opensm-" version ".tar.gz"))
(sha256
(base32 "19scwwpwqhqsyq4hbr5cflcmypss828lalxxd36yby7mbimca38y"))))
(base32 "0q74sx8y23h7picdzb4g5r84wcvc9hr9vzsdawkl812b38vmwcx3"))))
(build-system gnu-build-system)
(native-inputs
(list bison
@ -66,18 +66,20 @@ (define-public opensm
(inputs
(list rdma-core))
(arguments
`(#:configure-flags '("--disable-static")
#:phases
(modify-phases %standard-phases
(add-after 'install 'install-doc
(lambda* (#:key outputs #:allow-other-keys)
(let* ((base (assoc-ref outputs "out"))
(doc (string-append base "/share/doc/"
,name "-" ,version)))
(for-each (lambda (file)
(install-file file doc))
(find-files "doc"))
#t))))))
(list
#:configure-flags #~'("--disable-static")
#:phases
#~(modify-phases %standard-phases
(add-after 'install 'install-doc
(lambda* (#:key outputs #:allow-other-keys)
(let* ((base (assoc-ref outputs "out"))
(doc (string-append base "/share/doc/"
#$(package-name this-package)
"-"
#$(package-version this-package))))
(for-each (lambda (file)
(install-file file doc))
(find-files "doc"))))))))
(home-page "https://www.openfabrics.org/")
(synopsis "OpenIB InfiniBand Subnet Manager and management utilities")
(description "\
@ -183,7 +185,7 @@ (define-public ibutils
(define-public ucx
(package
(name "ucx")
(version "1.14.0")
(version "1.15.0")
(source (origin
(method git-fetch)
(uri (git-reference
@ -193,7 +195,7 @@ (define-public ucx
(patches (search-patches "ucx-tcp-iface-ioctl.patch"))
(sha256
(base32
"0ki2r768wqm92qv06wxrh3kv2nl2yj4ds9fz0s0b5rr2ycjiw9ir"))))
"1mk46vyfp8hsivk88s8gv0nf458jfs59fczpf66wwa3a9yp324jp"))))
(build-system gnu-build-system)
(arguments
(list

13
gnu/packages/fonts.scm
View file

@ -1015,15 +1015,16 @@ (define-public font-gnu-unifont
(define-public font-google-noto
(package
(name "font-google-noto")
(version "20171025")
(version "23.11.1")
(source
(origin
(method url-fetch/zipbomb)
(uri (string-append "https://noto-website-2.storage.googleapis.com/"
"pkgs/Noto-hinted.zip"))
(file-name (string-append name "-" version ".zip"))
(method git-fetch)
(uri (git-reference
(url "https://github.com/notofonts/notofonts.github.io")
(commit (string-append "noto-monthly-release-" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1bp42whyin7xcgmrbnfvz3rvd98xmxaz3ywqybbjmqzwaa9llyw3"))))
(base32 "0vvxhky35l4i0ha60yw0gj26f3v33hpf2zax17yyj16mww4cn4d8"))))
(build-system font-build-system)
(home-page "https://www.google.com/get/noto/")
(synopsis "Fonts to cover all languages")

9
gnu/packages/geo.scm
View file

@ -1940,7 +1940,7 @@ (define-public java-opening-hours-parser
(define-public josm
(package
(name "josm")
(version "18646")
(version "18822")
(source (origin
(method svn-fetch)
(uri (svn-reference
@ -1949,7 +1949,7 @@ (define-public josm
(recursive? #f)))
(sha256
(base32
"0zr3p1i39wi0f29lgb3xrnv6lijrq5ia8jxn4wnq1yz0xdlbg98i"))
"0b4q6n3jbqrh7dsfmcf2g0xdd1wjj62sjq8lwvggvrpqlk1fyn1b"))
(file-name (string-append name "-" version "-checkout"))
(modules '((guix build utils)))
(snippet
@ -1963,17 +1963,18 @@ (define-public josm
(list java-commons-jcs
java-commons-compress
java-jmapviewer
java-jsonp-api
java-jsonp-impl ; runtime dependency
java-jakarta-json
java-jsr305
java-metadata-extractor
java-opening-hours-parser
java-openjfx-media
java-parsson ; runtime dependency
java-signpost-core
java-svg-salamander))
(arguments
`(#:tests? #f
#:jar-name "josm.jar"
#:jdk ,openjdk11
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'rm-build.xml

10
gnu/packages/gnuzilla.scm
View file

@ -1058,10 +1058,12 @@ (define (runpaths-of-input label)
(lambda* (#:key (make-flags '()) (parallel-build? #t)
#:allow-other-keys)
(apply invoke "./mach" "build"
;; mach will use parallel build if possible by default
`(,@(if parallel-build?
'()
'("-j1"))
;; mach will use a wide parallel build if possible by
;; default, so reign it in if requested.
`(,(string-append
"-j" (number->string (if parallel-build?
(parallel-job-count)
1)))
,@make-flags))))
(add-after 'build 'neutralise-store-references
(lambda _

6
gnu/packages/guile-xyz.scm
View file

@ -1284,8 +1284,8 @@ (define-public guile2.0-pg
(license license:gpl3+)))
(define-public guile-prometheus
(let ((commit "35dc26c0ea44c3d70f1819f240d84e2cbb4b7b4c")
(revision "5"))
(let ((commit "4aaf902eb45b3a4c1003f854bda56c516fdf4f5b")
(revision "6"))
(package
(name "guile-prometheus")
(version (git-version "0" revision commit))
@ -1296,7 +1296,7 @@ (define-public guile-prometheus
(commit commit)))
(sha256
(base32
"07822jj4appw37lf444kc4xlgl7nm64mgldag56072l55kwashgb"))
"03sr7wgksi9ys6jyzsnwanl2qqa8csi8jzcgrc3wfzp17vcc16yi"))
(file-name (string-append name "-" version "-checkout"))))
(build-system gnu-build-system)
(native-inputs

8
gnu/packages/hardware.scm
View file

@ -1089,11 +1089,17 @@ (define-public openrgb
(("dependencies/json")
(string-append #$(this-package-input "nlohmann-json")
"/include/nlohmann")))))
(add-after 'unpack 'patch-chmod
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "scripts/build-udev-rules.sh"
(("/bin/chmod") (string-append (assoc-ref inputs "coreutils")
"/bin/chmod")))))
;; Call qmake instead of configure to create a Makefile.
(replace 'configure
(lambda _ (invoke "qmake" "PREFIX=/" "OpenRGB.pro"))))))
(inputs
(list hidapi
(list coreutils
hidapi
hueplusplus
nlohmann-json
libusb

41
gnu/packages/haskell-xyz.scm
View file

@ -65,6 +65,7 @@ (define-module (gnu packages haskell-xyz)
#:use-module (gnu packages haskell-check)
#:use-module (gnu packages haskell-crypto)
#:use-module (gnu packages haskell-web)
#:use-module (gnu packages icu4c)
#:use-module (gnu packages libffi)
#:use-module (gnu packages linux)
#:use-module (gnu packages llvm)
@ -8352,6 +8353,46 @@ (define-public ghc-text-conversions
(description "Safe conversions between textual types")
(license license:isc)))
(define-public ghc-text-icu
(package
(name "ghc-text-icu")
(version "0.8.0.4")
(source
(origin
(method url-fetch)
(uri (hackage-uri "text-icu" version))
(sha256
(base32 "1yj0jdjrsx12sy6lj1gizb2ys5likp9rcv8ryc6sjf2dw74097rd"))))
(build-system haskell-build-system)
(properties '((upstream-name . "text-icu")))
(inputs (list icu4c))
(native-inputs (list ghc-hunit
ghc-quickcheck
ghc-random
ghc-test-framework
ghc-test-framework-hunit
ghc-test-framework-quickcheck2
pkg-config))
(home-page "https://github.com/haskell/text-icu")
(synopsis "Bindings to the ICU library")
(description
"Haskell bindings to the International Components for Unicode (ICU) libraries.
These libraries provide robust and full-featured Unicode services on a wide
variety of platforms. . Features include: . * Both pure and impure bindings, to
allow for fine control over efficiency and ease of use. . * Breaking of strings
on character, word, sentence, and line boundaries. . * Access to the Unicode
Character Database (UCD) of character metadata. . * String collation functions,
for locales where the conventions for lexicographic ordering differ from the
simple numeric ordering of character codes. . * Character set conversion
functions, allowing conversion between Unicode and over 220 character encodings.
. * Unicode normalization. (When implementations keep strings in a normalized
form, they can be assured that equivalent strings have a unique binary
representation.) . * Regular expression search and replace. . * Security checks
for visually confusable (spoofable) strings. . * Bidirectional Unicode algorithm
. * Calendar objects holding dates and times. . * Number and calendar
formatting.")
(license license:bsd-3)))
(define-public ghc-text-short
(package
(name "ghc-text-short")

7
gnu/packages/image-processing.scm
View file

@ -1412,7 +1412,12 @@ (define-public insight-toolkit-4.12
(uri (string-append "mirror://sourceforge/itk/itk/4.12/"
"InsightToolkit-" version ".tar.xz"))
(sha256
(base32 "1qw9mxbh083siljygahl4gdfv91xvfd8hfl7ghwii19f60xrvn2w"))))))
(base32 "1qw9mxbh083siljygahl4gdfv91xvfd8hfl7ghwii19f60xrvn2w"))))
(arguments
(substitute-keyword-arguments (package-arguments insight-toolkit-4)
((#:configure-flags cf #~'())
;; error: ISO C++17 does not allow dynamic exception specifications
#~(cons* "-DCMAKE_CXX_FLAGS=-std=c++14" #$cf))))))
(define-public itk-snap
(package

153
gnu/packages/java.scm
View file

@ -518,6 +518,8 @@ (define-public icedtea-7
"/lib/arm")
("aarch64-linux"
"/lib/aarch64")
("powerpc-linux"
"/lib/ppc")
;; We need a catch-all, dropping
;; '-linux' works in most cases.
(_
@ -878,7 +880,14 @@ (define-public openjdk9
(build-system gnu-build-system)
(outputs '("out" "jdk" "doc"))
(arguments
`(#:tests? #f; require jtreg
`(#:imported-modules
((guix build ant-build-system)
,@%gnu-build-system-modules)
#:modules
((guix build utils)
(guix build gnu-build-system)
(ice-9 popen))
#:tests? #f; require jtreg
#:make-flags '("all")
#:disallowed-references ,(list (gexp-input icedtea-8)
(gexp-input icedtea-8 "jdk"))
@ -971,6 +980,80 @@ (define (icedtea-or-openjdk? path)
(find-files "."
"\\.c$|\\.h$"))
#t)))
;; By default OpenJDK only generates an empty keystore. In order to
;; be able to use certificates in Java programs we need to generate a
;; keystore from a set of certificates. For convenience we use the
;; certificates from the nss-certs package.
(add-after 'install 'install-keystore
(lambda* (#:key inputs outputs #:allow-other-keys)
(use-modules (ice-9 rdelim))
(let* ((keystore "cacerts")
(certs-dir (search-input-directory inputs
"etc/ssl/certs"))
(keytool (string-append (assoc-ref outputs "jdk")
"/bin/keytool")))
(define (extract-cert file target)
(call-with-input-file file
(lambda (in)
(call-with-output-file target
(lambda (out)
(let loop ((line (read-line in 'concat))
(copying? #f))
(cond
((eof-object? line) #t)
((string-prefix? "-----BEGIN" line)
(display line out)
(loop (read-line in 'concat) #t))
((string-prefix? "-----END" line)
(display line out)
#t)
(else
(when copying? (display line out))
(loop (read-line in 'concat) copying?)))))))))
(define (import-cert cert)
(format #t "Importing certificate ~a\n" (basename cert))
(let ((temp "tmpcert"))
(extract-cert cert temp)
(let ((port (open-pipe* OPEN_WRITE keytool
"-import"
"-alias" (basename cert)
"-keystore" keystore
"-storepass" "changeit"
"-file" temp)))
(display "yes\n" port)
(when (not (zero? (status:exit-val (close-pipe port))))
(format #t "failed to import ~a\n" cert)))
(delete-file temp)))
;; This is necessary because the certificate directory contains
;; files with non-ASCII characters in their names.
(setlocale LC_ALL "en_US.utf8")
(setenv "LC_ALL" "en_US.utf8")
(copy-file (string-append (assoc-ref outputs "out")
"/lib/security/cacerts")
keystore)
(chmod keystore #o644)
(for-each import-cert (find-files certs-dir "\\.pem$"))
(mkdir-p (string-append (assoc-ref outputs "out")
"/lib/security"))
(mkdir-p (string-append (assoc-ref outputs "jdk")
"/lib/security"))
;; The cacerts files we are going to overwrite are chmod'ed as
;; read-only (444) in icedtea-8 (which derives from this
;; package). We have to change this so we can overwrite them.
(chmod (string-append (assoc-ref outputs "out")
"/lib/security/" keystore) #o644)
(chmod (string-append (assoc-ref outputs "jdk")
"/lib/security/" keystore) #o644)
(install-file keystore
(string-append (assoc-ref outputs "out")
"/lib/security"))
(install-file keystore
(string-append (assoc-ref outputs "jdk")
"/lib/security")))))
;; Some of the libraries in the lib/ folder link to libjvm.so.
;; But that shared object is located in the server/ folder, so it
;; cannot be found. This phase creates a symbolic link in the
@ -1044,6 +1127,7 @@ (define (icedtea-or-openjdk? path)
("icedtea-8:jdk" ,icedtea-8 "jdk")
;; XXX: The build system fails with newer versions of GNU Make.
("make@4.2" ,gnu-make-4.2)
("nss-certs" ,nss-certs)
("unzip" ,unzip)
("which" ,which)
("zip" ,zip)))
@ -1126,6 +1210,7 @@ (define-public openjdk10
`(("openjdk9" ,openjdk9)
("openjdk9:jdk" ,openjdk9 "jdk")
("make@4.2" ,gnu-make-4.2)
("nss-certs" ,nss-certs)
("unzip" ,unzip)
("which" ,which)
("zip" ,zip)))))
@ -1152,6 +1237,7 @@ (define-public openjdk11
#:modules `((guix build gnu-build-system)
(guix build utils)
(ice-9 match)
(ice-9 popen)
(srfi srfi-1)
(srfi srfi-26))
#:disallowed-references (list (gexp-input openjdk10)
@ -1394,6 +1480,7 @@ (define (icedtea-or-openjdk? path)
openjdk10
`(,openjdk10 "jdk")
gnu-make-4.2
nss-certs
pkg-config
unzip
which
@ -13568,6 +13655,70 @@ (define-public java-jsonp-impl
parse, generate, transform and query) JSON messages. This package contains
a reference implementation of that API.")))
(define-public java-jakarta-json
(package
(name "java-jakarta-json")
(version "2.1.3")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/jakartaee/jsonp-api")
(commit (string-append version "-RELEASE"))))
(file-name (git-file-name name version))
(sha256
(base32
"1q600harqfhlf763l75j4fx7ai7ybp7ga06aiky2a2hg8mhz0s5f"))))
(build-system ant-build-system)
(arguments
`(#:jar-name "jakarta-json.jar"
#:source-dir "api/src/main/java"
#:tests? #f; no tests
#:jdk ,openjdk11))
(home-page "https://github.com/jakartaee/jsonp-api")
(synopsis "Portable API for JSON handling in Java")
(description "This project contains API and Compatible Implementation of
Jakarta JSON Processing specification. Jakarta JSON Processing provides
portable APIs to parse, generate, transform, and query JSON documents.")
;; with classpath exception
(license license:epl2.0)))
(define-public java-parsson
(package
(name "java-parsson")
(version "1.1.5")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/eclipse-ee4j/parsson")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"06vvr6qv1ihnk212gdxg4x0sd61lgxk7wf062s7gym5k2h7fms0p"))))
(build-system ant-build-system)
(arguments
`(#:jar-name "parsson.jar"
#:source-dir "impl/src/main/java"
#:test-dir "impl/src/test"
#:use-java-modules? #t
#:jdk ,openjdk11
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'copy-resources
(lambda _
(copy-recursively "impl/src/main/resources"
"build/classes"))))))
(inputs
(list java-jakarta-json))
(native-inputs
(list java-junit))
(home-page "https://github.com/eclipse-ee4j/parsson")
(synopsis "Implementation of Jakarta JSON API")
(description "Eclipse Parsson is an implementation of the Jakarta JSON
Processing specification.")
;; with classpath exception
(license license:epl2.0)))
(define-public java-xmp
(package
(name "java-xmp")

66
gnu/packages/libreoffice.scm
View file

@ -14,6 +14,7 @@
;;; Copyright © 2019 Chris Marusich <cmmarusich@gmail.com>
;;; Copyright © 2020 Marcin Karpezo <sirmacik@wioo.waw.pl>
;;; Copyright © 2023 Nicolas Graves <ngraves@ngraves.fr>
;;; Copyright © 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -50,6 +51,7 @@ (define-module (gnu packages libreoffice)
#:use-module (gnu packages boost)
#:use-module (gnu packages check)
#:use-module (gnu packages compression)
#:use-module (gnu packages cpp)
#:use-module (gnu packages cups)
#:use-module (gnu packages curl)
#:use-module (gnu packages cyrus-sasl)
@ -92,20 +94,19 @@ (define-module (gnu packages libreoffice)
(define-public ixion
(package
(name "ixion")
(version "0.17.0")
(source
(origin
(method url-fetch)
(uri (string-append "http://kohei.us/files/ixion/src/libixion-"
version ".tar.xz"))
(sha256
(base32
"07hhqkvns4da8xv990gr1smqz1zf40m531lg95nphfrz48wp3jak"))))
(version "0.19.0")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://gitlab.com/ixion/ixion")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"0nycbs3765wkaw9ff7aflm56ayxkn15dlfl5pbbb9b5i2rcv3dq6"))))
(build-system gnu-build-system)
(native-inputs
(list pkg-config))
(inputs
(list mdds python spdlog))
(native-inputs (list autoconf automake libtool pkg-config))
(inputs (list mdds python spdlog))
(home-page "https://gitlab.com/ixion/ixion")
(synopsis "General purpose formula parser and interpreter")
(description "Ixion is a library for calculating the results of formula
@ -117,22 +118,22 @@ (define-public ixion
(define-public orcus
(package
(name "orcus")
(version "0.17.2")
(source
(origin
(method url-fetch)
(uri (string-append "http://kohei.us/files/orcus/src/lib"
"orcus-" version ".tar.xz"))
(sha256
(base32
"1as04qb74jnlnwy4wh5jwaw2nnzgn2s3230ymvh3kx1w9r0rsl1h"))))
(version "0.19.0")
(source (origin
;; The test suite requires data files store with Git Large
;; File Storage.
(method git-fetch/lfs)
(uri (git-reference
(url "https://gitlab.com/orcus/orcus")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"02prj6kgph56fkr89k8wlqarrmx65cq92863i4rrny5sqr8c2llr"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags '("--disable-static")))
(native-inputs
(list pkg-config))
(inputs
(list ixion mdds python zlib))
(arguments (list #:configure-flags #~(list "--disable-static")))
(native-inputs (list autoconf automake libtool pkg-config))
(inputs (list ixion mdds python zlib))
(home-page "https://gitlab.com/orcus/orcus")
(synopsis "File import filter library for spreadsheet documents")
(description "Orcus is a library that provides a collection of standalone
@ -353,7 +354,7 @@ (define-public libcmis
(name "libcmis")
;; Note: Use an unreleased version because libreoffice requires it and
;; is the only user (see <https://github.com/tdf/libcmis/pull/43>).
(version "0.5.2-46-gf264a61")
(version "0.6.0")
(home-page "https://github.com/tdf/libcmis")
(source
(origin
@ -363,7 +364,7 @@ (define-public libcmis
(file-name (git-file-name name version))
(sha256
(base32
"06ff5vw0xrymvvna18wlaayyk20755sk2541i1gh7zpbmncs2ni6"))))
"17jx9fb7nmyp6jhz9nlmb3wcp8k03vhcv7sqql6a7jhsjnw3hq0k"))))
(build-system gnu-build-system)
(native-inputs
(list autoconf automake libtool cppunit pkg-config))
@ -897,7 +898,7 @@ (define dtoa
(define-public libreoffice
(package
(name "libreoffice")
(version "7.5.4.2")
(version "7.6.3.1")
(source
(origin
(method url-fetch)
@ -906,7 +907,7 @@ (define-public libreoffice
"https://download.documentfoundation.org/libreoffice/src/"
(version-prefix version 3) "/libreoffice-" version ".tar.xz"))
(sha256
(base32 "1s3592ick745kl60yjlv7ki3p7nnwswj0mgjh3nk6k7skyvx3fv8"))))
(base32 "148084acq370483y0xwvcvck30kxhr78cnmibp5lks17xqp5f9q7"))))
(build-system glib-or-gtk-build-system)
(arguments
(list
@ -1088,6 +1089,7 @@ (define (install-python-script name)
(list bison
cppunit
flex
frozen ;header-only library
pkg-config
python-wrapper
which

84
gnu/packages/linux.scm
View file

@ -493,7 +493,22 @@ (define (%upstream-linux-source version hash)
;; The current "stable" kernels. That is, the most recently released major
;; versions that are still supported upstream.
(define-public linux-libre-6.5-version "6.5.9")
(define-public linux-libre-6.6-version "6.6.1")
(define-public linux-libre-6.6-gnu-revision "gnu")
(define deblob-scripts-6.6
(linux-libre-deblob-scripts
linux-libre-6.6-version
linux-libre-6.6-gnu-revision
(base32 "0g8m0rb15b0231dv8ji456s75a67szsaim71may3yprplycz6pav")
(base32 "1hg3ck1j8288fhlhcvhgs1zzwh3i62nfvphw7x3vsaqr75kiwbjp")))
(define-public linux-libre-6.6-pristine-source
(let ((version linux-libre-6.6-version)
(hash (base32 "0d42b1hbvv9w3y3q4wydr6il0g5a823n54a06p4p5vcpgkadf7ns")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-6.6)))
(define-public linux-libre-6.5-version "6.5.11")
(define-public linux-libre-6.5-gnu-revision "gnu")
(define deblob-scripts-6.5
(linux-libre-deblob-scripts
@ -503,7 +518,7 @@ (define deblob-scripts-6.5
(base32 "066z5lw5vrfayhv23hpfcm6fh6b7zmn2v13kfv1g3z3jl1wblhfh")))
(define-public linux-libre-6.5-pristine-source
(let ((version linux-libre-6.5-version)
(hash (base32 "1mcg0lpxr832mwyqlbn0s5gssvsk2nn2xhq9w0qbymizf5j2yrn6")))
(hash (base32 "06dmb4hbwrms0lp4axphwgj8wbnzsym70sx55lxr501b53wlmqif")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-6.5)))
@ -511,52 +526,52 @@ (define-public linux-libre-6.5-pristine-source
;; The "longterm" kernels — the older releases with long-term upstream support.
;; Here are the support timelines:
;; <https://www.kernel.org/category/releases.html>
(define-public linux-libre-6.1-version "6.1.60")
(define-public linux-libre-6.1-version "6.1.62")
(define-public linux-libre-6.1-gnu-revision "gnu")
(define deblob-scripts-6.1
(linux-libre-deblob-scripts
linux-libre-6.1-version
linux-libre-6.1-gnu-revision
(base32 "1sf80f2i4vf888xjcn84ymn4w5ynn30ib9033zwmv7f09yvfhapy")
(base32 "1c73516nbhnz0cxjz38b5794dxygb8sznv9idiibw7ablmjbhd11")))
(base32 "1hdibv43xbn1lv83i6qjgfmf1bvqxvq17fryfsq4r4sjgs9212js")))
(define-public linux-libre-6.1-pristine-source
(let ((version linux-libre-6.1-version)
(hash (base32 "02pvymr1dgd36mp7yikxqqv0sfrpwi1grnvxvx6jbbx6wmx0wljq")))
(hash (base32 "1v453q4sf0j8708ivs1zmdf645hgimqvxfc8xz7czgnnmipn3zdr")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-6.1)))
(define-public linux-libre-5.15-version "5.15.137")
(define-public linux-libre-5.15-version "5.15.138")
(define-public linux-libre-5.15-gnu-revision "gnu")
(define deblob-scripts-5.15
(linux-libre-deblob-scripts
linux-libre-5.15-version
linux-libre-5.15-gnu-revision
(base32 "18ac30kxg2mf2f6gk3p935hzhz2qs110jy4xwk21kblnnkskbxj8")
(base32 "1c3lm0j401lv2lk39dmr4mlf5ic173snm7cc0cckl6czyvxr5ysy")))
(base32 "1idjrn2w8jrixj8ifkk1awxyyq5042nc4p2mld4rda96azlnp948")))
(define-public linux-libre-5.15-pristine-source
(let ((version linux-libre-5.15-version)
(hash (base32 "1xxjbxldrhmnh2q6rykpxyfbj8xqgl82q30n8sfavrzr14bb4jcp")))
(hash (base32 "1ajaxy97gx0c9cdxiyxa49ykfsykir22i9abfrcizh71ci0yb15g")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-5.15)))
(define-public linux-libre-5.10-version "5.10.199")
(define-public linux-libre-5.10-version "5.10.200")
(define-public linux-libre-5.10-gnu-revision "gnu1")
(define deblob-scripts-5.10
(linux-libre-deblob-scripts
linux-libre-5.10-version
linux-libre-5.10-gnu-revision
(base32 "1b33rkn32b923025iiz4xzxiy8y5ii9j5qk4021mg575890rl4ch")
(base32 "0nnp46mn32yk436swd2qh34igmzinfgkwvbzp3lqyy45f06hbc2j")))
(base32 "0xrrnmb5kcc5r21bdm24aq0fnkk1imn367c1cxlj78b6l6gigx4b")))
(define-public linux-libre-5.10-pristine-source
(let ((version linux-libre-5.10-version)
(hash (base32 "1h944syk7n6c4j1djlx19n77alzwbxcdza77c9ykicgfynhpgsm0")))
(hash (base32 "012i41bj8rcqn0vhfxrwq3gg82nb6pp2cwq8n146wj47pwgrcbcx")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-5.10)))
(define-public linux-libre-5.4-version "5.4.259")
(define-public linux-libre-5.4-version "5.4.260")
(define-public linux-libre-5.4-gnu-revision "gnu1")
(define deblob-scripts-5.4
(linux-libre-deblob-scripts
@ -566,27 +581,27 @@ (define deblob-scripts-5.4
(base32 "0sw67b2pk3lng4y67diqqnhxaggnp3nbkx8dxc5fs27rinfxr4m1")))
(define-public linux-libre-5.4-pristine-source
(let ((version linux-libre-5.4-version)
(hash (base32 "195v4fidavzm637glj6580006mrcaygnbj4za874imb62bxf9rpz")))
(hash (base32 "1zpbaipd2j3idj8h9iznlj0ywcq5nkhwj707a1f9ixf82h3q4c4q")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-5.4)))
(define-public linux-libre-4.19-version "4.19.297")
(define-public linux-libre-4.19-version "4.19.298")
(define-public linux-libre-4.19-gnu-revision "gnu1")
(define deblob-scripts-4.19
(linux-libre-deblob-scripts
linux-libre-4.19-version
linux-libre-4.19-gnu-revision
(base32 "0ghdizzs6969872rnjcv9p6sl9rcbs29v3ismk125yyvjaczd428")
(base32 "0pjal2cc2f99cvw8r4icb4l24j41k48jkj6bqk7pcahzcgx33ycb")
(base32 "1425mhkfxn18vxn05bb4h3li7x1jl7l1hf1zi8xhnqv3wa31h9wl")))
(define-public linux-libre-4.19-pristine-source
(let ((version linux-libre-4.19-version)
(hash (base32 "0c9xxqgv2i36hrr06dwz7f3idc04xpv0a5pxg08xdh03cnyf12cx")))
(hash (base32 "0mhgq6hdcls1af7nj999x1mds5b37s7vwin8nsb4q0lnx2y1da4x")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-4.19)))
(define-public linux-libre-4.14-version "4.14.328")
(define-public linux-libre-4.14-version "4.14.329")
(define-public linux-libre-4.14-gnu-revision "gnu1")
(define deblob-scripts-4.14
(linux-libre-deblob-scripts
@ -596,7 +611,7 @@ (define deblob-scripts-4.14
(base32 "1faagsj4i31z2bp83hflx3q9vrddjnn37a3ah2b47iaplva7z1nd")))
(define-public linux-libre-4.14-pristine-source
(let ((version linux-libre-4.14-version)
(hash (base32 "1igcpvnhwwrczfdsafmszvi0456k7f6j4cgpfw6v6afw09p95d8x")))
(hash (base32 "1dvb4xf0b7snabznl7bg7gga7ffdmywy8vr8q65pzl9yf6fnhdny")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-4.14)))
@ -629,6 +644,11 @@ (define (source-with-patches source patches)
(patches (append (origin-patches source)
patches))))
(define-public linux-libre-6.6-source
(source-with-patches linux-libre-6.6-pristine-source
(list %boot-logo-patch
%linux-libre-arm-export-__sync_icache_dcache-patch)))
(define-public linux-libre-6.5-source
(source-with-patches linux-libre-6.5-pristine-source
(list %boot-logo-patch
@ -748,6 +768,11 @@ (define (make-linux-libre-headers* version gnu-revision source)
(description "Headers of the Linux-Libre kernel.")
(license license:gpl2)))
(define-public linux-libre-headers-6.6
(make-linux-libre-headers* linux-libre-6.6-version
linux-libre-6.6-gnu-revision
linux-libre-6.6-source))
(define-public linux-libre-headers-6.5
(make-linux-libre-headers* linux-libre-6.5-version
linux-libre-6.5-gnu-revision
@ -1092,6 +1117,14 @@ (define* (make-linux-libre* version gnu-revision source supported-systems
;;; Generic kernel packages.
;;;
(define-public linux-libre-6.6
(make-linux-libre* linux-libre-6.6-version
linux-libre-6.6-gnu-revision
linux-libre-6.6-source
'("x86_64-linux" "i686-linux" "armhf-linux"
"aarch64-linux" "powerpc64le-linux" "riscv64-linux")
#:configuration-file kernel-config))
(define-public linux-libre-6.5
(make-linux-libre* linux-libre-6.5-version
linux-libre-6.5-gnu-revision
@ -6739,7 +6772,7 @@ (define-public ntfsfix/static
(define-public rdma-core
(package
(name "rdma-core")
(version "44.0")
(version "48.0")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/linux-rdma/rdma-core"
@ -6747,7 +6780,7 @@ (define-public rdma-core
version ".tar.gz"))
(sha256
(base32
"12w5v74wz1akac09frw7qk1yd06b00239zh7bvbvqyzjc0g61mi5"))))
"0h281dw2yph8pzfsr1wblqy6pb8nd9yj1pdf5c62zwc1l9b2fa3q"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f ;no tests
@ -8562,7 +8595,7 @@ (define-public procenv
(define-public libfabric
(package
(name "libfabric")
(version "1.11.2")
(version "1.19.0")
(source
(origin
(method url-fetch)
@ -8570,7 +8603,7 @@ (define-public libfabric
(string-append "https://github.com/ofiwg/libfabric/releases/download/v"
version "/libfabric-" version ".tar.bz2"))
(sha256
(base32 "1nnpfkwxhim2nqjkb1vwrb4wj4j3l6w6yvvy69fqam2snlhshazz"))))
(base32 "17pg0fb4fa77r1bmp0xk535m8n8fadpfdg93cb280ghhx55pck7i"))))
(build-system gnu-build-system)
(inputs `(("rdma-core" ,rdma-core)
,@(match (%current-system)
@ -8851,16 +8884,17 @@ (define-public mbpfan
(define-public psm2
(package
(name "psm2")
(version "11.2.230")
(version "12.0")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/intel/opa-psm2")
(commit (string-append "PSM2_" version))))
;; tag 'psm-v12.0' = commit ad5dd1b
(commit (string-append "psm-v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1bm7ndhi8qzmd0plnggj2h52yb34bab4k38530nsnkmv9smwdivl"))))
"04nar65ac11qqx41vkfs7iip8kfiah0zms7l4rmsxncpiz2iqfik"))))
(build-system gnu-build-system)
(arguments
(list #:make-flags

14
gnu/packages/lisp-check.scm
View file

@ -356,11 +356,11 @@ (define-public ecl-clunit
(sbcl-package->ecl-package sbcl-clunit))
(define-public sbcl-clunit2
(let ((commit "c3159275a6c5af166e60b592c3b7e22eaa69c048")
(let ((commit "b24c56851ee6ee6c4a9dc3725a634c06b604f207")
(revision "2"))
(package
(name "sbcl-clunit2")
(version (git-version "0.5.2" revision commit))
(version (git-version "0.6.1" revision commit))
(source
(origin
(method git-fetch)
@ -369,7 +369,7 @@ (define-public sbcl-clunit2
(commit commit)))
(file-name (git-file-name "cl-clunit2" version))
(sha256
(base32 "0n92z98dqfik3kfp25nz7yqycx4bpxlqbn69i5skcdnrj2ywmv01"))))
(base32 "03k4wc2zz31wcqcxy8fhq095i8xzcaxrzgrlrn2va10lcjs4v51b"))))
(build-system asdf-build-system/sbcl)
(synopsis "Unit testing framework for Common Lisp")
(description
@ -625,8 +625,8 @@ (define-public cl-kaputt
(sbcl-package->cl-source-package sbcl-kaputt))
(define-public sbcl-lift
(let ((commit "2594160d6ca3a77d8750110dfa63214256aab852")
(revision "2"))
(let ((commit "a7941845a9de72be60e66ea941aa34cbee35bf23")
(revision "3"))
(package
(name "sbcl-lift")
(version (git-version "1.7.1" revision commit))
@ -634,10 +634,10 @@ (define-public sbcl-lift
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/gwkkwg/lift")
(url "https://github.com/hraban/lift")
(commit commit)))
(sha256
(base32 "01xvz9sl5l5lai4h9dabmcjnm659wf5zllaxqbs55lffskp6jwq3"))
(base32 "1513n46fkqw8rnvz69s7xnwj476qm8ibdlwsr63qj9yh0mib0q6x"))
(file-name (git-file-name "lift" version))
(modules '((guix build utils)))
(snippet

284
gnu/packages/lisp-xyz.scm
View file

@ -1247,8 +1247,8 @@ (define-public ecl-tripod
(delete 'build-program))))))))
(define-public sbcl-trivial-timeout
(let ((commit "feb869357f40f5e109570fb40abad215fb370c6c")
(revision "1"))
(let ((commit "e70d9b4f7caeab83ea6ac50d724470fe49561e66")
(revision "2"))
(package
(name "sbcl-trivial-timeout")
(version (git-version "0.1.5" revision commit))
@ -1256,19 +1256,15 @@ (define-public sbcl-trivial-timeout
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/gwkkwg/trivial-timeout/")
(url "https://github.com/hraban/trivial-timeout")
(commit commit)))
(file-name (git-file-name "trivial-timeout" version))
(sha256
(base32 "1kninxwvvih9nhh7a9y8lfgi7pdr76675y1clw4ss17vz8fbim5p"))))
(base32 "0s8z9aj6b3kv21yiyk13cjylzf5zlnw9v86vcff477m1gk9yddjs"))))
(build-system asdf-build-system/sbcl)
(native-inputs
(list sbcl-lift))
(arguments
;; NOTE: (Sharlatan-20210202T231437+0000): Due to the age of this library
;; tests use some deprecated functionality and keep failing.
`(#:tests? #f))
(home-page "https://github.com/gwkkwg/trivial-timeout/")
(home-page "https://github.com/hraban/trivial-timeout")
(synopsis "Timeout library for Common Lisp")
(description
"This library provides an OS and implementation independent access to
@ -2260,8 +2256,9 @@ (define-public ecl-clx-truetype
(sbcl-package->ecl-package sbcl-clx-truetype))
(define-public sbcl-slynk
(let ((commit "df62abae73bd511885c9c7ec0ea7ea1469a00923")
(revision "8"))
;; Update together with emacs-sly.
(let ((commit "9c43bf65b967e12cef1996f1af5f0671d8aecbf4")
(revision "9"))
(package
(name "sbcl-slynk")
(version (git-version "1.0.43" revision commit))
@ -2273,7 +2270,7 @@ (define-public sbcl-slynk
(url "https://github.com/joaotavora/sly")
(commit commit)))
(sha256
(base32 "1nxijv52bja6la2i3asq7kklpj5li25454n52sgsc6xnnfvakbsv"))
(base32 "15nyr02ykkws4q79jcmxcawddg8sgq9v5l8k7jv7gg3hnpzxjlb2"))
(file-name (git-file-name "cl-slynk" version))))
(build-system asdf-build-system/sbcl)
(outputs '("out" "image"))
@ -2708,8 +2705,8 @@ (define-public ecl-cl-dot
(sbcl-package->ecl-package sbcl-cl-dot))
(define-public sbcl-cl-graph
(let ((commit "3cb786797b24883d784b7350e7372e8b1e743508")
(revision "1"))
(let ((commit "c617de35390cb02db88bc5b5febffafdb8947ae8")
(revision "2"))
(package
(name "sbcl-cl-graph")
(version (git-version "0.10.2" revision commit))
@ -2717,11 +2714,11 @@ (define-public sbcl-cl-graph
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/gwkkwg/cl-graph")
(url "https://github.com/hraban/cl-graph")
(commit commit)))
(file-name (git-file-name "cl-graph" version))
(sha256
(base32 "1748rj52f2jmd5jvsy9jwhn0zf73sjzjhwhnljvq6yi2kdqr30kl"))))
(base32 "0g1abkph9zb0m9zz6q2471ml9q9acdhwyapk8ra3bisqpwlxvpyf"))))
(build-system asdf-build-system/sbcl)
(arguments
;; TODO: (Sharlatan-20221118T215839+0000): Tests failed
@ -3610,8 +3607,8 @@ (define-public ecl-pythonic-string-reader
(sbcl-package->ecl-package sbcl-pythonic-string-reader))
(define-public sbcl-slime-swank
(let ((commit "0cc2e736112a0bc2a048ef6efd11dd67e3fbf7ad")
(revision "0"))
(let ((commit "735258a26bb97e85d25f39e4bef83c1f80c12f5d")
(revision "1"))
(package
(name "sbcl-slime-swank")
(version (git-version "2.28" revision commit))
@ -3623,7 +3620,7 @@ (define-public sbcl-slime-swank
(url "https://github.com/slime/slime/")
(commit commit)))
(sha256
(base32 "0iq9r4007rrnabj290y79i926x2m4j20j6b0x701pkywz926sn02"))
(base32 "0prskgzfqjmn8sc7p9nklnd0n1plwcvh40slgh23km31raplmzk7"))
(modules '((guix build utils)))
(snippet
;; The doc folder drags `gawk' into the closure. Doc is already
@ -5044,7 +5041,7 @@ (define-public ecl-cl-cffi-gtk
(define-public sbcl-cl-webkit
(package
(name "sbcl-cl-webkit")
(version "3.5.9")
(version "3.5.10")
(source
(origin
(method git-fetch)
@ -5054,7 +5051,7 @@ (define-public sbcl-cl-webkit
(file-name (git-file-name "cl-webkit" version))
(sha256
(base32
"00h61p5mrvvbycp703isy0wvgqlfb7k0cidw4vg75y7s29m3k6k0"))))
"0bn8idvbi58kg0g76lanvjzkgnkcy41yn9vbp7f80q9fa7w892rq"))))
(build-system asdf-build-system/sbcl)
(inputs
`(("cffi" ,sbcl-cffi)
@ -5601,8 +5598,8 @@ (define-public ecl-trivial-clipboard
(sbcl-package->ecl-package sbcl-trivial-clipboard))
(define-public sbcl-trivial-backtrace
(let ((commit "6eb65bde7229413040c81d42ea22f0e4c9c8cfc9")
(revision "1"))
(let ((commit "7f90b4a4144775cca0728791e4b92ac2557b07a1")
(revision "2"))
(package
(name "sbcl-trivial-backtrace")
(version (git-version "1.1.0" revision commit))
@ -5610,11 +5607,11 @@ (define-public sbcl-trivial-backtrace
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/gwkkwg/trivial-backtrace")
(url "https://github.com/hraban/trivial-backtrace")
(commit commit)))
(file-name (git-file-name "trivial-backtrace" version))
(sha256
(base32 "1mbaqiwj5034iw6jzw30jyhwzp1pvhnz1zcy0lns0z5j2h9ldapw"))))
(base32 "11j0p3vgmnn5q84xw7sacr5p3cvff2hfhsh2is8xpm2iwxc723kn"))))
(build-system asdf-build-system/sbcl)
(native-inputs
(list sbcl-lift))
@ -7730,8 +7727,8 @@ (define-public ecl-burgled-batteries3
(sbcl-package->ecl-package sbcl-burgled-batteries3))
(define-public sbcl-metabang-bind
(let ((commit "c93b7f7e1c18c954c2283efd6a7fdab36746ab5e")
(revision "1"))
(let ((commit "08196426cb099db0623e6cae2aeca566e0b788b2")
(revision "2"))
(package
(name "sbcl-metabang-bind")
(version (git-version "0.8.0" revision commit))
@ -7739,12 +7736,12 @@ (define-public sbcl-metabang-bind
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/gwkkwg/metabang-bind")
(url "https://github.com/hraban/metabang-bind")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"0hd0kr91795v77akpbcyqiss9p0p7ypa9dznrllincnmgvsxlmf0"))))
"14g7k3zhm8cd6bssc5mm5h6iq1dv5lfhiq33aimcmj5a6vbiq47d"))))
(build-system asdf-build-system/sbcl)
(native-inputs
(list sbcl-lift))
@ -9220,8 +9217,8 @@ (define-public ecl-periods
(sbcl-package->ecl-package sbcl-periods))
(define-public sbcl-metatilities-base
(let ((commit "6eaa9e3ff0939a93a92109dd0fcd218de85417d5")
(revision "1"))
(let ((commit "ef04337759972fd622c9b27b53149f3d594a841f")
(revision "2"))
(package
(name "sbcl-metatilities-base")
(version (git-version "0.6.6" revision commit))
@ -9229,12 +9226,12 @@ (define-public sbcl-metatilities-base
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/gwkkwg/metatilities-base")
(url "https://github.com/hraban/metatilities-base")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"0xpa86pdzlnf4v5g64j3ifaplx71sx2ha8b7vvakswi652679ma0"))))
"069rk5ncwvjnnzvvky6xiriynl72yzvjpnzl6jw9jf3b8na14zrk"))))
(build-system asdf-build-system/sbcl)
(native-inputs
(list sbcl-lift))
@ -9252,8 +9249,8 @@ (define-public ecl-metatilities-base
(sbcl-package->ecl-package sbcl-metatilities-base))
(define-public sbcl-cl-containers
(let ((commit "3d1df53c22403121bffb5d553cf7acb1503850e7")
(revision "3"))
(let ((commit "781ebfe0888bae46f07c018f7d473898b1bd4f5f")
(revision "4"))
(package
(name "sbcl-cl-containers")
(version (git-version "0.12.1" revision commit))
@ -9261,12 +9258,12 @@ (define-public sbcl-cl-containers
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/gwkkwg/cl-containers")
(url "https://github.com/hraban/cl-containers")
(commit commit)))
(file-name (git-file-name "cl-containers" version))
(sha256
(base32
"18s6jfq11n8nv9k4biz32pm1s7y9zl054ry1gmdbcf39nisy377y"))))
"1nrql8s1j123v5gscy99lxvhlzp0ijig9x94w30v3lwfa58hf90l"))))
(build-system asdf-build-system/sbcl)
(native-inputs
(list sbcl-lift))
@ -12135,6 +12132,50 @@ (define-public cl-jpeg
(define-public ecl-cl-jpeg
(sbcl-package->ecl-package sbcl-cl-jpeg))
(define-public sbcl-jpeg-turbo
(let ((commit "f79c646cc266c107bdace53572a31664754c6e0c")
(revision "1"))
(package
(name "sbcl-jpeg-turbo")
(version (git-version "1.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/shamazmazum/jpeg-turbo/")
(commit commit)))
(file-name (git-file-name "cl-jpeg-turbo" version))
(sha256
(base32 "1andd1ibbk3224idnpsnrn96flr5d1wm9ja3di57fs04wn577sag"))))
(build-system asdf-build-system/sbcl)
(arguments
(list #:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'fix-lib-paths
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "src/jpeg-turbo.lisp"
(("\"libturbojpeg\\.so\\.0\"")
(string-append "\""
(search-input-file inputs
"/lib/libturbojpeg.so")
"\""))))))))
(native-inputs
(list sbcl-fiveam))
(inputs
(list libjpeg-turbo sbcl-cffi))
(synopsis "Common Lisp wrapper for libjpeg-turbo")
(description
"This is a Common Lisp wrapper for libjpeg-turbo library which provides
TurboJPEG API for compressing and decompressing JPEG images.")
(home-page "https://github.com/shamazmazum/jpeg-turbo/")
(license license:bsd-2))))
(define-public cl-jpeg-turbo
(sbcl-package->cl-source-package sbcl-jpeg-turbo))
(define-public ecl-cl-jpeg-turbo
(sbcl-package->ecl-package sbcl-jpeg-turbo))
(define-public sbcl-png
(let ((commit "11b965fe378fd0561abe3616b18ff03af5179648")
(revision "1"))
@ -17097,12 +17138,21 @@ (define-public sbcl-trivial-shell
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/gwkkwg/trivial-shell")
(url "https://github.com/hraban/trivial-shell")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "08mpkl5ij5sjfsyn8pq2kvsvpvyvr7ha1r8g1224fa667b8k2q85"))))
(build-system asdf-build-system/sbcl)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'fix-paths
(lambda _
(substitute* "dev/definitions.lisp"
(("/bin/sh")
(which "sh"))))))))
(native-inputs
(list sbcl-lift))
(home-page "https://common-lisp.net/project/trivial-shell/")
@ -17687,31 +17737,34 @@ (define-public ecl-agnostic-lizard
(sbcl-package->ecl-package sbcl-agnostic-lizard))
(define-public sbcl-dynamic-classes
(package
(name "sbcl-dynamic-classes")
(version "1.0.2")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/gwkkwg/dynamic-classes")
(commit (string-append "version-" version))))
(file-name (git-file-name "dynamic-classes" version))
(sha256
(base32 "1z3ag6w4ff0v6715xa9zhvwjqnp4i6zrjfmxdz8m115sklbwgm6c"))))
(build-system asdf-build-system/sbcl)
(inputs
`(("metatilities-base" ,sbcl-metatilities-base)))
(arguments
;; NOTE: (Sharlatan-20210106222900+0000) Circular dependencies and failing
;; test suites. lift-standard.config contains referances to deprecated
;; functionality.
`(#:tests? #f))
(home-page "https://common-lisp.net/project/dynamic-classes/")
(synopsis "Dynamic class definition for Common Lisp")
(description "Dynamic-Classes helps to ease the prototyping process by
(let ((commit "ebd7405603f67b16e8f2bc08ce8e2bcfcf439501")
(revision "0"))
(package
(name "sbcl-dynamic-classes")
(version (git-version "1.0.2" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/hraban/dynamic-classes")
(commit commit)))
(file-name (git-file-name "dynamic-classes" version))
(sha256
(base32 "1k9lkchwyi2xhygp2v8ifq3kg1l3wcnihhzgr06jrivjxgdqpc1a"))))
(build-system asdf-build-system/sbcl)
(inputs
`(("metatilities-base" ,sbcl-metatilities-base)))
(arguments
;; NOTE: (Sharlatan-20210106222900+0000) Circular dependencies and failing
;; test suites. lift-standard.config contains referances to deprecated
;; functionality.
;; See https://github.com/hraban/dynamic-classes/issues/2
`(#:tests? #f))
(home-page "https://common-lisp.net/project/dynamic-classes/")
(synopsis "Dynamic class definition for Common Lisp")
(description "Dynamic-Classes helps to ease the prototyping process by
bringing dynamism to class definition.")
(license license:expat)))
(license license:expat))))
(define-public ecl-dynamic-classes
(sbcl-package->ecl-package sbcl-dynamic-classes))
@ -17720,41 +17773,47 @@ (define-public cl-dynamic-classes
(sbcl-package->cl-source-package sbcl-dynamic-classes))
(define-public sbcl-cl-markdown
;; NOTE: (Sharlatan-20210106214629+0000) latest version tag
;; "version-0.10.6_version-0.10.6" is failing to build due to missing system
;; #:container-dynamic-classes
(package
(name "sbcl-cl-markdown")
(version "0.10.4")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/gwkkwg/cl-markdown")
(commit (string-append "version-" version))))
(file-name (git-file-name "cl-markdown" version))
(sha256
(base32 "1wdjbdd1zyskxf7zlilcp6fmwkivybj0wjp64vvzb265d5xi7p8p"))))
(build-system asdf-build-system/sbcl)
(inputs
`(("anaphora" ,sbcl-anaphora)
("cl-containers" ,sbcl-cl-containers)
("cl-ppcre" ,sbcl-cl-ppcre)
("dynamic-classes" ,sbcl-dynamic-classes)
("metabang-bind" ,sbcl-metabang-bind)
("metatilities-base" ,sbcl-metatilities-base)))
(arguments
;; NOTE: (Sharlatan-20210107213629+0000) Tests depend on too many not
;; available systems, which themself are abandoned.
`(#:tests? #f))
(home-page "https://common-lisp.net/project/cl-markdown/")
(synopsis "Common Lisp rewrite of Markdown")
(description
"This is an implementation of a Markdown parser in Common Lisp.")
(license license:expat)))
;; The latest changes with fixes are not released yet, see
;; https://github.com/hraban/cl-markdown/issues/9
(let ((commit "3788802199228b49d0e06c3feb80c1c22af05cfc")
(revision "0"))
(package
(name "sbcl-cl-markdown")
(version (git-version "0.10.6" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/hraban/cl-markdown")
(commit commit)))
(file-name (git-file-name "cl-markdown" version))
(sha256
(base32 "1algqwmafipyf194cx9wfhg0pdx1ppx6s444p1pm8yaycbsyla1v"))))
(build-system asdf-build-system/sbcl)
(native-inputs
(list sbcl-lift sbcl-trivial-shell))
(inputs
(list sbcl-anaphora
sbcl-cl-containers
sbcl-cl-ppcre
sbcl-dynamic-classes
sbcl-metabang-bind
sbcl-metatilities-base))
(home-page "https://common-lisp.net/project/cl-markdown/")
(synopsis "Common Lisp rewrite of Markdown")
(description
"This is an implementation of a Markdown parser in Common Lisp.")
(license license:expat))))
(define-public ecl-cl-markdown
(sbcl-package->ecl-package sbcl-cl-markdown))
(let ((pkg (sbcl-package->ecl-package sbcl-cl-markdown)))
(package
(inherit pkg)
(arguments
;; XXX: Tests fail with "The function LIFT::GET-BACKTRACE-AS-STRING is
;; undefined" on ECL.
;; See https://github.com/hraban/cl-markdown/issues/11
'(#:tests? #f)))))
(define-public cl-markdown
(sbcl-package->cl-source-package sbcl-cl-markdown))
@ -18832,7 +18891,7 @@ (define-public cl-html-diff
(sbcl-package->cl-source-package sbcl-cl-html-diff))
(define-public sbcl-tooter
(let ((commit "2e1b22f0993419c1e7e6d10ead45d7bcafb5b6cb")
(let ((commit "2dcc2facddcacd79d0cce545a8c4b73c35826fc1")
(revision "4"))
(package
(name "sbcl-tooter")
@ -18845,10 +18904,13 @@ (define-public sbcl-tooter
(commit commit)))
(file-name (git-file-name "cl-tooter" version))
(sha256
(base32 "02ys58gzasvk7r84jmz6k522qcw2hkbgv8p0ax5i8dggjhr04cz2"))))
(base32 "1zisrmslj4rnibm02vxh7hbas2cfsjh6iizs2nfdg3a3pn7bhf6h"))))
(build-system asdf-build-system/sbcl)
(inputs
(list sbcl-cl-ppcre sbcl-documentation-utils sbcl-drakma
(list sbcl-alexandria
sbcl-cl-ppcre
sbcl-documentation-utils
sbcl-drakma
sbcl-yason))
(synopsis "Common Lisp client library for Mastodon instances")
(description
@ -18866,7 +18928,7 @@ (define-public cl-tooter
(define-public sbcl-croatoan
(package
(name "sbcl-croatoan")
(version "0.1")
(version "0.2")
(source
(origin
(method git-fetch)
@ -18875,7 +18937,7 @@ (define-public sbcl-croatoan
(commit (string-append "v" version))))
(file-name (git-file-name "cl-croatoan" version))
(sha256
(base32 "1whbvwc4df7zz0002xy3aczrpf4s3vk6kmyh9wydgwl112h060pd"))))
(base32 "0x2rlckyn8kn5mqy0fib8piggz694g3naarz2dvha1hsy4jhb1wg"))))
(build-system asdf-build-system/sbcl)
(arguments
'(#:phases
@ -19481,7 +19543,7 @@ (define-public sbcl-cl-mathstats
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/gwkkwg/cl-mathstats")
(url "https://github.com/hraban/cl-mathstats")
(commit commit)))
(file-name (git-file-name "cl-mathstats" version))
(sha256
@ -19491,7 +19553,7 @@ (define-public sbcl-cl-mathstats
(list sbcl-lift))
(inputs
(list sbcl-cl-containers sbcl-metatilities-base))
(home-page "https://github.com/gwkkwg/cl-mathstats")
(home-page "https://github.com/hraban/cl-mathstats")
(synopsis "Common Lisp collection of mathematical routines")
(description
"This package provides Common Lisp math and statistics routines.")
@ -21219,8 +21281,8 @@ (define-public cl-simple-inferiors
(sbcl-package->cl-source-package sbcl-simple-inferiors))
(define-public sbcl-metacopy
(let ((commit "1b5bf443206cc1dea7801ae23d1167bd02122d30")
(revision "1"))
(let ((commit "df7856f2a43fa91124fe780ef22f792040bc130c")
(revision "2"))
(package
(name "sbcl-metacopy")
(version (git-version "0.2.0" revision commit))
@ -21228,27 +21290,27 @@ (define-public sbcl-metacopy
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/gwkkwg/metacopy")
;; Upstream changed the maintaner.
;; legacy https://github.com/gwkkwg/metacopy
(url "https://github.com/hraban/metacopy")
(commit commit)))
(file-name (git-file-name "cl-metacopy" version))
(sha256
(base32 "1rzp112djgw5n76s6hy2aq92bc43p0zd5bgzvqwvgvws4pls42s9"))))
(base32 "0l5ryg8pvqz9sn9s8bsvd0plvcnm7crsx86iqk5wxblkialaizip"))))
(build-system asdf-build-system/sbcl)
(native-inputs
(list sbcl-asdf-system-connections sbcl-lift))
(inputs
(list sbcl-contextl sbcl-moptilities))
(home-page "https://github.com/gwkkwg/metacopy")
(home-page "https://github.com/hraban/metacopy")
(synopsis "Flexible Common Lisp shallow/deep copy mechanism")
(description
"This package provides a flexible shallow/deep copy mechanism for
Common Lisp.")
(license license:expat))))
;; NOTE: (Sharlatan-20221112T214131+0000): There is no ecl-moptilities variable
;; required for tests.
;;
;; ecl-metacopy
(define-public ecl-metacopy
(sbcl-package->ecl-package sbcl-metacopy))
(define-public cl-metacopy
(sbcl-package->cl-source-package sbcl-metacopy))

5
gnu/packages/lisp.scm
View file

@ -1061,8 +1061,9 @@ (define-public txr
'("txr-manpage.html" "txr-manpage.pdf")))))
(add-after 'install 'install-vim-files
(lambda _
(let ((syntax (string-append #$output
"/share/vim/vimfiles/syntax")))
(let ((syntax (string-append
#$output
"/share/vim/vimfiles/pack/guix/start/txr/syntax")))
(install-file "tl.vim" syntax)
(install-file "txr.vim" syntax)))))))
(native-inputs

147
gnu/packages/llvm.scm
View file

@ -26,6 +26,7 @@
;;; Copyright © 2022 John Kehayias <john.kehayias@protonmail.com>
;;; Copyright © 2022 Clément Lassieur <clement@lassieur.org>
;;; Copyright © 2022 Zhu Zihao <all_but_last@163.com>
;;; Copyright © 2023 Hilton Chain <hako@ultrarare.space>
;;;
;;; This file is part of GNU Guix.
;;;
@ -139,9 +140,19 @@ (define* (clang-runtime-from-llvm llvm
(patches (map search-patch patches)))
(llvm-monorepo (package-version llvm))))
(build-system cmake-build-system)
(native-inputs (package-native-inputs llvm))
(native-inputs
(if (version>=? version "15")
;; TODO: Remove this when GCC 12 is the default.
;; libfuzzer fails to build with GCC 11
(modify-inputs (package-native-inputs llvm)
(prepend gcc-12))
(package-native-inputs llvm)))
(inputs
(list llvm))
(append
(list llvm)
(if (version>=? version "15")
(list libffi)
'())))
(arguments
`(;; Don't use '-g' during the build to save space.
#:build-type "Release"
@ -150,6 +161,11 @@ (define* (clang-runtime-from-llvm llvm
(ice-9 match)
,@%cmake-build-system-modules)
#:phases (modify-phases (@ (guix build cmake-build-system) %standard-phases)
,@(if hash
'()
'((add-after 'unpack 'change-directory
(lambda _
(chdir "compiler-rt")))))
(add-after 'set-paths 'hide-glibc
;; Work around https://issues.guix.info/issue/36882. We need to
;; remove glibc from CPLUS_INCLUDE_PATH so that the one hardcoded
@ -342,6 +358,15 @@ (define* (clang-from-llvm llvm clang-runtime
(("@GLIBC_LIBDIR@")
(string-append libc "/lib"))))))
#t)))
,@(if (version>=? version "17")
'((add-after 'unpack 'include-test-runner
(lambda _
(substitute* "CMakeLists.txt"
((".*llvm_gtest" line)
(string-append
"add_subdirectory(${LLVM_THIRD_PARTY_DIR}/uni\
ttest third-party/unittest)\n" line))))))
'())
;; Awkwardly, multiple phases added after the same phase,
;; e.g. unpack, get applied in the reverse order. In other
;; words, adding 'change-directory last means it occurs
@ -574,11 +599,15 @@ (define-public (make-clang-toolchain clang libomp)
(define %llvm-monorepo-hashes
'(("14.0.6" . "14f8nlvnmdkp9a9a79wv67jbmafvabczhah8rwnqrgd5g3hfxxxx")
("15.0.7" . "12sggw15sxq1krh1mfk3c1f07h895jlxbcifpwk3pznh4m1rjfy2")))
("15.0.7" . "12sggw15sxq1krh1mfk3c1f07h895jlxbcifpwk3pznh4m1rjfy2")
("16.0.6" . "0jxmapg7shwkl88m4mqgfjv4ziqdmnppxhjz6vz51ycp2x4nmjky")
("17.0.3" . "1fhrnsv87if7kbqmrsxy2r7ykx3gnr9lmbmvkhvycc91ii4ihybx")))
(define %llvm-patches
'(("14.0.6" . ("clang-14.0-libc-search-path.patch"))
("15.0.7" . ("clang-15.0-libc-search-path.patch"))))
("15.0.7" . ("clang-15.0-libc-search-path.patch"))
("16.0.6" . ("clang-16.0-libc-search-path.patch"))
("17.0.3" . ("clang-17.0-libc-search-path.patch"))))
(define (llvm-monorepo version)
(origin
@ -703,34 +732,10 @@ (define-public llvm-14
("perl" ,perl)))))
(define-public clang-runtime-15
(let ((template (clang-runtime-from-llvm llvm-15)))
(package
(inherit template)
(arguments
(substitute-keyword-arguments (package-arguments template)
((#:phases phases '(@ (guix build cmake-build-system) %standard-phases))
#~(modify-phases #$phases
(add-after 'unpack 'change-directory
(lambda _
(chdir "compiler-rt")))))))
(native-inputs
(modify-inputs (package-native-inputs template)
(prepend gcc-12))) ;libfuzzer fails to build with GCC 11
(inputs
(modify-inputs (package-inputs template)
(append libffi))))))
(clang-runtime-from-llvm llvm-15))
(define-public clang-runtime-14
(let ((template (clang-runtime-from-llvm llvm-14)))
(package
(inherit template)
(arguments
(substitute-keyword-arguments (package-arguments template)
((#:phases phases '(@ (guix build cmake-build-system) %standard-phases))
#~(modify-phases #$phases
(add-after 'unpack 'change-directory
(lambda _
(chdir "compiler-rt"))))))))))
(clang-runtime-from-llvm llvm-14))
(define-public clang-15
(clang-from-llvm
@ -1458,6 +1463,74 @@ (define-public clang-3.5
#:legacy-build-shared-libs? #t
#:patches '("clang-3.5-libc-search-path.patch")))
(define-public llvm-16
(package
(inherit llvm-15)
(version "16.0.6")
(source (llvm-monorepo version))))
(define-public clang-runtime-16
(clang-runtime-from-llvm llvm-16))
(define-public clang-16
(clang-from-llvm
llvm-16 clang-runtime-16
#:tools-extra
(origin
(method url-fetch)
(uri (llvm-uri "clang-tools-extra"
(package-version llvm-16)))
(sha256
(base32
"0cbgffciql06a1i0ybyyqbnkkr4g7x8cxaar5a5v3415vd27hk0p")))))
(define-public libomp-16
(package
(inherit libomp-15)
(version (package-version llvm-16))
(source (llvm-monorepo version))
(native-inputs
(modify-inputs (package-native-inputs libomp-15)
(replace "clang" clang-16)
(replace "llvm" llvm-16)))))
(define-public clang-toolchain-16
(make-clang-toolchain clang-16 libomp-16))
(define-public llvm-17
(package
(inherit llvm-15)
(version "17.0.3")
(source (llvm-monorepo version))))
(define-public clang-runtime-17
(clang-runtime-from-llvm llvm-17))
(define-public clang-17
(clang-from-llvm
llvm-17 clang-runtime-17
#:tools-extra
(origin
(method url-fetch)
(uri (llvm-uri "clang-tools-extra"
(package-version llvm-17)))
(sha256
(base32
"0an16xdc8rgrdf0dcq3sdg82ajyb00h4bff9n0gm7gqf48ds0da8")))))
(define-public libomp-17
(package
(inherit libomp-15)
(version (package-version llvm-17))
(source (llvm-monorepo version))
(native-inputs
(modify-inputs (package-native-inputs libomp-15)
(replace "clang" clang-17)
(replace "llvm" llvm-17)))))
(define-public clang-toolchain-17
(make-clang-toolchain clang-17 libomp-17))
;; Default LLVM and Clang version.
(define-public libomp libomp-13)
(define-public llvm llvm-13)
@ -1602,6 +1675,20 @@ (define-public lld-11
(inputs (modify-inputs (package-inputs lld)
(replace "llvm" llvm-11)))))
(define-public lld-16
(package
(inherit lld-15)
(version (package-version llvm-16))
(source (llvm-monorepo version))
(inputs (list llvm-16))))
(define-public lld-17
(package
(inherit lld-15)
(version (package-version llvm-17))
(source (llvm-monorepo version))
(inputs (list llvm-17))))
(define-public lld lld-14)
(define* (make-lld-wrapper lld #:key lld-as-ld?)

3
gnu/packages/mail.scm
View file

@ -1867,7 +1867,8 @@ (define-public msmtp
(doc (string-append out "/share/doc/msmtp"))
(msmtpq "scripts/msmtpq")
(msmtpqueue "scripts/msmtpqueue")
(vimfiles (string-append out "/share/vim/vimfiles/syntax")))
(vimfiles (string-append
out "/share/vim/vimfiles/pack/guix/start/msmtp/syntax")))
(install-file (string-append msmtpq "/msmtpq") bin)
(install-file (string-append msmtpq "/msmtp-queue") bin)
(install-file (string-append msmtpqueue "/msmtp-enqueue.sh") bin)

66
gnu/packages/markup.scm
View file

@ -125,39 +125,39 @@ (define-public markdown
"See License.text in the distribution."))))
(define-public lowdown
(let ((commit "1de10c1d71bfb4348ae0beaec8b1547d5e114969")
(revision "1"))
(package
(name "lowdown")
(version (git-version "0.10.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/kristapsdz/lowdown")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "1wh07nkiihvp1m79sj4qlnqklnn0rfp3hwls8sqcp0bfd96wpa1h"))))
(build-system gnu-build-system)
(arguments
(list
#:test-target "regress"
#:phases
#~(modify-phases %standard-phases
(replace 'configure
(lambda _
(invoke "./configure"
(string-append "PREFIX=" #$output)
(string-append "MANDIR=" #$output "/share/man")))))
#:make-flags #~(list "CFLAGS=-fPIC")))
(native-inputs
(list which))
(home-page "https://kristaps.bsd.lv/lowdown/")
(synopsis "Simple Markdown translator")
(description "Lowdown is a Markdown translator producing HTML5,
roff documents in the ms and man formats, LaTeX, gemini, and terminal output.")
(license license:isc))))
(package
(name "lowdown")
(version "1.1.0")
(source
(origin
(method url-fetch)
(uri (string-append
"https://kristaps.bsd.lv/lowdown/snapshots/lowdown-"
version ".tar.gz"))
(sha256
(base32 "0y88gffrg1zrin0y53j4gbkmpia0r8p0kyklj501wavkqi83j7pk"))))
(build-system gnu-build-system)
(arguments
(list
#:test-target "regress"
#:phases
#~(modify-phases %standard-phases
(replace 'configure
(lambda _
(invoke "./configure"
(string-append "PREFIX=" #$output)
(string-append "MANDIR=" #$output "/share/man"))))
(replace 'install
(lambda _
(invoke "make" "install" "install_libs"))))
#:make-flags #~(list "CFLAGS=-fPIC")))
(native-inputs
(list which))
(home-page "https://kristaps.bsd.lv/lowdown/")
(synopsis "Simple Markdown translator")
(description "Lowdown is a Markdown translator producing HTML5, roff
documents in the ms and man formats, LaTeX, gemini, and terminal output.")
(license license:isc)))
(define-public discount
(package

1
gnu/packages/mastodon.scm
View file

@ -119,6 +119,7 @@ (define-public tuba
(list gdk-pixbuf ; so pixbuf loader cache (for webp) is generated
gettext-minimal
`(,glib "bin") ; for glib-compile-resources
gsettings-desktop-schemas ; for the org.gnome.system.proxy schema
pkg-config))
(inputs
(list gst-plugins-bad

109
gnu/packages/maths.scm
View file

@ -7594,60 +7594,65 @@ (define-public elpa-openmpi
(synopsis "Eigenvalue solvers for symmetric matrices (with MPI support)")))
(define-public elemental
(package
(name "elemental")
(version "0.87.7")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/elemental/Elemental")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1687xpjjzig27y2pnqv7hv09smpijyfdpz7qjgmcxf4shfajlfkc"))))
(build-system cmake-build-system)
(home-page "https://github.com/elemental/Elemental")
(native-inputs
(list gfortran))
(inputs
`(("blas" ,openblas)
("gfortran:lib" ,gfortran "lib")
("gmp" ,gmp)
("lapack" ,lapack)
("metis" ,metis)
("mpc" ,mpc)
("mpfr" ,mpfr)
("mpi" ,openmpi)
("qd" ,qd)))
(arguments
`(#:build-type "Release" ;default RelWithDebInfo not supported
#:configure-flags `("-DEL_DISABLE_PARMETIS:BOOL=YES"
"-DEL_AVOID_COMPLEX_MPI:BOOL=NO"
"-DEL_CACHE_WARNINGS:BOOL=YES"
"-DEL_TESTS:BOOL=YES"
"-DCMAKE_INSTALL_LIBDIR=lib"
"-DGFORTRAN_LIB=gfortran")
#:phases (modify-phases %standard-phases
(add-before 'check 'mpi-setup
,%openmpi-setup)
(add-before 'check 'setup-tests
(lambda _
;; Parallelism is done at the MPI layer.
(setenv "OMP_NUM_THREADS" "1")
#t))
(add-after 'install 'remove-tests
(lambda* (#:key outputs #:allow-other-keys)
;; Tests are installed, with no easy configuration
;; switch to prevent this, so delete them.
(delete-file-recursively
(string-append (assoc-ref outputs "out") "/bin"))
#t)))))
(synopsis "Dense and sparse-direct linear algebra and optimization")
(description "Elemental is a modern C++ library for distributed-memory
;; The build of 0.87.7 is failed for a long time due to new version of GCC. The
;; latest commit has fixes.
;; See https://github.com/elemental/Elemental/issues/254
(let ((commit "6eb15a0da2a4998bf1cf971ae231b78e06d989d9")
(revision "0"))
(package
(name "elemental")
(version (git-version "0.87.7" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/elemental/Elemental")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"06xcs4ic60ndcf2hq19gr8yjwdsnphpcyhapab41rkw726z4lm7p"))))
(build-system cmake-build-system)
(arguments
(list
#:build-type "Release" ;default RelWithDebInfo not supported
#:configure-flags
#~(list "-DEL_DISABLE_PARMETIS:BOOL=YES"
"-DEL_AVOID_COMPLEX_MPI:BOOL=NO"
"-DEL_CACHE_WARNINGS:BOOL=YES"
"-DEL_TESTS:BOOL=YES"
"-DCMAKE_INSTALL_LIBDIR=lib"
"-DGFORTRAN_LIB=gfortran")
#:phases
#~(modify-phases %standard-phases
(add-before 'check 'mpi-setup
#$%openmpi-setup)
(add-before 'check 'setup-tests
(lambda _ ;; Parallelism is done at the MPI layer.
(setenv "OMP_NUM_THREADS" "1")))
(add-after 'install 'remove-tests
(lambda _
;; Tests are installed, with no easy configuration
;; switch to prevent this, so delete them.
(delete-file-recursively
(string-append #$output "/bin/test")))))))
(native-inputs
(list gfortran))
(inputs
(list `(,gfortran "lib")
gmp
lapack
metis
mpc
mpfr
openmpi
qd
openblas))
(home-page "https://github.com/elemental/Elemental")
(synopsis "Dense and sparse-direct linear algebra and optimization")
(description "Elemental is a modern C++ library for distributed-memory
dense and sparse-direct linear algebra, conic optimization, and lattice
reduction.")
(license license:bsd-2)))
(license license:bsd-2))))
(define-public mcrl2
(package

61
gnu/packages/mes.scm
View file

@ -33,6 +33,7 @@ (define-module (gnu packages mes)
#:use-module (gnu packages texinfo)
#:use-module (guix build-system gnu)
#:use-module (guix download)
#:use-module (guix gexp)
#:use-module (guix git-download)
#:use-module (guix licenses)
#:use-module (guix packages)
@ -153,15 +154,16 @@ (define-public nyacc-1.00.2
(define-public mes
(package
(name "mes")
(version "0.24.2")
(version "0.25")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/mes/"
"mes-" version ".tar.gz"))
(sha256
(base32
"0vp8v88zszh1imm3dvdfi3m8cywshdj7xcrsq4cgmss69s2y1nkx"))))
(supported-systems '("armhf-linux" "i686-linux" "x86_64-linux"))
"0h49h85m1jkppfsv95zdxdrrw1q1mwswhq81lwxj1nbyasrm0lij"))))
(supported-systems '("aarch64-linux" "armhf-linux" "i686-linux"
"x86_64-linux" "riscv64-linux"))
(propagated-inputs (list mescc-tools nyacc-1.00.2))
(native-inputs
(append (list guile-3.0)
@ -173,8 +175,13 @@ (define-public mes
;; MesCC 64 bit .go files installed ready for use with Guile.
(list (cross-binutils "i686-unknown-linux-gnu")
(cross-gcc "i686-unknown-linux-gnu")))
(else
'())))
((string-prefix? "aarch64-linux" target-system)
;; Use cross-compiler rather than #:system "armhf-linux" to get
;; MesCC 64 bit .go files installed ready for use with Guile.
(let ((triplet "arm-linux-gnueabihf"))
(list (cross-binutils triplet) (cross-gcc triplet))))
(else
'())))
(list graphviz help2man
m2-planet
perl ;build-aux/gitlog-to-changelog
@ -206,26 +213,28 @@ (define-public mes
(define-public mescc-tools
(package
(name "mescc-tools")
(version "1.4.0")
(version "1.5.0")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://git.savannah.nongnu.org/r/mescc-tools.git")
(commit (string-append "Release_" version))
(recursive? #t))) ;for M2libc
(file-name (git-file-name name version))
(method url-fetch)
(uri (string-append "mirror://savannah/" name "/"
name "-" version ".tar.gz"))
(sha256
(base32
"0z2ni2qn2np1walcaqlxz8sinzb78d4hiq9glddzf26wxc226hs4"))))
"1vjczlajyrbjcx9ld35vhdqbxfdwwy3axg0jray3iwnrf70qr700"))))
(build-system gnu-build-system)
(supported-systems '("i686-linux" "x86_64-linux"
"armhf-linux" "aarch64-linux"
"riscv64-linux"))
(arguments
`(#:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out")))
#:test-target "test"
#:phases (modify-phases %standard-phases
(delete 'configure))))
(list
#:make-flags #~(list (string-append "PREFIX=" #$output))
#:test-target "test"
#:phases #~(modify-phases %standard-phases
(delete 'configure)
(add-after 'unpack 'patch-Kaem/test.sh
(lambda _
(substitute* "Kaem/test.sh"
(("#/usr/") "#! /usr")))))))
(native-inputs (list which))
(synopsis "Tools for the full source bootstrapping process")
(description
@ -239,19 +248,20 @@ (define-public mescc-tools
(define-public m2-planet
(package
(name "m2-planet")
(version "1.9.0")
(version "1.11.0")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/oriansj/m2-planet")
(commit (string-append "Release_" version))
(recursive? #t))) ;for M2libc
(file-name (git-file-name name version))
(method url-fetch)
(uri (string-append
"https://github.com/oriansj/M2-Planet/releases/download/"
"Release_" version "/" name "-" version ".tar.gz"))
(sha256
(base32
"0cgvvq91cbxxm93k8ayyvhpaf3c2lv10qw4wyqwn3hc1qb1cfyvr"))))
"1c510p55amxjyvjlx9jpa30gixlgmf6mmfnaqcs46412krymwg38"))))
(native-inputs (list mescc-tools))
(build-system gnu-build-system)
(supported-systems '("i686-linux" "x86_64-linux"
"armhf-linux" "aarch64-linux"
"riscv32-linux" "riscv64-linux"))
(arguments
`(#:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
,(string-append "CC=" (cc-for-target)))
@ -269,3 +279,4 @@ (define-public m2-planet
building GNU Mes.")
(home-page "https://github.com/oriansj/m2-planet")
(license gpl3+)))

6
gnu/packages/messaging.scm
View file

@ -2636,11 +2636,11 @@ (define-public telegram-purple
(license license:gpl2+)))
(define-public tdlib
(let ((commit "4d1d22d6f477d61f6ff2b8f6e49de1847092c5b4")
(let ((commit "4ed0b23c9c99868ab4d2d28e8ff244687f7b3144")
(revision "0"))
(package
(name "tdlib")
(version (git-version "1.8.16" revision commit))
(version (git-version "1.8.20" revision commit))
(source
(origin
(method git-fetch)
@ -2648,7 +2648,7 @@ (define-public tdlib
(url "https://github.com/tdlib/td")
(commit commit)))
(sha256
(base32 "0nv921k795kq0l993rxzd5pm5v3l3mnwbaxb7d7d0m0506l4w9fk"))
(base32 "16kprlcnphi89yfwgnlaxjwwb1xx24az8xd710rx8cslb4zv00qw"))
(file-name (git-file-name name version))))
(build-system cmake-build-system)
(arguments

24
gnu/packages/mold.scm
View file

@ -1,5 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2023 Zhu Zihao <all_but_last@163.com>
;;; Copyright © 2023 Efraim Flashner <efraim@flashner.co.il>
;;;
;;; This file is part of GNU Guix.
;;;
@ -34,7 +35,7 @@ (define-module (gnu packages mold)
(define-public mold
(package
(name "mold")
(version "1.10.1")
(version "2.3.2")
(source
(origin
(method git-fetch)
@ -43,10 +44,22 @@ (define-public mold
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1bqv1a93n3nks38k8fdc5i7v7ca2sav8n4xxaph0ikaqw1mkjcg7"))
(base32 "1p6w92caysy9h0vkl26iv3viv0lvwzvbd357yykls0p13hnzlzkr"))
(modules '((guix build utils)))
(snippet
#~(begin
;; Fix detection of i686 systems.
;; This can be removed with the next release of mold.
(substitute* "test/elf/common.inc"
(("echo i386") "echo i686"))
(substitute* '("test/elf/common.inc"
"test/elf/global-offset-table.sh"
"test/elf/i386_tls-module-base.sh"
"test/elf/large-alignment-dso.sh"
"test/elf/large-alignment.sh"
"test/elf/nocopyreloc.sh"
"test/elf/range-extension-thunk.sh")
(("MACHINE = i386") "MACHINE = i686"))
(for-each
(lambda (x)
(delete-file-recursively (string-append "third-party/" x)))
@ -55,7 +68,8 @@ (define-public mold
(arguments
(list
#:configure-flags #~(list "-DMOLD_USE_SYSTEM_MIMALLOC=ON"
"-DMOLD_USE_SYSTEM_TBB=ON")
"-DMOLD_USE_SYSTEM_TBB=ON"
"-DBUILD_TESTING=ON")
#:phases
#~(modify-phases %standard-phases
(add-before 'configure 'force-system-xxhash
@ -69,6 +83,10 @@ (define-public mold
(("CC=\"\\$\\{TEST_CC:-cc\\}\"") "CC=gcc")
(("CXX=\"\\$\\{TEST_CXX:-c\\+\\+\\}\"")
"CXX=g++"))))
(add-before 'configure 'skip-tbb-lto-test
(lambda _
;; This test needs tbb 2021.9.0 or newer
(delete-file "test/elf/lto-version-script.sh")))
(add-before 'configure 'disable-rpath-test
(lambda _
;; This test fails because mold expect the RUNPATH as-is,

8
gnu/packages/mpi.scm
View file

@ -141,7 +141,7 @@ (define-public hwloc-1
(define-public hwloc-2
(package
(inherit hwloc-1)
(version "2.9.2")
(version "2.9.3")
(source (origin
(method url-fetch)
(uri (string-append "https://download.open-mpi.org/release/hwloc/v"
@ -149,7 +149,7 @@ (define-public hwloc-2
"/hwloc-" version ".tar.bz2"))
(sha256
(base32
"1kv0n3b9knb8aawf0hxaxn9wc9bbpwh676r2gmb0pc7qfzvgv1qa"))))
"1v0dzzgzp40slakdwdb8vy0hy4m2ff3gnzqpzi8k8vbgap764h2w"))))
;; libnuma is no longer needed.
(inputs (modify-inputs (package-inputs hwloc-1)
@ -184,7 +184,7 @@ (define-public hwloc
(define-public openmpi
(package
(name "openmpi")
(version "4.1.5")
(version "4.1.6")
(source
(origin
(method url-fetch)
@ -192,7 +192,7 @@ (define-public openmpi
(version-major+minor version)
"/downloads/openmpi-" version ".tar.bz2"))
(sha256
(base32 "1qyvc77diyrxmviirdwqpibgm32c4vkdlvw8g79rsf2pq9mrhh56"))
(base32 "05g4245v0pdqcyjmgn50519ry5v5q8ig26iinmiynvaihm29jh7p"))
(patches (search-patches "openmpi-mtl-priorities.patch"))))
(properties

32
gnu/packages/multiprecision.scm
View file

@ -10,6 +10,7 @@
;;; Copyright © 2021 Vinicius Monego <monego@posteo.net>
;;; Copyright © 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2023 Janneke Nieuwenhuizen <janneke@gnu.org>
;;; Copyright © 2023 Sharlatan Hellseher <sharlatanus@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -251,30 +252,29 @@ (define-public irram
(define-public qd
(package
(name "qd")
(version "2.3.23")
(version "2.3.24")
(source
(origin
(method url-fetch)
(uri (string-append "https://crd-legacy.lbl.gov/~dhbailey/mpdist/qd-"
version ".tar.gz"))
(sha256
(base32 "09pfd77rmy370hy7qdqw84z21y9zpl3fcwzf93rhiv0kwhfg9smk"))))
(base32 "0f0fwsyh23p5zfyrj6n16q7b56g213fnhdc8dbl22r3fz1rnqyx4"))))
(build-system gnu-build-system)
(native-inputs
(list gfortran))
(native-inputs (list automake autoconf gfortran))
(arguments
`(#:configure-flags `("--disable-enable_fma" ;weird :/
"--disable-static"
"--enable-shared"
,,@(if (string-prefix? "aarch64"
(or (%current-target-system)
(%current-system)))
;; XXX: The qd_test test fails numerical
;; accuracy checks for 'dd_real::exp()' on
;; aarch64 with GCC 5.4 at -O2. Disabling
;; expensive optimizations lets it pass.
'("CXXFLAGS=-O3 -fno-expensive-optimizations")
'("CXXFLAGS=-O3")))))
(list
#:configure-flags
#~(list "--disable-enable_fma" ;weird :/
"--disable-static"
"--enable-shared"
#$@(if (target-aarch64?)
;; XXX: The qd_test test fails numerical
;; accuracy checks for 'dd_real::exp()' on
;; aarch64 with GCC 5.4 at -O2. Disabling
;; expensive optimizations lets it pass.
'("CXXFLAGS=-O3 -fno-expensive-optimizations")
'("CXXFLAGS=-O3")))))
(home-page "https://www.davidhbailey.com/dhbsoftware/")
(synopsis "Double-double and quad-double library")
(description "This package supports both a double-double

9
gnu/packages/music.scm
View file

@ -4982,7 +4982,7 @@ (define-public sfizz
(define-public musescore
(package
(name "musescore")
(version "4.0.2")
(version "4.1.1")
(source
(origin
(method git-fetch)
@ -4991,14 +4991,11 @@ (define-public musescore
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1yri94xs4xw0lsvmk5q7bqnpgmdadchfn08r7bb2y07jsi8qgm6w"))
(base32 "12h26k9qnsq027gdpch579nchwrqva1ymwm2fj5xmlh0aayrwy4d"))
(modules '((guix build utils)))
(snippet
'(begin
;; Remove unused libraries...
(for-each delete-file-recursively
'("thirdparty/freetype"))
;; ... and precompiled binaries.
;; Delete precompiled binaries.
(delete-file-recursively "src/diagnostics/crashpad_handler")
(substitute* "src/diagnostics/CMakeLists.txt"
(("install") "#install"))))))

47
gnu/packages/networking.scm
View file

@ -154,7 +154,6 @@ (define-module (gnu packages networking)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages qt)
#:use-module (gnu packages readline)
#:use-module (gnu packages ruby)
#:use-module (gnu packages samba)
#:use-module (gnu packages serialization)
#:use-module (gnu packages shells)
@ -867,25 +866,9 @@ (define-public nanomsg
(sha256
(base32 "01ddfzjlkf2dgijrmm3j3j8irccsnbgfvjcnwslsfaxnrmrq5s64"))))
(build-system cmake-build-system)
(outputs '("out" "doc"))
(arguments
`(#:configure-flags
(list
"-DNN_ENABLE_COVERAGE=ON")
#:phases
(modify-phases %standard-phases
(add-after 'install 'move-docs
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(doc (assoc-ref outputs "doc")))
(mkdir-p (string-append doc "/share/doc"))
(rename-file
(string-append out "/share/doc/nanomsg")
(string-append doc "/share/doc/nanomsg"))
#t))))))
(native-inputs
`(("asciidoctor" ,ruby-asciidoctor)
("pkg-config" ,pkg-config)))
(list "-DNN_ENABLE_COVERAGE=ON")))
(synopsis "Scalable socket library")
(description "Nanomsg is a socket library that provides several common
communication patterns. It aims to make the networking layer fast, scalable,
@ -4415,6 +4398,27 @@ (define-public nbd
network.")
(license license:gpl2)))
(define-public ngtcp2
(package
(name "ngtcp2")
(version "1.0.1")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/ngtcp2/ngtcp2/"
"releases/download/v" version "/"
"ngtcp2-" version ".tar.xz"))
(sha256
(base32 "0l84hnj9n4bfxjizgmqsqbz71jx7m00a7l1z43fg5ls3apx9ij11"))))
(build-system gnu-build-system)
(native-inputs (list cunit))
(home-page "https://nghttp2.org/ngtcp2/")
(synopsis "QUIC protocol implementation")
(description
"The ngtcp2 project is an effort to implement the RFC9000 (IETF)
QUIC protocol.")
(license license:expat)))
(define-public yggdrasil
(package
(name "yggdrasil")
@ -4540,7 +4544,7 @@ (define-public netdiscover
(define-public phantomsocks
(package
(name "phantomsocks")
(version "0.0.0-20230829023258-013a0002abe2")
(version "0.0.0-20231031033204-8b0ac27fc450")
(source (origin
(method git-fetch)
(uri (git-reference
@ -4549,10 +4553,11 @@ (define-public phantomsocks
(file-name (git-file-name name version))
(sha256
(base32
"0pqq4mh6dr7fb7i001wggwkxpvavxq0ps9h2cmm4gv8ygh4v6f10"))))
"1q4i8pgj6hzry9wzlczx729dmmgqdqfb26rfaim2ngmp1dyy9drl"))))
(build-system go-build-system)
(arguments
(list #:install-source? #f
(list #:go go-1.20
#:install-source? #f
#:import-path "github.com/macronut/phantomsocks"
#:build-flags #~'("-tags" #$(if (target-linux?)
"rawsocket"

25
gnu/packages/node.scm
View file

@ -738,14 +738,14 @@ (define-public llhttp-bootstrap
(define-public node-lts
(package
(inherit node)
(version "18.17.1")
(version "18.18.2")
(source (origin
(method url-fetch)
(uri (string-append "https://nodejs.org/dist/v" version
"/node-v" version ".tar.gz"))
(sha256
(base32
"0dachvhf5jxrb1av8mn2dikbhwklxsgc9y2zg4h50fcwh5d54mqi"))
"0ci1faxjsbp0lv05kskh5anfljn6zawqcf7dawiby5d5qg7x572h"))
(modules '((guix build utils)))
(snippet
'(begin
@ -903,7 +903,26 @@ (define-public node-lts
"/lib/node_modules/npm/node_modules"
"/tar/lib/write-entry.js")))
(substitute* file
(("this.stat.nlink > 1") "false")))))))))
(("this.stat.nlink > 1") "false")))))
(add-after 'install 'install-node-gyp-wrapper
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(dir (string-append out "/lib/node_modules/npm/bin/node-gyp-bin"))
(file (string-append dir "/node-gyp")))
(mkdir-p dir)
;; See https://github.com/npm/cli/issues/6842
(call-with-output-file file
(lambda (port)
(format port "#!~a/bin/sh
if [ \"x$npm_config_node_gyp\" = \"x\" ]; then
~a/bin/node \"~a/lib/node_modules/npm/node_modules/node-gyp/bin/node-gyp.js\" \"$@\"
else
\"$npm_config_node_gyp\" \"$@\"
fi"
(assoc-ref inputs "bash")
out
out)))
(chmod file #o555))))))))
(native-inputs
(list ;; Runtime dependencies for binaries used as a bootstrap.
c-ares-for-node

12
gnu/packages/package-management.scm
View file

@ -174,8 +174,8 @@ (define-public guix
;; Note: the 'update-guix-package.scm' script expects this definition to
;; start precisely like this.
(let ((version "1.4.0")
(commit "e863274e67e2242b970845783172c9f4e49405ca")
(revision 13))
(commit "a60ff4611a8814d1f33d64af07401762afbcc597")
(revision 14))
(package
(name "guix")
@ -191,7 +191,7 @@ (define-public guix
(commit commit)))
(sha256
(base32
"0g8p0w9qrqbzz3b4fzbvvqpdfgwhlxpz75n3ysa6haima5s19mp3"))
"08czk2789y21cydg1xwwrmah8hjaprdnzvb993n7d7d70ccxk5kz"))
(file-name (string-append "guix-" version "-checkout"))))
(build-system gnu-build-system)
(arguments
@ -1754,8 +1754,8 @@ (define-public guix-jupyter
(license license:gpl3+)))
(define-public nar-herder
(let ((commit "53682fac7e00cd2801406edbd014922c1720c347")
(revision "21"))
(let ((commit "bf539aa08edfe8010606a31c00e0296c3d400319")
(revision "22"))
(package
(name "nar-herder")
(version (git-version "0" revision commit))
@ -1766,7 +1766,7 @@ (define-public nar-herder
(commit commit)))
(sha256
(base32
"18mzrpc5ni8d6xbp1bg0nzdj0brmnji4jm1gyiq77dm17c118zyz"))
"1i9q7ys26r6y2xa4qqy21bcxlqiynxp3p1wl5gmyj33jnb9ryjby"))
(file-name (string-append name "-" version "-checkout"))))
(build-system gnu-build-system)
(arguments

20
gnu/packages/parallel.scm
View file

@ -9,7 +9,7 @@
;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com>
;;; Copyright © 2018–2022 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
;;; Copyright © 2019-2022 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2019-2023 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2020 Roel Janssen <roel@gnu.org>
;;; Copyright © 2021 Stefan Reichör <stefan@xsteve.at>
;;;
@ -185,7 +185,7 @@ (define-public xjobs
(define-public slurm
(package
(name "slurm")
(version "22.05.1")
(version "23.02.6")
(source (origin
(method url-fetch)
(uri (string-append
@ -193,7 +193,7 @@ (define-public slurm
version ".tar.bz2"))
(sha256
(base32
"0f3hhlki8g7slllsnyj1qikbsvr62i0hig85lcdcfnmsagzlhbyi"))
"08rz3r1rlnb3pmfdnbh542gm44ja0fdy8rkj4vm4lclc48cvqp2a"))
(modules '((guix build utils)))
(snippet
'(begin
@ -281,6 +281,20 @@ (define-public slurm
;; As noted in the link, YY.MM is the release scheme, and the 'maintenance'
;; digit does not introduce incompatibilities.
(define-public slurm-22.05
(package
(inherit slurm)
(version "22.05.1")
(source (origin
(inherit (package-source slurm))
(method url-fetch)
(uri (string-append
"https://download.schedmd.com/slurm/slurm-"
version ".tar.bz2"))
(sha256
(base32
"0f3hhlki8g7slllsnyj1qikbsvr62i0hig85lcdcfnmsagzlhbyi"))))))
(define-public slurm-21.08
(package
(inherit slurm)

28
gnu/packages/patches/agda-categories-use-stdlib-1.7.3.patch Normal file
View file

@ -0,0 +1,28 @@
From 76d3863a5e6e7b9ee948f10a3faec3420a2020f1 Mon Sep 17 00:00:00 2001
Message-ID: <76d3863a5e6e7b9ee948f10a3faec3420a2020f1.1698265016.git.dev@jpoiret.xyz>
From: Josselin Poiret <dev@jpoiret.xyz>
Date: Wed, 25 Oct 2023 22:15:43 +0200
Subject: [PATCH] Bump stdlib to 1.7.3
From: Josselin Poiret <dev@jpoiret.xyz>
---
agda-categories.agda-lib | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/agda-categories.agda-lib b/agda-categories.agda-lib
index 5b19c405..4d63d415 100644
--- a/agda-categories.agda-lib
+++ b/agda-categories.agda-lib
@@ -1,3 +1,3 @@
name: agda-categories
-depend: standard-library-1.7.2
+depend: standard-library-1.7.3
include: src/
base-commit: 9d61106740147a67fa2cae0a89ac066897b24a51
prerequisite-patch-id: 508dabd923ba9ac1ee4d8dab6697432b4bd8ba18
prerequisite-patch-id: b5f39b4fc9e4c9993ab31300de041ed2c7eb696b
--
2.41.0

51
gnu/packages/patches/agda-use-sphinx-5.patch Normal file
View file

@ -0,0 +1,51 @@
From 99ed1b59ef73fd35053810f6a09e034e1513caee Mon Sep 17 00:00:00 2001
Message-ID: <99ed1b59ef73fd35053810f6a09e034e1513caee.1698243851.git.dev@jpoiret.xyz>
From: Josselin Poiret <dev@jpoiret.xyz>
Date: Wed, 25 Oct 2023 16:23:32 +0200
Subject: [PATCH] Revert "Docs: bump Sphinx to 6.0.0"
From: Josselin Poiret <dev@jpoiret.xyz>
This reverts commit 40dd42eaa7c04e134fa38cb4f958414a76df27a7.
---
doc/user-manual/conf.py | 5 ++---
doc/user-manual/requirements.txt | 4 ++--
2 files changed, 4 insertions(+), 5 deletions(-)
diff --git a/doc/user-manual/conf.py b/doc/user-manual/conf.py
index 127f6582dc..d737ede19b 100644
--- a/doc/user-manual/conf.py
+++ b/doc/user-manual/conf.py
@@ -35,7 +35,7 @@ release = version
#
# If your change the version here also change it in the
# `requirements.txt` file [Issue #1936].
-needs_sphinx = '6.0.0'
+needs_sphinx = '5.0.0'
# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
@@ -43,8 +43,7 @@ needs_sphinx = '6.0.0'
extensions = [
'sphinx.ext.imgmath',
'sphinx.ext.ifconfig',
- 'sphinx.ext.imgconverter',
- 'sphinxcontrib.jquery'
+ 'sphinx.ext.imgconverter'
]
# Add any paths that contain templates here, relative to this directory.
diff --git a/doc/user-manual/requirements.txt b/doc/user-manual/requirements.txt
index 384b1466b4..656e6c9ac0 100644
--- a/doc/user-manual/requirements.txt
+++ b/doc/user-manual/requirements.txt
@@ -1,2 +1,2 @@
-Sphinx >= 7.2.5
-sphinx_rtd_theme >= 1.3.0
+Sphinx >= 5.0.0, != 5.2.0.post0
+sphinx_rtd_theme >= 1.0
base-commit: 08b79a684d712ba3dc4b26e5052ec49f49f5ff6c
--
2.41.0

95
gnu/packages/patches/clang-16.0-libc-search-path.patch Normal file
View file

@ -0,0 +1,95 @@
Clang attempts to guess file names based on the OS and distro (yes!),
but unfortunately, that doesn't work for us.
This patch makes it easy to insert libc's $libdir so that Clang passes the
correct absolute file name of crt1.o etc. to 'ld'. It also disables all
the distro-specific stuff and removes the hard-coded FHS directory names
to make sure Clang also works on foreign distros.
diff --git a/clang/lib/Driver/Distro.cpp b/clang/lib/Driver/Distro.cpp
index 87a0c5a58511..86ea82eda4b5 100644
--- a/clang/lib/Driver/Distro.cpp
+++ b/clang/lib/Driver/Distro.cpp
@@ -98,6 +98,10 @@ static Distro::DistroType DetectLsbRelease(llvm::vfs::FileSystem &VFS) {
}
static Distro::DistroType DetectDistro(llvm::vfs::FileSystem &VFS) {
+ // The compiler should always behave the same, even when used via Guix on a
+ // foreign distro.
+ return Distro::UnknownDistro;
+
Distro::DistroType Version = Distro::UnknownDistro;
// Newer freedesktop.org's compilant systemd-based systems
diff --git a/clang/lib/Driver/ToolChains/Cuda.cpp b/clang/lib/Driver/ToolChains/Cuda.cpp
index aa125bb308e8..8b86e144054c 100644
--- a/clang/lib/Driver/ToolChains/Cuda.cpp
+++ b/clang/lib/Driver/ToolChains/Cuda.cpp
@@ -124,6 +124,9 @@ CudaInstallationDetector::CudaInstallationDetector(
const Driver &D, const llvm::Triple &HostTriple,
const llvm::opt::ArgList &Args)
: D(D) {
+ // Don't look for CUDA in /usr.
+ return;
+
struct Candidate {
std::string Path;
bool StrictChecking;
diff --git a/clang/lib/Driver/ToolChains/Linux.cpp b/clang/lib/Driver/ToolChains/Linux.cpp
index c6fb290ffdb4..4736f4bb3392 100644
--- a/clang/lib/Driver/ToolChains/Linux.cpp
+++ b/clang/lib/Driver/ToolChains/Linux.cpp
@@ -189,6 +189,10 @@ Linux::Linux(const Driver &D, const llvm::Triple &Triple, const ArgList &Args)
Generic_GCC::PushPPaths(PPaths);
+ // Comment out the distro-specific tweaks so that they don't bite when
+ // using Guix on a foreign distro.
+#if 0
+
Distro Distro(D.getVFS(), Triple);
if (Distro.IsAlpineLinux() || Triple.isAndroid()) {
@@ -249,6 +253,7 @@ Linux::Linux(const Driver &D, const llvm::Triple &Triple, const ArgList &Args)
#ifdef ENABLE_LINKER_BUILD_ID
ExtraOpts.push_back("--build-id");
+#endif
#endif
// The selection of paths to try here is designed to match the patterns which
@@ -270,6 +275,7 @@ Linux::Linux(const Driver &D, const llvm::Triple &Triple, const ArgList &Args)
}
Generic_GCC::AddMultilibPaths(D, SysRoot, OSLibDir, MultiarchTriple, Paths);
+#if 0
addPathIfExists(D, concat(SysRoot, "/lib", MultiarchTriple), Paths);
addPathIfExists(D, concat(SysRoot, "/lib/..", OSLibDir), Paths);
@@ -298,9 +304,11 @@ Linux::Linux(const Driver &D, const llvm::Triple &Triple, const ArgList &Args)
addPathIfExists(D, concat(SysRoot, "/", OSLibDir, ABIName), Paths);
addPathIfExists(D, concat(SysRoot, "/usr", OSLibDir, ABIName), Paths);
}
+#endif
Generic_GCC::AddMultiarchPaths(D, SysRoot, OSLibDir, Paths);
+#if 0
// The deprecated -DLLVM_ENABLE_PROJECTS=libcxx configuration installs
// libc++.so in D.Dir+"/../lib/". Detect this path.
// TODO Remove once LLVM_ENABLE_PROJECTS=libcxx is unsupported.
@@ -310,6 +318,14 @@ Linux::Linux(const Driver &D, const llvm::Triple &Triple, const ArgList &Args)
addPathIfExists(D, concat(SysRoot, "/lib"), Paths);
addPathIfExists(D, concat(SysRoot, "/usr/lib"), Paths);
+#endif
+
+ // Add libc's lib/ directory to the search path, so that crt1.o, crti.o,
+ // and friends can be found.
+ addPathIfExists(D, "@GLIBC_LIBDIR@", Paths);
+
+ // Add GCC's lib/ directory so libstdc++.so can be found.
+ addPathIfExists(D, GCCInstallation.getParentLibPath(), Paths);
}
ToolChain::RuntimeLibType Linux::GetDefaultRuntimeLibType() const {

90
gnu/packages/patches/clang-17.0-libc-search-path.patch Normal file
View file

@ -0,0 +1,90 @@
Clang attempts to guess file names based on the OS and distro (yes!),
but unfortunately, that doesn't work for us.
This patch makes it easy to insert libc's $libdir so that Clang passes the
correct absolute file name of crt1.o etc. to 'ld'. It also disables all
the distro-specific stuff and removes the hard-coded FHS directory names
to make sure Clang also works on foreign distros.
diff --git a/clang/lib/Driver/Distro.cpp b/clang/lib/Driver/Distro.cpp
index 6e0087565941..c0a3ba7d7702 100644
--- a/clang/lib/Driver/Distro.cpp
+++ b/clang/lib/Driver/Distro.cpp
@@ -99,6 +99,10 @@ static Distro::DistroType DetectLsbRelease(llvm::vfs::FileSystem &VFS) {
}
static Distro::DistroType DetectDistro(llvm::vfs::FileSystem &VFS) {
+ // The compiler should always behave the same, even when used via Guix on a
+ // foreign distro.
+ return Distro::UnknownDistro;
+
Distro::DistroType Version = Distro::UnknownDistro;
// Newer freedesktop.org's compilant systemd-based systems
diff --git a/clang/lib/Driver/ToolChains/Cuda.cpp b/clang/lib/Driver/ToolChains/Cuda.cpp
index 3a577650eb08..ca3373edc127 100644
--- a/clang/lib/Driver/ToolChains/Cuda.cpp
+++ b/clang/lib/Driver/ToolChains/Cuda.cpp
@@ -128,6 +128,9 @@ CudaInstallationDetector::CudaInstallationDetector(
const Driver &D, const llvm::Triple &HostTriple,
const llvm::opt::ArgList &Args)
: D(D) {
+ // Don't look for CUDA in /usr.
+ return;
+
struct Candidate {
std::string Path;
bool StrictChecking;
diff --git a/clang/lib/Driver/ToolChains/Linux.cpp b/clang/lib/Driver/ToolChains/Linux.cpp
index 1ba222bf83b1..28766c5ab792 100644
--- a/clang/lib/Driver/ToolChains/Linux.cpp
+++ b/clang/lib/Driver/ToolChains/Linux.cpp
@@ -220,6 +220,10 @@ Linux::Linux(const Driver &D, const llvm::Triple &Triple, const ArgList &Args)
Generic_GCC::PushPPaths(PPaths);
+ // Comment out the distro-specific tweaks so that they don't bite when
+ // using Guix on a foreign distro.
+#if 0
+
Distro Distro(D.getVFS(), Triple);
if (Distro.IsAlpineLinux() || Triple.isAndroid()) {
@@ -280,6 +284,7 @@ Linux::Linux(const Driver &D, const llvm::Triple &Triple, const ArgList &Args)
#ifdef ENABLE_LINKER_BUILD_ID
ExtraOpts.push_back("--build-id");
+#endif
#endif
// The selection of paths to try here is designed to match the patterns which
@@ -301,6 +306,7 @@ Linux::Linux(const Driver &D, const llvm::Triple &Triple, const ArgList &Args)
}
Generic_GCC::AddMultilibPaths(D, SysRoot, OSLibDir, MultiarchTriple, Paths);
+#if 0
addPathIfExists(D, concat(SysRoot, "/lib", MultiarchTriple), Paths);
addPathIfExists(D, concat(SysRoot, "/lib/..", OSLibDir), Paths);
@@ -329,11 +335,21 @@ Linux::Linux(const Driver &D, const llvm::Triple &Triple, const ArgList &Args)
addPathIfExists(D, concat(SysRoot, "/", OSLibDir, ABIName), Paths);
addPathIfExists(D, concat(SysRoot, "/usr", OSLibDir, ABIName), Paths);
}
+#endif
Generic_GCC::AddMultiarchPaths(D, SysRoot, OSLibDir, Paths);
+#if 0
addPathIfExists(D, concat(SysRoot, "/lib"), Paths);
addPathIfExists(D, concat(SysRoot, "/usr/lib"), Paths);
+#endif
+
+ // Add libc's lib/ directory to the search path, so that crt1.o, crti.o,
+ // and friends can be found.
+ addPathIfExists(D, "@GLIBC_LIBDIR@", Paths);
+
+ // Add GCC's lib/ directory so libstdc++.so can be found.
+ addPathIfExists(D, GCCInstallation.getParentLibPath(), Paths);
}
ToolChain::RuntimeLibType Linux::GetDefaultRuntimeLibType() const {

29
gnu/packages/patches/emacs-debbugs-keep-patch-subject.patch
View file

@ -1,29 +0,0 @@
Preserve subject when replying to patch threads.
Upstream status: likely to be in the next release (bug#66330)
diff --git a/debbugs-gnu.el b/debbugs-gnu.el
index f366fba11d..cd549e364d 100644
--- a/debbugs-gnu.el
+++ b/debbugs-gnu.el
@@ -1747,6 +1747,12 @@ MERGED is the list of bugs merged with this one."
(format "Re: bug#%d: %s" id (alist-get 'subject status)))
(debbugs-gnu-summary-mode 1)))
+(defcustom debbugs-gnu-summary-keep-subject
+ (rx "[PATCH" (? (0+ (not (any digit "/]"))) (1+ digit) "/" (1+ digit)) "]")
+ "Regular expression which keeps the original message subject in replies."
+ :version "29.1"
+ :type 'regexp)
+
(defvar debbugs-gnu-summary-mode-map
(let ((map (make-sparse-keymap)))
(define-key map "C" #'debbugs-gnu-send-control-message)
@@ -1778,6 +1784,8 @@ MERGED is the list of bugs merged with this one."
(cons new new))
address))))))
,@(and debbugs-gnu-subject
+ (not (string-match-p debbugs-gnu-summary-keep-subject
+ debbugs-gnu-subject))
`((subject ,debbugs-gnu-subject)))))))
(defun debbugs-gnu-guess-current-id ()

105
gnu/packages/patches/ucx-tcp-iface-ioctl.patch
View file

@ -3,102 +3,121 @@ TCP network interfaces cannot be obtained via /sys/class/net. This patch
provides alternative code that uses the SIOCGIFCONF ioctl to get the
names of the available TCP network interfaces.
Initially submitted at <https://github.com/openucx/ucx/pull/4462>.
diff --git a/src/uct/tcp/tcp_iface.c b/src/uct/tcp/tcp_iface.c
index cad4a2709..7c1d2c9de 100644
index 6a6cd34fa..af32bb2e9 100644
--- a/src/uct/tcp/tcp_iface.c
+++ b/src/uct/tcp/tcp_iface.c
@@ -17,6 +17,8 @@
#include <sys/poll.h>
@@ -18,6 +18,8 @@
#include <netinet/tcp.h>
#include <dirent.h>
#include <float.h>
+#include <net/if.h>
+#include <sys/ioctl.h>
#define UCT_TCP_IFACE_NETDEV_DIR "/sys/class/net"
extern ucs_class_t UCS_CLASS_DECL_NAME(uct_tcp_iface_t);
@@ -586,6 +588,68 @@ static UCS_CLASS_DEFINE_NEW_FUNC(uct_tcp_iface_t, uct_iface_t, uct_md_h,
@@ -875,6 +877,85 @@ static UCS_CLASS_DEFINE_NEW_FUNC(uct_tcp_iface_t, uct_iface_t, uct_md_h,
uct_worker_h, const uct_iface_params_t*,
const uct_iface_config_t*);
+/* Fetch information about available network devices through an ioctl. */
+static ucs_status_t query_devices_ioctl(uct_md_h md,
+ uct_tl_device_resource_t **tl_devices_p,
+ unsigned *num_tl_devices_p)
+static ucs_status_t uct_tcp_query_devices_ioctl(uct_md_h md,
+ uct_tl_device_resource_t **devices_p,
+ unsigned *num_devices_p)
+{
+ int sock, err, i;
+ uct_tl_device_resource_t *resources, *tmp;
+ unsigned num_resources;
+ uct_tl_device_resource_t *devices, *tmp;
+ unsigned num_devices;
+ ucs_status_t status;
+ struct ifconf conf;
+ struct ifreq reqs[10];
+
+ conf.ifc_len = sizeof reqs;
+ conf.ifc_req = reqs;
+ conf.ifc_len = 0;
+ conf.ifc_req = NULL;
+
+ sock = socket(SOCK_STREAM, AF_INET, 0);
+ if (sock < 0) {
+ ucs_error("socket(2) failed: %m");
+ status = UCS_ERR_IO_ERROR;
+ goto out;
+ status = ucs_socket_create(AF_INET, SOCK_STREAM, &sock);
+ if (status != UCS_OK) {
+ goto out;
+ }
+
+ err = ioctl(sock, SIOCGIFCONF, &conf);
+ if (err < 0) {
+ ucs_error("SIOCGIFCONF ioctl failed: %m");
+ status = UCS_ERR_IO_ERROR;
+ goto out;
+ ucs_error("ioctl(SIOCGIFCONF) failed: %m");
+ status = UCS_ERR_IO_ERROR;
+ goto out;
+ }
+
+ resources = NULL;
+ num_resources = 0;
+ for (i = 0; i < conf.ifc_len / sizeof(struct ifreq); i++) {
+ const char *name = reqs[i].ifr_name;
+ conf.ifc_req = ucs_calloc(1, conf.ifc_len, "ifreq");
+ if (conf.ifc_req == NULL) {
+ ucs_error("memory alocation failed");
+ status = UCS_ERR_NO_MEMORY;
+ goto out;
+ }
+
+ if (!ucs_netif_is_active(name, AF_INET)) {
+ err = ioctl(sock, SIOCGIFCONF, &conf);
+ if (err < 0) {
+ ucs_error("ioctl(SIOCGIFCONF) failed: %m");
+ status = UCS_ERR_IO_ERROR;
+ goto out_free;
+ }
+
+ devices = NULL;
+ num_devices = 0;
+ for (i = 0; i < (conf.ifc_len / sizeof(struct ifreq)); i++) {
+ const char *name = conf.ifc_req[i].ifr_name;
+ sa_family_t family = conf.ifc_req[i].ifr_addr.sa_family;
+
+ if (!ucs_netif_is_active(name, family)) {
+ continue;
+ }
+
+ tmp = ucs_realloc(resources, sizeof(*resources) * (num_resources + 1),
+ "tcp resources");
+ tmp = ucs_realloc(devices, sizeof(*devices) * (num_devices + 1),
+ "tcp devices");
+ if (tmp == NULL) {
+ ucs_free(resources);
+ ucs_free(devices);
+ status = UCS_ERR_NO_MEMORY;
+ goto out;
+ goto out_free;
+ }
+ resources = tmp;
+ devices = tmp;
+
+ ucs_snprintf_zero(resources[i].name, sizeof(resources[i].name),
+ ucs_snprintf_zero(devices[num_devices].name,
+ sizeof(devices[num_devices].name),
+ "%s", name);
+ resources[i].type = UCT_DEVICE_TYPE_NET;
+ ++num_resources;
+ devices[num_devices].type = UCT_DEVICE_TYPE_NET;
+ ++num_devices;
+ }
+
+ *num_tl_devices_p = num_resources;
+ *tl_devices_p = resources;
+ status = UCS_OK;
+ *num_devices_p = num_devices;
+ *devices_p = devices;
+ status = UCS_OK;
+
+out_free:
+ ucs_free(conf.ifc_req);
+out:
+ if (sock >= 0) close(sock);
+ if (sock >= 0) {
+ close(sock);
+ }
+ return status;
+}
+
ucs_status_t uct_tcp_query_devices(uct_md_h md,
uct_tl_device_resource_t **devices_p,
unsigned *num_devices_p)
@@ -599,9 +663,9 @@ ucs_status_t uct_tcp_query_devices(uct_md_h md,
@@ -893,9 +974,9 @@ ucs_status_t uct_tcp_query_devices(uct_md_h md,
dir = opendir(UCT_TCP_IFACE_NETDEV_DIR);
if (dir == NULL) {
- ucs_error("opendir(%s) failed: %m", UCT_TCP_IFACE_NETDEV_DIR);
- status = UCS_ERR_IO_ERROR;
- goto out;
+ /* When /sys is unavailable, as can be the case in a container,
+ * resort to a good old 'ioctl'. */
+ return query_devices_ioctl(md, devices_p, num_devices_p);
+ /* When /sys is unavailable, as can be the case in a container,
+ * resort to a good old 'ioctl'. */
+ return uct_tcp_query_devices_ioctl(md, devices_p, num_devices_p);
}
devices = NULL;
@@ -655,7 +719,6 @@ ucs_status_t uct_tcp_query_devices(uct_md_h md,
@@ -963,7 +1044,6 @@ ucs_status_t uct_tcp_query_devices(uct_md_h md,
out_closedir:
closedir(dir);

4
gnu/packages/pdf.scm
View file

@ -117,7 +117,7 @@ (define-module (gnu packages pdf)
(define-public capypdf
(package
(name "capypdf")
(version "0.5.0")
(version "0.6.0")
(source (origin
(method git-fetch)
(uri (git-reference
@ -125,7 +125,7 @@ (define-public capypdf
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "1mb3i0jq04gg5cm1l07mn9kal5s748miql97j6fpaf1x1j2lcrsx"))))
(base32 "15l8zwc83l65xh739s0qddlv5qv537wnx74s8fcwlm1r8y7kf2x4"))))
(build-system meson-build-system)
(arguments
(list #:meson meson/newer

12
gnu/packages/python-check.scm
View file

@ -528,13 +528,13 @@ (define-public python-pytest-astropy-header
(define-public python-pytest-astropy
(package
(name "python-pytest-astropy")
(version "0.10.0")
(version "0.11.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pytest-astropy" version))
(sha256
(base32 "04g2rh261s3s6ym8mwi4iv2a6anbgwvwzcvkyilfck6yxrncdqw5"))))
(base32 "1d9rcxnc57rjp96xag1gq725pwl11b3k5hdaz7c3w5lixncsmbjf"))))
(build-system python-build-system)
(arguments (list #:tests? #f)) ; there are no tests
(native-inputs
@ -586,13 +586,13 @@ (define-public python-pytest-arraydiff
(define-public python-pytest-doctestplus
(package
(name "python-pytest-doctestplus")
(version "0.12.1")
(version "1.0.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pytest-doctestplus" version))
(sha256
(base32 "10ciqylgziihxwxryxvxgmkqgws51pqcarn0gbh1d4cxx55rx5vs"))))
(base32 "17ylfnrcvvp6sd13bfj40jl40paqmjsbywysszb3xqgdr86l8l7n"))))
(build-system pyproject-build-system)
(arguments
(list #:test-flags
@ -753,13 +753,13 @@ (define-public python-pytest-openfiles
(define-public python-pytest-remotedata
(package
(name "python-pytest-remotedata")
(version "0.4.0")
(version "0.4.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pytest-remotedata" version))
(sha256
(base32 "1j5106j331cfdyfcwzrbs3yby84mq1b0kddfysq12z2dwdcca8dy"))))
(base32 "0ndvnj9zghfj17haphrygiri9iy38wb8lwq1xdkfvlfd73v8ph05"))))
(build-system pyproject-build-system)
(arguments
(list

33
gnu/packages/python-science.scm
View file

@ -22,6 +22,7 @@
;;; Copyright © 2022 Eric Bavier <bavier@posteo.net>
;;; Copyright © 2022 Antero Mejr <antero@mailbox.org>
;;; Copyright © 2022 jgart <jgart@dismail.de>
;;; Copyright © 2023 Troy Figiel <troy@troyfigiel.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -349,6 +350,38 @@ (define-public python-scikit-optimize
@code{skopt} aims to be accessible and easy to use in many contexts.")
(license license:bsd-3)))
(define-public python-tdda
(package
(name "python-tdda")
(version "2.0.9")
(source
(origin
(method url-fetch)
(uri (pypi-uri "tdda" version))
(sha256
(base32 "1xs91s8b7cshjcqw88qsrjh10xly799k5rf2ycawqfz2mw8sy3br"))))
(build-system pyproject-build-system)
(arguments
'(#:phases (modify-phases %standard-phases
(add-after 'unpack 'relax-requirements
(lambda _
(substitute* "setup.py"
(("pandas>=1.5.2")
"pandas"))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "tdda" "test")))))))
(native-inputs (list python-numpy python-pandas))
(home-page "https://www.stochasticsolutions.com")
(synopsis "Test-driven data analysis library for Python")
(description
"The TDDA Python module provides command-line and Python API support
for the overall process of data analysis, through tools that peform
reference testing, constraint discovery for data, automatic inference
of regular expressions from text data and automatic test generation.")
(license license:expat))) ; MIT License
(define-public python-trimesh
(package
(name "python-trimesh")

35
gnu/packages/python-web.scm
View file

@ -5204,54 +5204,29 @@ (define-public python-google-auth-oauthlib
(define-public whoogle-search
(package
(name "whoogle-search")
(version "0.8.2")
(version "0.8.3")
(source (origin
(method url-fetch)
(uri (pypi-uri "whoogle-search" version))
(sha256
(base32
"1r6ymainwc3b8aar90b74mpnx3rsfscgzh0llwvsb03fbhiypw5g"))))
"09b9k97jflajvrs0npyz994rj8xkk400s98jw63b6vpsgw9q9nk4"))))
(build-system pyproject-build-system)
(arguments
(list
;; The tests need network access
#:tests? #f))
(propagated-inputs
(list python-attrs
python-beautifulsoup4
python-cachelib
python-certifi
python-cffi
(list python-beautifulsoup4
python-brotli
python-chardet
python-click
python-cryptography
python-cssutils
python-defusedxml
python-flask
python-flask-session
python-idna
python-itsdangerous
python-jinja2
python-markupsafe
python-more-itertools
python-packaging
python-pluggy
python-py
python-pycodestyle
python-pycparser
python-pyopenssl
python-pyparsing
python-pysocks
python-dateutil
python-dotenv
python-requests
python-soupsieve
python-stem
python-urllib3
python-waitress
python-wcwidth
python-werkzeug
python-dotenv))
python-waitress))
(home-page "https://github.com/benbusby/whoogle-search")
(synopsis "Self-hosted, ad-free, privacy-respecting metasearch engine")
(description

5
gnu/packages/python-xyz.scm
View file

@ -8726,6 +8726,7 @@ (define-public python-pikepdf
python-attrs
python-coverage
python-hypothesis
python-setuptools-scm
python-psutil
python-pytest
python-pytest-cov
@ -32572,13 +32573,13 @@ (define-public python-types-protobuf
(define-public python-types-pytz
(package
(name "python-types-pytz")
(version "2021.3.6")
(version "2023.3.1.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "types-pytz" version))
(sha256
(base32 "14yr5hg2ww8s4a0mz2bkd549fv8qgm538fnzxvqv92ld1pcpym3l"))))
(base32 "16mbinqac2fjjh4gqw2940q8ysjqwj0hrvj4p9mqz76l5hcx08yc"))))
(build-system python-build-system)
(home-page "https://github.com/python/typeshed")
(synopsis "Typing stubs for pytz")

112
gnu/packages/radio.scm
View file

@ -13,6 +13,7 @@
;;; Copyright © 2022 Greg Hogan <code@greghogan.com>
;;; Copyright © 2022 Ryan Tolboom <ryan@using.tech>
;;; Copyright © 2023 Sharlatan Hellseher <sharlatanus@gmail.com>
;;; Copyright © 2023 Efraim Flashner <efraim@flashner.co.il>
;;;
;;; This file is part of GNU Guix.
;;;
@ -218,49 +219,46 @@ (define-public liquid-dsp
(license license:expat)))
(define-public rtl-sdr
;; No tagged release since 2018
(let ((commit "5e73f90f1d85d8db2e583f3dbf1cff052d71d59b")
(revision "1"))
(package
(name "rtl-sdr")
(version (git-version "0.6.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://git.osmocom.org/rtl-sdr/")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "106fwzyr7cba952f3p3wm3hdqzm9zvm0v3gcz4aks2n7fnvrgrvn"))))
(build-system cmake-build-system)
(inputs
(list libusb))
(native-inputs
(list pkg-config))
(arguments
`(#:configure-flags '("-DDETACH_KERNEL_DRIVER=ON"
"-DINSTALL_UDEV_RULES=ON")
#:tests? #f ; No tests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-paths
(lambda* (#:key outputs #:allow-other-keys)
(substitute* "CMakeLists.txt"
(("DESTINATION \"/etc/udev/")
(string-append "DESTINATION \""
(assoc-ref outputs "out")
"/lib/udev/")))))
(add-after 'fix-paths 'fix-udev-rules
(lambda _
(substitute* "rtl-sdr.rules"
;; The plugdev group does not exist; use dialout as in
;; the hackrf package.
(("GROUP=\"plugdev\"")
"GROUP=\"dialout\"")))))))
(home-page "https://osmocom.org/projects/sdr/wiki/rtl-sdr")
(synopsis "Software defined radio driver for Realtek RTL2832U")
(description "DVB-T dongles based on the Realtek RTL2832U can be used as a
(package
(name "rtl-sdr")
(version "2.0.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://git.osmocom.org/rtl-sdr/")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0z8dn0gdava894fb9fs9gcwvmik31fcj6ldkggylc0mhgw5145pr"))))
(build-system cmake-build-system)
(inputs
(list libusb))
(native-inputs
(list pkg-config))
(arguments
`(#:configure-flags '("-DDETACH_KERNEL_DRIVER=ON"
"-DINSTALL_UDEV_RULES=ON")
#:tests? #f ; No tests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-paths
(lambda* (#:key outputs #:allow-other-keys)
(substitute* "CMakeLists.txt"
(("DESTINATION \"/etc/udev/")
(string-append "DESTINATION \""
(assoc-ref outputs "out")
"/lib/udev/")))))
(add-after 'fix-paths 'fix-udev-rules
(lambda _
(substitute* "rtl-sdr.rules"
;; The plugdev group does not exist; use dialout as in
;; the hackrf package.
(("GROUP=\"plugdev\"")
"GROUP=\"dialout\"")))))))
(home-page "https://osmocom.org/projects/sdr/wiki/rtl-sdr")
(synopsis "Software defined radio driver for Realtek RTL2832U")
(description "DVB-T dongles based on the Realtek RTL2832U can be used as a
cheap software defined radio, since the chip allows transferring the raw I/Q
samples to the host. @code{rtl-sdr} provides drivers for this purpose.
@ -275,7 +273,7 @@ (define-public rtl-sdr
To install the rtl-sdr udev rules, you must extend 'udev-service-type' with
this package. E.g.: @code{(udev-rules-service 'rtl-sdr rtl-sdr)}")
(license license:gpl2+))))
(license license:gpl2+)))
(define-public airspy
(let ((commit "6f92f47146aa8a8fce59b60927cf8c53da6851b3")
@ -1662,13 +1660,19 @@ (define-public wsjtx
(base32 "1lqd77v9xm58k9g9kfwxva3mmzm1yyk1v27nws5j1a293zfg2hkw"))))
(build-system qt-build-system)
(arguments
(list #:tests? #f)) ; No test suite
(list #:tests? #f ; No test suite
#:configure-flags
(if (this-package-native-input "ruby-asciidoctor")
#~'()
#~(list "-DWSJT_GENERATE_DOCS=OFF"))))
(native-inputs
(list asciidoc
gfortran
pkg-config
qttools-5
ruby-asciidoctor))
(append (list asciidoc
gfortran
pkg-config
qttools-5)
(if (supported-package? ruby-asciidoctor)
(list ruby-asciidoctor)
'())))
(inputs
(list boost
fftw
@ -1914,7 +1918,7 @@ (define-public rtl-433
(define-public multimon-ng
(package
(name "multimon-ng")
(version "1.2.0")
(version "1.3.0")
(source
(origin
(method git-fetch)
@ -1923,7 +1927,7 @@ (define-public multimon-ng
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "0hm7391z1iz2sk4xkwfphqz8qvihqjzsh45csz14gb4jfs1p6ks2"))))
(base32 "1gd3kxb1w2fc6waa8g7af036yicjbg4a7hs0dgdci4d3aqwyz690"))))
(build-system cmake-build-system)
(inputs
(list libx11 pulseaudio))
@ -2569,7 +2573,7 @@ (define-public dsdcc
(define-public sdrangel
(package
(name "sdrangel")
(version "7.16.0")
(version "7.17.0")
(source
(origin
(method git-fetch)
@ -2578,7 +2582,7 @@ (define-public sdrangel
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1c2pdxw2a3pysqlmr42gghg0ga33afwdp6wc97h7s6gwc5km6zlk"))))
(base32 "16hpnfzccpj8a3i24ryli870ym6kjih981sjapcqdc8va0q14qdz"))))
(build-system qt-build-system)
(native-inputs
(list doxygen graphviz pkg-config))

25
gnu/packages/ruby.scm
View file

@ -34,6 +34,7 @@
;;; Copyright © 2023 Yovan Naumovski <yovan@gorski.stream>
;;; Copyright © 2023 gemmaro <gemmaro.dev@gmail.com>
;;; Copyright © 2023 Janneke Nieuwenhuizen <janneke@gnu.org>
;;; Copyright © 2023 Zheng Junjie <873216071@qq.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -130,7 +131,13 @@ (define-public ruby-2.6
(build-system gnu-build-system)
(arguments
`(#:test-target "test"
#:configure-flags '("--enable-shared") ; dynamic linking
#:configure-flags
,(if (%current-target-system)
'(list (string-append
"LDFLAGS=-Wl,-rpath="
(assoc-ref %outputs "out") "/lib")
"--enable-shared")
''("--enable-shared")) ; dynamic linking
#:phases
(modify-phases %standard-phases
(add-before 'configure 'replace-bin-sh-and-remove-libffi
@ -148,6 +155,9 @@ (define-public ruby-2.6
"tool/rbinstall.rb")
(("/bin/sh") (which "sh")))
#t)))))
(native-inputs (if (%current-target-system)
(list this-package)
'()))
(inputs
(list readline openssl-1.1 libffi gdbm))
(propagated-inputs
@ -178,7 +188,13 @@ (define-public ruby-2.7
"042xrdk7hsv4072bayz3f8ffqh61i8zlhvck10nfshllq063n877"))))
(arguments
`(#:test-target "test"
#:configure-flags '("--enable-shared") ; dynamic linking
#:configure-flags
,(if (%current-target-system)
'(list (string-append
"LDFLAGS=-Wl,-rpath="
(assoc-ref %outputs "out") "/lib")
"--enable-shared")
''("--enable-shared")) ; dynamic linking
#:phases
(modify-phases %standard-phases
(add-before 'configure 'replace-bin-sh-and-remove-libffi
@ -205,7 +221,10 @@ (define-public ruby-2.7
(delete-file "test/ruby/test_io.rb"))))
'()))))
(native-inputs
(list autoconf))))
(append (if (%current-target-system)
(list this-package)
'())
(list autoconf)))))
(define ruby-2.7-fixed
(package

3
gnu/packages/rust-apps.scm
View file

@ -2206,7 +2206,8 @@ (define-public skim
(bin (string-append out "/bin"))
(share (string-append out "/share"))
(man (string-append out "/share/man"))
(vimfiles (string-append share "/vim/vimfiles/plugin"))
(vimfiles (string-append
share "/vim/vimfiles/pack/guix/start/skim/plugin"))
(bash-completion
(string-append share "/bash-completions/completions"))
(zsh-site (string-append share "/zsh/site-functions"))

66
gnu/packages/statistics.scm
View file

@ -672,14 +672,14 @@ (define-public r-lattice
(define-public r-matrix
(package
(name "r-matrix")
(version "1.6-1.1")
(version "1.6-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "Matrix" version))
(sha256
(base32
"1hlcxr38p4ybb67n25cc1ssh2q2r8cj0flc59lid8hclzvqv27ik"))))
"094n9qf5j7bzi4cyxhm276qx2b2qp676ad8w9gql0qhzhfc889li"))))
(properties `((upstream-name . "Matrix")))
(build-system r-build-system)
(propagated-inputs
@ -1178,14 +1178,14 @@ (define-public r-sendmailr
(define-public r-stringi
(package
(name "r-stringi")
(version "1.7.12")
(version "1.8.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "stringi" version))
(sha256
(base32
"02g0464sbprrbjlacx727p9ad1s5nbxl2mnvfmm9h7q000lsrs7g"))))
"0jm2f5wh231dzs46g7ic2k4633x9v9bd2a03dlpmq5rr46j299ay"))))
(build-system r-build-system)
(inputs (list icu4c))
(native-inputs (list pkg-config))
@ -1204,13 +1204,13 @@ (define-public r-stringi
(define-public r-stringr
(package
(name "r-stringr")
(version "1.5.0")
(version "1.5.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "stringr" version))
(sha256
(base32 "0fk34ql5ak57f06l10ai300kxay6r7kkkyfanh8r24qaf3bmkcaj"))))
(base32 "1pj5xwg8kq2jllmszgkw96qj37wlb0x0vx4f3m5j211zpd8yrbd4"))))
(build-system r-build-system)
(propagated-inputs
(list r-cli r-glue r-lifecycle r-magrittr r-rlang r-stringi r-vctrs))
@ -1448,13 +1448,13 @@ (define-public r-bh
(define-public r-evaluate
(package
(name "r-evaluate")
(version "0.22")
(version "0.23")
(source (origin
(method url-fetch)
(uri (cran-uri "evaluate" version))
(sha256
(base32
"0sz4zimz4brbd9sawdazfgipkmfzzdmdq01b5m8pnrql5xrxhiwh"))))
"0p540jl6sixpgk08cp2h9470d28p7n66pfafiskvz3rba0vrrky9"))))
(build-system r-build-system)
(home-page "https://github.com/hadley/evaluate")
(synopsis "Parsing and evaluation tools for R")
@ -1782,13 +1782,13 @@ (define-public r-r6
(define-public r-rlang
(package
(name "r-rlang")
(version "1.1.1")
(version "1.1.2")
(source (origin
(method url-fetch)
(uri (cran-uri "rlang" version))
(sha256
(base32
"16fsibxbh4fy62x6fw358qbniw085qs1wjyr75n22xv9g6kwjpjy"))))
"14l0dz36wav2jbz0dd3w34va68lrhr7fgd9dqf1v4nawdvff23ia"))))
(build-system r-build-system)
(home-page "http://rlang.tidyverse.org")
(synopsis "Functions for base types, core R and Tidyverse features")
@ -3063,13 +3063,13 @@ (define-public r-readr
(define-public r-plotrix
(package
(name "r-plotrix")
(version "3.8-2")
(version "3.8-4")
(source (origin
(method url-fetch)
(uri (cran-uri "plotrix" version))
(sha256
(base32
"07xwq3505qb2yak7pfda22yqwifj6m78f8b5rm0ym74808qrawmv"))))
"1mp8mb79prgf5fzlaix4fvslr4q67hrzxqdv3kr7mik1mf9jv8p6"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/plotrix")
(synopsis "Various plotting functions")
@ -3126,13 +3126,13 @@ (define-public r-latticeextra
(define-public r-rcpparmadillo
(package
(name "r-rcpparmadillo")
(version "0.12.6.4.0")
(version "0.12.6.6.0")
(source (origin
(method url-fetch)
(uri (cran-uri "RcppArmadillo" version))
(sha256
(base32
"1k7xq2yl4pkc7krz1bcdnx5kfj6n4zjmnm40nly2da2ji87agv49"))))
"171yflg07xi6570ich5gxhzsqqs7k3rxyhwg96amlkm1qn8v2pnk"))))
(properties `((upstream-name . "RcppArmadillo")))
(build-system r-build-system)
(propagated-inputs
@ -3195,14 +3195,14 @@ (define-public r-catools
(define-public r-rprojroot
(package
(name "r-rprojroot")
(version "2.0.3")
(version "2.0.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "rprojroot" version))
(sha256
(base32
"15zq606s544wmbvk5dw13xq0sspr9dsxyxlvzvn0r48f8x3l4q2h"))))
"16bf6ga5fgm83j3m67plw5i54az2vdbvw5m99ixaqkd24pxn7x5m"))))
(build-system r-build-system)
(native-inputs
(list r-knitr))
@ -3340,13 +3340,13 @@ (define-public r-blob
(define-public r-rsqlite
(package
(name "r-rsqlite")
(version "2.3.2")
(version "2.3.3")
(source (origin
(method url-fetch)
(uri (cran-uri "RSQLite" version))
(sha256
(base32
"09vbx3akqws8a07ai6qbp3jn1w05qsmazl79wl2dyvvjpzs8b62x"))))
"0i1cjhqcclglv62j4dclxraaj5jmqdwyj4bs3qfbd8jd8v5d1c9j"))))
(properties `((upstream-name . "RSQLite")))
(build-system r-build-system)
(propagated-inputs
@ -3370,13 +3370,13 @@ (define-public r-rsqlite
(define-public r-rcurl
(package
(name "r-rcurl")
(version "1.98-1.12")
(version "1.98-1.13")
(source (origin
(method url-fetch)
(uri (cran-uri "RCurl" version))
(sha256
(base32
"1ci6lsxm0f13yzw712gcbq23syl54x5llvhs2w1b8wwm9vqgx0qs"))))
"01pkmip1sllislmp34c25i9m9mlrid9b48xfjbf93sml55ijz985"))))
(properties `((upstream-name . "RCurl")))
(build-system r-build-system)
(arguments
@ -3412,13 +3412,13 @@ (define-public r-rcurl
(define-public r-xml
(package
(name "r-xml")
(version "3.99-0.14")
(version "3.99-0.15")
(source (origin
(method url-fetch)
(uri (cran-uri "XML" version))
(sha256
(base32
"1ygi65ddgbsamxw2rm0p2clfak1xj44xyisgk48y72cd9ldaddic"))))
"0giv03bixc4kcq4dmcwzra7gp01i41hfr1710fd1v2hacya4d8cq"))))
(properties
`((upstream-name . "XML")))
(build-system r-build-system)
@ -4543,13 +4543,13 @@ (define-public r-mvtnorm
(define-public r-matrixstats
(package
(name "r-matrixstats")
(version "1.0.0")
(version "1.1.0")
(source (origin
(method url-fetch)
(uri (cran-uri "matrixStats" version))
(sha256
(base32
"0vxd7g1fm4x0f72bs1xfik1d4yklvpjdyg1hpx86pl8fwr86i1wl"))))
"0h85hjvsmc8s3hyjdj83fykb2vl8jc7pb9ynp2xsl0q9v1sihrxl"))))
(properties `((upstream-name . "matrixStats")))
(build-system r-build-system)
(arguments
@ -6014,18 +6014,18 @@ (define-public r-minqa
(define-public r-rcppeigen
(package
(name "r-rcppeigen")
(version "0.3.3.9.3")
(version "0.3.3.9.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "RcppEigen" version))
(sha256
(base32
"0xhwgn77166ir7qnzl25mj0byskkqr0b36hihrpr2zaqsrzs8wsq"))))
"1faz1phvg7g14bchi88vizn5mfhgiwmsjg7jzkyf1yjg0f6vpsj1"))))
(properties `((upstream-name . "RcppEigen")))
(build-system r-build-system)
(propagated-inputs
(list r-rcpp r-matrix))
(list r-rcpp))
(home-page "http://eigen.tuxfamily.org")
(synopsis "Rcpp integration for the Eigen templated linear algebra library")
(description
@ -6060,14 +6060,14 @@ (define-public r-modelmetrics
(define-public r-matrixmodels
(package
(name "r-matrixmodels")
(version "0.5-2")
(version "0.5-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "MatrixModels" version))
(sha256
(base32
"0ap3mfzb2psjwlksfjzs2ycl5598bllwzx5hfmf9db4yjsydn1hw"))))
"03zjfxjk4l2dl1117slz163w0ky675d23sjfni4d7fdhqq359ny2"))))
(properties `((upstream-name . "MatrixModels")))
(build-system r-build-system)
(propagated-inputs
@ -6142,14 +6142,14 @@ (define-public r-nloptr
(define-public r-lme4
(package
(name "r-lme4")
(version "1.1-34")
(version "1.1-35.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "lme4" version))
(sha256
(base32
"1bbaxkrd5m3d40y6jdyrdr4vsjyzkfixbqjwj6c8inmks98f2wp8"))))
"0nzv1a22pfsf2ryw91h16ic4cb8y8g6wh0gx3msr7gv8dwwi3974"))))
(build-system r-build-system)
(propagated-inputs
(list r-boot
@ -6395,14 +6395,14 @@ (define-public r-tclust
(define-public r-ranger
(package
(name "r-ranger")
(version "0.15.1")
(version "0.16.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ranger" version))
(sha256
(base32
"0bibv9xf6w8k8nsc13f2yd4kx99aq0i758h3wfh089szgkpdjrad"))))
"12c52gqqwaaid5b062gad18ir1vala1z3a0z5j4af1xqzlxgk583"))))
(build-system r-build-system)
(propagated-inputs
(list r-rcpp r-matrix r-rcppeigen))

14
gnu/packages/tbb.scm
View file

@ -52,7 +52,19 @@ (define-public tbb
'(,@(if (target-riscv64?)
'("-DTBB_TEST_LINK_FLAGS=-latomic")
`())
"-DTBB_STRICT=OFF"))) ;; Don't fail on warnings
,@(if (target-arm32?)
'("-DTBB_TEST_COMPILE_FLAGS=-DTBB_TEST_LOW_WORKLOAD")
`())
"-DTBB_STRICT=OFF") ;; Don't fail on warnings
#:phases
(modify-phases %standard-phases
,@(if (target-arm32?)
`((add-after 'unpack 'adjust-test-suite
(lambda _
(substitute* "test/CMakeLists.txt"
;; Bus error, skipped on mips.
((".*test_malloc_pools.*") "")))))
'()))))
(home-page "https://www.threadingbuildingblocks.org")
(synopsis "C++ library for parallel programming")
(description

4
gnu/packages/tor.scm
View file

@ -63,14 +63,14 @@ (define-module (gnu packages tor)
(define-public tor
(package
(name "tor")
(version "0.4.8.7")
(version "0.4.8.9")
(source (origin
(method url-fetch)
(uri (string-append "https://dist.torproject.org/tor-"
version ".tar.gz"))
(sha256
(base32
"14blalf96240dg6crpmgyf2bdcj109dyx47h0w6a0a6vfjf2n3dj"))))
"0rfgn88izn74nh6gy42ggwmiicnylp73skrlwm61n4znj247vfsr"))))
(build-system gnu-build-system)
(arguments
(list #:configure-flags

45
gnu/packages/version-control.scm
View file

@ -3188,26 +3188,33 @@ (define-public git-lfs
#$(file-append (this-package-input "go-golang-org-x-net")
"/src/golang.org/x/net/publicsuffix/data")
"src/golang.org/x/net/publicsuffix/data")))
(add-before 'build 'man-gen
;; Without this, the binary generated in 'build
;; phase won't have any embedded usage-text.
(lambda _
(with-directory-excursion "src/github.com/git-lfs/git-lfs"
(invoke "make" "mangen"))))
(add-after 'build 'build-man-pages
(lambda _
(with-directory-excursion "src/github.com/git-lfs/git-lfs"
(invoke "make" "man"))))
(add-after 'install 'install-man-pages
(lambda* (#:key outputs #:allow-other-keys)
(with-directory-excursion "src/github.com/git-lfs/git-lfs/man"
(for-each
(lambda (manpage)
(install-file manpage
(string-append #$output "/share/man/man1")))
(find-files "." "^git-lfs.*\\.1$"))))))))
;; Only build the man pages if ruby-asciidoctor is available.
#$@(if (this-package-native-input "ruby-asciidoctor")
#~((add-before 'build 'man-gen
;; Without this, the binary generated in 'build
;; phase won't have any embedded usage-text.
(lambda _
(with-directory-excursion "src/github.com/git-lfs/git-lfs"
(invoke "make" "mangen"))))
(add-after 'build 'build-man-pages
(lambda _
(with-directory-excursion "src/github.com/git-lfs/git-lfs"
(invoke "make" "man"))))
(add-after 'install 'install-man-pages
(lambda* (#:key outputs #:allow-other-keys)
(with-directory-excursion "src/github.com/git-lfs/git-lfs/man"
(for-each
(lambda (manpage)
(install-file manpage
(string-append #$output "/share/man/man1")))
(find-files "." "^git-lfs.*\\.1$"))))))
#~()))))
;; make `ronn` available during build for man page generation
(native-inputs (list ronn-ng git-minimal ruby-asciidoctor))
(native-inputs
(append (list git-minimal)
(if (supported-package? ruby-asciidoctor)
(list ronn-ng ruby-asciidoctor)
'())))
(propagated-inputs
(list go-github-com-xeipuuv-gojsonschema
go-github-com-xeipuuv-gojsonreference

47
gnu/packages/video.scm
View file

@ -179,6 +179,7 @@ (define-module (gnu packages video)
#:use-module (gnu packages pulseaudio)
#:use-module (gnu packages python)
#:use-module (gnu packages python-build)
#:use-module (gnu packages python-check)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
@ -1782,14 +1783,14 @@ (define-public ffmpeg
(define-public ffmpeg-5
(package
(inherit ffmpeg)
(version "5.1.3")
(version "5.1.4")
(source (origin
(method url-fetch)
(uri (string-append "https://ffmpeg.org/releases/ffmpeg-"
version ".tar.xz"))
(sha256
(base32
"0biil32xnshg1b4lwzbdc5rxv1g7lpfsr5gdgaz96wlhzy9ka48v"))))))
"0qwhyhil805hns7yksdxagnrcc90h60al7lz1rc65kd1j2w3nf2l"))))))
(define-public ffmpeg-4
(package
@ -1812,14 +1813,14 @@ (define-public ffmpeg-4
(define-public ffmpeg-3.4
(package
(inherit ffmpeg-4)
(version "3.4.11")
(version "3.4.13")
(source (origin
(method url-fetch)
(uri (string-append "https://ffmpeg.org/releases/ffmpeg-"
version ".tar.xz"))
(sha256
(base32
"1rijdvcx8xjqwh084qchwz91vcj8wsvb4diax0g8miywpir00ccw"))))
"0np0yalqdrm7rn7iykgfzz3ly4vbgigrajg48c1l6n7qrzqvfszv"))))
(arguments
(substitute-keyword-arguments (package-arguments ffmpeg-4)
((#:modules modules %gnu-build-system-modules)
@ -1837,14 +1838,14 @@ (define-public ffmpeg-3.4
(define-public ffmpeg-2.8
(package
(inherit ffmpeg-3.4)
(version "2.8.20")
(version "2.8.22")
(source (origin
(method url-fetch)
(uri (string-append "https://ffmpeg.org/releases/ffmpeg-"
version ".tar.xz"))
(sha256
(base32
"1ivnfqmfnp3zmn1q2dxy4p85427y3r6d3jbnl5kprr7lqckf6rl5"))))
"0c8m4hhv2k5fybha908wzrpnf3wqkq52hayl658jq4bah0igdfqz"))))
(arguments
`(#:tests? #f ; XXX: Enable them later, if required
#:configure-flags
@ -2430,7 +2431,7 @@ (define-public gallery-dl
(define-public mpv-mpris
(package
(name "mpv-mpris")
(version "1.0")
(version "1.1")
(source
(origin
(method git-fetch)
@ -2439,7 +2440,7 @@ (define-public mpv-mpris
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "1vpx4kzyg4pssn1hql2ci4s9x08sdx2v0kphw4aryywnz04yjhzf"))))
(base32 "1384y8n3l0xk8hbad1nsj9ljzb1h02g3ln3jysd8bd6shbl0x4mx"))))
(build-system copy-build-system)
(arguments
'(#:install-plan
@ -2453,7 +2454,7 @@ (define-public mpv-mpris
(native-inputs
(list pkg-config))
(inputs
(list glib mpv))
(list ffmpeg glib mpv))
(home-page "https://github.com/hoyon/mpv-mpris")
(synopsis "MPRIS plugin for mpv")
(description "This package provides an @dfn{MPRIS} (Media Player Remote
@ -3272,33 +3273,45 @@ (define-public xvid
(define-public streamlink
(package
(name "streamlink")
(version "3.2.0")
(version "6.3.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "streamlink" version))
(sha256
(base32
"09nrspga15svzi0hmakcarbciav0nzf30hg1ff53gia473cd4w4p"))))
"0i2qym2plm4gpcq50vl67j69m8a4zz9mb8gi2xryx28pbnpdzh4k"))
(snippet
#~(begin (use-modules (guix build utils))
(substitute* "pyproject.toml"
(("trio >=0\\.22") "trio >=0.21"))))))
(build-system python-build-system)
(arguments
`(#:phases (modify-phases %standard-phases
`(#:phases
(modify-phases %standard-phases
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "python" "-m" "pytest")))))))
(native-inputs
(list python-freezegun python-mock python-pytest
python-requests-mock))
(list python-freezegun
python-requests-mock
python-pytest
python-pytest-asyncio
python-pytest-trio))
(propagated-inputs
(list python-pysocks
python-websocket-client
(list python-certifi
python-isodate
python-lxml
python-pycountry
python-pycryptodome
python-pysocks
python-requests
python-urllib3))
python-trio
python-trio-websocket
python-typing-extensions
python-urllib3
python-websocket-client))
(home-page "https://github.com/streamlink/streamlink")
(synopsis "Extract streams from various services")
(description "Streamlink is command-line utility that extracts streams

304
gnu/packages/vim.scm
View file

@ -31,17 +31,17 @@
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (gnu packages vim)
#:use-module ((guix licenses) #:prefix license:)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix gexp)
#:use-module (guix utils)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix build-system cmake)
#:use-module (guix build-system copy)
#:use-module (guix build-system gnu)
#:use-module (guix build-system python)
#:use-module (guix build-system pyproject)
#:use-module (guix build-system vim)
#:use-module (gnu packages)
#:use-module (gnu packages acl)
#:use-module (gnu packages admin) ; For GNU hostname
@ -299,12 +299,9 @@ (define-public vim-neocomplete
(sha256
(base32
"1h6sci5mhdfg6sjsjpi8l5li02hg858zcayiwl60y9j2gqnd18lv"))))
(build-system copy-build-system)
(build-system vim-build-system)
(arguments
'(#:install-plan
'(("autoload" "share/vim/vimfiles/")
("doc" "share/vim/vimfiles/")
("plugin" "share/vim/vimfiles/"))))
(list #:plugin-name "neocomplete"))
(synopsis "Next generation completion framework for Vim")
(description
"@code{neocomplete}, an abbreviation of 'neo-completion with cache',
@ -332,10 +329,9 @@ (define-public vim-neosnippet-snippets
(sha256
(base32
"151wpvbj6jb9jdkbhj3b77f5sq7y328spvwfbqyj1y32rg4ifmc6"))))
(build-system copy-build-system)
(build-system vim-build-system)
(arguments
'(#:install-plan
'(("neosnippets" "share/vim/vimfiles/"))))
(list #:plugin-name "neosnippet")) ; Extends neosnippet
(synopsis "Snippets for neosnippet")
(description
"@code{neosnippet-snippets} provides standard snippets for the Vim plugin
@ -361,17 +357,9 @@ (define-public vim-neosnippet
(sha256
(base32
"0k80syscmpnj38ks1fq02ds59g0r4jlg9ll7z4qc048mgi35alw5"))))
(build-system copy-build-system)
(build-system vim-build-system)
(arguments
'(#:install-plan
'(("autoload" "share/vim/vimfiles/")
("doc" "share/vim/vimfiles/")
("ftdetect" "share/vim/vimfiles/")
("ftplugin" "share/vim/vimfiles/")
("indent" "share/vim/vimfiles/")
("plugin" "share/vim/vimfiles/")
("rplugin" "share/vim/vimfiles/")
("syntax" "share/vim/vimfiles/"))))
(list #:plugin-name "neosnippet"))
(synopsis "Snippet support for Vim")
(description
"@code{neosnippet}, is a plugin for Vim which adds snippet support to Vim.
@ -400,12 +388,9 @@ (define-public vim-scheme
(sha256
(base32
"04h946vr4f8wxap3wzqs69y2v8n50g2zbk22jsg2kxr4c01z5cbw"))))
(build-system copy-build-system)
(build-system vim-build-system)
(arguments
'(#:install-plan
'(("ftplugin" "share/vim/vimfiles/")
("indent" "share/vim/vimfiles/")
("syntax" "share/vim/vimfiles/"))))
(list #:plugin-name "vim-scheme"))
(synopsis "Scheme syntax for Vim")
(description
"@code{vim-scheme} provides Scheme support for Vim (R7RS and CHICKEN).")
@ -428,10 +413,9 @@ (define-public vim-luna
(sha256
(base32
"0ka3qbhsh8lix1vyj4678j7dnchkd8khhirrnn3aylxxf8fpqyg8"))))
(build-system copy-build-system)
(build-system vim-build-system)
(arguments
'(#:install-plan
'(("colors" "share/vim/vimfiles/"))))
(list #:plugin-name "luna"))
(synopsis "Dark color theme for Vim")
(description
"@code{vim-luna} is a dark color theme for Vim.")
@ -455,11 +439,9 @@ (define-public vim-context-filetype
(sha256
(base32
"0alvrfhmd91zkd9h83s8wvgyq4iakcf6rybsyjd369qbgpcqky89"))))
(build-system copy-build-system)
(build-system vim-build-system)
(arguments
'(#:install-plan
'(("doc" "share/vim/vimfiles/")
("autoload" "share/vim/vimfiles/"))))
(list #:plugin-name "context_filetype"))
(synopsis "Context filetype library for Vim")
(description
"@code{vim-context-filetype} is context filetype library for Vim script.")
@ -479,15 +461,9 @@ (define-public vim-fugitive
(file-name (git-file-name name version))
(sha256
(base32 "138290g2aph1jjhaza6biky5qi4ka6435s01bwxivllgb53g3irc"))))
(build-system copy-build-system)
(build-system vim-build-system)
(arguments
'(#:install-plan
'(("autoload" "share/vim/vimfiles/")
("doc" "share/vim/vimfiles/")
("ftdetect" "share/vim/vimfiles/")
("ftplugin" "share/vim/vimfiles/")
("plugin" "share/vim/vimfiles/")
("syntax" "share/vim/vimfiles/"))))
(list #:plugin-name "fugitive"))
(home-page "https://github.com/tpope/vim-fugitive")
(synopsis "Vim plugin to work with Git")
(description "Vim-fugitive is a wrapper for Vim that complements the
@ -509,12 +485,9 @@ (define-public vim-airline
(sha256
(base32
"1aksmr73648pvyc75pfdz28k2d4ky52rn7xiwcv7lz87q3vqld7k"))))
(build-system copy-build-system)
(build-system vim-build-system)
(arguments
'(#:install-plan
'(("autoload" "share/vim/vimfiles/")
("doc" "share/vim/vimfiles/")
("plugin" "share/vim/vimfiles/"))))
(list #:plugin-name "airline"))
(synopsis "Statusline for Vim")
(description
"@code{vim-airline} is an extensible statusline for Vim.
@ -540,12 +513,9 @@ (define-public vim-airline-themes
(sha256
(base32
"1sb7nb7j7bz0pv1c9bgdy0smhr0jk2b1vbdv9yzghg5lrknpsbr6"))))
(build-system copy-build-system)
(build-system vim-build-system)
(arguments
'(#:install-plan
'(("autoload" "share/vim/vimfiles/")
("doc" "share/vim/vimfiles/")
("plugin" "share/vim/vimfiles/"))))
(list #:plugin-name "airline-themes"))
(synopsis "Collection of themes for Vim-airline")
(description
"@code{vim-airline-themes} is a collection of themes for @code{vim-airline}.")
@ -565,13 +535,9 @@ (define-public vim-syntastic
(file-name (git-file-name name version))
(sha256
(base32 "0j91f72jaz1s6aw1hpjiz30vk2ds2aqd9gisk91grsldy6nz6hhz"))))
(build-system copy-build-system)
(build-system vim-build-system)
(arguments
'(#:install-plan
'(("autoload" "share/vim/vimfiles/")
("doc" "share/vim/vimfiles/")
("plugin" "share/vim/vimfiles/")
("syntax_checkers" "share/vim/vimfiles/"))))
(list #:plugin-name "syntastic"))
(synopsis "Syntax checking plugin for Vim")
(description
"Vim-syntastic is a syntax checking plugin for Vim. It runs files through
@ -581,6 +547,17 @@ (define-public vim-syntastic
(home-page "https://github.com/vim-syntastic/syntastic")
(license license:wtfpl2)))
(define-public neovim-syntastic
(package
(inherit vim-syntastic)
(name "neovim-syntastic")
(synopsis "Syntax checking plugin for Neovim")
(description
"Vim-syntastic is a syntax checking plugin for Neovim. It runs files through
external syntax checkers and displays any resulting errors to the user. This
can be done on demand, or automatically as files are saved. If syntax errors
are detected, the user is notified.")))
(define-public vim-solarized
(let ((commit "62f656a02f93c5190a8753159e34b385588d5ff3")
(revision "1"))
@ -596,11 +573,15 @@ (define-public vim-solarized
(file-name (git-file-name name version))
(sha256
(base32 "0001mz5v3a8zvi3gzmxhi3yrsb6hs7qf6i497arsngnvj2cwn61d"))))
(build-system copy-build-system)
(build-system vim-build-system)
(arguments
'(#:install-plan
'(("vim-colors-solarized/colors" "share/vim/vimfiles/")
("vim-colors-solarized/doc" "share/vim/vimfiles/"))))
(list
#:plugin-name "solarized"
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'chdir
(lambda _
(chdir "vim-colors-solarized"))))))
(home-page "https://github.com/altercation/vim-colors-solarized")
(synopsis "Solarized color scheme for Vim")
(description
@ -631,9 +612,16 @@ (define-public vim-rainbow
(file-name (git-file-name name version))
(sha256
(base32 "1jya8wwlkmgs89hndrq6gsaskhk9g0fh62wdib8v9vz2x5g3738z"))))
(build-system copy-build-system)
(build-system vim-build-system)
(arguments
'(#:install-plan '(("opt" "share/vim/vimfiles/pack/rainbow/"))))
(list
#:plugin-name "rainbow"
#:mode "opt"
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'chdir
(lambda _
(chdir "opt/rainbow"))))))
(home-page "https://github.com/mason1920/rainbow")
(synopsis "Rainbow Parentheses Improved")
(description
@ -656,12 +644,11 @@ (define-public editorconfig-vim
(sha256
(base32
"0mp80bi2m56bb93szw87vy6q5s85yk9g91sl4pr51316rgdv5kkv"))))
(build-system copy-build-system)
(build-system vim-build-system)
(arguments
'(#:install-plan
'(("autoload" "share/vim/vimfiles/")
("doc" "share/vim/vimfiles/")
("plugin" "share/vim/vimfiles/"))))
(list
#:plugin-name "editorconfig"
#:vim? #t))
(home-page "https://editorconfig.org/")
(synopsis "EditorConfig plugin for Vim")
(description "EditorConfig makes it easy to maintain the correct coding
@ -686,11 +673,9 @@ (define-public neovim-packer
(sha256
(base32
"1xn08z3a21mgfvp5i1nv57jnldwxwnl5nkryiff3zc99b1mizigp"))))
(build-system copy-build-system)
(build-system vim-build-system)
(arguments
(list #:install-plan
#~'(("lua" "share/nvim/site/pack/guix/start/packer.nvim/")
("doc" "share/nvim/site/pack/guix/start/packer.nvim/"))))
(list #:plugin-name "packer.nvim"))
(home-page "https://github.com/wbthomason/packer.nvim")
(synopsis "Plugin manager for Neovim")
(description
@ -699,23 +684,6 @@ (define-public neovim-packer
is based on Vim's builtin plugin support.")
(license license:expat))))
(define-public neovim-syntastic
(package
(inherit vim-syntastic)
(name "neovim-syntastic")
(arguments
'(#:install-plan
'(("autoload" "share/nvim/site/")
("doc" "share/nvim/site/")
("plugin" "share/nvim/site/")
("syntax_checkers" "share/nvim/site/"))))
(synopsis "Syntax checking plugin for Neovim")
(description
"Vim-syntastic is a syntax checking plugin for Neovim. It runs files through
external syntax checkers and displays any resulting errors to the user. This
can be done on demand, or automatically as files are saved. If syntax errors
are detected, the user is notified.")))
(define-public neovim
(package
(name "neovim")
@ -889,12 +857,12 @@ (define-public vifm
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(vifm (string-append out "/share/vifm"))
(vimfiles (string-append out "/share/vim/vimfiles")))
(vimfiles (string-append
out "/share/vim/vimfiles/pack/guix/start/vifm")))
(copy-recursively (string-append vifm "/colors")
(string-append vimfiles "/colors"))
(copy-recursively (string-append vifm "/vim")
vimfiles)
(delete-file-recursively (string-append vifm "/colors"))
(delete-file-recursively (string-append vifm "/vim"))))))))
(native-inputs
(list groff)) ; for the documentation
@ -986,17 +954,9 @@ (define-public vim-guix-vim
(sha256
(base32
"013yn2n2nsspk12bldkc9xn4z4kjx9rvracbllc8i1nngldckxd0"))))
(build-system copy-build-system)
(build-system vim-build-system)
(arguments
'(#:install-plan
'(("autoload" "share/vim/vimfiles/")
("compiler" "share/vim/vimfiles/")
("doc" "share/vim/vimfiles/")
("indent" "share/vim/vimfiles/")
("ftdetect" "share/vim/vimfiles/")
("ftplugin" "share/vim/vimfiles/")
("plugin" "share/vim/vimfiles/")
("syntax" "share/vim/vimfiles/"))))
(list #:plugin-name "guix"))
(home-page "https://git.sr.ht/~efraim/guix.vim")
(synopsis "Guix integration in Vim")
(description "This package provides support for GNU Guix in Vim.")
@ -1015,11 +975,10 @@ (define-public vim-asyncrun
(sha256
(base32
"11zcw0sll6qg6ha0rr6n1cw5v73azvf7ycwn9lgiwa5cj7rrqjf4"))))
(build-system copy-build-system)
(build-system vim-build-system)
(arguments
'(#:install-plan
'(("plugin" "share/vim/vimfiles/")
("doc/" "share/vim/vimfiles/doc" #:include ("asyncrun.txt")))))
(list
#:plugin-name "asyncrun"))
(home-page "https://github.com/skywind3000/asyncrun.vim")
(synopsis "Run Async Shell Commands in Vim")
(description "This plugin takes the advantage of new APIs in Vim 8 (and
@ -1041,12 +1000,9 @@ (define-public vim-dispatch
(sha256
(base32
"1m8b5mn2zqlphzs6xfwykwmghf6p0wabrhpjmh7vav35jgcxc4wl"))))
(build-system copy-build-system)
(build-system vim-build-system)
(arguments
'(#:install-plan
'(("autoload" "share/vim/vimfiles/")
("doc" "share/vim/vimfiles/")
("plugin" "share/vim/vimfiles/"))))
(list #:plugin-name "dispatch"))
(home-page "https://github.com/tpope/vim-dispatch")
(synopsis "Asynchronous build and test dispatcher")
(description "Leverage the power of Vim's compiler plugins without being
@ -1071,11 +1027,9 @@ (define-public vim-gemini-vim
(file-name (git-file-name name version))
(sha256
(base32 "05ffhhfahjqwxyrqmsinsahrs15wknzl2qbj8mznyv319mn2civ2"))))
(build-system copy-build-system)
(build-system vim-build-system)
(arguments
`(#:install-plan
'(("ftdetect" "share/vim/vimfiles/")
("syntax" "share/vim/vimfiles/"))))
(list #:plugin-name "gemini"))
(home-page "https://git.sr.ht/~torresjrjr/gemini.vim")
(synopsis "Vim syntax highlighting plugin for Gemini")
(description "This Vim plugin provides a Vim syntax highlighting plugin
@ -1099,11 +1053,9 @@ (define-public vim-eunuch
(sha256
(base32
"1xadb22kd40swmww0qxmmkcpcq6viy8l167pjck5q32hfngll5d3"))))
(build-system copy-build-system)
(build-system vim-build-system)
(arguments
'(#:install-plan
'(("doc" "share/vim/vimfiles/")
("plugin" "share/vim/vimfiles/"))))
(list #:plugin-name "eunuch"))
(home-page "https://github.com/tpope/vim-eunuch")
(synopsis "Vim sugar for the UNIX shell commands")
(description "Vim sugar for the UNIX shell commands that need it the most.
@ -1127,13 +1079,9 @@ (define-public vim-slime
(file-name (git-file-name name version))
(sha256
(base32 "0k4b629jn6xlxyjxdl3cgm06v9dmx967rqnslv5m82c9kscwpyh4"))))
(build-system copy-build-system)
(build-system vim-build-system)
(arguments
`(#:install-plan
'(("autoload" "share/vim/vimfiles/")
("doc" "share/vim/vimfiles/")
("ftplugin" "share/vim/vimfiles/")
("plugin" "share/vim/vimfiles/"))))
(list #:plugin-name "vim-slime"))
(home-page "https://technotales.wordpress.com/2007/10/03/like-slime-for-vim/")
(synopsis "Vim plugin to give you some slime")
(description "SLIME is an Emacs plugin to turn Emacs into a Lisp IDE. You
@ -1159,28 +1107,29 @@ (define-public vim-vlime
(sha256
(base32 "1dfc1wyjsgkckrklkzvk4whaz3ahaka59rvm7rc724mabmk83pmp"))
(file-name (git-file-name name version))))
(build-system copy-build-system)
(build-system vim-build-system)
(arguments
'(#:install-plan
'(("vim/autoload" "share/vim/vimfiles/")
("vim/doc" "share/vim/vimfiles/")
("vim/ftplugin" "share/vim/vimfiles/")
("vim/syntax" "share/vim/vimfiles/")
("vim/test" "share/vim/vimfiles/")
;; This is so the Vimscript part of Vlime can find the lisp files.
("lisp" "share/vim/")
;; This is so lisp can load Vlime without the Vim part.
("lisp" "share/common-lisp/source/vlime"))
'(#:plugin-name "vlime"
#:phases
(modify-phases %standard-phases
;; Create a symbolic link to the .asd file so that
;; (asdf:load-system "vlime") finds the system.
(add-after 'install 'link-asd
(add-after 'symlink-files 'install-lisp-files
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(mkdir-p (string-append out "/share/common-lisp/systems/"))
(symlink (string-append out "/share/common-lisp/source/vlime/vlime.asd")
(string-append out "/share/common-lisp/systems/vlime.asd"))))))))
(let* ((out (assoc-ref outputs "out"))
(common-lisp (string-append out "/share/common-lisp")))
;; Create a symbolic link to the .asd file so that
;; (asdf:load-system "vlime") finds the system.
(copy-recursively "lisp" (string-append common-lisp "/source/vlime"))
(mkdir-p (string-append common-lisp "/systems/"))
(symlink (string-append common-lisp "/source/vlime/vlime.asd")
(string-append common-lisp "/systems/vlime.asd")))))
(add-after 'install 'symlink-files
(lambda* (#:key outputs plugin-name mode #:allow-other-keys)
(with-directory-excursion
(string-append (assoc-ref outputs "out")
"/share/vim/vimfiles/pack/guix/" mode "/" plugin-name)
(for-each (lambda (dir)
(symlink (string-append "./vim/" dir) dir))
(list "after" "autoload" "doc" "ftplugin" "syntax"))))))))
(propagated-inputs
(list cl-alexandria
cl-slime-swank
@ -1211,11 +1160,9 @@ (define-public vim-paredit
(file-name (git-file-name name version))
(sha256
(base32 "07d5s20r0ssd7rir45vy0fqlci44gha1a81rcilgar227f3nw328"))))
(build-system copy-build-system)
(build-system vim-build-system)
(arguments
'(#:install-plan
'(("doc" "share/vim/vimfiles/")
("plugin" "share/vim/vimfiles/"))))
(list #:plugin-name "paredit"))
(home-page "https://github.com/kovisoft/paredit")
(synopsis "Vim plugin for structured editing of Lisp S-expressions")
(description
@ -1237,11 +1184,9 @@ (define-public vim-surround
(file-name (git-file-name name version))
(sha256
(base32 "1b0bd5m5lv1p4d299mrwjfs2gk0zqwyaqdaid9hs9yqlxnr8s5nf"))))
(build-system copy-build-system)
(build-system vim-build-system)
(arguments
'(#:install-plan
'(("doc" "share/vim/vimfiles/")
("plugin" "share/vim/vimfiles/"))))
(list #:plugin-name "surround"))
(home-page "https://github.com/tpope/vim-surround")
(synopsis "Vim plugin for easy quoting and parenthesizing")
(description
@ -1262,12 +1207,9 @@ (define-public vim-gnupg
"/vim-gnupg-v" version ".tar.gz"))
(sha256
(base32 "02w8lgyyh7wgxysvmmcf9ja5c06vrbyh3alzvv97x8cfhrp0skn7"))))
(build-system copy-build-system)
(build-system vim-build-system)
(arguments
'(#:install-plan
'(("autoload" "share/vim/vimfiles/")
("doc" "share/vim/vimfiles/")
("plugin" "share/vim/vimfiles/"))))
(list #:plugin-name "vim-gnupg"))
(home-page "https://www.vim.org/scripts/script.php?script_id=3645")
(synopsis "Vim plugin for transparent editing of gpg encrypted files")
(description
@ -1293,12 +1235,9 @@ (define-public vim-ctrlp
(file-name (git-file-name name version))
(sha256
(base32 "0n68hg59h4rjn0ziqbsh5pr03l3kr98zk54659ny6vq107af1w96"))))
(build-system copy-build-system)
(build-system vim-build-system)
(arguments
'(#:install-plan
'(("autoload" "share/vim/vimfiles/")
("doc" "share/vim/vimfiles/")
("plugin" "share/vim/vimfiles/"))))
(list #:plugin-name "ctrlp.vim"))
(home-page "https://ctrlpvim.github.io/ctrlp.vim/")
(synopsis "Fuzzy file, buffer, mru, tag, etc. finder for Vim")
(description
@ -1330,12 +1269,9 @@ (define-public vim-mucomplete
(file-name (git-file-name name version))
(sha256
(base32 "054g80n09mmxxlh8xaic29bn8bgn3clvv732rymljdyvbj1mlhwd"))))
(build-system copy-build-system)
(build-system vim-build-system)
(arguments
'(#:install-plan
'(("autoload" "share/vim/vimfiles/")
("doc" "share/vim/vimfiles/")
("plugin" "share/vim/vimfiles/"))))
(list #:plugin-name "MUcomplete"))
(home-page "https://github.com/lifepillar/vim-mucomplete")
(synopsis "MUcomplete is a minimalist autocompletion plugin for Vim")
(description
@ -1359,12 +1295,9 @@ (define-public vim-gitgutter
(file-name (git-file-name name version))
(sha256
(base32 "0zpa7cs59a8sq0k3frlf9flpf30jcn239yrpmv40r7nqvxzglbpl"))))
(build-system copy-build-system)
(build-system vim-build-system)
(arguments
'(#:install-plan
'(("autoload" "share/vim/vimfiles/")
("doc" "share/vim/vimfiles/")
("plugin" "share/vim/vimfiles/"))))
(list #:plugin-name "gitgutter"))
(synopsis "Vim plugin which shows a git diff in the sign column")
(description
"A Vim plugin which shows a git diff in the sign column. It shows which
@ -1388,12 +1321,9 @@ (define-public vim-characterize
(file-name (git-file-name name version))
(sha256
(base32 "0ppsbsd696ih40d9f76mdl9sd9y7p2pvm65qmvq4b2zhkv4xbpxz"))))
(build-system copy-build-system)
(build-system vim-build-system)
(arguments
'(#:install-plan
'(("autoload" "share/vim/vimfiles/")
("doc" "share/vim/vimfiles/")
("plugin" "share/vim/vimfiles/"))))
(list #:plugin-name "characterize"))
(home-page "https://github.com/tpope/vim-characterize")
(synopsis "Vim plugin for showing Unicode character metadata")
(description
@ -1422,13 +1352,9 @@ (define-public vim-tagbar
(file-name (git-file-name name version))
(sha256
(base32 "1fqfs8msmr6d4kpvxqp14sdjvp5fj52q5w5kz71myzcd4kqzmirp"))))
(build-system copy-build-system)
(build-system vim-build-system)
(arguments
'(#:install-plan
'(("autoload" "share/vim/vimfiles/")
("doc" "share/vim/vimfiles/")
("plugin" "share/vim/vimfiles/")
("syntax" "share/vim/vimfiles/"))
'(#:plugin-name "tagbar"
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'link-universal-ctags
@ -1463,15 +1389,9 @@ (define-public vim-nerdtree
(file-name (git-file-name name version))
(sha256
(base32 "1si8qla86ng8cffbmfrk9gss0i3912yw0f1ph4bsiq0kk837lccp"))))
(build-system copy-build-system)
(build-system vim-build-system)
(arguments
'(#:install-plan
'(("autoload" "share/vim/vimfiles/")
("doc" "share/vim/vimfiles/")
("lib" "share/vim/vimfiles/")
("nerdtree_plugin" "share/vim/vimfiles/")
("plugin" "share/vim/vimfiles/")
("syntax" "share/vim/vimfiles/"))))
(list #:plugin-name "nerdtree"))
(home-page "https://github.com/preservim/nerdtree")
(synopsis "Tree explorer plugin for Vim")
(description
@ -1493,13 +1413,9 @@ (define-public vim-nerdcommenter
(file-name (git-file-name name version))
(sha256
(base32 "1ka2rqn7rby55aps3iblh1dcqxm7m7qx72mpkz6y2aaj8mkj0zyd"))))
(build-system copy-build-system)
(build-system vim-build-system)
(arguments
(list
#:install-plan
#~`(("autoload" "share/vim/vimfiles/")
("doc" "share/vim/vimfiles/")
("plugin" "share/vim/vimfiles/"))))
(list #:plugin-name "nerdcommenter"))
(home-page "https://github.com/preservim/nerdcommenter")
(synopsis "Vim plugin for easy commenting of code")
(description

4
gnu/packages/web-browsers.scm
View file

@ -586,7 +586,7 @@ (define-public vimb
(define-public nyxt
(package
(name "nyxt")
(version "3.9.1")
(version "3.9.2")
(source
(origin
(method git-fetch)
@ -595,7 +595,7 @@ (define-public nyxt
(commit version)))
(sha256
(base32
"1x7ia43yh024hwwsh2a6g2daznkzgjlisnxvjfcb9sgvfqfa368i"))
"1v85jn46d9vacjig6n9z797fch88fw6vzwbfdzlqdkm86vvm8dwn"))
(file-name (git-file-name "nyxt" version))
(modules '((guix build utils)))
(snippet

40
gnu/packages/web.scm
View file

@ -64,6 +64,7 @@
;;; Copyright © 2023 David Thompson <dthompson2@worcester.edu>
;;; Copyright © 2023 Christopher Howard <christopher@librehacker.com>
;;; Copyright © 2023 Felix Lechner <felix.lechner@lease-up.com>
;;; Copyright © 2023 Evgeny Pisemsky <evgeny@pisemsky.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -1004,7 +1005,7 @@ (define-public nginx-module-vts
(define-public lighttpd
(package
(name "lighttpd")
(version "1.4.72")
(version "1.4.73")
(source (origin
(method url-fetch)
(uri (string-append "https://download.lighttpd.net/lighttpd/"
@ -1012,7 +1013,7 @@ (define-public lighttpd
"lighttpd-" version ".tar.xz"))
(sha256
(base32
"1v2m9vavrg3ibbl0kfq3rjlnqicbrlrkqih1iisa0m5pd56xxjpp"))))
"1a2cx3di07wf8qii7dpk4yr5wvaz8c9na1x7523smc0lng81d241"))))
(build-system gnu-build-system)
(arguments
(list #:configure-flags
@ -4955,8 +4956,8 @@ (define-public python-tibanna
(license license:expat)))
(define-public guix-data-service
(let ((commit "1c7539418743e0dfe3a9cad22c414fd732daef8f")
(revision "42"))
(let ((commit "37a07c2d6e8285877ad0440a7e4ae286b7b65177")
(revision "43"))
(package
(name "guix-data-service")
(version (string-append "0.0.1-" revision "." (string-take commit 7)))
@ -4968,7 +4969,7 @@ (define-public guix-data-service
(file-name (git-file-name name version))
(sha256
(base32
"1gp4mhjssxky0jjjz916rfgz4w2f327wfd5ixb6lb00ydlfh5mws"))))
"0h83j10bq7dyda2idbqh5y6dcvmbl3xgc147yq4pk6bkh10y29y6"))))
(build-system gnu-build-system)
(arguments
(list
@ -7910,6 +7911,35 @@ (define-public geomyidae
@end enumerate\n")
(license license:expat)))
(define-public monsterid
(let ((commit "5597f177b473343ff5cad9a6e0e5b255312c6096")
(revision "0"))
(package
(name "monsterid")
(version (git-version "0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/splitbrain/monsterID")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "0ixyrrcbw96plcdna2rx1pqwisqy9hnr57kvamgj13lzlv2whdb3"))))
(build-system copy-build-system)
(arguments
'(#:install-plan '(("monsterid.php" "share/web/monsterid/")
("parts/" "share/web/monsterid/parts/"
#:include-regexp ("\\.png$")))))
(home-page "https://www.splitbrain.org/projects/monsterid")
(synopsis "The original MonsterID implementation")
(description
"MonsterID is a method to generate a unique monster image based upon a
certain identifier (IP address, email address, whatever). It can be
used to automatically provide personal avatar images in blog comments
or other community services.")
(license license:expat))))
(define-public cat-avatar-generator
(let ((commit "9360ea33f79d1dad3e43494b09878b5e3f6b41fa")
(revision "1"))

58
gnu/packages/wm.scm
View file

@ -64,6 +64,7 @@
;;; Copyright © 2023 Jonathan Brielamier <jonathan.brielmaier@web.de>
;;; Copyright © 2023 Vessel Wave <vesselwave@disroot.org>
;;; Copyright © 2023 Nicolas Graves <ngraves@ngraves.fr>
;;; Copyright © 2023 Jaeme Sifat <jaeme@runbox.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -786,7 +787,7 @@ (define-public i3lock-fancy
(define-public icewm
(package
(name "icewm")
(version "3.4.3")
(version "3.4.4")
(source (origin
(method url-fetch)
(uri (string-append
@ -794,7 +795,7 @@ (define-public icewm
version "/icewm-" version ".tar.lz"))
(sha256
(base32
"1r2x7acjahq4666mds1di46zc32sl80592wllghqcp5800jpjcjm"))))
"0cdsb2d45dwcr2dm4jfh0z5g6pkb0ghd4jaybxqiz74mbw5rmjhv"))))
(build-system gnu-build-system)
(native-inputs (list pkg-config))
(inputs (list fontconfig
@ -1083,7 +1084,8 @@ (define-public fluxbox
(add-after 'install 'install-vim-files
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(syntax (string-append out "/share/vim/vimfiles/syntax")))
(syntax (string-append
out "/share/vim/vimfiles/pack/guix/start/fluxbox/syntax")))
(copy-recursively "3rd/vim/vim/syntax" syntax)
#t)))
(add-after 'install 'install-xsession
@ -1490,6 +1492,56 @@ (define-public cwm
project derived from the original Calm Window Manager.")
(license license:isc)))
(define-public dunst
(package
(name "dunst")
(version "1.9.2")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/dunst-project/dunst")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "17zrw7jrnlyln81pxw7p4jgvl7j1w1gf488nfskhns6j6dcz90gh"))))
(build-system gnu-build-system)
(arguments
(list
#:tests? #f ;no check target
#:make-flags #~(list (string-append "CC="
#$(cc-for-target))
(string-append "PREFIX=" %output)
(string-append "SYSCONFDIR=" %output "/etc")
;; Otherwise it tries to install service file
;; to "dbus" store directory.
(string-append "SERVICEDIR_DBUS=" %output
"/share/dbus-1/services")
"dunstify")
#:phases #~(modify-phases %standard-phases
(delete 'configure))))
(native-inputs (list pkg-config perl ;for pod2man
which))
(inputs (list dbus
(librsvg-for-system) ;for svg support
glib
cairo
pango
libnotify ;for dunstify
libx11
libxscrnsaver
libxinerama
libxrandr
libxdg-basedir
wayland)) ;for wayland support
(home-page "https://dunst-project.org/")
(synopsis "Customizable and lightweight notification daemon")
(description
"Dunst is a highly configurable and minimalistic notification daemon.
It provides @code{org.freedesktop.Notifications} D-Bus service, so it is
started automatically on the first call via D-Bus.")
(license license:bsd-3)))
(define-public dwl
(package
(name "dwl")

9
gnu/tests.scm
View file

@ -33,6 +33,10 @@ (define-module (gnu tests)
#:use-module (gnu services base)
#:use-module (gnu services shepherd)
#:use-module (guix discovery)
#:use-module (guix monads)
#:use-module ((guix store) #:select (%store-monad))
#:use-module ((guix utils)
#:select (%current-system %current-target-system))
#:use-module (srfi srfi-1)
#:use-module (srfi srfi-9 gnu)
#:use-module (ice-9 match)
@ -284,8 +288,9 @@ (define (write-system-test test port)
(define-gexp-compiler (compile-system-test (test <system-test>)
system target)
"Compile TEST to a derivation."
;; XXX: SYSTEM and TARGET are ignored.
(system-test-value test))
(mparameterize %store-monad ((%current-system system)
(%current-target-system target))
(system-test-value test)))
(define (test-modules)
"Return the list of modules that define system tests."

5
gnu/tests/networking.scm
View file

@ -349,9 +349,8 @@ (define marionette
;; Make sure the PID file is created.
(test-assert "PID file"
(marionette-eval
'(file-exists? "/var/run/inetd.pid")
marionette))
(wait-for-file "/var/run/inetd.pid" marionette
#:timeout 30))
;; Test the echo service.
(test-equal "echo response"

2
guix/build-system/ant.scm
View file

@ -103,6 +103,7 @@ (define* (ant-build name inputs
(build-target "jar")
(jar-name #f)
(main-class #f)
(use-java-modules? #f)
(test-include (list "**/*Test.java"))
(test-exclude (list "**/Abstract*.java"))
(source-dir "src")
@ -131,6 +132,7 @@ (define builder
#:build-target #$build-target
#:jar-name #$jar-name
#:main-class #$main-class
#:use-java-modules? #$use-java-modules?
#:test-include (list #$@test-include)
#:test-exclude (list #$@test-exclude)
#:source-dir #$source-dir

157
guix/build-system/vim.scm Normal file
View file

@ -0,0 +1,157 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2022 Jonathan Scoresby <me@jonscoresby.com>
;;; Copyright © 2023 Efraim Flashner <efraim@flashner.co.il>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (guix build-system vim)
#:use-module (guix store)
#:use-module (guix utils)
#:use-module (guix gexp)
#:use-module (guix monads)
#:use-module (guix packages)
#:use-module (guix search-paths)
#:use-module (guix build-system)
#:use-module (guix build-system copy)
#:use-module (guix build-system gnu)
#:export (%vim-build-system-modules vim-build vim-build-system))
;; Commentary:
;;
;; Standard package installer for vim and neovim plugins.
;; This is implemented as an extension of the `copy-build-system'
;; and takes advantage of vim and neovim's built-in package manager.
;; It extends the installation procedure from the copy-build-system
;; to put files in the correct place and then generates help tags.
;;
;; Code:
(define %vim-build-system-modules
;; Build-side modules imported by default.
`((guix build vim-build-system)
,@%copy-build-system-modules))
(define (default-vim)
"Return the default Vim package."
;; Lazily resolve the binding to avoid a circular dependency.
(let ((vim (resolve-interface '(gnu packages vim))))
(module-ref vim 'vim)))
(define (default-neovim)
"Return the default Neovim package."
(let ((vim (resolve-interface '(gnu packages vim))))
(module-ref vim 'neovim)))
(define* (lower name
#:key source
inputs
native-inputs
outputs
system
target
(vim? #f)
(neovim? #f)
(plugin-name name)
(vim (default-vim))
(neovim (default-neovim))
#:allow-other-keys #:rest arguments)
"Return a bag for NAME."
(let* ((private-keywords '(#:target #:vim #:neovim #:inputs #:native-inputs))
(vim? (or (string-prefix? "vim-" name)
vim?))
(neovim? (or (string-prefix? "neovim-" name)
neovim?))
(vim-inputs (append (if vim?
`(("vim" ,vim))
'())
(if neovim?
`(("neovim" ,neovim))
'())))
(vim-arguments (append arguments
`(#:vim? ,vim?
#:neovim? ,neovim?))))
(bag (name name)
(system system)
(host-inputs `(,@(if source
`(("source" ,source))
'()) ,@inputs
;; Keep the standard inputs of 'gnu-build-system'.
,@(standard-packages)))
(build-inputs `(,@vim-inputs ,@native-inputs))
(outputs outputs)
(build vim-build)
(arguments (strip-keyword-arguments private-keywords vim-arguments)))))
(define* (vim-build name inputs
#:key guile
source
(vim? #f)
(neovim? #f)
(mode "start")
(plugin-name name)
(install-plan ''())
(phases '(@ (guix build vim-build-system) %standard-phases))
(outputs '("out"))
(search-paths '())
(system (%current-system))
(substitutable? #t)
(imported-modules %vim-build-system-modules)
(modules '((guix build vim-build-system)
(guix build utils))))
(define build
(with-imported-modules imported-modules
#~(begin
(use-modules #$@modules)
#$(with-build-variables inputs outputs
#~(vim-build #:name #$name
#:vim? #$vim?
#:neovim? #$neovim?
#:mode #$mode
#:plugin-name #$plugin-name
#:install-plan #$(if (pair? install-plan)
(sexp->gexp install-plan)
install-plan)
#:source #+source
#:system #$system
#:phases #$(if (pair? phases)
(sexp->gexp phases)
phases)
#:outputs %outputs
#:search-paths '#$(sexp->gexp
(map search-path-specification->sexp
search-paths))
#:inputs
%build-inputs)))))
(mlet %store-monad
((guile (package->derivation (or guile (default-guile))
system #:graft? #f)))
(gexp->derivation name
build
#:system system
#:target #f
#:graft? #f
#:substitutable? substitutable?
#:guile-for-build guile)))
(define vim-build-system
(build-system (name 'vim)
(description "The standard Vim build system")
(lower lower)))
;;; vim.scm ends here

31
guix/build/ant-build-system.scm
View file

@ -37,6 +37,7 @@ (define-module (guix build ant-build-system)
(define* (default-build.xml jar-name prefix #:optional
(source-dir ".") (test-dir "./test") (main-class #f)
(use-java-modules? #f)
(test-include '("**/*Test.java"))
(test-exclude '("**/Abstract*Test.java")))
"Create a simple build.xml with standard targets for Ant."
@ -65,7 +66,7 @@ (define* (default-build.xml jar-name prefix #:optional
(value "first")))
(property (@ (environment "env")))
(path (@ (id "classpath"))
(pathelement (@ (location "${env.CLASSPATH}"))))
(pathelement (@ (path "${env.CLASSPATH}"))))
(target (@ (name "manifest"))
(mkdir (@ (dir "${manifest.dir}")))
@ -79,18 +80,30 @@ (define* (default-build.xml jar-name prefix #:optional
(mkdir (@ (dir "${classes.dir}")))
(javac (@ (includeantruntime "false")
(srcdir ,source-dir)
(destdir "${classes.dir}")
(classpath (@ (refid "classpath"))))))
(destdir "${classes.dir}"))
,(if use-java-modules?
`((modulepath (@ (refid "classpath"))))
'())
(classpath (@ (refid "classpath")))))
(target (@ (name "compile-tests"))
(mkdir (@ (dir "${test.classes.dir}")))
(javac (@ (includeantruntime "false")
(srcdir ,test-dir)
(destdir "${test.classes.dir}"))
(classpath
(pathelement (@ (path "${env.CLASSPATH}")))
(pathelement (@ (location "${classes.dir}")))
(pathelement (@ (location "${test.classes.dir}"))))))
,(if use-java-modules?
`((classpath
(pathelement
(@ (path "${env.CLASSPATH}")))
(pathelement
(@ (location "${classes.dir}")))
(pathelement
(@ (location "${test.classes.dir}")))))
'())
(classpath
(pathelement (@ (path "${env.CLASSPATH}")))
(pathelement (@ (location "${classes.dir}")))
(pathelement (@ (location "${test.classes.dir}"))))))
(target (@ (name "check")
(depends "compile-tests"))
@ -156,13 +169,15 @@ (define* (configure #:key inputs outputs (jar-name #f)
(source-dir "src")
(test-dir "src/test")
(main-class #f)
(use-java-modules? #f)
(test-include '("**/*Test.java"))
(test-exclude '("**/Abstract*.java")) #:allow-other-keys)
(when jar-name
(default-build.xml jar-name
(string-append (assoc-ref outputs "out")
"/share/java")
source-dir test-dir main-class test-include test-exclude))
source-dir test-dir main-class use-java-modules?
test-include test-exclude))
(setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
(setenv "CLASSPATH" (generate-classpath inputs))
#t)

19
guix/build/git.scm
View file

@ -1,5 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014, 2016, 2019, 2023 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -33,10 +34,13 @@ (define-module (guix build git)
;;; Code:
(define* (git-fetch url commit directory
#:key (git-command "git") recursive?)
#:key (git-command "git")
lfs? recursive?)
"Fetch COMMIT from URL into DIRECTORY. COMMIT must be a valid Git commit
identifier. When RECURSIVE? is true, all the sub-modules of URL are fetched,
recursively. Return #t on success, #f otherwise."
identifier. When LFS? is true, configure Git to also fetch Large File
Storage (LFS) files; it assumes that the @code{git-lfs} extension is available
in the environment. When RECURSIVE? is true, all the sub-modules of URL are
fetched, recursively. Return #t on success, #f otherwise."
;; Disable TLS certificate verification. The hash of the checkout is known
;; in advance anyway.
@ -57,6 +61,11 @@ (define* (git-fetch url commit directory
(with-directory-excursion directory
(invoke git-command "init" "--initial-branch=main")
(invoke git-command "remote" "add" "origin" url)
(when lfs?
(setenv "HOME" "/tmp")
(invoke git-command "lfs" "install"))
(if (zero? (system* git-command "fetch" "--depth" "1" "origin" commit))
(invoke git-command "checkout" "FETCH_HEAD")
(begin
@ -81,11 +90,13 @@ (define* (git-fetch url commit directory
(define* (git-fetch-with-fallback url commit directory
#:key (git-command "git") recursive?)
#:key (git-command "git")
lfs? recursive?)
"Like 'git-fetch', fetch COMMIT from URL into DIRECTORY, but fall back to
alternative methods when fetching from URL fails: attempt to download a nar,
and if that also fails, download from the Software Heritage archive."
(or (git-fetch url commit directory
#:lfs? lfs?
#:recursive? recursive?
#:git-command git-command)
(download-nar directory)

13
guix/build/guile-build-system.scm
View file

@ -28,6 +28,7 @@ (define-module (guix build guile-build-system)
#:use-module (ice-9 format)
#:use-module (guix build utils)
#:export (target-guile-effective-version
target-guile-scm+go
%standard-phases
guile-build))
@ -44,7 +45,17 @@ (define* (target-guile-effective-version #:optional guile)
(string? line)
line)))
(define (file-sans-extension file) ;TODO: factorize
(define* (target-guile-scm+go output #:optional guile)
"Return paths under `output' for scm and go files for effective version of
GUILE or whichever `guile' is in $PATH. Raises an error if they cannot be
determined."
(let* ((version (or (target-guile-effective-version guile)
(error "Cannot determine the effective target guile version.")))
(scm (string-append output "/share/guile/site/" version))
(go (string-append output "/lib/guile/" version "/site-ccache")))
(values scm go)))
(define (file-sans-extension file) ;TODO: factorize
"Return the substring of FILE without its extension, if any."
(let ((dot (string-rindex file #\.)))
(if dot

3
guix/build/minetest-build-system.scm
View file

@ -126,7 +126,8 @@ (define files (find-files "." ".png$"))
(/ total-old-size (expt 1024 2))
(/ total-new-size (expt 1024 2)))))))
(define name-regexp (make-regexp "^name[ ]*=(.+)$"))
(define name-regexp
(make-regexp "^name[[:space:]]*=[[:space:]]*([[:graph:]]+)[[:space:]]*$"))
(define* (read-mod-name mod.conf #:optional not-found)
"Read the name of a mod from MOD.CONF. If MOD.CONF

15
guix/build/syscalls.scm
View file

@ -192,6 +192,7 @@ (define-module (guix build syscalls)
terminal-window-size
terminal-columns
terminal-rows
terminal-string-width
openpty
login-tty
@ -2336,6 +2337,20 @@ (define* (terminal-rows #:optional (port (current-output-port)))
always a positive integer."
(terminal-dimension window-size-rows port (const 25)))
(define terminal-string-width
(let ((mbstowcs (syscall->procedure int "mbstowcs" (list '* '* size_t)))
(wcswidth (syscall->procedure int "wcswidth" (list '* size_t))))
(lambda (str)
"Return the width of a string as it would be printed on the terminal.
This procedure accounts for characters that have a different width than 1, such
as CJK double-width characters."
(let ((wchar (make-bytevector (* (+ (string-length str) 1) 4))))
(mbstowcs (bytevector->pointer wchar)
(string->pointer str)
(string-length str))
(wcswidth (bytevector->pointer wchar)
(string-length str))))))
(define openpty
(let ((proc (syscall->procedure int "openpty" '(* * * * *)
#:library "libutil")))

119
guix/build/vim-build-system.scm Normal file
View file

@ -0,0 +1,119 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2022 Jonathan Scoresby <me@jonscoresby.com>
;;; Copyright © 2023 Efraim Flashner <efraim@flashner.co.il>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (guix build vim-build-system)
#:use-module ((guix build copy-build-system)
#:prefix copy:)
#:use-module (guix build utils)
#:use-module (ice-9 match)
#:use-module (ice-9 ftw)
#:use-module (srfi srfi-1)
#:use-module (srfi srfi-26)
#:export (%standard-phases vim-build))
;; Commentary:
;;
;; System for installing vim and neovim plugins. It downloads
;; the source and copies the appropriate files to vim and nvim
;; packpaths. It then generates helptags.
;;
;; Code:
(define copy:install
(assoc-ref copy:%standard-phases 'install))
(define vim-path
"/share/vim/vimfiles/pack/guix/")
(define nvim-path
"/share/nvim/site/pack/guix/")
(define* (install #:key plugin-name
install-plan
neovim?
vim?
mode
outputs
#:allow-other-keys)
(let* ((include-regexp '(".*\\/.*\\/.*"))
(exclude-regexp '("^scripts/.*"
"tests?/.*" "^t/.*"
"assets/.*"
".*\\/\\..*"))
(vim-install
(if vim?
`(("." ,(string-append vim-path mode "/" plugin-name "/")
#:include-regexp ,include-regexp
#:exclude-regexp ,exclude-regexp))
'()))
(neovim-install
(if neovim?
`(("." ,(string-append nvim-path mode "/" plugin-name "/")
#:include-regexp ,include-regexp
#:exclude-regexp ,exclude-regexp))
'())))
(copy:install #:outputs outputs
#:install-plan (append vim-install
neovim-install
install-plan))))
(define* (generate-helptags #:key plugin-name
neovim?
vim?
mode
outputs
#:allow-other-keys)
(define (vim-generate-helptags output)
(invoke "vim" "--clean" "-en" "--cmd"
(string-append "helptags "
output vim-path mode "/" plugin-name "/doc")
"--cmd" "q"))
(define (neovim-generate-helptags output)
(invoke "nvim" "--clean" "--headless" "-en" "--cmd"
(string-append "helptags "
output nvim-path mode "/" plugin-name "/doc")
"--cmd" "q"))
(when (scandir "./doc")
(let ((out (assoc-ref outputs "out")))
(when vim?
(vim-generate-helptags out))
(when neovim?
(neovim-generate-helptags out)))))
(define %standard-phases
;; Everything is as with the Copy Build System except for
;; the addition of the generate-helptags phase and a few
;; custom actions are added to the install phase
(modify-phases copy:%standard-phases
(replace 'install install)
(add-after 'install 'generate-helptags generate-helptags)))
(define* (vim-build #:key inputs
(phases %standard-phases)
#:allow-other-keys #:rest args)
"Build the given package, applying all of PHASES in order."
(apply copy:copy-build
#:inputs inputs
#:phases phases
args))
;;; vim-build-system.scm ends here

2
guix/download.scm
View file

@ -129,7 +129,7 @@ (define %mirrors
"ftp://ftp.hu.netfilter.org/"
"ftp://www.lt.netfilter.org/pub/")
(kernel.org
"http://linux-kernel.uio.no/pub/"
"https://cdn.kernel.org/pub/"
"http://ftp.be.debian.org/pub/"
"https://mirrors.edge.kernel.org/pub/"
"ftp://ftp.funet.fi/pub/mirrors/ftp.kernel.org/pub/")

97
guix/git-download.scm
View file

@ -4,6 +4,7 @@
;;; Copyright © 2017 Christopher Baines <mail@cbaines.net>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
;;; Copyright © 2023 Simon Tournier <zimon.toutoune@gmail.com>
;;; Copyright © 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -54,6 +55,7 @@ (define-module (guix git-download)
git-reference-recursive?
git-fetch
git-fetch/lfs
git-version
git-file-name
git-predicate))
@ -79,30 +81,36 @@ (define (git-package)
(let ((distro (resolve-interface '(gnu packages version-control))))
(module-ref distro 'git-minimal)))
(define* (git-fetch/in-band ref hash-algo hash
#:optional name
#:key (system (%current-system))
(guile (default-guile))
(git (git-package)))
"Return a fixed-output derivation that performs a Git checkout of REF, using
GIT and GUILE (thus, said derivation depends on GIT and GUILE).
(define (git-lfs-package)
"Return the default 'git-lfs' package."
(let ((distro (resolve-interface '(gnu packages version-control))))
(module-ref distro 'git-lfs)))
This method is deprecated in favor of the \"builtin:git-download\" builder.
It will be removed when versions of guix-daemon implementing
\"builtin:git-download\" will be sufficiently widespread."
(define* (git-fetch/in-band* ref hash-algo hash
#:optional name
#:key (system (%current-system))
(guile (default-guile))
(git (git-package))
git-lfs)
"Shared implementation code for git-fetch/in-band & friends. Refer to their
respective documentation."
(define inputs
`(("git" ,(or git (git-package)))
;; When doing 'git clone --recursive', we need sed, grep, etc. to be
;; available so that 'git submodule' works.
`(,(or git (git-package))
,@(if git-lfs
(list git-lfs)
'())
,@(if (git-reference-recursive? ref)
(standard-packages)
;; TODO: remove (standard-packages) after
;; 48e528a26f9c019eeaccf5e3de3126aa02c98d3b is merged into master;
;; currently when doing 'git clone --recursive', we need sed, grep,
;; etc. to be available so that 'git submodule' works.
(map second (standard-packages))
;; The 'swh-download' procedure requires tar and gzip.
`(("gzip" ,(module-ref (resolve-interface '(gnu packages compression))
'gzip))
("tar" ,(module-ref (resolve-interface '(gnu packages base))
'tar))))))
(list (module-ref (resolve-interface '(gnu packages compression))
'gzip)
(module-ref (resolve-interface '(gnu packages base))
'tar)))))
(define guile-json
(module-ref (resolve-interface '(gnu packages guile)) 'guile-json-4))
@ -126,7 +134,7 @@ (define modules
(define build
(with-imported-modules modules
(with-extensions (list guile-json gnutls ;for (guix swh)
(with-extensions (list guile-json gnutls ;for (guix swh)
guile-lzlib)
#~(begin
(use-modules (guix build git)
@ -134,6 +142,9 @@ (define build
#:select (set-path-environment-variable))
(ice-9 match))
(define lfs?
(call-with-input-string (getenv "git lfs?") read))
(define recursive?
(call-with-input-string (getenv "git recursive?") read))
@ -144,18 +155,17 @@ (define recursive?
#+(file-append glibc-locales "/lib/locale"))
(setlocale LC_ALL "en_US.utf8")
;; The 'git submodule' commands expects Coreutils, sed,
;; grep, etc. to be in $PATH.
(set-path-environment-variable "PATH" '("bin")
(match '#+inputs
(((names dirs outputs ...) ...)
dirs)))
;; The 'git submodule' commands expects Coreutils, sed, grep,
;; etc. to be in $PATH. This also ensures that git extensions are
;; found.
(set-path-environment-variable "PATH" '("bin") '#+inputs)
(setvbuf (current-output-port) 'line)
(setvbuf (current-error-port) 'line)
(git-fetch-with-fallback (getenv "git url") (getenv "git commit")
#$output
#:lfs? lfs?
#:recursive? recursive?
#:git-command "git")))))
@ -175,18 +185,49 @@ (define recursive?
(git-reference-url ref))))
("git commit" . ,(git-reference-commit ref))
("git recursive?" . ,(object->string
(git-reference-recursive? ref))))
(git-reference-recursive? ref)))
("git lfs?" . ,(if git-lfs "#t" "#f")))
#:leaked-env-vars '("http_proxy" "https_proxy"
"LC_ALL" "LC_MESSAGES" "LANG"
"COLUMNS")
#:system system
#:local-build? #t ;don't offload repo cloning
#:local-build? #t ;don't offload repo cloning
#:hash-algo hash-algo
#:hash hash
#:recursive? #t
#:guile-for-build guile)))
(define* (git-fetch/in-band ref hash-algo hash
#:optional name
#:key (system (%current-system))
(guile (default-guile))
(git (git-package)))
"Return a fixed-output derivation that performs a Git checkout of REF, using
GIT and GUILE (thus, said derivation depends on GIT and GUILE).
This method is deprecated in favor of the \"builtin:git-download\" builder.
It will be removed when versions of guix-daemon implementing
\"builtin:git-download\" will be sufficiently widespread."
(git-fetch/in-band* ref hash-algo hash name
#:system system
#:guile guile
#:git git))
(define* (git-fetch/lfs ref hash-algo hash
#:optional name
#:key (system (%current-system))
(guile (default-guile))
(git (git-package))
(git-lfs (git-lfs-package)))
"Like git-fetch/in-band, but with support for the Git Large File
Storage (LFS) extension."
(git-fetch/in-band* ref hash-algo hash name
#:system system
#:guile guile
#:git git
#:git-lfs git-lfs))
(define* (git-fetch/built-in ref hash-algo hash
#:optional name
#:key (system (%current-system)))

4
guix/git.scm
View file

@ -33,6 +33,8 @@ (define-module (guix git)
#:use-module (guix store)
#:use-module (guix utils)
#:use-module (guix records)
#:use-module ((guix build syscalls)
#:select (terminal-string-width))
#:use-module (guix gexp)
#:autoload (guix git-download)
(git-reference-url git-reference-commit git-reference-recursive?)
@ -154,7 +156,7 @@ (define %
;; TODO: Both should be handled & exposed by the PROGRESS-BAR API instead.
(define width
(max (- (current-terminal-columns)
(string-length label) 7)
(terminal-string-width label) 7)
3))
(define grain

58
guix/inferior.scm
View file

@ -872,14 +872,17 @@ (define* (cached-channel-instance store
(authenticate? #t)
(cache-directory (%inferior-cache-directory))
(ttl (* 3600 24 30))
validate-channels)
(reference-channels '())
(validate-channels (const #t)))
"Return a directory containing a guix filetree defined by CHANNELS, a list of channels.
The directory is a subdirectory of CACHE-DIRECTORY, where entries can be
reclaimed after TTL seconds. This procedure opens a new connection to the
build daemon. AUTHENTICATE? determines whether CHANNELS are authenticated.
VALIDATE-CHANNELS, if specified, must be a one argument procedure accepting a
list of channels that can be used to validate the channels; it should raise an
exception in case of problems."
VALIDATE-CHANNELS must be a four-argument procedure used to validate channel
instances against REFERENCE-CHANNELS; it is passed as #:validate-pull to
'latest-channel-instances' and should raise an exception in case a target
channel commit is deemed \"invalid\"."
(define commits
;; Since computing the instances of CHANNELS is I/O-intensive, use a
;; cheaper way to get the commit list of CHANNELS. This limits overhead
@ -927,30 +930,31 @@ (define add-temp-root*
(if (file-exists? cached)
cached
(begin
(when (procedure? validate-channels)
(validate-channels channels))
(run-with-store store
(mlet* %store-monad ((instances
-> (latest-channel-instances store channels
#:authenticate?
authenticate?))
(profile
(channel-instances->derivation instances)))
(mbegin %store-monad
;; It's up to the caller to install a build handler to report
;; what's going to be built.
(built-derivations (list profile))
(run-with-store store
(mlet* %store-monad ((instances
-> (latest-channel-instances store channels
#:authenticate?
authenticate?
#:current-channels
reference-channels
#:validate-pull
validate-channels))
(profile
(channel-instances->derivation instances)))
(mbegin %store-monad
;; It's up to the caller to install a build handler to report
;; what's going to be built.
(built-derivations (list profile))
;; Cache if and only if AUTHENTICATE? is true.
(if authenticate?
(mbegin %store-monad
(symlink* (derivation->output-path profile) cached)
(add-indirect-root* cached)
(return cached))
(mbegin %store-monad
(add-temp-root* (derivation->output-path profile))
(return (derivation->output-path profile))))))))))
;; Cache if and only if AUTHENTICATE? is true.
(if authenticate?
(mbegin %store-monad
(symlink* (derivation->output-path profile) cached)
(add-indirect-root* cached)
(return cached))
(mbegin %store-monad
(add-temp-root* (derivation->output-path profile))
(return (derivation->output-path profile)))))))))
(define* (inferior-for-channels channels
#:key

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