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Author SHA1 Message Date
Jonathan Brielmaier
1e5656e7bd
news: Add copyright line for myself. 
* etc/news.scm: Add myself to the copyright headers.
 2021-12-04 15:10:29 +01:00
jgart
da70132ee9
gnu: janet: Update to 1.19.0. 
* gnu/packages/lisp.scm (janet): Update to 1.19.0.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-12-04 13:51:49 +01:00
cage
612fe425b4
gnu: tinmop: Update to 0.9.2. 
* gnu/packages/web-browsers.scm (tinmop): Update to 0.9.2.
  [inputs]: Move nano, openssl and xdg-utils to...
  [native-inputs]: ... here. Add automake, autoconf and mandoc. Remove curl
  and gnupg.
  [arguments]: Add 'fix-configure.ac' phase.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-12-04 13:44:17 +01:00
Ricardo Wurmus
18a85213ae
gnu: pigx-sars-cov2-ww: Update to 0.0.4. 
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.4.
[inputs]: Add bbmap, bedtools, fastp, ivar, and r-r-utils.
 2021-12-04 12:42:51 +01:00
Ricardo Wurmus
ce9bfcddb5
gnu: imp: Update to 2.15.0. 
* gnu/packages/bioinformatics.scm (imp): Update to 2.15.0.
[arguments]: Disable one more test.
 2021-12-03 22:29:52 +01:00
Ricardo Wurmus
dcf857e486
gnu: Add r-fpeek. 
* gnu/packages/cran.scm (r-fpeek): New variable.
 2021-12-03 22:29:40 +01:00
Liliana Marie Prikler
15404ff19b
gnu: emacs: Load package descriptors from packages referenced by subdirs.el 
* gnu/packages/aux-files/emacs/guix-emacs.el
(guix-emacs--non-core-load-path): New procedure.
(guix-emacs-autoload-packages): Use it here.
(guix-emacs-load-package-descriptors): New procedure.
* gnu/packages/emacs.scm (emacs)[install-site-start]: Install advice to run
‘guix-emacs-load-package-descriptors’.
 2021-12-03 21:39:50 +01:00
Liliana Marie Prikler
98cec36957
build-system: emacs: Keep -pkg.el files. 
Partly fixes <https://bugs.gnu.org/48331> -- package descriptions can now be
found in the install directory.

* guix/build/emacs-build-system.scm (%default-exclude): Remove "-pkg\\.el$".
 2021-12-03 21:39:50 +01:00
Liliana Marie Prikler
4baeb72717
gnu: emacs: Make DocView PDF work out of the box. 
* gnu/packages/emacs.scm (emacs)[patch-program-file-names]: Add patches for
the programs “gs”, “dvipdf”, “ps2pdf” and “pdftotext”.
[inputs]: Add ghostscript and poppler.
 2021-12-03 21:39:49 +01:00
Liliana Marie Prikler
f725279cdd
gnu: emacs: Find real GVFS processes. 
* gnu/packages/emacs.scm (emacs)[#:phases]<patch-program-file-names>: Expand
calls to “tramp-compat-process-running-p” so that Guix wrappers are also
matched.
 2021-12-03 21:39:49 +01:00
phodina
269baba919
gnu: Add valeronoi. 
* gnu/packages/engineering.scm (valeronoi): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-03 21:38:30 +01:00
jgart
19528e39bb
gnu: st: Install terminfo files. 
* gnu/packages/suckless.scm (st)[native-inputs]: Add ncurses.
[make-flags](TERMINFO): New flag.
[phases](inhibit-terminfo-install): Remove phase.

Signed-off-by: Raghav Gururajan <rg@raghavgururajan.name>
 2021-12-03 15:27:41 -05:00
Morgan Smith
170cb4c881
gnu: emacs-org: Preserve version information. 
* gnu/packages/emacs-xyz.scm (emacs-org)[#:phases]: Prevent install phase from
deleting the version information.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-03 21:14:25 +01:00
Nicolas Goaziou
85ed37c170
gnu: emacs-consult-notmuch: Update to 0.6. 
* gnu/packages/emacs-xyz.scm (emacs-consult-notmuch): Update to 0.6.
 2021-12-03 19:43:12 +01:00
Nicolas Goaziou
6557f17000
gnu: emacs-helm: Update to 3.8.2. 
* gnu/packages/emacs-xyz.scm (emacs-helm): Update to 3.8.2.
 2021-12-03 19:41:27 +01:00
Nicolas Goaziou
a7776d5ac0
gnu: emacs-vertico: Update to 0.17. 
* gnu/packages/emacs-xyz.scm (emacs-vertico): Update to 0.17.
 2021-12-03 19:36:35 +01:00
Ricardo Wurmus
b8d6e77476
gnu: python-ont-fast5-api: Update to 4.0.0. 
* gnu/packages/bioinformatics.scm (python-ont-fast5-api): Update to 4.0.0.
[source]: Remove bundled plugin binaries.
[arguments]: Install plugin from inputs.
[inputs]: Add vbz-compression.
[propagated-inputs]: Remove python-six; add python-packaging.
 2021-12-03 14:55:38 +01:00
Ricardo Wurmus
d0aa14a43d
gnu: Add vbz-compression. 
* gnu/packages/bioinformatics.scm (vbz-compression): New variable.
 2021-12-03 14:55:38 +01:00
Mathieu Othacehe
3354e41c1e
system: vm: Remove the vga argument. 
* gnu/system/vm.scm (common-qemu-options): Remove the "-vga std" argument that
is the default since QEMU 2.2.

Suggested-by: Attila Lendvai <attila@lendvai.name>
 2021-12-03 14:25:57 +01:00
Attila Lendvai
b42bfbdfe5
guix system vm: Add --no-graphic CLI argument. 
It configures QEMU to use the tty it was started in for IO (as opposed to
opening a separate graphical window).  This enables copy-pasting and
scrollback.  Exit QEMU with C-a x.

* gnu/system/vm.scm (system-qemu-image/shared-store-script): Also add the
'-nographic' QEMU argument when called with #:graphic? #false.
* guix/scripts/system.scm (system-derivation-for-action): Propagate
the #:graphic? keyword arg.
(perform-action): Add and propagate the #:graphic? keyword arg.
(show-help): Add --no-graphic CLI arg.
(%options): Process the new --no-graphic CLI arg.
(process-action): Feed in the CLI arg through the #:graphic? keyword arg.
* doc/guix.texi (Invoking guix system): Add example to combine guix system and
invoking the vm start script into one command.  Split the description of the
various options into separate paragraphs.  Add a paragraph to describe
--no-graphic.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-12-03 14:18:32 +01:00
Charles
5a18cf3604
gnu: cl-coalton: Update to 0.0.1-2.012f6c8. 
* gnu/packages/lisp-xyz.scm (sbcl-coalton): Update to 0.0.1-2.012f6c8.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-12-03 14:08:14 +01:00
Charles
6e0c4a28b9
gnu: cl-float-features: Update to 1.0.0-2.c1f86ae. 
* gnu/packages/lisp-xyz.scm (sbcl-float-features): Update to 1.0.0-2.c1f86ae.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-12-03 13:59:46 +01:00
Ricardo Wurmus
b7aaf6c418
gnu: ivar: Disable parallel tests. 
* gnu/packages/bioinformatics.scm (ivar)[arguments]: Disable parallel tests.
 2021-12-03 13:48:41 +01:00
Ricardo Wurmus
aa2d5ca02e
gnu: Remove python2-biom-format. 
There are no users of this variant, and the current version of biom-format
does not support Python 2.

* gnu/packages/bioinformatics.scm (python2-biom-format): Remove variable.
(python-biom-format)[properties]: Remove field.
 2021-12-03 13:31:32 +01:00
Ricardo Wurmus
8fa7de386c
gnu: r-flowclust: Add gsl. 
* gnu/packages/bioconductor.scm (r-flowclust)[inputs]: Remove accidentally
committed comment character.
 2021-12-03 13:31:32 +01:00
Mark H Weaver
3e9dc2754e
gnu: icecat: Remove vestigial icecat-78-makeicecat.patch. 
This is a followup to commit a63231003e.

* gnu/packages/patches/icecat-78-makeicecat.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2021-12-03 04:45:15 -05:00
Mathieu Othacehe
c0d9ba22d0
gnu: cuirass: Update to 1.1.0-6.df8837c. 
* gnu/packages/ci.scm (cuirass): Update to 1.1.0-6.df8837c.
 2021-12-03 10:41:37 +01:00
jgart
fcf7e6513c
gnu: python-pandocfilters: Update to 1.5.0. 
* gnu/packages/textutils.scm (python-pandocfilters): Update to 1.5.0.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-12-03 10:41:37 +01:00
Mark H Weaver
d49e7a592f
gnu: icecat: Fix CVE-2021-43527. 
* gnu/packages/patches/icecat-CVE-2021-43527.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gnuzilla.scm (icecat-source): Apply it.
 2021-12-03 04:37:42 -05:00
Mark H Weaver
080a5de2ee
gnu: nss: Fix CVE-2021-43527 via graft. 
* gnu/packages/patches/nss-CVE-2021-43527.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/nss.scm (nss/fixed): New variable
(nss)[replacement]: New field.
 2021-12-03 04:37:21 -05:00
Ricardo Wurmus
345b341919
gnu: openjdk16: Use MAKE-FILE-WRITABLE. 
* gnu/packages/java.scm (openjdk16)[arguments]: Do not shell out to "chmod".
 2021-12-02 23:58:56 +01:00
Arne Babenhauserheide
68e71fbb17
gnu: Add openjdk17. 
* gnu/packages/java.scm (openjdk17): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2021-12-02 23:58:53 +01:00
Leo Famulari
f697fc267c
doc: Give more details about generating patches with base commit information. 
* doc/contributing.texi (Submitting Patches): Talk more about '--base'.
 2021-12-02 14:31:13 -05:00
Ricardo Wurmus
1f5c1bc024
gnu: python2-decorator: Downgrade to 4.3.0 
* gnu/packages/python-xyz.scm (python2-decorator): Keep at 4.3.0.
(python-decorator)[properties]: Add python2-variant.
 2021-12-02 18:56:29 +01:00
Ricardo Wurmus
a2423c0ca4
gnu: ribodiff: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Remove trailing #T
from build phase.
 2021-12-02 18:32:33 +01:00
Ricardo Wurmus
1123d25830
gnu: ribodiff: Disable broken test. 
* gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Add build phase
'disable-plot-test.
 2021-12-02 18:32:10 +01:00
Ricardo Wurmus
f28f5be11d
gnu: python2-statsmodels: Downgrade to 0.9.0. 
* gnu/packages/statistics.scm (python2-statsmodels): Downgrade to 0.9.0.
 2021-12-02 18:31:38 +01:00
Ricardo Wurmus
31d372cd8a
gnu: khmer: Fix build with Python 3.8. 
* gnu/packages/bioinformatics.scm (khmer)[source]: Remove trailing #T.
[arguments]: Remove trailing #T from build phases; add build phase
'python-3.8-compatibility.
 2021-12-02 18:24:31 +01:00
Ricardo Wurmus
32d5fb01f8
gnu: python-biom-format: Update to 2.1.10. 
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.10.
[source]: Simplify snippet.
[arguments]: Add phase 'relax; remove trailing #T from other build phases.
[propagated-inputs]: Add python-anndata; replace python-pandas-0.25 with
python-pandas.
 2021-12-02 18:02:07 +01:00
jgart
fab80c3672
gnu: Add trayer-srg. 
* gnu/packages/wm.scm (trayer-srg): New variable.

Co-authored-by: Disseminate Dissent <disseminatedissent@protonmail.com>
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-12-02 15:44:31 +01:00
Ricardo Wurmus
28ad55a59d
gnu: pardre: Update to 2.2.5. 
* gnu/packages/bioinformatics.scm (pardre): Update to 2.2.5.
[arguments]: Remove trailing #T and update comment about tests.
 2021-12-02 15:40:46 +01:00
Ricardo Wurmus
fc20fad6f7
gnu: pardre: Use C++ bindings for MPI. 
* gnu/packages/bioinformatics.scm (pardre)[inputs]: Replace openmpi with
openmpi-c++.
 2021-12-02 15:40:46 +01:00
Ricardo Wurmus
2d6be35ea2
gnu: Add openmpi-c++. 
* gnu/packages/mpi.scm (openmpi-c++): New variable.
 2021-12-02 15:40:45 +01:00
Liliana Marie Prikler
df4f960cb8
gnu: Add libconfini. 
* gnu/packages/cpp.scm (libconfini): New variable.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-12-02 15:38:17 +01:00
Vinicius Monego
2d92b3bbb6
gnu: shotcut: Update to 21.10.31. 
* gnu/packages/video.scm (shotcut): Update to 21.10.31.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-12-02 15:29:33 +01:00
Vinicius Monego
82e5a1b4c3
gnu: kdenlive: Update to 21.08.3. 
* gnu/packages/kde.scm (kdenlive): Update to 21.08.3.
[arguments]: Pass "-DBUILD_TESTING=off" to #:configure-flags as tests are
currently disabled.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-12-02 15:29:33 +01:00
Vinicius Monego
6fc0cfe1b5
gnu: mlt: Update to 7.2.0. 
* gnu/packages/video.scm (mlt): Update to 7.2.0.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-12-02 15:29:33 +01:00
jgart
e8d5dd5c9b
gnu: ccls: Update to 0.20210330. 
* gnu/packages/cpp.scm (ccls): Update to 0.20210330.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-12-02 15:26:05 +01:00
Artyom V. Poptsov
a4cc1ae446
gnu: guile-udev: Update to 0.2.0 
* gnu/packages/guile-xyz.scm (guile-udev): Update to 0.2.0.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-12-02 15:05:28 +01:00
Ricardo Wurmus
46b73fd22d
gnu: python-ipython: Update to 7.20.0. 
* gnu/packages/python-xyz.scm (python-ipython): Update to 7.20.0.
 2021-12-02 13:42:17 +01:00