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Author SHA1 Message Date
Navid Afkhami
8f084b2c7c
gnu: r-doubletcollection: Add missing inputs. 
If these Python packages are not available at runtime the package tries to
install them automatically via Conda.

* gnu/packages/bioinformatics.scm (r-doubletcollection)[propagated-inputs]:
Add python, python-scrublet, and python-doubletdetection.
 2023-03-03 23:49:14 +01:00
Tobias Geerinckx-Rice
73cb232442
gnu: linux-libre-documentation: Honour ‘--cores’. 
* gnu/packages/linux.scm (linux-libre-documentation)[arguments]:
Respect PARALLEL-BUILD? and PARALLEL-JOB-COUNT.
 2023-02-26 01:00:07 +01:00
Bruno Victal
cd22932945
services: desktop: Set default value for geoclue-service-type. 
This follows up on commit ae0975332c60818793c6c63a3646c982d686bf49?.

* gnu/services/desktop.scm (geoclue-service-type): Set default-value.

Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
 2023-02-26 01:00:07 +01:00
Bruno Victal
2799ad4423
services: dbus: Deprecate 'dbus-service' procedure. 
* doc/guix.texi (Desktop Services): Replace with 'dbus-root-service-type'.
Document dbus-configuration.
* gnu/services/dbus.scm (dbus-service): Define with 'define-deprecated'.
* gnu/services/desktop.scm (desktop-services-for-system): Replace with
dbus-root-service-type.
* gnu/system/install.scm (%installation-services): Ditto.
* gnu/tests/base.scm (%avahi-os): Ditto.
* gnu/tests/docker.scm (%docker-os): Ditto.
* gnu/tests/lightdm.scm (minimal-desktop-services): Ditto.
* gnu/tests/virtualization.scm (%libvirt-os): Ditto.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 17:55:35 +01:00
Bruno Victal
7c23dab85c
services: spice: Deprecate 'spice-vdagent-service' procedure. 
* doc/guix.texi (Miscellaneous Services): Replace 'spice-vdagent-service' with
'spice-vdagent-service-type'. Document <spice-vdagent-configuration>.
* gnu/services/spice.scm (spice-vdagent-service): Deprecate procedure.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 17:55:35 +01:00
Bruno Victal
e24555234a
services: lirc: Deprecate 'lirc-service' procedure. 
* doc/guix.texi (Miscellaneous Services): Replace 'lirc-service' with 'lirc-service-type'.
Document <lirc-configuration>.
* gnu/services/lirc.scm (<lirc-configuration>): Set default values based on
the arguments from the now deprecated 'lirc-service' procedure.
(lirc-service-type): Set default value.
(lirc-service): Deprecate procedure.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 17:55:34 +01:00
Bruno Victal
eddd9b1240
services: vpn: Deprecate 'openvpn-client-service' & 'openvpn-server-service' procedures. 
* doc/guix.texi (VPN Services): Replace 'openvpn-client-service' & 'openvpn-server-service' procedures
with their service-type counterparts.
* gnu/services/vpn.scm (openvpn-client-service, openvpn-server-service): Deprecate procedure.
(openvpn-server-service-type, openvpn-client-service-type): Set default value.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 17:55:34 +01:00
Bruno Victal
c6cbce9ad8
services: mail: Deprecate 'dovecot-service' procedure. 
* doc/guix.texi (Mail Services): Replace 'dovecot-service' with 'dovecot-service-type'.
* gnu/services/mail.scm (dovecot-service-type): Set default value.
(dovecot-service): Deprecate procedure.
* gnu/tests/mail.scm (%dovecot-os): Use dovecot-service-type.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 17:55:34 +01:00
Bruno Victal
be1435d668
services: desktop: Deprecate 'bluetooth-service' procedure. 
* doc/guix.texi (Desktop Services): Remove mention of 'bluetooth-service'.
* gnu/services/desktop.scm (bluetooth-service): Deprecate procedure.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 17:55:34 +01:00
Bruno Victal
ae0975332c
services: desktop: Deprecate 'geoclue-service' procedure. 
* doc/guix.texi (Desktop Services): Replace 'geoclue-service' with 'geoclue-service-type'.
* gnu/services/desktop.scm (<geoclue-configuration>): Set default values
based on the values from the now deprecated geoclue-service procedure.
(geoclue-service): Deprecate procedure.
(desktop-services-for-system): Use geoclue-service-type.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 17:55:34 +01:00
Bruno Victal
e8f161ea11
services: desktop: Deprecate 'udisks-service' procedure. 
* doc/guix.texi (Desktop Services): Replace 'udisks-service' with 'udisks-service-type'.
Document <udisks-configuration>.
* gnu/packages/kde-multimedia.scm (k3b)[description]: Replace 'udisks-service' with 'udisks-service-type'.
* gnu/services/desktop.scm (udisks-service-type): Set default value.
(udisks-service): Deprecate procedure.
(desktop-services-for-system): Use udisks-service-type.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 17:55:34 +01:00
Bruno Victal
ffc5d42fc2
services: dbus: Deprecate 'polkit-service' procedure. 
* doc/guix.texi (Desktop Services): Replace 'polkit-service' with 'polkit-service-type'.
* gnu/services/dbus.scm (polkit-service): Deprecate procedure.
* gnu/tests/docker.scm (%docker-os): Use polkit-service-type.
* gnu/tests/virtualization.scm (%libvirt-os): Ditto.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 17:55:34 +01:00
Bruno Victal
c3dc13e29c
services: desktop: Deprecate 'accountsservice-service' procedure. 
* doc/guix.texi (Desktop Services): Replace 'accountsservice-service'
with 'accountsservice-service-type'.
* gnu/services/desktop.scm (accountsservice-service): Deprecate procedure.
(desktop-services-for-system): Use accountsservice-service-type.
* gnu/tests/lightdm.scm (minimal-desktop-services): Ditto.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 17:55:33 +01:00
Bruno Victal
ca3a73de3d
services: elogind-configuration: Do not ignore 'handle-hibernate-key' by default. 
* gnu/services/desktop.scm (<elogind-configuration>)[handle-hibernate-key]: Set default value to 'hibernate.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 17:55:33 +01:00
Bruno Victal
00767d967d
services: desktop: Deprecate 'elogind-service' procedure. 
* doc/guix.texi (Desktop Services): Replace 'elogind-service' with
'elogind-service-type'.
* gnu/services/desktop.scm (elogind-service): Deprecate procedure.
(desktop-services-for-system): Use elogind-service-type.
* gnu/tests/lightdm.scm (minimal-desktop-services): Ditto.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 17:55:33 +01:00
Bruno Victal
3b2e88011a
services: ssh: Deprecate 'dropbear-service' procedure. 
* doc/guix.texi (Networking Services): Replace 'dropbear-service' with
'dropbear-service-type'.
* gnu/services/ssh.scm (dropbear-service): Deprecate procedure.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 17:55:33 +01:00
Bruno Victal
0e21015fd2
services: ssh: Deprecate 'lsh-service' procedure. 
* doc/guix.texi (Networking Services): Remove mention of lsh-service.
Document lsh-service-type and lsh-service-configuration.
* gnu/services/ssh.scm (<lsh-configuration>): Set default values based
on the now deprecated 'lsh-service' procedure.
(lsh-service-type): Set default value.
(lsh-service): Deprecate procedure.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 17:55:33 +01:00
Bruno Victal
31b1e22926
services: base: Deprecate 'rngd-service' procedure. 
* doc/guix.texi (Base Services): Replace rngd-service with rngd-service-type.
Document <rngd-configuration>.
* gnu/services/base.scm (<rngd-configuration>): Set default values from
the values in the now deprecated 'rngd-service' procedure.
(rngd-service): Deprecate procedure.
(rngd-service-type): Set default value.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 17:55:33 +01:00
Bruno Victal
2e7516168e
services: base: Deprecate 'udev-service' procedure. 
* doc/guix.texi (Base Services): Replace udev-service with udev-service-type.
Document <udev-configuration>. Use @defun @-commands for udev-rules-service,
udev-rule and file->udev-rule.
* gnu/services/base.scm (udev-service): Deprecate procedure.
* gnu/system/install.scm (%installation-services): Use udev-service-type.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 17:55:32 +01:00
Bruno Victal
6edacf2491
services: base: Deprecate 'syslog-service' procedure. 
* doc/guix.texi (Base Services): Replace syslog-service with syslog-service-type.
* gnu/services/base.scm (%default-syslog.conf): Place before <syslog-configuration>.
(syslog-service-type): Set default value.
(syslog-service): Deprecate procedure.
(%base-services): Use syslog-service-type.
* gnu/system/hurd.scm (%base-services/hurd): Ditto.
* gnu/system/install.scm (%installation-services): Ditto.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 17:55:32 +01:00
Bruno Victal
98e9dc6ab7
services: base: Deprecate 'nscd-service' procedure. 
* doc/guix.texi (Application Setup): Compress @cindex entries.
(Base Services): Compress @cindex entries. Delete %nscd-default-configuration.
Replace 'nscd-service' with 'nscd-service-type'.
* gnu/services/base.scm (%nscd-default-configuration): Deprecate variable.
(nscd-service): Deprecate procedure.
* gnu/system/install.scm (%installation-services): Use nscd-service-type.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 17:55:32 +01:00
Bruno Victal
5bd5e77281
doc: kmscon-service-type: Use @defvar @-command. 
* doc/guix.texi (Base Services): Use @defvar @-command for kmscon-service-type.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 17:55:32 +01:00
Bruno Victal
4892c0186e
services: base: Deprecate 'agetty-service' procedure. 
* doc/guix.texi (Base Services): Replace agetty-service with
agetty-service-type.
* gnu/services/base.scm (agetty-service): Deprecate procedure.
* gnu/system/examples/beaglebone-black.tmpl
(operating-system)[services]: Use agetty-service-type.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 17:55:32 +01:00
Bruno Victal
ad665a38fc
services: base: Deprecate 'mingetty-service' procedure. 
* doc/guix.texi (Base Services): Replace mingetty-service with
mingetty-service-type.
* gnu/services/base.scm (mingetty-service): Deprecate procedure.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 17:55:32 +01:00
Bruno Victal
6dd635b4cf
services: base: Deprecate 'login-service' procedure. 
* doc/guix.texi (Base Services): Replace with login-service-type.
* gnu/services/base.scm (login-service): Deprecate procedure.
* gnu/system/install.scm (%installation-services): Use login-service-type.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 17:55:32 +01:00
Bruno Victal
cb00e600ff
services: base: Deprecate 'host-name-service' procedure. 
* doc/guix.texi (operating-system Reference): Reorder cross-reference.
Add an anchor to be used ...
(Base services): ... here by host-name-service-type. Document
host-name-service-type.
* gnu/services/base.scm: Export host-name-service-type.
(host-name-service): Deprecate procedure.
* gnu/system.scm (operating-system-default-essential-services): Use
host-name-service-type.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 17:55:31 +01:00
Navid Afkhami
c6480edbe3
gnu: Add r-seurat-utils. 
* gnu/packages/bioinformatics.scm (r-seurat-utils): New variable.
 2023-03-03 15:11:43 +01:00
Navid Afkhami
03ef0914d5
gnu: Add r-hgnchelper. 
* gnu/packages/cran.scm (r-hgnchelper): New variable.
 2023-03-03 15:11:43 +01:00
Navid Afkhami
9aad3dfd7b
gnu: Add r-tictoc. 
* gnu/packages/bioinformatics.scm (r-tictoc): New variable.
 2023-03-03 15:11:43 +01:00
Navid Afkhami
573b65f51e
gnu: Add r-ggexpress. 
* gnu/packages/bioinformatics.scm (r-ggexpress): New variable.
 2023-03-03 15:11:43 +01:00
Navid Afkhami
fd099793c8
gnu: Add r-markdownreports. 
* gnu/packages/bioinformatics.scm (r-markdownreports): New variable.
 2023-03-03 15:11:43 +01:00
Navid Afkhami
8eb8af7e30
gnu: Add r-markdownhelpers. 
* gnu/packages/bioinformatics.scm (r-markdownhelpers): New variable.
 2023-03-03 15:11:43 +01:00
Navid Afkhami
ba47b0fceb
gnu: Add r-codeandroll2. 
* gnu/packages/bioinformatics.scm (r-codeandroll2): New variable.
 2023-03-03 15:11:43 +01:00
Navid Afkhami
877e2e7cf3
gnu: Add r-readwriter. 
* gnu/packages/bioinformatics.scm (r-readwriter): New variable.
 2023-03-03 15:11:43 +01:00
Navid Afkhami
351de7426c
gnu: Add r-stringendo. 
* gnu/packages/bioinformatics.scm (r-stringendo): New variable.
 2023-03-03 15:11:42 +01:00
Sharlatan Hellseher
6385070190
gnu: Add julia-astrotime. 
* gnu/packages/julia-xyz.scm (julia-astrotime): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 12:30:50 +01:00
Sharlatan Hellseher
39f02b5760
gnu: Add julia-muladdmacro. 
* gnu/packages/julia-xyz.scm (julia-muladdmacro): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 12:30:49 +01:00
Sharlatan Hellseher
549c227f3c
gnu: Add julia-itemgraphs. 
* gnu/packages/julia-xyz.scm (julia-itemgraphs): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 12:30:47 +01:00
Sharlatan Hellseher
16c7becdc7
gnu: Add julia-lightgraphs. 
* gnu/packages/julia-xyz.scm (julia-lightgraphs): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 12:30:46 +01:00
Sharlatan Hellseher
7f53aa7aa8
gnu: Add julia-arnoldimethod. 
* gnu/packages/julia-xyz.scm (julia-arnoldimethod): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 12:30:45 +01:00
Sharlatan Hellseher
a6fc3bc163
gnu: Add julia-inflate. 
* gnu/packages/julia-xyz.scm (julia-inflate): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 12:30:43 +01:00
Sharlatan Hellseher
b7804b473f
gnu: Add julia-earthorientation. 
* gnu/packages/julia-xyz.scm (julia-earthorientation): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 12:30:40 +01:00
Sharlatan Hellseher
a0ca88b1a6
gnu: Add julia-remotefiles. 
* gnu/packages/julia-xyz.scm (julia-remotefiles): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 12:30:37 +01:00
Sharlatan Hellseher
f808ce789d
gnu: Add julia-optionaldata. 
* gnu/packages/julia-xyz.scm (julia-optionaldata): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 12:30:33 +01:00
Sharlatan Hellseher
e21c19b2ad
gnu: Add julia-leapseconds. 
* gnu/packages/julia-xyz.scm (julia-leapseconds): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 12:30:24 +01:00
Ludovic Courtès
58f20fa818
git-download: Apply Git attributes on checkouts coming from SWH. 
Fixes a bug whereby CR/LF conversion, for instance, would not be applied
on Git repositories retrieved from SWH:

  https://sympa.inria.fr/sympa/arc/swh-devel/2023-03/msg00000.html

Reported by Simon Tournier <simon.tournier@inserm.fr>.
Suggested by Valentin Lorentz <valentin.lorentz@inria.fr>.
Co-authored by Simon Tournier <simon.tournier@inserm.fr>.

* guix/git-download.scm (git-fetch)[build]: Add Git operations conditioned by
'.gitattributes' on the result from SWH.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-03-03 12:28:22 +01:00
Navid Afkhami
4f681cdbc2
gnu: Add r-oscope. 
* gnu/packages/bioconductor.scm (r-oscope): New variable.
 2023-03-03 12:04:24 +01:00
Guillaume Le Vaillant
98cac9dcab
gnu: cl-tripod: Fix build. 
* gnu/packages/lisp-xyz.scm (sbcl-tripod)[arguments]: Use the 'assoc-ref' form
  for the bin output.
  (cl-tripod)[outputs]: Remove bin.
  (ecl-tripod)[outputs]: Remove bin.
  [arguments]: Remove 'build-program' phase.
 2023-03-03 10:38:41 +01:00
Guillaume Le Vaillant
a359b744ce
gnu: eisl: Update to 2.72. 
* gnu/packages/lisp.scm (eisl): Update to 2.72.
  [arguments]: Update 'fix-paths' phase.
 2023-03-03 09:52:52 +01:00
Guillaume Le Vaillant
d5e41d7166
gnu: gcl: Update to 2.6.14. 
* gnu/packages/lisp.scm (gcl): Update to 2.6.14.
 2023-03-03 09:52:52 +01:00