62da3f9837
gnu: python-pairtools: Update to 1.0.2.
...
* gnu/packages/bioinformatics.scm (python-pairtools): Update to 1.0.2.
[source]: Update Github URL.
[arguments]: Update patch in "fix-references" phase.
[native-inputs]: Remove python-nose.
[inputs]: Remove.
[propagated-inputs]: Add python-bioframe, python-pandas, python-pysam,
python-pyyaml, and python-scipy.
[home-page]: Update.
2022-12-02 21:46:36 +01:00
089b2e4f65
gnu: python-pairtools: Run tests conditionally.
...
* gnu/packages/bioinformatics.scm (python-pairtools)[arguments]: Run tests
conditionally.
2022-12-02 21:46:36 +01:00
631ea9a411
gnu: python-pybedtools: Use pyproject-build-system.
...
* gnu/packages/bioinformatics.scm (python-pybedtools)[build-system]: Use
pyproject-build-system.
[arguments]: Import (guix build pyproject-build-system).
2022-12-02 21:46:36 +01:00
a268b1ba91
gnu: python-htsget: Update to 0.2.6.
...
* gnu/packages/bioinformatics.scm (python-htsget): Update to 0.2.6.
[build-system]: Use pyproject-build-system.
2022-12-02 21:46:35 +01:00
16ecce39d2
gnu: python-cellbender: Update to 0.2.2.
...
* gnu/packages/bioinformatics.scm (python-cellbender): Update to 0.2.2.
[build-system]: Use pyproject-build-system.
2022-12-02 21:46:35 +01:00
9ef6286bc3
gnu: Add bgpq3.
...
* gnu/packages/networking.scm (bgpq3): New variable.
Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
2022-11-27 01:00:00 +01:00
83350bf56b
gnu: rust-zerocopy: Add 0.6.1.
...
* gnu/packages/crates-io.scm (rust-zerocopy-0.6): New variable.
(rust-zerocopy-0.3): Inherit from it.
2022-12-02 19:35:46 +01:00
d65afc9f5a
gnu: rust-zerocopy-derive: Add 0.3.2.
...
* gnu/packages/crates-io.scm (rust-zerocopy-derive-0.3): New variable.
(rust-zerocopy-derive-0.2): Inherit from it.
2022-12-02 19:35:46 +01:00
3c8bd23d0a
gnu: Add rust-sha1-smol.
...
* gnu/packages/crates-io.scm (rust-sha1-smol-1): New variable.
2022-12-02 19:35:46 +01:00
ddb87e8acc
gnu: rust-md-5: Add 0.10.5.
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* gnu/packages/crates-io.scm (rust-md-5-0.10): New variable.
(rust-md-5-0.9): Inherit from it.
2022-12-02 19:35:45 +01:00
3492a01928
gnu: rust-md5-asm: Update to 0.5.0.
...
* gnu/packages/crates-io.scm (rust-md5-asm-0.5): New variable.
(rust-md5-asm-0.4): Inherit from it.
2022-12-02 19:35:45 +01:00
3d90b39d9e
gnu: Add rust-atomic.
...
* gnu/packages/crates-io.scm (rust-atomic-0.5): New variable.
2022-12-02 19:35:45 +01:00
26582405c3
gnu: rust-memoffset: Add 0.7.1.
...
* gnu/packages/crates-io.scm (rust-memoffset-0.7): New variable.
(rust-memoffset-0.6): Inherit from it.
2022-12-02 19:35:45 +01:00
5e8f23a7fd
gnu: rust-gl: Add 0.14.
...
* gnu/packages/crates-graphics.scm (rust-gl-0.14): New variable.
(rust-gl-0.11): Inherit.
2022-12-02 19:35:45 +01:00
365b0b5533
gnu: ungoogled-chromium: Use git tag in ungoogled origin.
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* gnu/packages/chromium.scm (%ungoogled-origin)[uri]: Use %UNGOOGLED-REVISION
instead of commit identifier.
2022-12-02 19:10:51 +01:00
11b0670a9d
gnu: kicad: Remove obsolete phases.
...
* gnu/packages/engineering.scm (kicad)[arguments]: Remove two phases.
2022-12-02 19:08:27 +01:00
ea0e6e5d65
gnu: golly: Update to 4.2.
...
* gnu/packages/games.scm (golly): Update to 4.2.
[arguments]: Remove configure phase.
[inputs]: Remove PYTHON-2 and WXWIDGETS-GTK2. Add PYTHON, SDL2, and
WXWIDGETS. Remove labels while at it.
2022-12-02 19:08:27 +01:00
6aac95ae2b
gnu: python-wxpython: Update to 4.2.0.
...
* gnu/packages/wxwidgets.scm (python-wxpython): Update to 4.2.0.
[propagated-inputs]: Add PYTHON-ATTRDICT.
2022-12-02 19:08:27 +01:00
f16358144f
gnu: wxWidgets: Update to 3.2.1.
...
* gnu/packages/wxwidgets.scm (wxwidgets): Update to 3.2.1.
[source](modules, snippet): New fields.
[inputs]: Remove SDL. Add CATCH-FRAMEWORK, EXPAT, GSTREAMER,
GST-PLUGINS-BASE, LIBNOTIFY, LIBPNG, LIBSECRET, PCRE, SDL2,
WEBKITGTK-WITH-LIBSOUP2, and ZLIB
[arguments]: Add "--enable-mediactrl" and "--enable-gui" to #:configure-flags.
Remove aarch64 workaround. Install catch header in refer-to-inputs phase.
Add phase to adjust WebKitGTK version.
(wxwidgets-3.1, wxwidgets-gtk2-3.1): Remove variables.
(wxwidgets-3.0, (wxwidgets-gtk2-3.0): New variables.
(wxsvg)[inputs]: Change from WXWIDGETS-3.1 to WXWIDGETS.
* gnu/packages/audio.scm (audacity)[inputs]: Likewise.
* gnu/packages/cdrom.scm (dvdstyler)[inputs]: Likewise.
* gnu/packages/astronomy.scm (imppg)[inputs]: Change from WXWIDGETS to
WXWIDGETS-3.0.
* gnu/packages/ftp.scm (filezilla)[inputs]: Likewise.
* gnu/packages/games.scm (megaglest)[inputs]: Likewise.
* gnu/packages/geo.scm (opencpn)[inputs]: Likewise.
* gnu/packages/music.scm (sooperlooper)[inputs]: Likewise.
* gnu/packages/engineering.scm (kicad)[arguments]: Enable EGL support.
2022-12-02 19:08:27 +01:00
8737ee0479
gnu: wxWidgets: Remove input labels.
...
* gnu/packages/wxwidgets.scm (wxwidgets)[inputs]: Remove labels.
[arguments]: Use SEARCH-INPUT-FILE.
(wxwidgets-gtk2)[inputs]: Use MODIFY-INPUTS.
2022-12-02 19:08:27 +01:00
2cf835ae28
gnu: jucipp: Update to 1.7.2.
...
* gnu/packages/text-editors.scm (jucipp): Update to 1.7.2.
[arguments]: Skip one more test.
2022-12-02 19:08:26 +01:00
fa3dac025a
gnu: universal-ctags: Update to 5.9.20221127.0.
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* gnu/packages/code.scm (universal-ctags): Update to 5.9.20221127.0.
2022-12-02 19:08:26 +01:00
62ddd3bc80
gnu: Add python-fanc.
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* gnu/packages/bioinformatics.scm (python-fanc): New variable.
Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de>
2022-12-02 17:43:20 +01:00
ee069ec651
gnu: Add python-genomic-regions.
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* gnu/packages/bioinformatics.scm (python-genomic-regions): New variable.
Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de>
2022-12-02 17:20:54 +01:00
9ddc4e5b03
gnu: python-msgpack-numpy: Update to 0.4.8.
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* gnu/packages/python-science.scm (python-msgpack-numpy): Update to 0.4.8.
2022-12-02 15:04:15 +01:00
0c2dad9951
gnu: Add python-pybloom-live.
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* gnu/packages/python-xyz.scm (python-pybloom-live): New variable.
2022-12-02 15:03:00 +01:00
840d543939
gnu: python-xxhash: Update to 3.1.0.
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* gnu/packages/digest.scm (python-xxhash): Update to 3.1.0.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-setuptools-scm.
2022-12-02 15:03:00 +01:00
4781f0458d
Revert "gnu: linux-libre: Move info manual to doc output."
...
This reverts commit 748ec62882
2022-12-01 21:37:12 -05:00
2775bb95c7
gnu: ungoogled-chromium: Update to 108.0.5359.71-1.
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* gnu/packages/chromium.scm (%preserved-third-party-files): Adjust for M108.
(%chromium-version): Set to 108.0.5359.71-1.
(%arch-revision): Bump to newer commit.
(%ungoogled-origin): Update hash.
(%gcc-patches): Remove.
(%reverse-patches): Remove one patch.
(%arch-patches): New variable.
(%patches): New variable.
(ungoogled-chromium-snippet): Apply %PATCHES instead of individual variables.
(ungoogled-chromium)[source]: Update hash.
[arguments]: Adjust configure flag.
[inputs]: Change from HARFBUZZ-3 to HARFBUZZ-5.
2022-12-02 00:21:25 +01:00
503fb0dcb4
gnu: ungoogled-chromium: Generalize OpenJPEG substitution.
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* gnu/packages/chromium.scm (ungoogled-chromium)[arguments]: Don't hard code
openjpeg version.
2022-12-02 00:21:25 +01:00
1a8d063a44
gnu: harfbuzz: Add 5.3.1.
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* gnu/packages/gtk.scm (harfbuzz-5): New variable.
2022-12-02 00:21:25 +01:00
c091339204
gnu: balsa: Update to 2.6.4.
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* gnu/packages/mail.scm (balsa): Update to 2.6.4.
2022-12-02 00:21:25 +01:00
dee7c94b59
gnu: balsa: Add release-monitoring-url.
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* gnu/packages/mail.scm (balsa)[properties]: New field.
2022-12-02 00:21:25 +01:00
168afe2976
gnu: svt-av1: Update to 1.3.0.
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* gnu/packages/video.scm (svt-av1): Update to 1.3.0.
[supported-systems]: Remove.
[description]: Update.
2022-12-02 00:21:25 +01:00
84c577d7a7
gnu: QtWebEngine: Simplify code to remove third-party files.
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* gnu/packages/qt.scm (remove-third-party-files): Simplify some procedures.
2022-12-02 00:21:25 +01:00
9252f14722
gnu: qtwebengine@6: Fix third-party code removal snippet.
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* gnu/packages/qt.scm (qtwebengine-5)[source](snippet): Move code to delete
third-party files out to ...
(remove-third-party-files): ... this new variable.
(qtwebengine)[source](snippet): Use that variable instead of the broken
duplicate implementation. Adjust PRESERVED-THIRD-PARTY-FILES accordingly.
[native-inputs]: Add PYTHON-BEAUTIFULSOUP4.
2022-12-02 00:21:25 +01:00
6f0a8371fe
gnu: gn: Use G-expression.
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* gnu/packages/build-tools.scm (gn)[arguments]: Convert to G-expression.
2022-12-02 00:21:24 +01:00
e069db7e30
gnu: gn: Remove input labels.
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* gnu/packages/build-tools.scm (gn)[native-inputs]: Remove labels.
2022-12-02 00:21:24 +01:00
c02a77bdd6
gnu: gn: Update to 0.0-2072.1c4151f.
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* gnu/packages/build-tools.scm (gn): Update to 0.0-2072.1c4151f.
[arguments]: Adjust create-last-commit-position phase to be identical with
upstream code.
2022-12-02 00:21:24 +01:00
34a70b1f86
gnu: balsa: Fix build.
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* gnu/packages/mail.scm (balsa)[arguments]: Add #:phase to build with newer
WebKitGTK.
[inputs]: Change from GTKSOURCEVIEW to GTKSOURCEVIEW-4.
2022-12-02 00:21:24 +01:00
00ddf185e6
services: networking: Avoid 'match' on records.
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* gnu/services/networking.scm (dhcp-client-shepherd-service): Use
accessors instead of 'match'.
(inetd-shepherd-service): Likewise.
(tor-shepherd-service): Likewise.
(network-manager-service-type): Likewise.
(modem-manager-service-type): Likewise.
(wpa-supplicant-service-type): Likewise.
(openvswitch-activation): Likewise.
(openvswitch-shepherd-service): Likewise.
(dhcpd-shepherd-service): Use 'match-record' instead of 'match'.
(dhcpd-activation): Likewise.
(ntp-server->string): Likewise.
(ntp-shepherd-service): Likewise.
(tor-configuration->torrc): Likewise.
(network-manager-activation): Likewise.
(network-manager-environment): Likewise.
(network-manager-shepherd-service): Likewise.
(usb-modeswitch-configuration->udev-rules): Likewise.
(wpa-supplicant-shepherd-service): Likewise.
(iptables-shepherd-service): Likewise.
(nftables-shepherd-service): Likewise.
(keepalived-shepherd-service): Likewise.
2022-12-02 00:03:40 +01:00
adfe1064c8
services: base: Use 'match-record' instead of 'match'.
...
* gnu/services/base.scm (agetty-shepherd-service)
(mingetty-shepherd-service)
(nscd.conf-file)
(udev-shepherd-service)
(udev-etc)
(gpm-shepherd-service)
(network-set-up/linux)
(network-tear-down/linux)
(static-networking-shepherd-service)
(greetd-agreety-tty-session-command)
(greetd-agreety-tty-xdg-session-command): Use 'match-record' instead of
'match'.
(guix-accounts): Use <guix-configuration> accessors.
(udev-service-type): Use <udev-configuration> accessors.
2022-12-02 00:02:13 +01:00
4c8eea027a
home: services: Use 'match-record' instead of 'match'.
...
* gnu/home/services/mcron.scm (home-mcron-shepherd-services): Use
'match-record' instead of 'match'.
* gnu/home/services/shells.scm (home-bash-extensions): Likewise.
* gnu/home/services/xdg.scm (serialize-xdg-desktop-entry): Likewise.
2022-12-02 00:02:13 +01:00
7c1161dba4
records: 'match-record' checks fields at macro-expansion time.
...
This allows 'match-record' to be more efficient (field offsets are
computed at compilation time) and to report unknown fields at
macro-expansion time.
* guix/records.scm (map-fields): New macro.
(define-record-type*)[rtd-identifier]: New procedure.
Define TYPE as a macro and use a separate identifier for the RTD.
(lookup-field, match-record-inner): New macros.
(match-record): Rewrite in terms of 'match-error-inner'.
* tests/records.scm ("match-record, simple")
("match-record, unknown field"): New tests.
* gnu/services/cuirass.scm (cuirass-shepherd-service): Rename 'log-file'
local variable to 'main-log-file'.
* gnu/services/getmail.scm (serialize-getmail-configuration-file): Move
after <getmail-configuration-file> definition.
2022-12-02 00:02:12 +01:00
594f5ef351
gnu: Add alfa.
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* gnu/packages/astronomy.scm (alfa): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-12-02 00:02:12 +01:00
8e416c979d
gnu: guile-gcrypt: Update to 0.4.0.
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* gnu/packages/gnupg.scm (guile-gcrypt): Update to 0.4.0.
2022-12-02 00:02:12 +01:00
c7793b82ef
gnu: raspberry-pi: Add a bootloader-chain for the Raspberry Pi and os examples.
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* gnu/packages/raspberry-pi.scm (grub-efi-bootloader-chain-raspi-64): New
bootloader variable, capable to boot a Raspberry Pi over network or from a
local storage.
* gnu/system/examples/raspberry-pi-64.tmpl: New operating-system example.
* gnu/system/examples/raspberry-pi-64-nfs-root.tmpl: New operating-system
example for booting over network.
* Makefile.am (EXAMPLES): Register the new files.
Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-12-01 14:31:29 -05:00
0ea8328052
gnu: raspberry-pi: New make-raspi-bcm28-dtbs procedure.
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* gnu/packages/raspberry-pi.scm (make-raspi-bcm28-dtbs): New procedure.
Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-12-01 14:31:29 -05:00
4e2e4b222f
gnu: raspberry-pi: Add helpers for config.txt file generation.
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* gnu/packages/raspberry-pi.scm (raspi-config-file, raspi-custom-txt):
New functions.
(%raspi-config-txt, %raspi-bcm27-dtb-txt, %raspi-bcm28-dtb-txt
%raspi-u-boot-bootloader-txt): New variables.
Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-12-01 14:31:29 -05:00
13f9110e5f
gnu: raspberry-pi: Add defconfig objects to build customized Linux kernels.
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gnu/packages/raspberry-pi.scm (make-raspi-defconfig): New procedure.
(%bcm2709-defconfig, %bcm2711-defconfig, %bcm2711-defconfig-64)
(%bcmrpi3-defconfig): New variables.
Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-12-01 14:31:28 -05:00
Ricardo Wurmus
Felix Lechner
Marius Bakke
Navid Afkhami
Maxim Cournoyer
Ludovic Courtès
Sharlatan Hellseher
Stefan