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Author SHA1 Message Date
Ricardo Wurmus
2345cd49de
gnu: Add go-github-com-biogo-store-step. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-step): New variable.
 2022-08-16 16:18:57 +02:00
Ricardo Wurmus
c42745ba39
gnu: Add go-github-com-biogo-store-llrb. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-llrb): New variable.
 2022-08-16 16:18:48 +02:00
Ricardo Wurmus
5fae9e158d
gnu: Add go-github-com-biogo-store-kdtree. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-kdtree): New variable.
 2022-08-16 16:18:40 +02:00
Ricardo Wurmus
a33ee9bd51
gnu: Add go-github-com-biogo-store-interval. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-interval): New variable.
 2022-08-16 16:18:31 +02:00
Ricardo Wurmus
2b4dcc477b
gnu: Add go-github-com-biogo-graph. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-graph): New variable.
 2022-08-16 16:09:54 +02:00
Ricardo Wurmus
872e17ddc1
gnu: Add stpipeline. 
* gnu/packages/bioinformatics.scm (stpipeline): New variable.
 2022-08-16 15:22:07 +02:00
Ricardo Wurmus
9c2400c282
gnu: Add python-taggd. 
* gnu/packages/bioinformatics.scm (python-taggd): New variable.
 2022-08-16 15:22:07 +02:00
Ricardo Wurmus
a60412019e
gnu: Add python-sqlitedict. 
* gnu/packages/databases.scm (python-sqlitedict): New variable.
 2022-08-16 15:22:06 +02:00
Ricardo Wurmus
752be79bf3
gnu: htseq: Update to 2.0.2. 
* gnu/packages/bioinformatics.scm (htseq): Update to 2.0.2.
[source]: Fetch from git repository.
[arguments]: Delete 'build phase; run tests with pytest in 'check phase.
[propagated-inputs]: Add python-matplotlib and python-pysam.
[inputs]: Remove python-matplotlib and python-pysam.
[native-inputs]: Add python-pandas, python-pytest, python-scipy, and swig.
[synopsis]: Update.
[description]: Update.
 2022-08-16 15:22:06 +02:00
Andrew Tropin
0598b5d143
gnu: emacs-geiser-guile: Update guile input to guile-3.0-latest. 
* gnu/packages/emacs-xyz.scm (emacs-geiser-guile)[inputs]: Update guile to
guile-3.0-latest.
 2022-08-16 09:20:45 +03:00
(
ace7b5babe
gnu: terminals: Deprecate wterm. 
`wterm` no longer works with modern Wayland, and has been unmaintained
since early 2021. See issue #52029.

* gnu/packages/terminals.scm (wterm): Deprecate in favour of `foot`.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2022-08-16 09:21:52 +08:00
Marius Bakke
302b3cdca3
gnu: python-daemon: Remove unused input. 
* gnu/packages/python-xyz.scm (python-daemon)[native-inputs]: Remove
PYTHON-UNITTEST2.
 2022-08-16 00:43:46 +02:00
Marius Bakke
b38df69c2c
gnu: python-case: Remove unused input. 
* gnu/packages/python-xyz.scm (python-case)[propagated-inputs]: Remove
PYTHON-UNITTEST2.
 2022-08-16 00:43:45 +02:00
Marius Bakke
afdcd03689
gnu: python-posix-ipc: Remove unused input. 
* gnu/packages/python-xyz.scm (python-posix-ipc)[native-inputs]: Remove.
 2022-08-16 00:43:45 +02:00
Marius Bakke
d23a04e52e
gnu: python-pyu2f: Remove unused inputs. 
* gnu/packages/python-crypto.scm (python-pyu2f)[native-inputs]: Remove.
 2022-08-16 00:43:45 +02:00
Marius Bakke
24834c2722
gnu: python-pymysql: Remove unused input. 
* gnu/packages/databases.scm (python-pymysql)[native-inputs]: Remove
PYTHON-UNITTEST2.
 2022-08-16 00:43:45 +02:00
Marius Bakke
715a5efc49
gnu: python-pyclipper: Update to 1.3.0.post3. 
* gnu/packages/python-xyz.scm (python-pyclipper): Update to 1.3.0.post3.
[source](uri): Use tarball instead of zipball.
[source](snippet): Adjust for renamed file.
[arguments]: Likewise.
[propagated-inputs]: Remove.
[native-inputs]: Remove PYTHON-UNITTEST2 and UNZIP.  Add PYTHON-SETUPTOOLS-SCM.
 2022-08-16 00:43:45 +02:00
Marius Bakke
90ec03cae3
gnu: python-ufo2ft: Add missing input. 
* gnu/packages/fontutils.scm (python-ufo2ft)[native-inputs]: Add
PYTHON-SETUPTOOLS-SCM.
 2022-08-16 00:43:44 +02:00
Marius Bakke
46b3fb82f8
gnu: python-afdko: Add missing input. 
* gnu/packages/fontutils.scm (python-afdko)[native-inputs]: Add
PYTHON-SETUPTOOLS-SCM.
 2022-08-16 00:43:44 +02:00
Marius Bakke
b74744fee6
gnu: python-ufoprocessor: Add missing input. 
* gnu/packages/fontutils.scm (python-ufoprocessor)[native-inputs]: Add
PYTHON-SETUPTOOLS-SCM.
 2022-08-16 00:43:44 +02:00
Marius Bakke
5f2c529a59
gnu: python-fontparts: Add missing input. 
* gnu/packages/fontutils.scm (python-fontparts-bootstrap)[native-inputs]: Add
PYTHON-SETUPTOOLS-SCM.
 2022-08-16 00:43:44 +02:00
Marius Bakke
a038bfc481
gnu: python-booleanoperations: Add missing input. 
* gnu/packages/graphics.scm (python-booleanoperations)[native-inputs]: Add
PYTHON-SETUPTOOLS-SCM.
 2022-08-16 00:43:44 +02:00
Marius Bakke
faea55669f
gnu: python-mando: Update to 0.7.1. 
* gnu/packages/python-xyz.scm (python-mando): Update to 0.7.1.
[arguments]: Override check phase.
 2022-08-16 00:43:44 +02:00
Marius Bakke
46cb02c7cb
gnu: python-radon: Permit newer versions of mando. 
* gnu/packages/python-xyz.scm (python-radon)[arguments]: Add setup.py
substitution.
 2022-08-16 00:43:44 +02:00
Marius Bakke
389ae75a37
gnu: python-lz4: Update to 4.0.2. 
* gnu/packages/python-compression.scm (python-lz4): Update to 4.0.2.
[native-inputs]: Remove PYTHON-NOSE.  Add PYTHON-PKGCONFIG and PYTHON-PSUTIL.
[arguments]: Override check phase.
 2022-08-16 00:43:43 +02:00
Marius Bakke
7e0116740b
gnu: python-mypy: Update to 0.971. 
* gnu/packages/patches/python-mypy-12332.patch,
gnu/packages/patches/python-mypy-use-sys-path.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/python-check.scm (python-mypy): Update to 0.971.
[source](patches): Remove.
[arguments]: Skip one test.
 2022-08-16 00:43:43 +02:00
Marius Bakke
1e969dafb7
gnu: libreoffice: Remove obsolete workaround. 
* gnu/packages/libreoffice.scm (libreoffice)[arguments]: Don't pass LDFLAGS.
 2022-08-16 00:43:43 +02:00
Tobias Geerinckx-Rice
97386910fb
gnu: encodings: Update to 1.0.6. 
* gnu/packages/xorg.scm (encodings): Update to 1.0.6.
 2022-08-14 02:00:54 +02:00
Tobias Geerinckx-Rice
73eca39df7
gnu: mu: Update to 1.8.9. 
* gnu/packages/mail.scm (mu): Update to 1.8.9.
[arguments]: Adjust the 'patch-bin-references phase accordingly.
 2022-08-14 02:00:00 +02:00
Ricardo Wurmus
c3c2dfdb5e
gnu: plink-ng: Build sources from 2.0 directory 
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Disable tests; adjust
make flags; enter 2.0 directory in 'chdir phase; replace 'install phase.
[inputs]: Add zstd:lib.
 2022-08-15 18:08:20 +02:00
Tobias Geerinckx-Rice
d248d8b519
gnu: rnnoise: Remove input labels. 
* gnu/packages/xiph.scm (rnnoise)[native-inputs]:
Remove input labels.
 2022-08-14 02:00:01 +02:00
Tobias Geerinckx-Rice
2388d2d3f7
gnu: rnnoise: Unhide and rename variable. 
* gnu/packages/xiph.scm (xiph-rnnoise): Rename to…
(rnnoise): …this.  Adjust all users.
[properties]: Remove HIDDEN? property as it is no longer ambiguous.
 2022-08-14 02:00:01 +02:00
Tobias Geerinckx-Rice
2790d118b2
gnu: noise-suppression-for-voice: Rename from ‘rnnoise’. 
This is a set of plug-ins *based on* Xiph's rnnoise package (also in Guix).

* gnu/packages/pulseaudio.scm (rnnoise): Rename this variable…
(noise-suppression-for-voice): …to this.
[noisetorch](inputs): Adjust its only user.
 2022-08-14 02:00:01 +02:00
Tobias Geerinckx-Rice
8e82a70a4f
gnu: noisetorch: Update to 0.12.2. 
* gnu/packages/pulseaudio.scm (noisetorch): Update to 0.12.2.
[source]: Switch to maintained fork.
[arguments]: Update all ‘paths’ accordingly.  Rename 'symlink-rnnoise
phase to 'copy-rnnoise-library and do so.  Remove 'gen-version.go phase.
Don't explicitly return #f from phases.
[home-page]: Update to match SOURCE.
 2022-08-14 02:00:01 +02:00
Tobias Geerinckx-Rice
39b77ed3aa
gnu: openvpn: Update to 2.5.7. 
* gnu/packages/vpn.scm (openvpn): Update to 2.5.7.
 2022-08-14 02:00:01 +02:00
Tobias Geerinckx-Rice
0d92088d5c
gnu: nftables: Update to 1.0.5. 
* gnu/packages/linux.scm (nftables): Update to 1.0.5.
 2022-08-14 02:00:01 +02:00
Tobias Geerinckx-Rice
4985043c7c
gnu: libnftnl: Update to 1.2.3. 
* gnu/packages/linux.scm (libnftnl): Update to 1.2.3.
 2022-08-14 02:00:00 +02:00
Tobias Geerinckx-Rice
ab34425e53
gnu: bird: Update to 2.0.10. 
* gnu/packages/networking.scm (bird): Update to 2.0.10.
 2022-08-14 02:00:00 +02:00
Tobias Geerinckx-Rice
3ee8a17eff
gnu: catfish: Update to 4.16.4. 
* gnu/packages/xfce.scm (catfish): Update to 4.16.4.
 2022-08-14 02:00:00 +02:00
Tobias Geerinckx-Rice
367b045c55
gnu: libupnp: Update to 1.14.13. 
* gnu/packages/upnp.scm (libupnp): Update to 1.14.13.
 2022-08-14 02:00:00 +02:00
Tobias Geerinckx-Rice
25e9bb05da
gnu: os-prober: Update to 1.81. 
* gnu/packages/bootloaders.scm (os-prober): Update to 1.81.
 2022-08-14 02:00:00 +02:00
Maxime Devos
de29a26008
guile-fibers: Backport the ‘epoll instance is dead’ bugfix. 
This fixes some indeterministic test failures for gnunet-scheme observed while
developing gnunet-scheme.  The following checks were made:

All dependents compile for x86_64:

$ ./pre-inst-env guix build shepherd gnunet-scheme guix-build-coordinator nar-herder guix-data-service guile-fibers --system=x86_64-linux

Everything except guix-build-coordinator (which depends on the
non-cross-compilable sqitch) cross-compile from x86_64 to aarch64-linux-gnu:

$ ./pre-inst-env guix build shepherd gnunet-scheme nar-herder  guile-fibers --system=x86_64-linux --target=aarch64-linux-gnu

I tried testing for reproducibility but the check phase took to long.
However, you can compare the hash you get against the hash I got:

$ ./pre-inst-env guix hash --serializer=nar $(./pre-inst-env guix build guile-fibers --no-grafts --system=x86_64-linux) 0qsaqx27b6q2s22h7y93417ijpkwl6gc1fhhck8aha6bvmawk5h0

I tried an emulated build for another architecture, but there the tests took
overly long.

There were no lint warnings for guile-fibers.

* gnu/packages/patches/guile-fibers-epoll-instance-is-dead.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Register the patch.
* gnu/packages/guile-xyz.scm (guile-fibers)[source]{patches}: Use the patch.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2022-08-15 15:51:27 +02:00
Mathieu Othacehe
3084fc28fd
Revert "gnu: python-lxml: Update to 4.6.5." 
This reverts commit 2365e8435a as it triggers
>15k rebuilds: https://ci.guix.gnu.org/eval/543158.
 2022-08-15 15:45:46 +02:00
Maximilian Heisinger
9ddd37d6ab
gnu: Add kissat. 
* gnu/packages/maths.scm (kissat): New variable.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2022-08-15 15:15:11 +02:00
Danny Milosavljevic
2365e8435a
gnu: python-lxml: Update to 4.6.5. 
* gnu/packages/xml.scm (python-lxml): Update to 4.6.5.
 2022-08-15 14:48:41 +02:00
Maxim Cournoyer
d8537c68d0
gnu: Add python-robotframework-sshtunnellibrary. 
* gnu/packages/python-xyz.scm (python-robotframework-sshtunnellibrary): New variable.
 2022-08-15 08:30:14 -04:00
Maxim Cournoyer
21f1a47097
gnu: Add python-sshtunnel. 
* gnu/packages/python-xyz.scm (python-sshtunnel): New variable.
 2022-08-15 08:30:14 -04:00
Mathieu Othacehe
0e53328a8a
gnu: torsocks: Wrap lines. 
* gnu/packages/tor.scm (torsocks)[source, arguments]: Wrap long lines
and remove a trailing #t.
 2022-08-15 11:21:22 +02:00
Jim Newsome
ae549cf48f
gnu: torsocks: Update to 2.4.0. 
* gnu/packages/tor.scm (torsocks): Update to 2.4.0.
[native-inputs]: Add autoconf, automake, libtool because torsocks releases
no longer pre-run autogen.sh.
[synopsis, description]: Clarify that applications do not need to be
socks-aware to be used with torsocks.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2022-08-15 11:20:28 +02:00
Mathieu Othacehe
6b2d29a6f5
Revert "gnu: python-lsp-server: Update to 1.5.0." 
This reverts commit 07f807f12c because it
requires a python-pluggy update which seems to cause some issues.
 2022-08-15 11:08:05 +02:00