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Author SHA1 Message Date
Ludovic Courtès 6d54f1987f
gnu: vtk: Remove input labels. 
* gnu/packages/image-processing.scm (vtk)[inputs]: Remove labels.
 2022-04-01 18:01:07 +02:00
Ludovic Courtès c3a20d91f9
gnu: vtk@6: Depend on Python 2.x, not 3.x. 
* gnu/packages/image-processing.scm (vtk-6)[native-inputs]: Replace
PYTHON with PYTHON-2.
 2022-04-01 18:01:06 +02:00
Ludovic Courtès 2a363bb5d3
weather: Colorize the output. 
* guix/colors.scm (coloring-procedure): Export.
* guix/scripts/weather.scm (report-server-coverage): Highlight the
server name and colorize the availability ratio.
 2022-04-01 18:01:06 +02:00
Ludovic Courtès c1093dc7a6
gnu: libtool: Add 2.4.7. 
* gnu/packages/autotools.scm (libtool-2.4.7): New variable.
 2022-04-01 18:01:06 +02:00
Ludovic Courtès 0fffcfa41d
gnu: libressl: Add 'release-monitoring-url' property. 
* gnu/packages/tls.scm (libressl)[properties]: New field.
 2022-04-01 18:01:06 +02:00
jgart b724c847a2
gnu: cl-usocket: Update to 0.8.4. 
* gnu/packages/lisp-xyz.scm (sbcl-usocket): Update to 0.8.4.
  [inputs]: Use new style.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2022-04-01 13:33:56 +02:00
Sébastien Lerique fc94e93c4b
gnu: libfido2: Fix cross-compilation. 
* gnu/packages/security-token.scm (libfido2)[arguments]: Set the
PKG_CONFIG_EXECUTABLE variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-03-31 18:57:05 +03:00
Sébastien Lerique 89f3275ff5
gnu: libfido2: Use new style for inputs. 
* gnu/packages/security-token.scm (libfido2)[inputs]: Use new style.
Sort alphabetically.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-03-31 18:40:08 +03:00
Raphaël Mélotte via Guix-patches 4cfc1c433d
gnu: tio: Update to 1.36. 
* gnu/packages/terminals.scm (tio): Update to 1.36.
[native-inputs]: Add pkg-config.
[inputs]: Add libinih.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-03-31 18:25:31 +03:00
Christian Gelinek 9f82d1f1c0
gnu: iverilog: Add zlib dependency for LXT dump file format support. 
* gnu/packages/fpga.scm (iverilog)[native-inputs]: Add zlib.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-03-31 18:22:58 +03:00
cage 58874999c9
gnu: gmid: Update to 1.8.3. 
* gnu/packages/web.scm (gmid): Update to 1.8.3.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-03-31 18:19:19 +03:00
Collin J. Doering c5ffc9b65d
gnu: plantuml: Update to 1.2022.3. 
* gnu/packages/uml.scm (plantuml): Update to 1.2022.3.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-03-31 17:52:19 +03:00
Ricardo Wurmus 05e68f31ba
gnu: python-velocyto: Set cache directory for Numba. 
* gnu/packages/bioinformatics.scm (python-velocyto)[arguments]: Add phase
'set-numba-cache-dir.
 2022-03-31 16:02:21 +02:00
Efraim Flashner 8f3dc994bb
gnu: wfmash: Enable test suite. 
* gnu/packages/bioinformatics.scm (wfmash)[arguments]: Don't disable
tests. Add custom 'check phase based on upstream's own CI tests.
[native-inputs]: Add samtools.
 2022-03-31 16:29:34 +03:00
Arun Isaac 1ca9d9e194
gnu: Add wfmash. 
* gnu/packages/bioinformatics.scm (wfmash): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-03-31 16:14:53 +03:00
Arun Isaac 8524904e08
gnu: atomic-queue: Do not look for boost when cross-compiling. 
* gnu/packages/cpp.scm (atomic-queue)[arguments]: When cross-compiling, add a
do-not-check-for-boost phase.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-03-31 16:14:53 +03:00
Arun Isaac a83918837e
gnu: atomic-queue: Run tests correctly. 
* gnu/packages/cpp.scm (atomic-queue)[arguments]: In the check phase, run
tests instead of returning a function to run them.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-03-31 16:14:52 +03:00
Arun Isaac 7d331dd203
gnu: htslib: Add bzip2 and xz to inputs. 
htslib links to libbz2 from bzip2 and liblzma from xz. Therefore, bzip2 and xz
should be listed in inputs even though they are already present implicitly in
native-inputs. Else, cross-compilation will fail.

* gnu/packages/bioinformatics.scm (htslib)[inputs]: Add bzip2 and xz.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-03-31 16:14:52 +03:00
Arun Isaac 973ee1c91d
gnu: gsl: Force bootstrap when cross-compiling to riscv64-linux. 
* gnu/packages/maths.scm (gsl)[arguments]: Force an autotools bootstrap
when cross-compiling to riscv64-linux.
[native-inputs]: Add autoconf, automake and libtool when cross-compiling
to riscv64-linux.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-03-31 16:14:52 +03:00
Ricardo Wurmus a69a44bf59
gnu: python-loompy: Update to 3.0.7. 
* gnu/packages/bioinformatics.scm (python-loompy): Update to 3.0.7.
[arguments]: Add build phases 'fix-h5py-error and 'set-numba-cache-dir;
respect TESTS? argument in 'check phase.
[propagated-inputs]: Add python-click, python-numba, and
python-numpy-groupies.
 2022-03-31 14:37:58 +02:00
Ricardo Wurmus 38b2026515
gnu: Add python-numpy-groupies. 
* gnu/packages/python-science.scm (python-numpy-groupies): New variable.
 2022-03-31 14:37:58 +02:00
Arun Isaac 668d52a815
gnu: Add riscv-pk. 
* gnu/packages/virtualization.scm (riscv-pk): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-03-31 15:20:11 +03:00
Arun Isaac 9afad0c16e
gnu: spike: Substitute path to dtc instead of wrapping executables. 
* gnu/packages/virtualization.scm (spike)[arguments]: Delete the wrap-binary
phase. Add a configure-dtc-path phase that substitutes the absolute path to
dtc.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-03-31 15:20:08 +03:00
Ricardo Wurmus dda555fead
gnu: python-anndata: Update to 0.8.0. 
* gnu/packages/python-xyz.scm (python-anndata): Update to 0.8.0.
[arguments]: Remove build phase 'relax-dependency-requirements.
 2022-03-31 10:36:31 +02:00
Ricardo Wurmus ea403bf290
gnu: python-h5py: Update to 3.6.0. 
* gnu/packages/python-xyz.scm (python-h5py): Update to 3.6.0.
[arguments]: Set HDF5_DIR variable instead of patching files.
 2022-03-31 10:36:31 +02:00
Ricardo Wurmus 967d5fd5c2
gnu: python2-h5py: Detach version and source from python-h5py. 
* gnu/packages/python-xyz.scm (python2-h5py): Override source and version
field.
(python-h5py)[properties]: Record python2-variant.
 2022-03-31 10:36:31 +02:00
Efraim Flashner ecb2603046
gnu: weechat: Update to 3.5. 
* gnu/packages/irc.scm (weechat): Update to 3.5.
[inputs]: Add zstd:lib.
 2022-03-30 20:52:14 +03:00
Efraim Flashner cb00a5fd85
gnu: msmtp: Update to 1.8.20. 
* gnu/packages/mail.scm (msmtp): Update to 1.8.20.
 2022-03-30 20:24:55 +03:00
Efraim Flashner 96a1d6b7a0
gnu: ncdu-2: Update to 2.1.1. 
* gnu/packages/ncdu.scm (ncdu-2): Update to 2.1.1.
 2022-03-30 19:58:29 +03:00
Efraim Flashner 693212087d
gnu: ncdu2: Set upstream name. 
* gnu/packages/ncdu.scm (ncdu-2)[properties]: New field.
 2022-03-30 19:58:29 +03:00
Ricardo Wurmus 1c2da66035
gnu: anonip: Update to 1.1.0. 
* gnu/packages/web.scm (anonip): Update to 1.1.0.
[source]: Fetch from git.
[arguments]: Run tests with pytest.
[native-inputs]: Add python-pytest and python-pytest-cov.
 2022-03-30 15:33:22 +02:00
Mathieu Othacehe 643d05eb20
lsof: Prevent mass-rebuild. 
* gnu/packages/lsof.scm (lsof): Set LINUX_CONF_CC variable only when
cross-compiling.
 2022-03-30 14:40:04 +02:00
Brian Kubisiak 2387adf600
gnu: lbzip2: Fix cross-compilation. 
* gnu/packages/compression.scm (lbzip2)[arguments]: Search (or
native-inputs inputs) for gnulib-tool.py.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2022-03-30 12:34:36 +02:00
Brian Kubisiak a006b7d347
gnu: lsof: Fix cross-compilation. 
* gnu/packages/lsof (lsof)[arguments]: Add LINUX_CONF_CC environment
variable.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2022-03-30 11:50:58 +02:00
Leo Famulari 457999ce36
gnu: Mutt: Update to 2.2.2. 
* gnu/packages/mail.scm (mutt): Update to 2.2.2.
 2022-03-29 23:33:07 -04:00
Leo Famulari 1d62b15dc1
gnu: linux-libre 4.9: Update to 4.9.309. 
* gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.309.
(linux-libre-4.9-pristine-source): Update hash.
 2022-03-29 13:40:14 -04:00
Leo Famulari 555b2b0bd0
gnu: linux-libre 4.14: Update to 4.14.274. 
* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.274.
(linux-libre-4.14-pristine-source): Update hash.
 2022-03-29 13:40:14 -04:00
Leo Famulari ef57c59046
gnu: linux-libre 4.19: Update to 4.19.237. 
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.237.
(linux-libre-4.19-pristine-source): Update hash.
 2022-03-29 13:40:14 -04:00
Leo Famulari 5721cb284a
gnu: linux-libre 5.4: Update to 5.4.188. 
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.188.
(linux-libre-5.4-pristine-source): Update hash.
 2022-03-29 13:40:14 -04:00
Leo Famulari ded6beb9a7
gnu: linux-libre 5.10: Update to 5.10.109. 
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.109.
(linux-libre-5.10-pristine-source): Update hash.
 2022-03-29 13:40:13 -04:00
Leo Famulari 916b333e86
gnu: linux-libre 5.15: Update to 5.15.32. 
* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.32.
(linux-libre-5.15-pristine-source): Update hash.
 2022-03-29 13:40:13 -04:00
Leo Famulari c2a141156e
gnu: linux-libre 5.16: Update to 5.16.18. 
* gnu/packages/linux.scm (linux-libre-5.16-version): Update to 5.16.18.
(linux-libre-5.16-pristine-source): Update hash.
 2022-03-29 13:40:13 -04:00
Leo Famulari 89af5cd2a9
gnu: linux-libre 5.17: Update to 5.17.1. 
* gnu/packages/linux.scm (linux-libre-5.17-version): Update to 5.17.1.
(linux-libre-5.17-pristine-source): Update hash.
 2022-03-29 13:40:13 -04:00
cage 4b8500e7cb
gnu: gmid: Update to 1.8.2. 
* gnu/packages/web.scm (gmid): Update to 1.8.2.
[native-inputs]: Remove which.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2022-03-29 12:53:26 -04:00
Kyle Meyer 6c317e02ee
gnu: git-annex: Update to 10.20220322. 
* gnu/packages/haskell-apps.scm (git-annex): Update to 10.20220322.
[inputs]: Add ghc-http-client-restricted.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2022-03-29 12:53:26 -04:00
Kyle Meyer e59069fe2b
gnu: Add ghc-http-client-restricted. 
* gnu/packages/haskell-web.scm (ghc-http-client-restricted): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2022-03-29 12:53:26 -04:00
Kyle Meyer f40c72327e
gnu: ghc-http-client-tls: Update to 0.3.6.1. 
* gnu/packages/haskell-web.scm (ghc-http-client-tls): Update to 0.3.6.1.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2022-03-29 12:53:26 -04:00
Kyle Meyer d2984784fd
gnu: ghc-http-client: Update to 0.7.11. 
* gnu/packages/haskell-web.scm (ghc-http-client): Update to 0.7.11.
[inputs]: Add ghc-iproute.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2022-03-29 12:53:25 -04:00
Mădălin Ionel Patrașcu 591007f7d1
gnu: r-signac: Update to 1.6.0-2.458e647. 
* gnu/packages/bioinformatics.scm (r-signac): Update to 1.6.0-2.458e647.
[propagated-inputs]: Remove r-annotationfilter, r-biocgenerics, r-biostrings,
r-biovizbase, and r-ggbio; add r-qlcmatrix and r-tidyselect.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2022-03-29 17:40:17 +02:00
Ricardo Wurmus 977a33139e
gnu: plink-ng: Update to 2.00a3-20220315. 
* gnu/packages/bioinformatics.scm (plink-ng): Update to 2.00a3-20220315.
 2022-03-29 15:33:55 +02:00