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Author SHA1 Message Date
Ricardo Wurmus 23322c2de8
gnu: tophat: Remove trailing #T from build phases and snippet. 
* gnu/packages/bioinformatics.scm (tophat)[source]: Remove trailing #T from
snippet.
[arguments]: Remove trailing #T from build phases.
 2022-12-13 16:31:55 +01:00
Ricardo Wurmus b339e181e1
gnu: python-bx-python: Update to 0.9.0. 
* gnu/packages/bioinformatics.scm (python-bx-python): Update to 0.9.0.
[build-system]: Use pyproject-build-system.
[arguments]: Add phase 'build-extensions and 'disable-cython-doctests.
[native-inputs]: Replace python-nose with python-pytest.
 2022-12-13 16:31:55 +01:00
Ricardo Wurmus de30c74b63
gnu: bioawk: Use gexp. 
* gnu/packages/bioinformatics.scm (bioawk)[arguments]: Use gexp and simplify
'install phase.
 2022-12-13 16:31:55 +01:00
Ricardo Wurmus 057579495f
gnu: blasr-libcpp: Remove trailing #T from build phases. 
* gnu/packages/bioinformatics.scm (blasr-libcpp)[arguments]: Remove
trailing #T from build phases.
 2022-12-13 16:31:55 +01:00
Ricardo Wurmus eaf5198a5e
gnu: pbbam: Drop input labels. 
* gnu/packages/bioinformatics.scm (pbbam)[native-inputs]: Drop labels.
 2022-12-13 16:31:55 +01:00
Ricardo Wurmus 8b2fdcb2c3
gnu: pbbam: Update to 2.1.0. 
* gnu/packages/bioinformatics.scm (pbbam): Update to 2.1.0.
 2022-12-13 16:31:55 +01:00
Ricardo Wurmus 684d046e6c
gnu: pbcopper: Update to 2.0.0. 
* gnu/packages/bioinformatics.scm (pbcopper): Update to 2.0.0.
 2022-12-13 16:31:55 +01:00
Ricardo Wurmus 53f65f7315
gnu: bedtools: Remove unnecessary quasiquotation. 
* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Remove quasiquote.
[native-inputs]: Drop input label.
 2022-12-13 16:31:54 +01:00
Ricardo Wurmus 4f1a36bd7b
gnu: bamutils: Update to 1.0.15. 
* gnu/packages/bioinformatics.scm (bamutils): Update to 1.0.15.
[arguments]: Remove quasiquoting; remove USER_WARNINGS from make-flags.
[native-inputs]: Update libstatgen.
 2022-12-13 16:31:54 +01:00
Ricardo Wurmus 8cc22866c2
gnu: bamtools: Update to 2.5.2. 
* gnu/packages/bioinformatics.scm (bamtools): Update to 2.5.2.
[arguments]: Enable tests; remove extra phases.
[inputs]: Add jsoncpp.
[native-inputs]: Add pkg-config.
 2022-12-13 16:31:54 +01:00
Ricardo Wurmus 6d2afaf25b
gnu: aragorn: Update to 1.2.41. 
* gnu/packages/bioinformatics.scm (aragorn): Update to 1.2.41.
[source]: Fetch C source file from new location.
[arguments]: Drop trailing #T in build phases; use gexp.
[native-inputs]: Add origin for man page.
[home-page]: Update to new home page.
[license]: Update to GPLv3+.
 2022-12-13 16:31:54 +01:00
Maxim Cournoyer 93b0c1e35e
gnu: Add rpi-imager. 
* gnu/packages/raspberry-pi.scm (rpi-imager): New variable.
 2022-12-13 10:11:20 -05:00
jgart 87638cdd48
gnu: mercury: Update to 22.01.4. 
* gnu/packages/mercury.scm (mercury-minimal): Update to 22.01.4.
[arguments]: Remove obsolete and non-existent file from being patched.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2022-12-13 13:42:12 +00:00
jgart 1810d67ad4
gnu: mercury-minimal: Update to 22.01.4. 
* gnu/packages/mercury.scm (mercury-minimal): Update to 22.01.4.
[arguments]: Remove obsolete file path, update libatomic-ops, and update
libgc-8.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2022-12-13 13:42:12 +00:00
Sharlatan Hellseher 0682e7c2e3
gnu: python-h5netcdf: Update to 1.1.0. 
* gnu/packages/python-xyz.scm (python-h5netcdf): Update to 1.1.0.
[build-system]: Use pyproject-build-system, to simplify package.
[description]: Style content and add links to referenced projects.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2022-12-13 13:42:11 +00:00
Sharlatan Hellseher 1a0dcc2112
gnu: python-asdf-astropy: Update to 0.3.0. 
* gnu/packages/astronomy.scm (python-asdf-astropy): Update to 0.3.0.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2022-12-13 13:42:11 +00:00
EuAndreh 866eb7fffb
gnu: Add tmux-plugin-resurrect. 
* gnu/packages/tmux.scm (tmux-plugin-resurrect): New variable.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2022-12-13 13:42:11 +00:00
Paul A. Patience 36bd9121d6
gnu: Add rust-csv-index-0.1. 
* gnu/packages/crates-io.scm (rust-csv-index-0.1): New variable.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2022-12-13 13:42:11 +00:00
Martin Schmidt 34cf5e06a9
gnu: nheko: Support video calls. 
* gnu/packages/messaging.scm (nheko)[inputs]: Replace GST-PLUGINS-GOOD with
GST-PLUGINS-GOOD-QT to fix video calls.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2022-12-13 13:42:11 +00:00
Martin Schmidt 27efd3ed3c
gnu: Add gst-plugins-good-qt. 
* gnu/packages/gstreamer.scm (gst-plugins-good-qt): New variable.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2022-12-13 13:42:11 +00:00
Christopher Baines 2fb187ed7c
gnu: guix-data-service: Update to 0.0.1-36.7b69611. 
* gnu/packages/web.scm (guix-data-service): Update to 0.0.1-36.7b69611.
 2022-12-13 13:42:11 +00:00
Ricardo Wurmus 81841559f4
gnu: kaldi: Update to 0-1.be22248. 
* gnu/packages/machine-learning.scm (kaldi): Update to 0-1.be22248.
 2022-12-13 14:38:13 +01:00
Ricardo Wurmus f764947dab
gnu: kaldi: Remove trailing #T from build phases. 
* gnu/packages/machine-learning.scm (kaldi)[arguments]: Remove trailing #T
from build phases.
 2022-12-13 14:38:12 +01:00
Ricardo Wurmus c978ae3c6b
gnu: kaldi-gstreamer-server: Update to 0-3.f79e204. 
* gnu/packages/machine-learning.scm (kaldi-gstreamer-server): Update to
0-3.f79e204.
 2022-12-13 14:38:12 +01:00
Ricardo Wurmus 8466aceb13
gnu: kaldi-gstreamer-server: Drop input labels. 
* gnu/packages/machine-learning.scm (kaldi-gstreamer-server)[inputs]: Drop
package labels.
 2022-12-13 14:38:12 +01:00
Ricardo Wurmus 79cf84c7ab
gnu: kaldi-gstreamer-server: Remove trailing #T from build phases. 
* gnu/packages/machine-learning.scm (kaldi-gstreamer-server)[arguments]:
Remove trailing #T from build phases.
 2022-12-13 14:38:12 +01:00
Ricardo Wurmus 01f4617b99
gnu: gst-kaldi-nnet2-online: Update to 0-3.7888ae5. 
* gnu/packages/machine-learning.scm (gst-kaldi-nnet2-online): Update to
0-3.7888ae5.
[arguments]: Do to quote list; remove trailing #T from build phases; augment
CPLUS_INCLUDE_PATH instead of replacing it.
[inputs]: Replace openfst with openfst-1.7.3.
 2022-12-13 14:38:03 +01:00
Pierre Neidhardt 417604ec25
gnu: sbcl-alloy: Update to 20221126. 
* gnu/packages/lisp-xyz.scm (sbcl-alloy): Update to 20221126.
 2022-12-13 11:18:59 +01:00
Pierre Neidhardt 706dead679
gnu: sbcl-3b-bmfont: Update to 20220327. 
* gnu/packages/lisp-xyz.scm (sbcl-3b-bmfont): Update to 20220327.
 2022-12-13 11:18:59 +01:00
Pierre Neidhardt e7eefbf85c
gnu: Add cl-sdf. 
* gnu/packages/lisp-xyz.scm (cl-sdf, ecl-sdf, sbcl-sdf): New variables.
 2022-12-13 11:18:59 +01:00
Pierre Neidhardt f0ebbe1598
gnu: sbcl-cl-vectors: Build all subsystems. 
* gnu/packages/lisp-xyz.scm (sbcl-cl-vectors)[arguments]: Build cl-paths,
cl-aa and cl-aa-misc as well.
 2022-12-13 11:18:59 +01:00
Pierre Neidhardt 4f64d30b5d
gnu: Add cl-binpack. 
* gnu/packages/lisp-xyz.scm (cl-binpack, ecl-binpack, sbcl-binpack): New variables.
 2022-12-13 11:18:59 +01:00
Pierre Neidhardt 63b508e4fb
gnu: Add cl-uax-14. 
* gnu/packages/lisp-xyz.scm (cl-uax-14, ecl-uax-14, sbcl-uax-14): New variables.
 2022-12-13 11:18:59 +01:00
Pierre Neidhardt 752b65935d
gnu: Add cl-font-discovery. 
* gnu/packages/lisp-xyz.scm (cl-font-discovery, ecl-font-discovery,
sbcl-font-discovery): New variables.
 2022-12-13 11:18:59 +01:00
Pierre Neidhardt 206b97c102
gnu: Add cl-colored. 
* gnu/packages/lisp-xyz.scm (cl-colored, ecl-colored, sbcl-colored): New variables.
 2022-12-13 11:18:59 +01:00
Bruno Victal ca735decfb
gnu: mympd: Update to 10.1.6. 
* gnu/packages/mpd.scm (mympd): Update to 10.1.6.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2022-12-13 14:17:30 +08:00
Robby Zambito 648b1605dd
gnu: gauche: Update to 0.9.12 
* gnu/packages/scheme.scm (gauche): Update to 0.9.12.
[source]: Project migrated to GitHub.
libatomic-ops is no longer in the Gauche source tree.
[arguments]: Renamed network test file.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2022-12-13 14:10:26 +08:00
Ricardo Wurmus e84042fdd4
gnu: cnvkit: Update to 0.9.9. 
* gnu/packages/bioinformatics.scm (cnvkit): Update to 0.9.9.
[build-system]: Use pyproject-build-system.
[arguments]: Relax restriction on python-joblib.
[propagated-inputs]: Add python-pomegranate and python-scikit-learn.
 2022-12-13 00:08:54 +01:00
Ricardo Wurmus 1369b53d49
gnu: seqmagick: Update to 0.8.4. 
* gnu/packages/bioinformatics.scm (seqmagick): Update to 0.8.4.
[build-system]: Use pyproject-build-system.
[inputs]: Add python-pygtrie.
[native-inputs]: Replace python-nose with python-pytest.
 2022-12-13 00:08:54 +01:00
Ricardo Wurmus 9bf2101049
gnu: python-flasgger: Update to 0.9.5. 
* gnu/packages/python-xyz.scm (python-flasgger): Update to 0.9.5.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom 'check phase; add 'prepare-check phase; disable
"test_swag" test via #:test-flags.
[native-inputs]: Add python-apispec-webframeworks and python-flask-jwt.
 2022-12-13 00:08:54 +01:00
Ricardo Wurmus 8c197f990b
gnu: python-pyjwt: Update to 2.6.0. 
* gnu/packages/python-xyz.scm (python-pyjwt): Update to 2.6.0.
[build-system]: Use pyproject-build-system.
[arguments]: Remove.
[native-inputs]: Add pytohn-coverage, python-pre-commit, python-sphinx, and
python-sphinx-rtd-theme.
 2022-12-13 00:08:54 +01:00
Ricardo Wurmus 99a29b4933
gnu: python-apispec: Update to 6.0.2. 
* gnu/packages/python-xyz.scm (python-apispec): Update to 6.0.2.
[build-system]: Use pyproject-build-system.
[arguments]: Disable test through test-flags, not by replacing the 'check
phase.
[propagated-inputs]: Remove python-pyyaml; add python-packaging.
[native-inputs]: Add python-flake8, python-flake8-bugbear, python-mypy,
python-pre-commit, and python-pyyaml.
 2022-12-13 00:08:54 +01:00
Ricardo Wurmus 0fcba8b01c
gnu: python-marshmallow: Update to 3.19.0. 
* gnu/packages/python-xyz.scm (python-marshmallow): Update to 3.19.0.
[build-system]: Use pyproject-build-system.
[propagated-inputs]: Remove python-dateutil and python-simplejson; add
python-packaging.
[native-inputs]: Add python-flake8, python-flake8-bugbear, python-mypy,
python-pre-commit, and python-simplejson.
 2022-12-13 00:08:54 +01:00
Ricardo Wurmus 71dc990f22
gnu: python-flask-restful: Update to 0.3.9. 
* gnu/packages/python-web.scm (python-flask-restful): Update to 0.3.9.
[source]: Remove patch.
[build-system]: Use pyproject-build-system.
[arguments]: Disable "test_redirect" test; remove 'fix-imports phase.
[native-inputs]: Replace python-nose with python-pytest.
* gnu/local.mk (dist_patch_DATA): Remove patch.
* gnu/packages/patches/python-flask-restful-werkzeug-compat.patch: Remove file.
 2022-12-13 00:08:54 +01:00
Ricardo Wurmus 461dff2651
gnu: python-cgatcore: Update to 0.6.14. 
* gnu/packages/bioinformatics.scm (python-cgatcore): Update to 0.6.14.
[build-system]: Use pyproject-build-system.
[arguments]: Disable broken tests with #:test-flags; do not replace 'check
phase; add phase 'sqlite-compatibility.
[native-inputs]: Drop input labels.
 2022-12-13 00:08:54 +01:00
Ricardo Wurmus 2f1d8fb129
gnu: python-apsw: Update to 3.40.0.0. 
* gnu/packages/databases.scm (python-apsw): Update to 3.40.0.0.
[source]: Remove obsolete patch.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-cython.
[arguments]: Move build-extensions phase before build phase.
* gnu/local.mk (dist_patch_DATA): Remove patch.
* gnu/packages/patches/python-apsw-3.39.2.1-test-fix.patch: Remove file.
 2022-12-13 00:08:54 +01:00
Ricardo Wurmus 08b9e29d46
gnu: python-bokeh: Skip failing PIL test. 
The test compares base64-encoded gifs; the gifs look identical but the
base64-encoded data differs.  Since the result seems fine, disabling this PIL
test is probably okay.

* gnu/packages/python-xyz.scm (python-bokeh)[arguments]: Ignore failing
test_transform_PIL test.
 2022-12-13 00:08:13 +01:00
Ricardo Wurmus b72df3bbb3
gnu: python-dna-features-viewer: Update to 3.1.1. 
* gnu/packages/bioinformatics.scm (python-dna-features-viewer):
Update to 3.1.1.
[build-system]: Use pyproject-build-system.
[arguments]: Add build phase to fix a compatibility problem with biopython.
[propagated-inputs]: Add python-packaging.
 2022-12-13 00:07:23 +01:00
Ricardo Wurmus b66b6bdf70
gnu: python-hicexplorer: Update to 3.7.2. 
* gnu/packages/bioinformatics.scm (python-hicexplorer): Update to 3.7.2.
[build-system]: Use pyproject-build-system.
[arguments]: Use gexp; remove phase "loosen-up-requirements"; add test-flags
to skip some tests; add phase "remove-dependency-on-krbalancing" to remove a
dependency on an unlicensed package; add phase "fix-references"; add phase
"run-only-low-mem-tests".
[propagated-inputs]: Remove python-configparser and python-six; add
python-biopython, python-cleanlab-1, python-fit-nbinom, python-graphviz,
python-hic2cool, python-hicmatrix, python-hyperopt, python-imbalanced-learn,
python-ipykernel, python-psutil, python-pybedtools, python-pygenometracks,
python-scikit-learn, and python-tqdm.
[native-inputs]: Add graphviz.
 2022-12-13 00:07:23 +01:00
Ricardo Wurmus c3e330cf36
gnu: python-pygenometracks: Update to 3.5. 
* gnu/packages/bioinformatics.scm (python-pygenometracks): Update to 3.5.
[build-system]: Use pyproject-build-system.
[arguments]: Quote phases instead of full list of arguments; remove trailing #T
from build phase.
 2022-12-13 00:07:22 +01:00