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2022-12-13gnu: bioawk: Use gexp.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bioawk)[arguments]: Use gexp and simplify 'install phase.
2022-12-13gnu: blasr-libcpp: Remove trailing #T from build phases.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (blasr-libcpp)[arguments]: Remove trailing #T from build phases.
2022-12-13gnu: pbbam: Drop input labels.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pbbam)[native-inputs]: Drop labels.
2022-12-13gnu: pbbam: Update to 2.1.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pbbam): Update to 2.1.0.
2022-12-13gnu: pbcopper: Update to 2.0.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pbcopper): Update to 2.0.0.
2022-12-13gnu: bedtools: Remove unnecessary quasiquotation.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Remove quasiquote. [native-inputs]: Drop input label.
2022-12-13gnu: bamutils: Update to 1.0.15.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bamutils): Update to 1.0.15. [arguments]: Remove quasiquoting; remove USER_WARNINGS from make-flags. [native-inputs]: Update libstatgen.
2022-12-13gnu: bamtools: Update to 2.5.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bamtools): Update to 2.5.2. [arguments]: Enable tests; remove extra phases. [inputs]: Add jsoncpp. [native-inputs]: Add pkg-config.
2022-12-13gnu: aragorn: Update to 1.2.41.Ricardo Wurmus
* 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+.
2022-12-13gnu: Add rpi-imager.Maxim Cournoyer
* gnu/packages/raspberry-pi.scm (rpi-imager): New variable.
2022-12-13gnu: mercury: Update to 22.01.4.jgart
* 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>
2022-12-13gnu: mercury-minimal: Update to 22.01.4.jgart
* 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>
2022-12-13gnu: python-h5netcdf: Update to 1.1.0.Sharlatan Hellseher
* 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>
2022-12-13gnu: python-asdf-astropy: Update to 0.3.0.Sharlatan Hellseher
* gnu/packages/astronomy.scm (python-asdf-astropy): Update to 0.3.0. Signed-off-by: Christopher Baines <mail@cbaines.net>
2022-12-13gnu: Add tmux-plugin-resurrect.EuAndreh
* gnu/packages/tmux.scm (tmux-plugin-resurrect): New variable. Signed-off-by: Christopher Baines <mail@cbaines.net>
2022-12-13gnu: Add rust-csv-index-0.1.Paul A. Patience
* gnu/packages/crates-io.scm (rust-csv-index-0.1): New variable. Signed-off-by: Christopher Baines <mail@cbaines.net>
2022-12-13gnu: nheko: Support video calls.Martin Schmidt
* 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>
2022-12-13gnu: Add gst-plugins-good-qt.Martin Schmidt
* gnu/packages/gstreamer.scm (gst-plugins-good-qt): New variable. Signed-off-by: Christopher Baines <mail@cbaines.net>
2022-12-13gnu: guix-data-service: Update to 0.0.1-36.7b69611.Christopher Baines
* gnu/packages/web.scm (guix-data-service): Update to 0.0.1-36.7b69611.
2022-12-13gnu: kaldi: Update to 0-1.be22248.Ricardo Wurmus
* gnu/packages/machine-learning.scm (kaldi): Update to 0-1.be22248.
2022-12-13gnu: kaldi: Remove trailing #T from build phases.Ricardo Wurmus
* gnu/packages/machine-learning.scm (kaldi)[arguments]: Remove trailing #T from build phases.
2022-12-13gnu: kaldi-gstreamer-server: Update to 0-3.f79e204.Ricardo Wurmus
* gnu/packages/machine-learning.scm (kaldi-gstreamer-server): Update to 0-3.f79e204.
2022-12-13gnu: kaldi-gstreamer-server: Drop input labels.Ricardo Wurmus
* gnu/packages/machine-learning.scm (kaldi-gstreamer-server)[inputs]: Drop package labels.
2022-12-13gnu: kaldi-gstreamer-server: Remove trailing #T from build phases.Ricardo Wurmus
* gnu/packages/machine-learning.scm (kaldi-gstreamer-server)[arguments]: Remove trailing #T from build phases.
2022-12-13gnu: gst-kaldi-nnet2-online: Update to 0-3.7888ae5.Ricardo Wurmus
* 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.
2022-12-13gnu: sbcl-alloy: Update to 20221126.Pierre Neidhardt
* gnu/packages/lisp-xyz.scm (sbcl-alloy): Update to 20221126.
2022-12-13gnu: sbcl-3b-bmfont: Update to 20220327.Pierre Neidhardt
* gnu/packages/lisp-xyz.scm (sbcl-3b-bmfont): Update to 20220327.
2022-12-13gnu: Add cl-sdf.Pierre Neidhardt
* gnu/packages/lisp-xyz.scm (cl-sdf, ecl-sdf, sbcl-sdf): New variables.
2022-12-13gnu: sbcl-cl-vectors: Build all subsystems.Pierre Neidhardt
* gnu/packages/lisp-xyz.scm (sbcl-cl-vectors)[arguments]: Build cl-paths, cl-aa and cl-aa-misc as well.
2022-12-13gnu: Add cl-binpack.Pierre Neidhardt
* gnu/packages/lisp-xyz.scm (cl-binpack, ecl-binpack, sbcl-binpack): New variables.
2022-12-13gnu: Add cl-uax-14.Pierre Neidhardt
* gnu/packages/lisp-xyz.scm (cl-uax-14, ecl-uax-14, sbcl-uax-14): New variables.
2022-12-13gnu: Add cl-font-discovery.Pierre Neidhardt
* gnu/packages/lisp-xyz.scm (cl-font-discovery, ecl-font-discovery, sbcl-font-discovery): New variables.
2022-12-13gnu: Add cl-colored.Pierre Neidhardt
* gnu/packages/lisp-xyz.scm (cl-colored, ecl-colored, sbcl-colored): New variables.
2022-12-13gnu: mympd: Update to 10.1.6.Bruno Victal
* gnu/packages/mpd.scm (mympd): Update to 10.1.6. Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
2022-12-13gnu: gauche: Update to 0.9.12Robby Zambito
* 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>
2022-12-13gnu: cnvkit: Update to 0.9.9.Ricardo Wurmus
* 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.
2022-12-13gnu: seqmagick: Update to 0.8.4.Ricardo Wurmus
* 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.
2022-12-13gnu: python-flasgger: Update to 0.9.5.Ricardo Wurmus
* 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.
2022-12-13gnu: python-pyjwt: Update to 2.6.0.Ricardo Wurmus
* 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.
2022-12-13gnu: python-apispec: Update to 6.0.2.Ricardo Wurmus
* 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.
2022-12-13gnu: python-marshmallow: Update to 3.19.0.Ricardo Wurmus
* 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.
2022-12-13gnu: python-flask-restful: Update to 0.3.9.Ricardo Wurmus
* 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.
2022-12-13gnu: python-cgatcore: Update to 0.6.14.Ricardo Wurmus
* 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.
2022-12-13gnu: python-apsw: Update to 3.40.0.0.Ricardo Wurmus
* 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.
2022-12-13gnu: python-bokeh: Skip failing PIL test.Ricardo Wurmus
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.
2022-12-13gnu: python-dna-features-viewer: Update to 3.1.1.Ricardo Wurmus
* 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.
2022-12-13gnu: python-hicexplorer: Update to 3.7.2.Ricardo Wurmus
* 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.
2022-12-13gnu: python-pygenometracks: Update to 3.5.Ricardo Wurmus
* 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.
2022-12-13gnu: python-hicmatrix: Update to 16.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 16. [build-system]: Use pyproject-build-system. [arguments]: Shuffle the quote.
2022-12-13gnu: python-biopython: Update to 1.80.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.80. [build-system]: Use pyproject-build-system. [arguments]: Remove trailing #T from build phase.
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