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2021-12-08gnu: python2-markupsafe: Downgrade to 1.1.1....* gnu/packages/python-xyz.scm (python2-markupsafe): Downgrade to 1.1.1, because that's the last version to support Python 2. Ricardo Wurmus
2021-12-08gnu: ocaml-mcl: Add -fcommon to compiler flags....* gnu/packages/machine-learning.scm (ocaml-mcl)[arguments]: Add -fcommon. Ricardo Wurmus
2021-12-08gnu: paml: Pass -fcommon to compiler....* gnu/packages/bioinformatics.scm (paml)[arguments]: Set CFLAGS. Ricardo Wurmus
2021-12-08gnu: paml: Remove trailing #T....* gnu/packages/bioinformatics.scm (paml)[arguments]: Remove trailing #T from build phases. Ricardo Wurmus
2021-12-08gnu: sambamba: Remove trailing #T....* gnu/packages/bioinformatics.scm (sambamba)[arguments]: Remove trailing #T from build phases. Ricardo Wurmus
2021-12-08gnu: discrover: Add texlive-fonts-ec to inputs....* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Add texlive-fonts-ec. Ricardo Wurmus
2021-12-08gnu: discrover: Remove trailing #T....* gnu/packages/bioinformatics.scm (discrover)[arguments]: Remove trailing #T from build phases. Ricardo Wurmus
2021-12-08gnu: tbsp: Update to 1.0.0-2.dc30c03....* gnu/packages/bioinformatics.scm (tbsp): Update to 1.0.0-2.dc30c03. [arguments]: Relax requirement on matplot. This may turn out to be a mistake. [inputs]: Replace python-biopython with python-biopython-1.73. Ricardo Wurmus
2021-12-08gnu: mantis: Update to 0.1-2.b6979a2....* gnu/packages/bioinformatics.scm (mantis): Update to 0.1-2.b6979a2. [arguments]: Disable the use of SSE4.2 instructions. [native-inputs]: Build with GCC 7. Ricardo Wurmus
2021-12-08gnu: imp: Disable tests....* gnu/packages/bioinformatics.scm (imp)[arguments]: Disable unreliable test suite. Ricardo Wurmus
2021-12-08gnu: snap-aligner: Update to 2.0.0....* gnu/packages/bioinformatics.scm (snap-aligner): Update to 2.0.0. Ricardo Wurmus
2021-12-08gnu: snap-aligner: Remove trailing #T....* gnu/packages/bioinformatics.scm (snap-aligner)[arguments]: Remove trailing #T from 'install phase. Ricardo Wurmus
2021-12-08gnu: snap-aligner: Run tests conditionally....* gnu/packages/bioinformatics.scm (snap-aligner)[arguments]: Respect TESTS? option. Ricardo Wurmus
2021-12-08gnu: khmer: Cythonize source files....* gnu/packages/bioinformatics.scm (khmer)[source]: Remove generated files. [arguments]: Add phase 'do-use-cython to patch the setup.py to generate cpp files from Cython sources; add 'build-extensions phase; replace 'check phase. Ricardo Wurmus
2021-12-08gnu: cwltool: Update to 3.1.20211107152837....* gnu/packages/bioinformatics.scm (cwltool): Update to 3.1.20211107152837. [arguments]: Adjust phase 'loosen-version-restrictions; remove trailing #T from build phases; fix /bin/sh invocations in test files. Ricardo Wurmus
2021-12-08gnu: monero: Improve check phase....* gnu/packages/finance.scm (monero)[arguments]: Take 'tests?' parameter into consideration in 'check' phase. Guillaume Le Vaillant
2021-12-08gnu: monero-gui: Update to 0.17.3.0....* gnu/packages/finance.scm (monero-gui): Update to 0.17.3.0. Guillaume Le Vaillant
2021-12-08gnu: monero: Update to 0.17.3.0....* gnu/packages/finance.scm (monero): Update to 0.17.3.0. * gnu/packages/patches/monero-use-system-miniupnpc.patch: Update patch. Guillaume Le Vaillant
2021-12-08gnu: python-userspacefs: Update to 2.0.4....* gnu/packages/python-xyz.scm (python-userspacefs): Update to 2.0.4. Efraim Flashner
2021-12-08gnu: python-dropbox: Update to 11.25.0....* gnu/packages/file-systems.scm (python-dropbox): Update to 11.25.0. [propagated-inputs]: Remove python-certifi, python-chardet, and python-urllib3. Efraim Flashner
2021-12-08gnu: lollypop: Update to 1.4.24....* gnu/packages/gnome.scm (lollypop): Update to 1.4.24. [native-inputs]: Remove INTLTOOL and ITSTOOL. Add GETTEXT-MINIMAL. Marius Bakke
2021-12-08gnu: python-toolz: Update to 0.11.2....* gnu/packages/python-xyz.scm (python-toolz): Update to 0.11.2. Marius Bakke
2021-12-08gnu: python-django: Update to 3.2.10 [fixes CVE-2021-4442]....* gnu/packages/django.scm (python-django): Update to 3.2.10. Marius Bakke
2021-12-08gnu: python-django@2.2: Update to 2.2.25 [fixes CVE-2021-4442]....* gnu/packages/django.scm (python-django-2.2): Update to 2.2.25. Marius Bakke
2021-12-08gnu: hitch: Update to 1.7.2....* gnu/packages/web.scm (hitch): Update to 1.7.2. Marius Bakke
2021-12-08gnu: lollypop: Build with libsoup@2....* gnu/packages/gnome.scm (lollypop)[inputs]: Change from LIBSOUP to LIBSOUP-MINIMAL-2. Marius Bakke
2021-12-08gnu: rhythmbox: Adjust inputs....* gnu/packages/gnome.scm (rhythmbox)[inputs]: Change from PYTHON2-PYGOBJECT to PYTHON-PYGOBJECT. Add LIBSOUP-MINIMAL-2. Marius Bakke
2021-12-08gnu: labelme: Loosen Python requirements....* gnu/packages/image-processing.scm (labelme)[arguments]: Patch setup.py so it does not require a specific version of Matplotlib. Marius Bakke
2021-12-08nls: Update 'es' translation.Julien Lepiller
2021-12-07gnu: icecat: Update to 91.4.0-guix0-preview1 [security fixes]....Includes fixes for CVE-2021-43536, CVE-2021-43537, CVE-2021-43538, CVE-2021-43539, CVE-2021-43541, CVE-2021-43542, CVE-2021-43543, CVE-2021-43545, CVE-2021-43546, and MOZ-2021-0009. * gnu/packages/gnuzilla.scm (%icecat-version, %icecat-build-id): Update. (icecat-source): Remove icecat-CVE-2021-43527.patch, which is now included in upstream icecat. Update the gnuzilla commit, base version, and hashes. * gnu/packages/patches/icecat-CVE-2021-43527.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. Mark H Weaver
2021-12-07gnu: Add kiwix-tools....* gnu/packages/web.scm (kiwix-tools): New variable. Signed-off-by: Leo Famulari <leo@famulari.name> Denis 'GNUtoo' Carikli
2021-12-07gnu: newick-utils: Pass -fcommon to compiler....* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Set CFLAGS. Ricardo Wurmus
2021-12-07gnu: blasr: Update to 5.3.5....* gnu/packages/bioinformatics.scm (blasr): Update to 5.3.5. Ricardo Wurmus
2021-12-07gnu: blasr: Remove trailing #T....* gnu/packages/bioinformatics.scm (blasr)[arguments]: Remove trailing #T from build phase. Ricardo Wurmus
2021-12-07gnu: blasr-libcpp: Update to 5.3.5....* gnu/packages/bioinformatics.scm (blasr-libcpp): Update to 5.3.5. [inputs]: Add htslib. Ricardo Wurmus
2021-12-07gnu: htseq: Update to 0.12.3....* gnu/packages/bioinformatics.scm (htseq): Update to 0.12.3. Ricardo Wurmus
2021-12-07gnu: clipper: Update to 2.0.1....* gnu/packages/bioinformatics.scm (clipper): Update to 2.0.1. [source]: Add snippet to remove pre-compiled files. [arguments]: Disable tests, delete 'sanity-check phase, and add 'use-python3-for-cython phase. Ricardo Wurmus
2021-12-07gnu: pbbam: Update to 1.7.0....* gnu/packages/bioinformatics.scm (pbbam): Update to 1.7.0. [arguments]: Remove phase 'find-googletest; add phase 'patch-tests. [propagated-inputs]: Add pbcopper. Ricardo Wurmus
2021-12-07gnu: dovecot-pigeonhole: Update to 0.5.17.1....* gnu/packages/mail.scm (dovecot-pigeonhole): Update to 0.5.17.1. Tobias Geerinckx-Rice
2021-12-07gnu: dovecot: Update to 2.3.17.1....* gnu/packages/mail.scm (dovecot): Update to 2.3.17.1. Tobias Geerinckx-Rice
2021-12-07gnu: bwa-pssm: Fix build....* gnu/packages/bioinformatics.scm (bwa-pssm)[arguments]: Add phase 'patch-C-error. Ricardo Wurmus
2021-12-07gnu: Add pbcopper....* gnu/packages/bioinformatics.scm (pbcopper): New variable. Ricardo Wurmus
2021-12-07gnu: giac: Update to 1.7.0-43....* gnu/packages/algebra.scm (giac): Update to 1.7.0-43. Nicolas Goaziou
2021-12-07gnu: python-ndg-httpsclient: Add missing input....* gnu/packages/python-web.scm (python-ndg-httpsclient)[propagated-inputs]: Add python-pyasn1. Ricardo Wurmus
2021-12-07gnu: fsom: Build with GCC 6....* gnu/packages/bioinformatics.scm (fsom)[native-inputs]: Add gcc-6. [arguments]: Remove trailing #T. Ricardo Wurmus
2021-12-07gnu: python-velocyto: Remove generated C files....* gnu/packages/bioinformatics.scm (python-velocyto)[source]: Remove all generated .c files. Ricardo Wurmus
2021-12-07gnu: python-schema-salad: Update to 8.2.20211116214159....* gnu/packages/bioinformatics.scm (python-schema-salad): Update to 8.2.20211116214159. [arguments]: Remove trailing #T. [propagated-inputs]: Replace python-cachecontrol-0.11 with python-cachecontrol. [native-inputs]: Add python-black. Ricardo Wurmus
2021-12-07gnu: taxtastic: Update to 0.9.2....* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.9.2. [arguments]: Delete 'sanity-check and 'python37-compatibility phases; adjust 'prepare-directory phase. Ricardo Wurmus
2021-12-07gnu: taxtastic: Run tests conditionally....* gnu/packages/bioinformatics.scm (taxtastic)[arguments]: Respect TESTS? option. Ricardo Wurmus
2021-12-07gnu: python-dendropy: Update to 4.5.1....* gnu/packages/bioinformatics.scm (python-dendropy): Update to 4.5.1. [arguments]: Skip failing tests. Ricardo Wurmus
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