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* gnu: python2-scipy: Override native inputs.Ricardo Wurmus2021-12-09
| | | | | * gnu/packages/python-science.scm (python2-scipy)[native-inputs]: Override; replace gfortran with gfortran-7; add gcc-7.
* gnu: python2-matplotlib: Fix mpl_toolkits module.Ricardo Wurmus2021-12-09
| | | | | * gnu/packages/python-xyz.scm (python2-matplotlib)[arguments]: Add phase 'create-init-file; restore 'sanity-check phase.
* gnu: Add gfortran-7.Ricardo Wurmus2021-12-09
| | | | * gnu/packages/gcc.scm (gfortran-7): New variable.
* gnu: python-slepc4py: Update to 3.16.1.Ludovic Courtès2021-12-08
| | | | | | | | This is a followup 5b4d1e57b6d4931f6ee2a50abf84222fe015d045. * gnu/packages/maths.scm (slepc-openmpi)[inputs]: Move ARPACK-NG-OPENMPI to... [propagated-inputs]: ... here. (python-slepc4py): Update to 3.16.1.
* gnu: python-petsc4py: Update to 3.16.1.Ludovic Courtès2021-12-08
| | | | | | This is a followup to 07ac13a26a0d7c8319afb42c55fc2116ec44668f. * gnu/packages/maths.scm (python-petsc4py): Update to 3.16.1.
* gnu: geeqie: Fix X11 error at startup.Ludovic Courtès2021-12-08
| | | | | | | | | | Fixes <https://issues.guix.gnu.org/52089>. Reported by Maxim Cournoyer <maxim.cournoyer@gmail.com>. Patch provided by John Kehayias <john.kehayias@protonmail.com>. * gnu/packages/patches/geeqie-clutter.patch: New file. * gnu/packages/image-viewers.scm (geeqie)[sources]: Use it. * gnu/local.mk (dist_patch_DATA): Add it.
* gnu: mumps: Allow compilation with GCC 10.Ludovic Courtès2021-12-08
| | | | | | | | Following the suggestion at <https://community.freefem.org/t/compline-on-macos-10-15-6/543>. * gnu/packages/maths.scm (mumps)[arguments]: In 'configure' phase, add '-fallow-argument-mismatch' to 'OPTF'.
* maint: Don't require unsupported packages such as GNOME on i686-linux.Ludovic Courtès2021-12-08
| | | | | * etc/release-manifest.scm (%system-manifest): Filter out PACKAGE when it doesn't pass 'supported-package?'.
* services: %desktop-services: Use SDDM rather than GDM on non-x86_64.Ludovic Courtès2021-12-08
| | | | | | | | | | | This works around the fact that Rust is currently unavailable in Guix on platforms other than x86_64-linux: https://lists.gnu.org/archive/html/guix-devel/2021-11/msg00197.html * gnu/services/desktop.scm (desktop-services-for-system): New procedure. (%desktop-services): Turn into a macro.
* system: Mark 'services' field as thunked.Ludovic Courtès2021-12-08
| | | | | | | This allows us to make services dependent on (%current-system), for example. * gnu/system.scm (<operating-system>)[services]: Mark as thunked.
* gnu: idutils: Fix build with glibc 2.33.Ludovic Courtès2021-12-08
| | | | | * gnu/packages/idutils.scm (idutils)[source]: Remove reference to 'gets' from "lib/stdio.in.h".
* gnu: libtorrent-rasterbar: Build with default cmake.Efraim Flashner2021-12-08
| | | | | * gnu/packages/bittorrent.scm (libtorrent-rasterbar)[arguments]: Remove cmake flag.
* gnu: tadbit: Update to 1.0.1-1.5c4c1dd.Ricardo Wurmus2021-12-08
| | | | | | * gnu/packages/bioinformatics.scm (tadbit): Update to 1.0.1-1.5c4c1dd. [arguments]: Remove trailing #T from build phases; pass -fcommon to test binaries; run tests conditionally.
* gnu: python2-sphinx: Remove websupport test.Ricardo Wurmus2021-12-08
| | | | | * gnu/packages/sphinx.scm (python2-sphinx)[arguments]: Remove websupport test file.
* gnu: python2-sphinxcontrib-websupport: Downgrade to 1.1.2.Ricardo Wurmus2021-12-08
| | | | | | | | * gnu/packages/sphinx.scm (python2-sphinxcontrib-websupport): Downgrade to 1.1.2. [arguments]: Override; delete 'sanity-check phase. [propagated-inputs]: Override and add python2-six. (python-sphinxcontrib-websupport)[properties]: Record python2-variant.
* gnu: python2-jinja2: Downgrade to 2.11.3Ricardo Wurmus2021-12-08
| | | | | | * gnu/packages/python-xyz.scm (python2-jinja2): Downgrade to the last version supporting Python 2. (python-jinja2)[properties]: Record python2-variant.
* gnu: python2-markupsafe: Downgrade to 1.1.1.Ricardo Wurmus2021-12-08
| | | | | * gnu/packages/python-xyz.scm (python2-markupsafe): Downgrade to 1.1.1, because that's the last version to support Python 2.
* gnu: ocaml-mcl: Add -fcommon to compiler flags.Ricardo Wurmus2021-12-08
| | | | * gnu/packages/machine-learning.scm (ocaml-mcl)[arguments]: Add -fcommon.
* gnu: paml: Pass -fcommon to compiler.Ricardo Wurmus2021-12-08
| | | | * gnu/packages/bioinformatics.scm (paml)[arguments]: Set CFLAGS.
* gnu: paml: Remove trailing #T.Ricardo Wurmus2021-12-08
| | | | | * gnu/packages/bioinformatics.scm (paml)[arguments]: Remove trailing #T from build phases.
* gnu: sambamba: Remove trailing #T.Ricardo Wurmus2021-12-08
| | | | | * gnu/packages/bioinformatics.scm (sambamba)[arguments]: Remove trailing #T from build phases.
* gnu: discrover: Add texlive-fonts-ec to inputs.Ricardo Wurmus2021-12-08
| | | | | * gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Add texlive-fonts-ec.
* gnu: discrover: Remove trailing #T.Ricardo Wurmus2021-12-08
| | | | | * gnu/packages/bioinformatics.scm (discrover)[arguments]: Remove trailing #T from build phases.
* gnu: tbsp: Update to 1.0.0-2.dc30c03.Ricardo Wurmus2021-12-08
| | | | | | * 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.
* gnu: mantis: Update to 0.1-2.b6979a2.Ricardo Wurmus2021-12-08
| | | | | | * 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.
* gnu: imp: Disable tests.Ricardo Wurmus2021-12-08
| | | | | * gnu/packages/bioinformatics.scm (imp)[arguments]: Disable unreliable test suite.
* gnu: snap-aligner: Update to 2.0.0.Ricardo Wurmus2021-12-08
| | | | * gnu/packages/bioinformatics.scm (snap-aligner): Update to 2.0.0.
* gnu: snap-aligner: Remove trailing #T.Ricardo Wurmus2021-12-08
| | | | | * gnu/packages/bioinformatics.scm (snap-aligner)[arguments]: Remove trailing #T from 'install phase.
* gnu: snap-aligner: Run tests conditionally.Ricardo Wurmus2021-12-08
| | | | | * gnu/packages/bioinformatics.scm (snap-aligner)[arguments]: Respect TESTS? option.
* gnu: khmer: Cythonize source files.Ricardo Wurmus2021-12-08
| | | | | | * 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.
* gnu: cwltool: Update to 3.1.20211107152837.Ricardo Wurmus2021-12-08
| | | | | | * 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.
* gnu: lollypop: Build with libsoup@2.Marius Bakke2021-12-08
| | | | | * gnu/packages/gnome.scm (lollypop)[inputs]: Change from LIBSOUP to LIBSOUP-MINIMAL-2.
* gnu: rhythmbox: Adjust inputs.Marius Bakke2021-12-08
| | | | | * gnu/packages/gnome.scm (rhythmbox)[inputs]: Change from PYTHON2-PYGOBJECT to PYTHON-PYGOBJECT. Add LIBSOUP-MINIMAL-2.
* gnu: labelme: Loosen Python requirements.Marius Bakke2021-12-08
| | | | | * gnu/packages/image-processing.scm (labelme)[arguments]: Patch setup.py so it does not require a specific version of Matplotlib.
* gnu: newick-utils: Pass -fcommon to compiler.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Set CFLAGS.
* gnu: blasr: Update to 5.3.5.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/bioinformatics.scm (blasr): Update to 5.3.5.
* gnu: blasr: Remove trailing #T.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/bioinformatics.scm (blasr)[arguments]: Remove trailing #T from build phase.
* gnu: blasr-libcpp: Update to 5.3.5.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/bioinformatics.scm (blasr-libcpp): Update to 5.3.5. [inputs]: Add htslib.
* gnu: htseq: Update to 0.12.3.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/bioinformatics.scm (htseq): Update to 0.12.3.
* gnu: clipper: Update to 2.0.1.Ricardo Wurmus2021-12-07
| | | | | | | * 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.
* gnu: pbbam: Update to 1.7.0.Ricardo Wurmus2021-12-07
| | | | | | * gnu/packages/bioinformatics.scm (pbbam): Update to 1.7.0. [arguments]: Remove phase 'find-googletest; add phase 'patch-tests. [propagated-inputs]: Add pbcopper.
* gnu: bwa-pssm: Fix build.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/bioinformatics.scm (bwa-pssm)[arguments]: Add phase 'patch-C-error.
* gnu: Add pbcopper.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/bioinformatics.scm (pbcopper): New variable.
* gnu: python-ndg-httpsclient: Add missing input.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/python-web.scm (python-ndg-httpsclient)[propagated-inputs]: Add python-pyasn1.
* gnu: fsom: Build with GCC 6.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/bioinformatics.scm (fsom)[native-inputs]: Add gcc-6. [arguments]: Remove trailing #T.
* gnu: python-velocyto: Remove generated C files.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/bioinformatics.scm (python-velocyto)[source]: Remove all generated .c files.
* gnu: python-schema-salad: Update to 8.2.20211116214159.Ricardo Wurmus2021-12-07
| | | | | | | | | * 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.
* gnu: taxtastic: Update to 0.9.2.Ricardo Wurmus2021-12-07
| | | | | | * gnu/packages/bioinformatics.scm (taxtastic): Update to 0.9.2. [arguments]: Delete 'sanity-check and 'python37-compatibility phases; adjust 'prepare-directory phase.
* gnu: taxtastic: Run tests conditionally.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/bioinformatics.scm (taxtastic)[arguments]: Respect TESTS? option.
* gnu: python-dendropy: Update to 4.5.1.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/bioinformatics.scm (python-dendropy): Update to 4.5.1. [arguments]: Skip failing tests.
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