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2021-02-01gnu: Adjust package collection to Wrap using GUIX_PYTHONPATH.Maxim Cournoyer
This change was automated using: $ git ls-files | grep .scm | \ xargs sed 's/(getenv "PYTHONPATH")/(getenv "GUIX_PYTHONPATH")/' -i $ git ls-files | grep .scm | \ xargs sed 's/`("PYTHONPATH"/`("GUIX_PYTHONPATH"/' -i * gnu/packages/admin.scm (nmap): (dstat): Wrap using GUIX_PYTHONPATH. * gnu/packages/audio.scm (jack-2): (carla): Likewise. * gnu/packages/benchmark.scm (fio): Likewise. * gnu/packages/bioinformatics.scm (couger): Likewise. (gess, find-circ, filtlong, nanopolish): Likewise. * gnu/packages/cdrom.scm (cdemu-client): Likewise. * gnu/packages/chemistry.scm (avogadro): Likewise. * gnu/packages/connman.scm (econnman): Likewise. * gnu/packages/cups.scm (hplip): Likewise. * gnu/packages/debug.scm (scanmem): Likewise. * gnu/packages/display-managers.scm (lightdm): Likewise. * gnu/packages/ebook.scm (cozy): Likewise. * gnu/packages/education.scm (anki): Likewise. * gnu/packages/engineering.scm (kicad, volk, freecad): Likewise. * gnu/packages/game-development.scm (renpy): Likewise. * gnu/packages/games.scm (roguebox-adventures) (seahorse-adventures, kajongg): Likewise. * gnu/packages/gimp.scm (gimp, glimpse): Likewise. * gnu/packages/glib.scm (itstool): Likewise. * gnu/packages/gnome.scm (gnome-music, gtg, rhythmbox): Likewise. (eolie, d-feet, gedit, caribou, gnome-shell, authenticator) (gnome-todo, orca, passwordsafe, terminator, setzer) (libratbag, komikku): Likewise. * gnu/packages/gps.scm (gpsd): Likewise. * gnu/packages/gtk.scm (gtk-doc): Likewise. * gnu/packages/ibus.scm (ibus, ibus-libpinyin, ibus-anthy) (ibus-libhangul): Likewise. * gnu/packages/inkscape.scm (inkscape-1.0): Likewise. * gnu/packages/linux.scm (bcc): Likewise. * gnu/packages/mail.scm (notifymuch): Likewise. * gnu/packages/maths.scm (units): Likewise. * gnu/packages/music.scm (solfege): Likewise. * gnu/packages/networking.scm (blueman): Likewise. * gnu/packages/patchutils.scm (patchwork): Likewise. * gnu/packages/photo.scm (rapid-photo-downloader, entangle): Likewise. * gnu/packages/plotutils.scm (asymptote): Likewise. * gnu/packages/presentation.scm (presentty): Likewise. * gnu/packages/screen.scm (byobu): Likewise. * gnu/packages/storage.scm (ceph): Likewise. * gnu/packages/syndication.scm (liferea): Likewise. * gnu/packages/task-management.scm (blanket): Likewise. * gnu/packages/text-editors.scm (manuskript): Likewise. * gnu/packages/version-control.scm (gitless, cgit, git-when-merged) (git-imerge): Likewise. * gnu/packages/video.scm (pitivi): Likewise. * gnu/packages/virtualization.scm (criu): Likewise. * gnu/packages/xfce.scm (catfish): Likewise.
2021-02-01gnu: python-loompy: Do not set PYTHONPATH.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python-loompy) [phases]{check}: Do not set PYTHONPATH.
2021-02-01gnu: python-scanpy: Do not set PYTHONPATH.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python-scanpy)[phases] {check}: Do not set PYTHONPATH.
2021-02-01gnu: python-screed: Adjust following Python build system changes.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python-screed)[arguments]: Remove field, no longer necessary.
2021-02-01gnu: bamm: Update following changes to the Python build system.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (bamm): Delete trailing #t. [phases]{check}: Override rather than delete phase. Remove trailing #t. {post-install-check}: Delete phase. {wrap-executable}: Also wrap with the new GUIX_PYTHONPATH.
2021-02-01gnu: python-pysam: Adjust following Python build system changes.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Remove the '#:modules' argument. [phases]: Remove trailing #t. {check}: Do not manually set PYTHONPATH.
2021-02-01gnu: python-pybedtools: Streamline following Python build system changes.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python-pybedtools): Remove trailing #t. [phases]{check}: Do not manually set PYTHONPATH. [arguments]: Remove the '#:modules' argument.
2021-01-29gnu: Replace all uses of texlive-union by texlive-updmap.cfg.Maxim Cournoyer
* doc/build.scm (pdf-manual) Replace texlive-union by texlive-updmap.cfg. * gnu/packages/algebra.scm (pari-gp): Likewise. * gnu/packages/bioinformatics.scm (discrover, velvet): Likewise. * gnu/packages/chez.scm (chez-scheme, chez-web, chez-sockets): Likewise. * gnu/packages/docbook.scm (dblatex): Likewise. * gnu/packages/emacs-xyz.scm (emacs-auctex): Likewise. * gnu/packages/engineering.scm (fastcap): Likewise. * gnu/packages/guile-xyz.scm (emacsy, guile-cv): Likewise. * gnu/packages/lisp.scm (sbcl): Likewise. * gnu/packages/maths.scm (octave, hypre): Likewise. * gnu/packages/music.scm (lilypond): Likewise. * gnu/packages/plotutils.scm (asymptote): Likewise. * gnu/packages/python-xyz.scm (python-numpy-documentation) (python-matplotlib-documentation, python-ipython-documentation) (python-pypandoc): Likewise. * gnu/packages/radio.scm (gnuradio, libosmo-dsp): Likewise. * gnu/packages/scheme.scm (mit-scheme): Likewise. * gnu/packages/statistics.scm (r-with-tests): Likewise. * gnu/packages/tex.scm (simple-texlive-package) (texlive-xmltex, texlive-tiny, texlive-jadetex, teximpatient, lyx): Likewise.
2021-01-13Merge branch 'staging' into 'core-updates'.Maxim Cournoyer
Conflicts: gnu/local.mk gnu/packages/cmake.scm gnu/packages/curl.scm gnu/packages/gl.scm gnu/packages/glib.scm gnu/packages/guile.scm gnu/packages/node.scm gnu/packages/openldap.scm gnu/packages/package-management.scm gnu/packages/python-xyz.scm gnu/packages/python.scm gnu/packages/tls.scm gnu/packages/vpn.scm gnu/packages/xorg.scm
2020-12-29gnu: r-ggbio: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-ggbio): Move from here... * gnu/packages/bioconductor.scm (r-ggbio): ...to here.
2020-12-29gnu: r-gqtlstats: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-gqtlstats): Move from here... * gnu/packages/bioconductor.scm (r-gqtlstats): ...to here.
2020-12-29gnu: r-snpstats: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-snpstats): Move from here... * gnu/packages/bioconductor.scm (r-snpstats): ...to here.
2020-12-29gnu: r-homo-sapiens: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-homo-sapiens): Move from here... * gnu/packages/bioconductor.scm (r-homo-sapiens): ...to here. Replace 'string-append' by 'bioconductor-uri' with 'annotation'.
2020-12-29gnu: r-erma: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-erma): Move from here... * gnu/packages/bioconductor.scm (r-erma): ...to here.
2020-12-29gnu: r-ldblock: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-ldblock): Move from here... * gnu/packages/bioconductor.scm (r-ldblock): ...to here.
2020-12-29gnu: r-gqtlstats: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-gqtlstats): Move from here... * gnu/packages/bioconductor.scm (r-gqtlstats): ...to here.
2020-12-29gnu: r-gviz: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-gviz): Move from here... * gnu/packages/bioconductor.scm (r-gviz): ...to here.
2020-12-29gnu: r-gwascat: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-gwascat): Move from here... * gnu/packages/bioconductor.scm (r-gwascat): ...to here.
2020-12-29gnu: r-sushi: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-sushi): Move from here... * gnu/packages/bioconductor.scm (r-sushi): ...to here.
2020-12-23gnu: discrover: Use new texlive package names.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Replace "texlive-fonts-cm" and "texlive-fonts-amsfonts" with their new names "texlive-cm" and "texlive-amsfonts", respectively.
2020-12-23gnu: discrover: Remove obsolete build phase.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (discrover)[arguments]: Remove obsolete build phase setenv-HOME.
2020-12-20gnu: kentutils: Build with OpenSSL 1.1.Marius Bakke
* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Change from OPENSSL-1.0 to OPENSSL.
2020-12-20gnu: kentutils: Add a file name for the "samtabix" input.Marius Bakke
* gnu/packages/bioinformatics.scm (kentutils)[native-inputs]: For "samtabix", add a file name on the origin.
2020-12-09gnu: r-keggrest: Update to 1.30.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.30.1.
2020-12-09gnu: r-genomeinfodb: Update to 1.26.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.26.2.
2020-12-09gnu: r-biocstyle: Update to 2.18.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.18.1.
2020-12-09gnu: r-rhtslib: Propagate zlib.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhtslib)[inputs]: Move zlib from here... [propagated-inputs]: ...to here. (r-variantannotation, r-rsamtools, r-bamsignals, r-rhdf5, r-methylkit)[inputs]: Remove zlib. * gnu/packages/bioconductor.scm (r-diffbind, r-quasr, r-cytolib, r-ncdfflow, r-flowworkspace, r-seqbias)[inputs]: Remove zlib.
2020-12-09gnu: r-gqtlstats: Update to 1.21.3.zimoun
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.21.3.
2020-12-09gnu: r-gqtlbase: Update to 1.21.1.zimoun
Co-authored-by: Ricardo Wurmus <rekado@elephly.net> * gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.21.1. [arguments]: Add phase to patch broken NAMESPACE file.
2020-12-09gnu: r-biocviews: Update to 1.58.1.zimoun
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.58.1. Co-authored-by: Ricardo Wurmus <reka@elephly.net>.
2020-12-09gnu: r-rhdf5: Update to 2.34.0.zimoun
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.34.0. [propagated-inputs]: Add r-rhdf5filters. [arguments]: Avoid to have a plain directory on the list of libraries to link. Co-authored-by: Ricardo Wurmus <reka@elephly.net>.
2020-12-09gnu: Add r-rhdf5filters.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhdf5filters): New variable.
2020-12-09gnu: r-genomationdata: Update to 1.22.0.zimoun
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.22.0.
2020-12-09gnu: r-sushi: Update to 1.28.0.zimoun
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.28.0.
2020-12-09gnu: r-gwascat: Update to 2.22.0.zimoun
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.22.0. [propagated-inputs]: Add r-biocfilecache, r-readr, r-snpstats, and r-variantannotation; remove r-biocgenerics, r-ggplot2, r-rsamtools, and r-rtracklayer.
2020-12-09gnu: r-gviz: Update to 1.34.0.zimoun
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.34.0.
2020-12-09gnu: r-ldblock: Update to 1.20.0.zimoun
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.20.0.
2020-12-09gnu: r-erma: Update to 1.6.0.zimoun
* gnu/packages/bioinformatics.scm (r-erma): Update to 1.6.0.
2020-12-09gnu: r-snpstats: Update to 1.40.0.zimoun
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.40.0.
2020-12-09gnu: r-ggbio: Update to 1.38.0.zimoun
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.38.0.
2020-12-09gnu: r-biovizbase: Update to 1.38.0.zimoun
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.38.0.
2020-12-09gnu: r-organismdbi: Update to 1.32.0.zimoun
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.32.0.
2020-12-09gnu: r-ensembldb: Update to 2.14.0.zimoun
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.14.0.
2020-12-09gnu: r-dirichletmultinomial: Update to 1.32.0.zimoun
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.32.0.
2020-12-09gnu: r-complexheatmap: Update to 2.6.2.Roel Janssen
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.6.2; [propagated-inputs]: Add r-cairo, r-digest, r-iranges, r-matrixstats, and r-s4vectors.
2020-12-09gnu: r-genomicfiles: Update to 1.26.0.zimoun
* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.26.0. [propagated-inputs]: Add r-matrixgenerics.
2020-12-09gnu: r-gage: Update to 2.40.0.zimoun
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.40.0.
2020-12-09gnu: r-keggrest: Update to 1.30.0.zimoun
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.30.0.
2020-12-09gnu: r-fastseg: Update to 1.36.0.zimoun
* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.36.0.
2020-12-09gnu: r-annotationhub: Update to 2.22.0.zimoun
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.22.0.
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