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* gnu: abjad: Move python-ply to propagated-inputs.•••* gnu/packages/music.scm (abjad)[ntaive-inputs]: Move python-ply ... [propagated-inputs]: ... to here. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> jgart2021-07-221-2/+2
* gnu: python-abjad: Rename to abjad.•••* gnu/packages/music.scm (abjad): Rename from python-abjad. (python-abjad): Keep as deprecated package. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> jgart2021-07-221-2/+5
* gnu: python-pysam: Make the check phase honor the tests? argument.•••* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Adjust custom 'check phase to skip tests when #:tests is #f. Efraim Flashner2021-07-221-15/+16
* gnu: python-pysam: Update to 0.16.0.1.•••* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.16.0.1. [arguments]: Update custom 'check phase. [propagated-inputs]: Replace htslib-1.9 with 1.10. [native-inputs]: Add python-pytest. Replace samtools-1.9 with 1.10, bcftools-1.9 with 1.10. (bcftools-1.9): Replace with bcftools-1.10. [native-inputs]: Replace htslib-1.9 with 1.10. (samtools-1.9): Replace with samtools-1.10. [inputs]: Replace htslib-1.9 with 1.10. Efraim Flashner2021-07-221-25/+26
* gnu: Add htslib-1.10.•••* gnu/packages/bioinformatics.scm (htslib-1.10): New variable. Efraim Flashner2021-07-221-0/+13
* gnu: python-biopython: Update to 1.73.•••* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73. Efraim Flashner2021-07-221-2/+2
* gnu: onionshare: Update to 2.3.2.•••* gnu/packages/tor.scm (onionshare-cli, onionshare): Update to 2.3.2. (onionshare)[inputs]: Add python-colorama. [arguments]: Insert "import pytest" for later "pytest.mark.skip". Eric Bavier2021-07-211-2/+8
* gnu: Add emacs-seeing-is-believing.•••* gnu/packages/emacs-xyz.scm (emacs-seeing-is-believing): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Joseph LaFreniere2021-07-221-0/+28
* gnu: guile-git: Update to 0.5.2.•••Fixes <https://issues.guix.gnu.org/48855>. Reported by Maxim Cournoyer <maxim.cournoyer@gmail.com>. * gnu/packages/guile.scm (guile-git): Update to 0.5.2. Ludovic Courtès2021-07-221-2/+2
* gnu: extempore: Update to 0.8.9.•••* gnu/packages/music.scm (extempore): Update to 0.8.6. [source]: Portaudio is no more in-tree. [arguments]: Load external libraries through patched CMakeLists.txt. [phases]: Symlink assets. * gnu/packages/patches/extempore-unbundle-external-dependencies.patch: Update accordingly. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Giacomo Leidi2021-07-212-95/+251
* gnu: Add python-sparqlkernel.•••* gnu/packages/jupyter.scm (python-sparqlkernel): New variable. Lars-Dominik Braun2021-07-211-0/+47
* gnu: Add python-sparqlwrapper.•••* gnu/packages/rdf.scm (python-sparqlwrapper): New variable. Lars-Dominik Braun2021-07-211-0/+27
* gnu: Add python-bash-kernel.•••* gnu/packages/jupyter.scm (python-bash-kernel): New variable. Lars-Dominik Braun2021-07-211-0/+41
* gnu: Add r-battenberg.•••* gnu/packages/bioinformatics.scm (r-battenberg): New variable. Lars-Dominik Braun2021-07-211-0/+30
* gnu: Add r-ascat.•••* gnu/packages/bioinformatics.scm (r-ascat): New variable. Lars-Dominik Braun2021-07-211-0/+29
* gnu: Add nanosv.•••* gnu/packages/bioinformatics.scm (nanosv): New variable. Lars-Dominik Braun2021-07-211-0/+23
* gnu: Add python-pyvcf.•••* gnu/packages/bioinformatics.scm (python-pyvcf): New variable. Lars-Dominik Braun2021-07-211-0/+37
* gnu: checkm: Rename and update to 1.1.3.•••Renamed from python2-checkm-genome to checkm to better reflect its status as standalone-application and support for Python 3. * gnu/packages/bioinformatics.scm (python2-checkm-genome): Redirect to… (checkm): …here and update to 1.1.3. [propagated-inputs]: Move to inputs. [inputs]: Use Python 3 dependencies. [home-page]: Point to real home-page. Lars-Dominik Braun2021-07-211-13/+20
* gnu: Add tombo.•••* gnu/packages/bioinformatics.scm (tombo): New variable. Lars-Dominik Braun2021-07-211-0/+33
* gnu: Add r-rmisc.•••* gnu/packages/cran.scm (r-rmisc): New variable. Lars-Dominik Braun2021-07-211-0/+21
* gnu: Add r-glinternet.•••* gnu/packages/statistics.scm (r-glinternet): New variable. Lars-Dominik Braun2021-07-211-0/+24
* gnu: Add r-naniar.•••* gnu/packages/statistics.scm (r-naniar): New variable. Lars-Dominik Braun2021-07-211-0/+38
* gnu: Add r-norm.•••* gnu/packages/statistics.scm (r-norm): New variable. Lars-Dominik Braun2021-07-211-0/+20
* gnu: txr: Reduce closure size.•••* gnu/packages/lisp.scm (txr)[inputs]: Replace bash by bash-minimal. Guillaume Le Vaillant2021-07-211-1/+1
* gnu: catfish: Update to 4.16.1.•••* gnu/packages/xfce.scm (catfish): Update to 4.16.1. [inputs]: Add xfconf. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Michael Rohleder2021-07-211-2/+3
* gnu: Add libgpiod.•••* gnu/packages/linux.scm (libgpiod): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Ivan Gankevich2021-07-201-0/+37
* gnu: dealii: Update to 9.3.1 and clean up.•••The cleanup notably: * Builds and installs the documentation into a separate doc output (in the process moving around some files erroneously installed into the root directory); and * Removes unnecessary inputs and moves some inputs into propagated-inputs (the candidates of which were determined with a search for "include.*LIBNAME" in include/deal.II). * gnu/packages/maths.scm (dealii): Reword comments. [version]: Update to 9.3.1. [outputs]: New field including doc output. [native-inputs]: New field. [inputs]: Sort them. Remove p4est (deal.II interfaces with it only when MPI is enabled). Move boost, suitesparse and tbb to... [propagated-inputs]: ...here. New field including hdf5, which is actually supported in deal.II without MPI. [arguments]<#:tests?>: New argument. The tests were not being run before anyway. <#:configure-flags>[-DDEAL_II_COMPONENT_DOCUMENTATION]: New flag. [-DDEAL_II_DOCREADME_RELDIR]: New flag. Prevents the LICENSE.md, README.md, detailed.log and summary.log files from being installed in the root directory (though note that the logs are removed in the new remove-build-logs phase). [-DDEAL_II_DOCHTML_RELDIR]: New flag. [-DDEAL_II_COMPILE_EXAMPLES]: New flag. [-DDEAL_II_EXAMPLES_RELDIR]: New flag. Prevents the examples directory from being installed in the root directory. [-DCMAKE_POSITION_INDEPENDENT_CODE]: Remove flag. The issue has been resolved. <#:phases>{remove-build-logs}: New phase. [home-page]: Add trailing slash. (dealii-openmpi): Use package/inherit. [inputs]: Sort them. Remove mumps-metis-openmpi (deal.II no longer interfaces with MUMPS). Move hdf5-parallel-openmpi, openmpi, p4est-openmpi, petsc-openmpi and slepc-openmpi to... [propagated-inputs]: ...here. New field. [arguments]<#:configure-flags>: Rename cf variable to flags. <#:phases>{mpi-setup}: Remove phase which is unused because the tests are disabled. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Paul A. Patience2021-07-201-33/+62
* gnu: xorg.scm: Add missing module import.•••This is a follow-up to 1a4c7ddefe2a1c853fb99989e21f867e1965ec59. * gnu/packages/xorg.scm: Add missing module import. Efraim Flashner2021-07-201-0/+1
* gnu: Add python-tldr.•••* gnu/packages/python-xyz.scm (python-tldr): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Tanguy Le Carrour2021-07-201-1/+38
* gnu: rust-openssl-sys-extras-0.7: Skip build.•••* gnu/packages/crates-io.scm (rust-openssl-sys-extras-0.7) [arguments]: Skip build. [inputs]: Remove openssl-1.0. Efraim Flashner2021-07-201-3/+2
* gnu: rust-openssl-0.7: Skip build.•••* gnu/packages/crates-io.scm (rust-openssl-0.7)[arguments]: Skip build. Remove tests keyword. [inputs]: Remove openssl-1.0. Efraim Flashner2021-07-201-4/+2
* gnu: rust-sha1-0.2: Skip tests.•••* gnu/packages/crates-io.scm (rust-sha1-0.2)[arguments]: Skip tests. [inputs]: Remove openssl-1.0. Efraim Flashner2021-07-201-4/+3
* gnu: gpodder: Make the check phase honor the tests? argument.•••* gnu/packages/gpodder.scm (gpodder)[arguments]: Adjust custom 'check phase to skip tests when #:tests? is #f. Efraim Flashner2021-07-201-2/+3
* gnu: gpodder: Add bash-minimal.•••* gnu/packages/gpodder.scm (gpodder)[inputs]: Add bash-minimal. Efraim Flashner2021-07-201-1/+3
* gnu: gpodder: Add python-mutagen (fixes one of its addons).•••* gnu/packages/gpodder.scm (gpodder)[inputs]: Added python-mutagen. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> raingloom2021-07-201-0/+2
* gnu: xpra: Add bash-minimal.•••* gnu/packages/xorg.scm (xpra)[inputs]: Add bash-minimal. Efraim Flashner2021-07-201-1/+1
* gnu: xpra: Update to 4.2.1.•••* gnu/packages/xorg.scm (xpra): Update to 4.2.1. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Matthew James Kraai2021-07-201-2/+2
* gnu: pipe-viewer: Correct references to youtube-dl program.•••* gnu/packages/videos.scm (pipe-viewer)[phases](patch-source): Modify. Raghav Gururajan2021-07-201-1/+5
* gnu: claws-mail: Use absolute paths to referenced programs.•••* gnu/packages/mail.scm (claws-mail)[phases](patch-source): New phase. [inputs]: Add mailutils and sendmail. Raghav Gururajan2021-07-201-0/+12
* gnu: python-graph-tool: Sort inputs alphabetically.•••* gnu/packages/graph.scm (python-graph-tool)[native-inputs]: Sort alphabetically. [inputs]: Same. [propagated-inputs]: Same. Efraim Flashner2021-07-201-10/+10
* gnu: Add sequeler.•••* gnu/packages/databases.scm (sequeler): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Alexandre Hannud Abdo2021-07-201-0/+58
* gnu: python-graph-tool: Update to 2.43.•••* gnu/packages/graph.scm (python-graph-tool): Update to 2.43. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Alexandre Hannud Abdo2021-07-201-2/+2
* gnu: txr: Update to 266.•••* gnu/packages/lisp.scm (txr)[version]: Update to 266. [inputs]: Add bash. [arguments]<#:phases>{inhibit-doc-syms-generation}: Correct the path to doc-syms.tl to its new location. {fix-tests}: Fix another test. {fix-paths}: New phase. Co-authored-by: Guillaume Le Vaillant <glv@posteo.net> Paul A. Patience2021-07-201-4/+13
* gnu: txr: Fix license installation.•••The install-license-files phase was installing LICENSE-CYG when it shouldn't have, because that license applies only to TXR builds for Microsoft Windows; and it was also ignoring the METALICENSE file. However, TXR's Makefile was already installing the LICENSE and METALICENSE files into share/txr (the datadir), so redirect them into the appropriate doc directory and delete the install-license-files phase. * gnu/packages/lisp.scm (txr)[arguments]<#:phases> {fix-license-installation}: New phase. {install-license-files}: Delete phase. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net> Paul A. Patience2021-07-201-0/+9
* gnu: txr: Build documentation.•••* gnu/packages/lisp.scm (man-for-txr): New variable. (txr)[native-inputs]: New field. [inputs]: Move above the arguments field. [arguments]<#:phases>{inhibit-doc-syms-generation, build-doc, install-doc}: New phases. {fix-tests}: Add after the unpack phase rather than after the configure phase so that all file-modifying phases are performed after unpacking. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net> Paul A. Patience2021-07-201-6/+90
* gnu: cl-authentic: Update to 0.1.2-2.4e9194d.•••* gnu/packages/lisp-xyz.scm (sbcl-authentic): Update to 0.1.2-2.4e9194d. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net> Charles2021-07-201-4/+4
* gnu: icedove: Update to 78.12.0 [security fixes].•••Fixes CVE-2021-29969 and CVE-2021-29976. * gnu/packages/gnuzilla.scm (icedove): Update to 78.12.0. Jonathan Brielmaier2021-07-191-4/+4
* gnu: Add searx.•••* gnu/packages/search.scm (searx): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Vinicius Monego2021-07-191-1/+52
* gnu: Add python-langdetect.•••* gnu/packages/python-xyz.scm (python-langdetect): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Vinicius Monego2021-07-191-0/+20
* gnu: Add nomad-optimizer.•••* gnu/packages/maths.scm (nomad-optimizer): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Paul A. Patience2021-07-191-0/+148
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