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2023-05-13gnu: python-rapidjson: Use pyproject-build-system.Ricardo Wurmus
* gnu/packages/python-web.scm (python-rapidjson)[build-system]: Use pyproject-build-system. [arguments]: Do not use custom 'build and 'check phases.
2023-05-13gnu: python-markdown-it-py: Simplify by using pyproject-build-system.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-markdown-it-py)[arguments]: Remove custom 'build and 'install phases. [build-system]: Use pyproject-build-system.
2023-05-13gnu: python-sphinx-panels: Use older docutils.Ricardo Wurmus
* gnu/packages/sphinx.scm (python-sphinx-panels)[propagated-inputs]: Replace python-docutils with python-docutils-0.15. [build-system]: Use pyproject-build-system. [arguments]: Remove custom 'check phase.
2023-05-13gnu: ghc-tasty: Add missing dependency on i686-linux.Lars-Dominik Braun
Fixes <https://issues.guix.gnu.org/63421>. * gnu/packages/haskell-check.scm (ghc-tasty)[inputs]: Conditionally add ghc-unbounded-delays.
2023-05-12gnu: python-orjson: Fix version string of Python module.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-orjson)[arguments]: Remove invalid characters from version string.
2023-05-12gnu: python-orjson: Reuse phases from pyproject-build-system.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-orjson)[arguments]: Include modules from pyproject-build-system; use their 'build and 'install phases instead of duplicating their contents.
2023-05-12gnu: python-canonicaljson: Use pyproject-build-system.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-canonicaljson)[arguments]: Remove custom 'build, 'check, and 'install phases. [build-system]: Use pyproject-build-system.
2023-05-12gnu: python-pyproject-metadata: Simplify by using pyproject-build-system.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-pyproject-metadata)[arguments]: Remove. [build-system]: Use pyproject-build-system.
2023-05-12gnu: python-seaborn: Simplify by using pyproject-build-system.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-seaborn)[arguments]: Remove. [build-system]: Use pyproject-build-system.
2023-05-12gnu: shrinkwrap: Use pyproject-build-system.Ricardo Wurmus
* gnu/packages/python-xyz.scm (shrinkwrap)[arguments]: Remove. [build-system]: Use pyproject-build-system.
2023-05-12gnu: jamm: Use G-expression.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (jamm)[arguments]: Use G-expression.
2023-05-12gnu: arriba: Use SEARCH-INPUT-FILE and -DIRECTORY.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (arriba)[arguments]: Use SEARCH-INPUT-DIRECTORY and SEARCH-INPUT-FILE; use G-expression; drop trailing #T from build phases.
2023-05-12gnu: multichoose: Clean up.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (multichoos): Fix indentation. [arguments]: Use G-expression.
2023-05-12gnu: samblaster: Update to 0.1.26.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (samblaster): Update to 0.1.26.
2023-05-12gnu: samblaster: Simplify.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (samblaster): Fix indentation. [arguments]: Use G-expression; drop trailing #T from 'install phase. [description]: Use double spacing between all sentences.
2023-05-12gnu: methyldackel: Update to 0.6.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (methyldackel): Update to 0.6.1. [arguments]: Set LIBBIGWIG variable instead of patching Makefile. [inputs]: Replace htslib-1.9 with htslib.
2023-05-12gnu: methyldackel: Simplify arguments.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Use list, drop argument list. [native-inputs]: Drop package label.
2023-05-12gnu: phast: Simplify by using G-expression.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (phast)[arguments]: Use G-expression and drop trailing #T from build phases.
2023-05-12gnu: ribotaper: Simplify with G-expression.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ribotaper)[arguments]: Use G-expression and drop trailing #T from build phase.
2023-05-12gnu: sra-tools: Do link with libxml2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use G-expression for clarity; drop trailing #T from build phases; modify 'configure phase to dynamically link with libxml2. [inputs]: Drop package labels; add libxml2.
2023-05-12gnu: ncbi-vdb: Ensure that vdb-sqlite is installed.Ricardo Wurmus
The most important change here is the addition of the 'install-libs phase. All other changes are just the result of switching to G-expressions. * gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Add 'install-libs phase; use G-expression; drop trailing #T from build phases. [inputs]: Drop package labels.
2023-05-12gnu: Add python-mgatk.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (python-mgatk): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2023-05-12system: default-skeletons: Merge search-paths of multiple profiles.宋文武
Fixes <https://issues.guix.gnu.org/20255>. * gnu/system/shadow.scm (default-skeletons)[bash_profile, zprofile]: Merge search-paths from multiple profiles via "guix package".
2023-05-12gnu: Add Free as in Freedom (2.0).宋文武
* gnu/packages/fsf.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
2023-05-12gnu: sbcl-serapeum: Update to 20230511.Pierre Neidhardt
* gnu/packages/lisp-xyz.scm (sbcl-serapeum): Update to 20230511.
2023-05-12gnu: python-lightning-cloud: Use older version of fastapi.Ricardo Wurmus
The variant of the fastapi package must match that of python-pytorch-lightning. * gnu/packages/machine-learning.scm (python-lightning-cloud) [propagated-inputs]: Replace python-fastapi with python-fastapi-for-pytorch-lightning.
2023-05-12gnu: Add python-optparse-pretty.Mădălin Ionel Patrașcu
* gnu/packages/python-xyz.scm (python-optparse-pretty): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-05-12gnu: Add r-dropletutils.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-dropletutils): New variable.
2023-05-12gnu: Add r-ggpattern.Mădălin Ionel Patrașcu
* gnu/packages/cran.scm (r-ggpattern): New variable.
2023-05-12gnu: Add r-gridpattern.Mădălin Ionel Patrașcu
* gnu/packages/cran.scm (r-gridpattern): New variable.
2023-05-11gnu: texlive-datetime2: Add needed propagated-inputs.Greg Hogan
Required packages can be seen with: $ rg RequirePackage $(guix build texlive-datetime2) * gnu/packages/tex.scm (texlive-datetime2)[propagated-inputs]: Add TEXLIVE-ETOOLBOX, TEXLIVE-LATEX-XKEYVAL, and TEXLIVE-TRACKLANG. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2023-05-11gnu: Add emacs-framemove.Fabio Natali
* gnu/packages/emacs-xyz.scm (emacs-framemove): New variable. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2023-05-11gnu: texlive-ddphonism: Replace deprecated input.Simon Tournier
* gnu/packages/tex.scm (texlive-ddphonism)[propagated-inputs]: Replace deprecated texlive-latex-tools by texlive-tools. Signed-off-by: Josselin Poiret <dev@jpoiret.xyz>
2023-05-11gnu: texlive-totpages: Replace deprecated input.Simon Tournier
* gnu/packages/tex.scm (texlive-totpages)[propagated-inputs]: Replace deprecated texlive-latex-graphics by texlive-graphics. Signed-off-by: Josselin Poiret <dev@jpoiret.xyz>
2023-05-11gnu: texlive-totcount: Replace deprecated input.Simon Tournier
* gnu/packages/tex.scm (texlive-totcount)[propagated-inputs]: Replace deprecated texlive-latex-graphics by texlive-graphics. Signed-off-by: Josselin Poiret <dev@jpoiret.xyz>
2023-05-11gnu: texlive-ncctools: Replace deprecated input.Simon Tournier
* gnu/packages/tex.scm (texlive-ncctools)[propagated-inputs]: Replace deprecated texlive-latex-graphics by texlive-graphics. Signed-off-by: Josselin Poiret <dev@jpoiret.xyz>
2023-05-11gnu: texlive-soulutf8: Replace deprecated inputs.Simon Tournier
* gnu/packages/tex.scm (texlive-soulutf8)[propagated-inputs]: Replace deprecated texlive-generic-etexcmds by texlive-etexcmds and deprecated texlive-generic-infwarerr by texlive-infwarerr. Signed-off-by: Josselin Poiret <dev@jpoiret.xyz>
2023-05-11gnu: texlive-xetex: Replace deprecated inputs.Simon Tournier
* gnu/packages/tex.scm (texlive-xetex)[propagated-inputs]: Replace deprecated texlive-generic-atbegshi by texlive-atbegshi and deprecated texlive-latex-atveryend by texlive-atveryend. Signed-off-by: Josselin Poiret <dev@jpoiret.xyz>
2023-05-11gnu: python-skranger: Install library.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-skranger)[arguments]: Install the library that we've just built.
2023-05-11gnu: Add python-skranger.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-skranger): New variable.
2023-05-11Revert "gnu: Add python-pytest-enabler."Ricardo Wurmus
This reverts commit 0a8c46e89f095a9ec3632d43920ac3cce49f16d5. An older version of python-pytest-enabler already exists in (gnu packages check).
2023-05-11gnu: lagrange: Update to 1.15.9.Efraim Flashner
* gnu/packages/web-browsers.scm (lagrange): Update to 1.15.9.
2023-05-11gnu: mutt: Update to 2.2.10.Efraim Flashner
* gnu/packages/mail.scm (mutt): Update to 2.2.10.
2023-05-11gnu: qiv: Update to 2.3.3.Efraim Flashner
* gnu/packages/image-viewers.scm (qiv): Update to 2.3.3.
2023-05-11gnu: git-annex: Update to 10.20230407.Efraim Flashner
* gnu/packages/haskell-apps.scm (git-annex): Update to 10.20230407.
2023-05-11gnu: global: Update to 6.6.10.Efraim Flashner
* gnu/packages/code.scm (global): Update to 6.6.10.
2023-05-11tests: vnstat: Avoid call to 'getservbyname'.Ludovic Courtès
This would break "make as-derivation" because /etc/services is unavailable in the build environment: [ 38/ 80] loading... 95.0% of 40 filesBacktrace: In guix/build/compile.scm: 249:8 19 (compile-files "." "/gnu/store/s5nadqd6hkzivkxp33svwqslfn608ng5-guix-system-tests" ("gnu/tests/audio.scm" "gnu/tests/base.scm" "gnu/tests/ci.scm" "gnu/tests/cups.scm" "gnu/tests/d…" …) …) […] In unknown file: 0 (getserv "discard" "tcp") ERROR: In procedure getserv: In procedure getserv: no such service discard builder for `/gnu/store/…-guix-system-tests.drv' failed with exit code 1 * gnu/tests/vnstat.scm (run-vnstat-test): Hard-code 'guest-port' instead of calling 'getservbyname'.
2023-05-11.guix-authorizations: Authorize Josselin Poiret.Maxim Cournoyer
* .guix-authorizations (jpoiret): Add OpenPGP key fingerprint.
2023-05-11gnu: Add python-omnipath.Ricardo Wurmus
* gnu/packages/python-web.scm (python-omnipath): New variable.
2023-05-11gnu: Add python-inflect.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-inflect): New variable.
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