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2023-04-26gnu: python-umap-learn: Patch for sklearn/numpy compatibility.Ricardo Wurmus
* gnu/packages/machine-learning.scm (python-umap-learn)[arguments]: Add phase 'numpy-compatibility.
2023-04-26gnu: python-tables: Build cython files from source.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-tables)[source]: Remove generated C files. [arguments]: Remove trailing #T from build phases; use G-expression; override library directories. [inputs]: Add c-blosc and lzo.
2023-04-26gnu: python-bokeh: Add missing input.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-bokeh)[native-inputs]: Add python-mock.
2023-04-26gnu: python-tornado: Run a lot more tests and fix collections.Ricardo Wurmus
* gnu/packages/python-web.scm (python-tornado)[arguments]: Do run tests; add phase 'fix-collections.
2023-04-26gnu: nikola: Add input.Andreas Enge
* gnu/packages/python-xyz.scm (nikola)[propagated-inputs]: Add python-toml.
2023-04-26gnu: cl-mock: Update to 1.1.0-0.01762fd.Sharlatan Hellseher
* gnu/packages/lisp-xyz.scm (sbcl-cl-mock): Update to 1.1.0-0.01762fd. [arguments]: Build cl-mock and cl-mock-basic systems. [inputs]: Add sbcl-bordeaux-threads. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2023-04-26gnu: cl-fast-ecs: Update to 0.2.2.Sharlatan Hellseher
* gnu/packages/lisp-xyz.scm (sbcl-cl-fast-ecs): Update to 0.2.2. [native-inputs]: Add sbcl-chlorophyll, sbcl-cl-mock. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2023-04-26gnu: Add cl-chlorophyll.Sharlatan Hellseher
* gnu/packages/lisp-xyz.scm (cl-chlorophyll, ecl-chlorophyll, sbcl-chlorophyll): New variables. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2023-04-26gnu: cl-nclasses: Update to 0.4.0.Artyom Bologov
gnu/packages/lisp-xyz.scm (sbcl-nclasses): Update to 0.4.0. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2023-04-26gnu: flwrap: Update to 1.3.6.Guillaume Le Vaillant
* gnu/packages/radio.scm (flwrap): Update to 1.3.6.
2023-04-26gnu: pdf2djvu: Update to 0.9.19.Guillaume Le Vaillant
* gnu/packages/djvu.scm (pdf2djvu): Update to 0.9.19.
2023-04-26gnu: xonsh: Add missing input.jgart
Xonsh vim emulation mode/environment variable does not work without this. * gnu/packages/shell.scm (xonsh)[inputs]: Add PYTHON-PROMPT-TOOLKIT. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2023-04-26gnu: plocate: Update to 1.1.18.kiasoc5
* gnu/packages/search.scm (plocate): Update to 1.1.18. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2023-04-26gnu: emacs-vertico: Update to 1.3.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-vertico): Update to 1.3.
2023-04-26gnu: Add emacs-lojban.Christine Lemmer-Webber
* gnu/packages/emacs-xyz.scm (emacs-lojban): New variable. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2023-04-26gnu: valgrind: Update to 3.20.0.zimoun
* gnu/packages/valgrind.scm (valgrind): Update to 3.20.0. Remove patch. [arguments]<phases>: Remove trailing #t. * gnu/packages/patches/valgrind-enable-arm.patch: Delete file. * gnu/packages/valgrind.scm (dist_patch_DATA): Unregister patch. Signed-off-by: Andreas Enge <andreas@enge.fr>
2023-04-26gnu: lz4: Remove valgrind from native-inputs.zimoun
* gnu/compression.scm (lz4)[native-inputs]: Remove valgrind. [arguments]<phases>: Remove trailing #t. Signed-off-by: Andreas Enge <andreas@enge.fr>
2023-04-26gnu: python-ipykernel: Fix build.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-ipykernel)[build-system]: Use pyproject-build-system. [arguments]: Use pyproject-build-system modules; add build phase 'hide-zmq-deprecation-warnings.
2023-04-26news: Add 'de' translation.Florian Pelz
* etc/news.scm: Add German translation of core-updates entry.
2023-04-26gnu: python-jupyter-client: Disable one test.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-jupyter-client)[arguments]: Begrudgingly disable one failing test, because there is no information on why it fails.
2023-04-26gnu: python-jupyter-client-bootstrap: Hide zmq deprecation warning.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-jupyter-client-bootstrap)[arguments]: Add phase 'hide-zmq-deprecation-warning.
2023-04-26gnu: python-jupyter-client-bootstrap: Use pyproject-build-system.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-jupyter-client-bootstrap)[build-system]: Use pyproject-build-system.
2023-04-26news: Add entry for 'core-updates' merge.Ludovic Courtès
* etc/news.scm: Add entry.
2023-04-26gnu: python-distributed: Fix build.Ricardo Wurmus
* gnu/packages/python-science.scm (python-distributed)[build-system]: Use pyproject-build-system. [arguments]: Hide deprecation warnings from tornado, because they break almost all tests; disable three more tests.
2023-04-26gnu: cppcheck: Update to 2.10.3.Efraim Flashner
* gnu/packages/check.scm (cppcheck): Update to 2.10.3. [home-page]: Update to new home-page.
2023-04-26gnu: cppcheck: Skip failing test.Efraim Flashner
* gnu/packages/patches/check.scm (cppcheck)[source]: Add patch. * gnu/packages/patches/cppcheck-disable-char-signedness-test.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it.
2023-04-26gnu: graphviz: Remove version 2.38.Andreas Enge
This is a follow-up to commit 370cb92eaa089af19c08d9a7b4f5a96ac5b27716 . * gnu/packages/graphviz.scm: Drop imported modules. (graphviz-2.38): Remove package.
2023-04-25gnu: lcov: Update to 1.16.Ludovic Courtès
* gnu/packages/code.scm (lcov): Update to 1.16.
2023-04-25gnu: perl-io-compress: Update to 2.204.Ludovic Courtès
* gnu/packages/perl-compression.scm (perl-io-compress): Update to 2.204.
2023-04-25gnu: perl-compress-raw-bzip2: Update to 2.204.Ludovic Courtès
* gnu/packages/perl-compression.scm (perl-compress-raw-bzip2): Update to 2.204.
2023-04-25gnu: perl-compress-raw-zlib: Update to 2.204.Ludovic Courtès
* gnu/packages/perl-compression.scm (perl-compress-raw-zlib): Update to 2.204. [arguments]: Remove.
2023-04-25gnu: gnutls: Don't embed a phase inside another phase.Efraim Flashner
* gnu/packages/tls.scm (gnutls)[arguments]: Adjust powerpc-linux phase 'increase-test-timeout to not be embedded inside another phase.
2023-04-25gnu: mpdevil: Add missing input.Efraim Flashner
* gnu/packages/mpd.scm (mpdevil)[native-inputs]: Add gettext-minimal.
2023-04-25gnu: presage: Build with c++-14.Efraim Flashner
* gnu/packages/fcitx.scm (presage)[arguments]: Adjust configure-flags to use c++-14 cor CFLAGS and CXXFLAGS.
2023-04-25gnu: libpst: Fix python detection.Efraim Flashner
* gnu/packages/mail.scm (libpst)[arguments]: Add a phase to detect newer versions of python3. [native-inputs]: Add autoconf, automake, gettext-minimal, libool.
2023-04-25gnu: perl-data-dumper: Update to 2.183.Ricardo Wurmus
* gnu/packages/perl.scm (perl-data-dumper): Update to 2.183.
2023-04-25gnu: cwltool: Use pyproject-build-system.Ricardo Wurmus
"setup.py install is deprecated. Use build and pip and other standards-based tools." It then falls back to attempting to install packages via pip. * gnu/packages/bioinformatics.scm (cwltool)[build-system]: Use pyproject-build-system.
2023-04-25gnu: python-schema-salad: Use pyproject-build-system.Ricardo Wurmus
The python-build-system fails with "setuptools.installer is deprecated. Requirements should be satisfied by a PEP 517 installer." This, in turn, causes all Python packages to be ignored and "pip install" to be invoked for them. * gnu/packages/bioinformatics.scm (python-schema-salad)[build-system]: Use pyproject-build-system.
2023-04-25gnu: gfeeds: Add missing gettext-minimal.Liliana Marie Prikler
* gnu/packages/syndication.scm (gfeeds)[inputs]: Add gettext-minimal.
2023-04-25gnu: syndication-domination: Update to 1.0-1-7592032.Liliana Marie Prikler
* gnu/packages/syndication.scm (syndication-domination): Update to 1.0-1-7592032.
2023-04-25gnu: evolution: Update to 3.46.4.Liliana Marie Prikler
* gnu/packages/gnome.scm (evolution): Update to 3.46.4.
2023-04-25gnu: evolution-data-server: Update to 3.46.4.Liliana Marie Prikler
* gnu/packages/gnome.scm (evolution-data-server): Update to 3.46.4.
2023-04-25gnu: adapterremoval: Update to 2.3.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (adapterremoval): Update to 2.3.3. [arguments]: Simplify. [inputs]: Reformat.
2023-04-25gnu: ocaml-lwt: Add ocaml4.07 variant.Efraim Flashner
* gnu/packages/ocaml.scm (ocaml-lwt)[properties]: New field. (ocaml4.07-lwt): New variable.
2023-04-25gnu: perl-crypt-openssl-rsa: Update to 0.33.Efraim Flashner
* gnu/packages/tls.scm (perl-crypt-openssl-rsa): Update to 0.33.
2023-04-25gnu: bedtools-2.18: Fix build.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Fix operators in 'compatibility phase.
2023-04-25gnu: hisat: Build with GCC 10.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (hisat)[native-inputs]: Add gcc-10.
2023-04-25gnu: kallisto: Update to 0.48.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (kallisto): Update to 0.48.0. [arguments]: Remove trailing #T from build phase.
2023-04-25gnu: bpp-core: Build with GCC 10.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bpp-core)[native-inputs]: Add gcc-10.
2023-04-25gnu: vcflib: Update to 1.0.9.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.9. [source]: Update snippet. [inputs]: Add curl, pybind11, and wfa2-lib. [arguments]: Adjust and reformat.
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