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2023-04-27gnu: vcflib: Use libwfa2.pc.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (vcflib)[source]: Use pkg-config to look for libwfa2. [inputs]: Move wfa2-lib from here... [propagated-inputs]: ...to here. [arguments]: Drop WFA_LINK_LIBRARIES option; fix typo in build phase name; patch IntervalTree.h includes; add libwfa2 to pkg-config file.
2023-04-27gnu: wfa2-lib: Install pkg-config file.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (wfa2-lib)[arguments]: Install libwfa2.pc.
2023-04-27gnu: express: Adjust bamtools location.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (express)[arguments]: Modify location of libbamtools.so in 'use-shared-boost-libs-and-set-bamtools-paths; drop trailing #T.
2023-04-27gnu: python-tinycss2: Simplify.Ricardo Wurmus
* gnu/packages/python-web.scm (python-tinycss2)[build-system]: Use pyproject-build-system. [arguments]: Remove.
2023-04-27gnu: python-openapi-core: Add missing input.Ricardo Wurmus
* gnu/packages/python-web.scm (python-openapi-core)[build-system]: Use pyproject-build-system. [arguments]: Do not override 'check phase; specify #:test-flags. [native-inputs]: Add python-mock.
2023-04-27gnu: libwebsockets: Update to 4.3.2.Ricardo Wurmus
* gnu/packages/web.scm (libwebsockets): Update to 4.3.2. [arguments]: Remove. [source]: Use GIT-FILE-NAME.
2023-04-27gnu: python-google-cloud-storage: Add missing input.Ricardo Wurmus
* gnu/packages/python-web.scm (python-google-cloud-storage)[native-inputs]: Add python-mock.
2023-04-27gnu: python-google-resumable-media: Add missing input.Ricardo Wurmus
* gnu/packages/python-web.scm (python-google-resumable-media)[native-inputs]: Add python-mock.
2023-04-27gnu: python-aws-xray-sdk: Update to 2.12.0.Ricardo Wurmus
* gnu/packages/python-web.scm (python-aws-xray-sdk): Update to 2.12.0. [build-system]: Use pyproject-build-system. [arguments]: Specify #:test-flags; do not override 'check phase; add 'pre-check phase. [native-inputs]: Add python-httpx, python-mock, python-pytest-asyncio, and python-pytest-benchmark.
2023-04-27gnu: python-httpx: Update to 0.24.0.Ricardo Wurmus
* gnu/packages/python-web.scm (python-httpx): Update to 0.24.0. [build-system]: Use pyproject-build-system. [arguments]: Remove custom check phase in favor of specifying #:test-flags. [native-inputs]: Add python-hatchling and python-hatch-fancy-pypi-readme. (python-httpx-bootstrap)[native-inputs]: Add python-hatchling and python-hatch-fancy-pypi-readme.
2023-04-27gnu: python-httpcore: Update to 0.17.0.Ricardo Wurmus
* gnu/packages/python-web.scm (python-httpcore): Update to 0.17.0. [build-system]: Use pyproject-build-system. [arguments]: Remove custom check phase; specify #:test-flags; disable broken tests.
2023-04-27gnu: python-h11: Update to 0.14.0.Ricardo Wurmus
* gnu/packages/python-web.scm (python-h11): Update to 0.14.0. [build-system]: Use pyproject-build-system. [arguments]: Remove.
2023-04-27gnu: python-wsproto: Update to 1.2.0.Ricardo Wurmus
* gnu/packages/python-web.scm (python-wsproto): Update to 1.2.0. [build-system]: Use pyproject-build-system. [arguments]: Remove.
2023-04-26gnu: python-dendropy: Fix build.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-dendropy)[native-inputs]: Add python-pytest. [arguments]: Add phase 'python-compatibility; remove 'skip-broken-tests; add #:test-flags; do not delete test files. [build-system]: Use pyproject-build-system.
2023-04-26gnu: python-watchgod: Update to 0.8.1.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-watchgod): Update to 0.8.1. [build-system]: Use pyproject-build-system. [arguments]: Specify #:test-flags instead of overwriting 'check phase. [native-inputs]: Add python-anyio.
2023-04-26gnu: python-fastjsonschema: Use pyproject-build-system.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-fastjsonschema): Reindent. [build-system]: Use pyproject-build-system. [arguments]: Remove custom check phase; update comment on why tests are disabled.
2023-04-26gnu: python-rapidjson: Update to 1.10.Ricardo Wurmus
* gnu/packages/python-web.scm (python-rapidjson): Update to 1.10. [source]: Simplify snippet. [arguments]: Run tests conditionally; do not delete test files.
2023-04-26gnu: rapidjson: Update to 1.1.0-1.949c771.Ricardo Wurmus
* gnu/packages/patches/rapidjson-gcc-compat.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. * gnu/packages/web.scm (rapidjson): Update to 1.1.0-1.949c771. [source]: Remove obsolete patch.
2023-04-26gnu: python-multiprocess: Update to 0.70.14.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-multiprocess): Update to 0.70.14. [build-system]: Use pyproject-build-system. [arguments]: Adjust directory containing tests; disable two more tests; replace check phase instead of deleting and adding it; run tests conditionally.
2023-04-26gnu: python-dill: Update to 0.3.6.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-dill): Update to 0.3.6. [build-system]: Use pyproject-build-system. [arguments]: Run tests conditionally; drop trailing #T from build phase.
2023-04-26gnu: python-jupyterlab-widgets: Update to 1.1.4.Ricardo Wurmus
* gnu/packages/jupyter.scm (python-jupyterlab-widgets): Update to 1.1.4. [build-system]: Use pyproject-build-system.
2023-04-26gnu: python-fire: Add missing input.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-fire)[native-inputs]: Add python-mock.
2023-04-26gnu: gitg: Fix build.Liliana Marie Prikler
* gnu/packages/patches/gitg-fix-positional-argument.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it here. * gnu/packages/gnome.scm (gitg)[source]<patches>: Use it here.
2023-04-26gnu: gnome-2048: Fix build.Liliana Marie Prikler
* gnu/packages/patches/gnome-2048-fix-positional-argument.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it here. * gnu/packages/games.scm (gnome-2048)[source]<patches>: Use it here.
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.
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