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* gnu: yubico-piv-tool: Update to 2.3.1.•••* gnu/packages/security-token.scm (yubico-piv-tool): Update to 2.3.1. [source]: Fetch from Github repository. [build-system]: Use cmake-build-system. Ricardo Wurmus2023-04-271-8/+9
* gnu: Add cl-prompter.•••* gnu/packages/lisp-xyz.scm (cl-prompter, ecl-prompter, sbcl-prompter): New variables. Pierre Neidhardt2023-04-271-0/+64
* gnu: python-docutils-0.15: Add missing input.•••* gnu/packages/python-xyz.scm (python-docutils-0.15)[native-inputs]: Add python-setuptools-57. Ricardo Wurmus2023-04-271-1/+3
* gnu: gdcm: Disable dependent tests.•••* gnu/packages/bioinformatics.scm (gdcm)[arguments]: Disable tests that depend on the output of a disabled test. Ricardo Wurmus2023-04-271-0/+5
* gnu: freebayes: Update to 1.3.7.•••* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.7. [arguments]: Do not use "grep -P" in tests; drop trailing #T. Ricardo Wurmus2023-04-271-15/+12
* gnu: vcflib: Use libwfa2.pc.•••* 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. Ricardo Wurmus2023-04-271-5/+14
* gnu: wfa2-lib: Install pkg-config file.•••* gnu/packages/bioinformatics.scm (wfa2-lib)[arguments]: Install libwfa2.pc. Ricardo Wurmus2023-04-271-0/+23
* gnu: express: Adjust bamtools location.•••* gnu/packages/bioinformatics.scm (express)[arguments]: Modify location of libbamtools.so in 'use-shared-boost-libs-and-set-bamtools-paths; drop trailing #T. Ricardo Wurmus2023-04-271-21/+21
* gnu: python-tinycss2: Simplify.•••* gnu/packages/python-web.scm (python-tinycss2)[build-system]: Use pyproject-build-system. [arguments]: Remove. Ricardo Wurmus2023-04-271-25/+1
* gnu: python-openapi-core: Add missing input.•••* 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. Ricardo Wurmus2023-04-271-14/+11
* gnu: libwebsockets: Update to 4.3.2.•••* gnu/packages/web.scm (libwebsockets): Update to 4.3.2. [arguments]: Remove. [source]: Use GIT-FILE-NAME. Ricardo Wurmus2023-04-271-9/+3
* gnu: python-google-cloud-storage: Add missing input.•••* gnu/packages/python-web.scm (python-google-cloud-storage)[native-inputs]: Add python-mock. Ricardo Wurmus2023-04-271-1/+1
* gnu: python-google-resumable-media: Add missing input.•••* gnu/packages/python-web.scm (python-google-resumable-media)[native-inputs]: Add python-mock. Ricardo Wurmus2023-04-271-0/+1
* gnu: python-aws-xray-sdk: Update to 2.12.0.•••* 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. Ricardo Wurmus2023-04-271-40/+34
* gnu: python-httpx: Update to 0.24.0.•••* 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. Ricardo Wurmus2023-04-271-25/+24
* gnu: python-httpcore: Update to 0.17.0.•••* 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. Ricardo Wurmus2023-04-271-10/+22
* gnu: python-h11: Update to 0.14.0.•••* gnu/packages/python-web.scm (python-h11): Update to 0.14.0. [build-system]: Use pyproject-build-system. [arguments]: Remove. Ricardo Wurmus2023-04-271-10/+3
* gnu: python-wsproto: Update to 1.2.0.•••* gnu/packages/python-web.scm (python-wsproto): Update to 1.2.0. [build-system]: Use pyproject-build-system. [arguments]: Remove. Ricardo Wurmus2023-04-271-10/+3
* gnu: python-dendropy: Fix build.•••* 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. Ricardo Wurmus2023-04-261-19/+22
* gnu: python-watchgod: Update to 0.8.1.•••* 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. Ricardo Wurmus2023-04-261-11/+8
* gnu: python-fastjsonschema: Use pyproject-build-system.•••* 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. Ricardo Wurmus2023-04-261-24/+17
* gnu: python-rapidjson: Update to 1.10.•••* gnu/packages/python-web.scm (python-rapidjson): Update to 1.10. [source]: Simplify snippet. [arguments]: Run tests conditionally; do not delete test files. Ricardo Wurmus2023-04-261-9/+6
* gnu: rapidjson: Update to 1.1.0-1.949c771.•••* 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. Ricardo Wurmus2023-04-263-99/+34
* gnu: python-multiprocess: Update to 0.70.14.•••* 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. Ricardo Wurmus2023-04-261-18/+22
* gnu: python-dill: Update to 0.3.6.•••* 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. Ricardo Wurmus2023-04-261-7/+7
* gnu: python-jupyterlab-widgets: Update to 1.1.4.•••* gnu/packages/jupyter.scm (python-jupyterlab-widgets): Update to 1.1.4. [build-system]: Use pyproject-build-system. Ricardo Wurmus2023-04-261-4/+5
* gnu: python-fire: Add missing input.•••* gnu/packages/python-xyz.scm (python-fire)[native-inputs]: Add python-mock. Ricardo Wurmus2023-04-261-2/+2
* gnu: gitg: Fix build.•••* 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. Liliana Marie Prikler2023-04-263-1/+39
* gnu: gnome-2048: Fix build.•••* 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. Liliana Marie Prikler2023-04-263-1/+40
* gnu: python-umap-learn: Patch for sklearn/numpy compatibility.•••* gnu/packages/machine-learning.scm (python-umap-learn)[arguments]: Add phase 'numpy-compatibility. Ricardo Wurmus2023-04-261-0/+12
* gnu: python-tables: Build cython files from source.•••* 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. Ricardo Wurmus2023-04-261-34/+47
* gnu: python-bokeh: Add missing input.•••* gnu/packages/python-xyz.scm (python-bokeh)[native-inputs]: Add python-mock. Ricardo Wurmus2023-04-261-0/+1
* gnu: python-tornado: Run a lot more tests and fix collections.•••* gnu/packages/python-web.scm (python-tornado)[arguments]: Do run tests; add phase 'fix-collections. Ricardo Wurmus2023-04-261-11/+27
* gnu: nikola: Add input.•••* gnu/packages/python-xyz.scm (nikola)[propagated-inputs]: Add python-toml. Andreas Enge2023-04-261-0/+1
* gnu: cl-mock: Update to 1.1.0-0.01762fd.•••* 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> Sharlatan Hellseher2023-04-261-6/+11
* gnu: cl-fast-ecs: Update to 0.2.2.•••* 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> Sharlatan Hellseher2023-04-261-3/+3
* gnu: Add cl-chlorophyll.•••* gnu/packages/lisp-xyz.scm (cl-chlorophyll, ecl-chlorophyll, sbcl-chlorophyll): New variables. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net> Sharlatan Hellseher2023-04-261-0/+31
* gnu: cl-nclasses: Update to 0.4.0.•••gnu/packages/lisp-xyz.scm (sbcl-nclasses): Update to 0.4.0. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net> Artyom Bologov2023-04-261-6/+6
* gnu: flwrap: Update to 1.3.6.•••* gnu/packages/radio.scm (flwrap): Update to 1.3.6. Guillaume Le Vaillant2023-04-261-2/+2
* gnu: pdf2djvu: Update to 0.9.19.•••* gnu/packages/djvu.scm (pdf2djvu): Update to 0.9.19. Guillaume Le Vaillant2023-04-261-2/+2
* gnu: xonsh: Add missing input.•••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> jgart2023-04-261-0/+1
* gnu: plocate: Update to 1.1.18.•••* gnu/packages/search.scm (plocate): Update to 1.1.18. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr> kiasoc52023-04-261-2/+2
* gnu: emacs-vertico: Update to 1.3.•••* gnu/packages/emacs-xyz.scm (emacs-vertico): Update to 1.3. Nicolas Goaziou2023-04-261-2/+2
* gnu: Add emacs-lojban.•••* gnu/packages/emacs-xyz.scm (emacs-lojban): New variable. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr> Christine Lemmer-Webber2023-04-261-0/+26
* gnu: valgrind: Update to 3.20.0.•••* 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> zimoun2023-04-263-35/+4
* gnu: lz4: Remove valgrind from native-inputs.•••* gnu/compression.scm (lz4)[native-inputs]: Remove valgrind. [arguments]<phases>: Remove trailing #t. Signed-off-by: Andreas Enge <andreas@enge.fr> zimoun2023-04-261-9/+3
* gnu: python-ipykernel: Fix build.•••* 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. Ricardo Wurmus2023-04-261-3/+12
* gnu: python-jupyter-client: Disable one test.•••* gnu/packages/python-xyz.scm (python-jupyter-client)[arguments]: Begrudgingly disable one failing test, because there is no information on why it fails. Ricardo Wurmus2023-04-261-1/+6
* gnu: python-jupyter-client-bootstrap: Hide zmq deprecation warning.•••* gnu/packages/python-xyz.scm (python-jupyter-client-bootstrap)[arguments]: Add phase 'hide-zmq-deprecation-warning. Ricardo Wurmus2023-04-261-0/+8
* gnu: python-jupyter-client-bootstrap: Use pyproject-build-system.•••* gnu/packages/python-xyz.scm (python-jupyter-client-bootstrap)[build-system]: Use pyproject-build-system. Ricardo Wurmus2023-04-261-1/+1
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