| Commit message (Collapse) | Author | Age |
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* gnu/packages/jupyter.scm (python-jupyter-packaging): New variable.
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* gnu/packages/python-xyz.scm (python-deprecation): New variable.
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* gnu/packages/check.scm (python-testpath): Update to 0.4.4.
[arguments]: Build the package as intended with flit.
[native-inputs]: Add python-flit.
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* gnu/packages/python-xyz.scm (python-flit): Update to 3.2.0.
[source]: Fetch from git repository to include flit_core.
[arguments]: Add phases to bootstrap the build.
[propagated-inputs]: Add python-pytoml and python-toml.
[native-inputs]: Add python-docutils, python-responses,
python-pygments-github-lexers, python-pytest, python-pytest-cov,
python-sphinx, python-sphinxcontrib-github-alt, and python-testpath.
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* gnu/packages/sphinx.scm (python-sphinxcontrib-github-alt): New variable.
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* gnu/packages/python-web.scm (python-requests-unixsocket): New variable.
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* gnu/packages/python-xyz.scm (python-pygments-github-lexers): New variable.
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* gnu/packages/python-build.scm (python-pytoml): New variable.
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* gnu/packages/python-xyz.scm (python2-ipykernel): Remove variable.
(python-ipykernel)[properties]: Remove python2-variant.
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* gnu/packages/python-xyz.scm (python2-jupyter-console): Remove variable.
(python-jupyter-console)[properties]: Remove python2-variant.
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* gnu/packages/python-xyz.scm (python2-jupyter-core): Remove variable.
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* gnu/packages/python-xyz.scm (python2-ipyparallel): Remove variable.
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* gnu/packages/python-xyz.scm (python2-matplotlib-documentation): Remove variable.
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* gnu/packages/python-xyz.scm (python-nbformat): Update to 5.1.3.
[arguments]: Remove to enable tests.
[native-inputs]: Add python-pytest.
[properties]: Add python2-variant.
(python2-nbformat): Keep at version 4.4.0; override version and source field.
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* gnu/packages/python-xyz.scm (python-nbconvert): Update to 6.0.7.
[arguments]: Remove configure flags, enable tests, override check phase.
[propagated-inputs]: Add python-defusedxml, python-nbclient,
python-pandocfilters, python-jupyterlab-pygments, and python-testpath.
[properties]: Add python2-variant.
(python2-nbconvert): Override version, source, arguments, and
propagated-inputs.
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* gnu/packages/jupyter.scm (python-nbclient): New variable.
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* gnu/packages/jupyter.scm (python-jupyterlab-pygments): New variable.
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* gnu/packages/python-xyz.scm (python-nest-asyncio): New variable.
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* gnu/packages/python-xyz.scm (python-notebook)[propagated-inputs]: Add
python-argon2-cffi, python-ipykernel, python-ipython-genutils, python-jinja2,
python-jupyter-client, python-pyzmq, python-tornado-6, and python-traitlets.
[native-inputs]: Remove python-nose and python-sphinx; add python-coverage,
python-nbval, python-pytest, python-pytest-cov, and
python-requests-unixsocket.
[arguments]: Use pytest instead of nosetests.
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* gnu/packages/python-xyz.scm (python-notebook): Update to 6.3.0.
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* gnu/packages/python-xyz.scm (python-widgetsnbextension)[propagated-inputs]:
Add python-argon2-cffi and python-terminado.
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* gnu/packages/python-xyz.scm (python-ipykernel): Update to 5.5.3.
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* gnu/packages/python-xyz.scm (python-jupyter-client): Update to 6.1.12.
[propagated-inputs]: Add python-dateutil and python-tornado-6.
[native-inputs]: Add python-pytest.
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* gnu/packages/python-xyz.scm (python-jupyter-core): Update to 4.7.1.
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* gnu/packages/python-web.scm (python-terminado): Update to 0.9.4.
[propagated-inputs]: Replace python-tornado with python-tornado-6.
[native-inputs]: Replace python-nose with python-pytest.
[home-page]: Follow redirect.
[arguments]: Update check phase.
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* gnu/packages/web.scm (esbuild): Update to 0.11.9.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
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* gnu/packages/visidata.scm (visidata): Update to 2.4.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
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* gnu/packages/gnu-doc.scm (gnu-standards): Update to 2020-11-25.
[source]: Make file-name more descriptive. Use version variable for
revision.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
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* gnu/packages/tex.scm: New variable.
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This fixes: <https://issues.guix.gnu.org/47727>. The OCR prompt detection is
failing, so remove it altogether. It looks like the test doesn't need the
prompt detection delay to work properly.
* gnu/tests/base.scm (run-halt-test): Remove failing OCR detection.
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Fixes <https://bugs.gnu.org/46737>.
PostgreSQL running with a different socket directory to the default one in the
package itself breaks some services, this commit restores the previous
behaviour where PostgreSQL by default will run with a socket directory that
matches the default used by PostgreSQL packaged for Guix.
Switching to a different default value can happen, but only alongside changing
the PostgreSQL package.
* gnu/services/databases.scm (<postgresql-config-file>)[socket-directory]:
Change default to #false.
* doc/guix.texi (Database Services): Update documentation, and specify a
different value for disabling connections via sockets.
* gnu/tests/guix.scm (%guix-data-service-os): Use default PostgreSQL
behaviour.
* gnu/tests/monitoring.scm (%zabbix-os): Likewise.
* gnu/tests/web.scm (patchwork-os): Likewise.
Signed-off-by: Leo Famulari <leo@famulari.name>
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* gnu/packages/guile-xyz.scm (guile-picture-language): Update to
0.0.1-5.a1322bf.
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* gnu/services/networking.scm (ipfs-service-type)[description]: Avoid
abbreviation.
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It is tested whether the IPFS service listens
at the gateway and API ports and whether it
is possible to upload and download a bytevector.
* gnu/tests/networking.scm
(%ipfs-os): New variable.
(run-ipfs-test): New procedure.
(%test-ipfs): New system test.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/tests.scm
(<marionette-configuration>): Add 'extensions' field.
(marionette-shepherd-service): Honour the field.
(with-import-modules-and-extensions): Define a combination
of 'with-import-modules' and 'with-extensions'.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/services/networking.scm (ipfs-service-type)
(%ipfs-home-mapping, %ipfs-environment)
(%ipfs-accounts, %ipfs-home): New variables.
(ipfs-configuration, ipfs-configuration?)
(ipfs-configuration-package, ipfs-configuration-gateway)
(ipfs-configuration-api, ipfs-shepherd-service)
(ipfs-binary, %ipfs-activation): New procedures.
* doc/guix.texi (Networking Services): Document it.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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Apparently, during grafting, Guix can somehow mangle compiled
Racket CS files (.zo) such that Racket will refuse to load them.
(Maybe it has something to do with compression?)
So, we stop patching Racket sources with absolute paths to store
files (i.e. for foreign libraries to dlopen).
Instead, we put them in a data file that doesn't get compiled or,
in one case, embed it in C.
Fixes https://issues.guix.gnu.org/47064
* gnu/packages/patches/racket-sh-via-rktio.patch: New file.
Adds a special case at the C level, controlled by a preprocessor macro,
to handle attempts to execute "/bin/sh".
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/scheme.scm (racket)[source](patches): Apply it.
(racket)[arguments](#:configure-flags): Add the CPP flag to enable it.
(racket)[arguments](#:modules): Use srfi-1.
(racket)[arguments](#:phases): Remove 'patch-/bin/sh and 'pre-configure.
Change 'pre-configure-minimal to just change directory.
Add 'patch-config.rktd-lib-search-dirs after 'build and before 'install
to configure Racket's "lib-search-dirs".
(racket, racket-minimal)[inputs]: Add bash-minimal as an explicit input.
(racket-minimal)[source]: Adjust to inherit patches from racket.
(racket-minimal)[arguments]: Inherit from racket: changes no longer needed.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/packages/bioconductor.scm (r-txdb-dmelanogaster-ucsc-dm6-ensgene):
New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
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* gnu/services.scm (%modify-service): Add clause for DELETE syntax.
(modify-services): Use FILTER-MAP; adjust docstring.
* doc/guix.texi (System Services): Mention alternative syntax.
(X Window): Use MODIFY-SERVICES syntax.
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* gnu/packages/lisp-xyz.scm (sbcl-bodge-queue, cl-bodge-queue,
ecl-bodge-queue): New variables.
Co-authored-by: Guillaume Le Vaillant <glv@posteo.net>
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* gnu/packages/music.scm (hydrogen): Update to 1.0.2.
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* gnu/packages/graphics.scm (openvdb): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
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* gnu/packages/tex.scm: New variable.
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Fixes CVE-2021-28165 - jetty server high CPU when client send data length >
17408, CVE-2021-28164 - Normalize ambiguous URIs and CVE-2021-28163 - Exclude
webapps directory from deployment scan.
* gnu/packages/java.scm (java-eclipse-jetty-util): Update to 9.4.39.
(java-eclipse-jetty-util-ajax): New variable.
(java-eclipse-jetty-util, java-eclipse-jetty-io, java-eclipse-jetty-http)
(java-eclipse-jetty-jmx, java-eclipse-jetty-server)
(java-eclipse-jetty-security, java-eclipse-jetty-servlet)
(java-eclipse-jetty-xml, java-eclipse-jetty-webapp): Disable tests.
[native-inputs]: Remove test dependencies.
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* gnu/packages/messaging.scm (hangups)[arguments]: Use custom 'check
phase.
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* gnu/packages/messaging.scm (hangups)[arguments]: Adjust custom
'relax-dependencies phase to allow more dependency versions.
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* gnu/packages/python-web.scm (python-mechanicalsoup): Update to
1.0.0.
[arguments]: Enable tests.
[native-inputs]: Add python-pytest-flake8, python-pytest-httpbin,
python-pytest-cov, python-pytest-mock, python-pytest-runner,
python-requests-mock.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
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This fixes the following error when running the "docker-system" test:
In ice-9/ftw.scm:
553:30 1 (_ #<directory stream db6660>)
In unknown file:
0 (readdir #<directory stream db6660>)
ERROR: In procedure readdir:
In procedure readdir: Cannot allocate memory
* gnu/tests/docker.scm (%test-docker-system): Bump image building VM memory
size to 1024 MiB.
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* gnu/system/vm.scm (system-docker-image): Add a memory-size argument and pass
it to expression->derivation-in-linux-vm.
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* gnu/packages/game-development.scm (python2-renpy): Update to 7.4.4.
(python2-pygame-sdl2)[renpy-version]: Likewise.
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