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2021-04-13gnu: Add r-hmm.Roel Janssen
* gnu/packages/cran.scm (r-hmm): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2021-04-13gnu: python-tinycss2: Enable tests.Ricardo Wurmus
* gnu/packages/python-web.scm (python-tinycss2)[source]: Fetch from git repository to include tests. [arguments]: Build from source with flit. [native-inputs]: Add python-flit, python-pytest, python-pytest-cov, python-pytest-flake8, and python-pytest-isort.
2021-04-13gnu: python-ipywidgets: Update to 7.6.3.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-ipywidgets): Update to 7.6.3. [propagated-inputs]: Add python-ipython, python-jupyterlab-widgets, and python-nbformat. [native-inputs]: Remove python-nose; add python-mock and ptyhon-pytest-cov.
2021-04-13gnu: python-widgetsnbextension: Remove unnecessary inputs.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-widgetsnbextension)[propagated-inputs]: Remove python-argon2-cffi, python-ipykernel, and python-terminado. [native-inputs]: Remove python-certifi and python-nose.
2021-04-13gnu: Add python-jupyterlab-widgets.Ricardo Wurmus
* gnu/packages/jupyter.scm (python-jupyterlab-widgets): New variable.
2021-04-13gnu: Add python-jupyter-packaging.Ricardo Wurmus
* gnu/packages/jupyter.scm (python-jupyter-packaging): New variable.
2021-04-13gnu: Add python-deprecation.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-deprecation): New variable.
2021-04-13gnu: python-testpath: Update to 0.4.4.Ricardo Wurmus
* gnu/packages/check.scm (python-testpath): Update to 0.4.4. [arguments]: Build the package as intended with flit. [native-inputs]: Add python-flit.
2021-04-13gnu: python-flit: Update to 3.2.0.Ricardo Wurmus
* 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.
2021-04-13gnu: Add python-sphinxcontrib-github-alt.Ricardo Wurmus
* gnu/packages/sphinx.scm (python-sphinxcontrib-github-alt): New variable.
2021-04-13gnu: Add python-requests-unixsocket.Ricardo Wurmus
* gnu/packages/python-web.scm (python-requests-unixsocket): New variable.
2021-04-13gnu: Add python-pygments-github-lexers.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-pygments-github-lexers): New variable.
2021-04-13gnu: Add python-pytoml.Ricardo Wurmus
* gnu/packages/python-build.scm (python-pytoml): New variable.
2021-04-13gnu: Remove python2-ipykernel.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python2-ipykernel): Remove variable. (python-ipykernel)[properties]: Remove python2-variant.
2021-04-13gnu: Remove python2-jupyter-console.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python2-jupyter-console): Remove variable. (python-jupyter-console)[properties]: Remove python2-variant.
2021-04-13gnu: Remove python2-jupyter-core.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python2-jupyter-core): Remove variable.
2021-04-13gnu: Remove python2-ipyparallel.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python2-ipyparallel): Remove variable.
2021-04-13gnu: Remove python2-matplotlib-documentation.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python2-matplotlib-documentation): Remove variable.
2021-04-13gnu: python-nbformat: Update to 5.1.3.Ricardo Wurmus
* 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.
2021-04-13gnu: python-nbconvert: Update to 6.0.7.Ricardo Wurmus
* 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.
2021-04-13gnu: Add python-nbclient.Ricardo Wurmus
* gnu/packages/jupyter.scm (python-nbclient): New variable.
2021-04-13gnu: Add python-jupyterlab-pygments.Ricardo Wurmus
* gnu/packages/jupyter.scm (python-jupyterlab-pygments): New variable.
2021-04-13gnu: Add python-nest-asyncio.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-nest-asyncio): New variable.
2021-04-13gnu: python-notebook: Update inputs.Ricardo Wurmus
* 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.
2021-04-13gnu: python-notebook: Update to 6.3.0.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-notebook): Update to 6.3.0.
2021-04-13gnu: python-widgetsnbextension: Add missing inputs.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-widgetsnbextension)[propagated-inputs]: Add python-argon2-cffi and python-terminado.
2021-04-13gnu: python-ipykernel: Update to 5.5.3.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-ipykernel): Update to 5.5.3.
2021-04-13gnu: python-jupyter-client: Update to 6.1.12.Ricardo Wurmus
* 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.
2021-04-13gnu: python-jupyter-core: Update to 4.7.1.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-jupyter-core): Update to 4.7.1.
2021-04-13gnu: python-terminado: Update to 0.9.4.Ricardo Wurmus
* 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.
2021-04-13gnu: esbuild: Update to 0.11.9.Ryan Prior
* gnu/packages/web.scm (esbuild): Update to 0.11.9. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-04-13gnu: visidata: Update to 2.4.Ryan Prior
* gnu/packages/visidata.scm (visidata): Update to 2.4. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-04-13gnu: gnu-standards: Update to 2020-11-25.Morgan Smith
* 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>
2021-04-13gnu: Add texlive-xcharter.Paul Garlick
* gnu/packages/tex.scm: New variable.
2021-04-13tests: halt: Fix it.Mathieu Othacehe
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.
2021-04-12services: postgresql: Change service default socket directory.Christopher Baines
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>
2021-04-12gnu: guile-picture-language: Update to 0.0.1-5.a1322bf.Ricardo Wurmus
* gnu/packages/guile-xyz.scm (guile-picture-language): Update to 0.0.1-5.a1322bf.
2021-04-12etc/committer: Add missing newline.Morgan Smith
* etc/committer.scm.in (main): Add newline to message. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2021-04-12etc/committer: Use git plumbing instead of porcelain.Morgan Smith
* etc/committer.scm.in (diff-info): Use "git diff-files" instead of "git diff". (old-sexp): Use "git cat-file" instead of "git show". Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2021-04-12doc: Document 'gnu-build-system' keyword parameters.Ludovic Courtès
* doc/guix.texi (Build Systems): Document keyword parameters of 'gnu-build-system'.
2021-04-12doc: Move list of build phases to "Build Phases".Ludovic Courtès
Before this change, the 'gnu-build-system' phases were listed in the "Build Systems" section, and then summarized in the "Build Phases" section. This moves everything to "Build Phases". * doc/guix.texi (Build Systems): Move phase table to... (Build Phases): ... here. Rearrange surrounding text.
2021-04-12channels: Build user channels with '-O1'.Ludovic Courtès
This should noticeably speed up compilation for channels with many files. * guix/channels.scm (standard-module-derivation)[build]: Define 'optimizations-for-level' and '-O1'. Pass #:optimization-options to 'compile-files'.
2021-04-12services: ipfs: Tweak description.Ludovic Courtès
* gnu/services/networking.scm (ipfs-service-type)[description]: Avoid abbreviation.
2021-04-12gnu: tests: Test basic funtionality of the IPFS service.Maxime Devos
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>
2021-04-12tests: Support package extensions in the backdoor REPL.Maxime Devos
* 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>
2021-04-12Add (guix ipfs).Ludovic Courtès
This module allows for communicating with the IPFS gateway over the HTTP interface. The commit has been cherry-picked from <https://issues.guix.gnu.org/33899>. The procedures for adding and restoring file trees have been removed as according to a reply issue 33899, a different format will be used. The procedure 'add-data' has been exported as it will be used in the system test for IPFS. * guix/ipfs.scm: New file. * Makefile.am (MODULES): Add it. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-04-12services: Add ipfs-service-typeMaxime Devos
* 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>
2021-04-12gnu: racket: Don't inject store paths into Racket files.Philip McGrath
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>
2021-04-12gnu: Add r-txdb-dmelanogaster-ucsc-dm6-ensgene.hli
* gnu/packages/bioconductor.scm (r-txdb-dmelanogaster-ucsc-dm6-ensgene): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2021-04-12services: Support DELETE in MODIFY-SERVICES macro.Ricardo Wurmus
* 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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