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2021-04-13gnu: python-flit: Update to 3.2.0....* 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. Ricardo Wurmus
2021-04-13gnu: Add python-sphinxcontrib-github-alt....* gnu/packages/sphinx.scm (python-sphinxcontrib-github-alt): New variable. Ricardo Wurmus
2021-04-13gnu: Add python-requests-unixsocket....* gnu/packages/python-web.scm (python-requests-unixsocket): New variable. Ricardo Wurmus
2021-04-13gnu: Add python-pygments-github-lexers....* gnu/packages/python-xyz.scm (python-pygments-github-lexers): New variable. Ricardo Wurmus
2021-04-13gnu: Add python-pytoml....* gnu/packages/python-build.scm (python-pytoml): New variable. Ricardo Wurmus
2021-04-13gnu: Remove python2-ipykernel....* gnu/packages/python-xyz.scm (python2-ipykernel): Remove variable. (python-ipykernel)[properties]: Remove python2-variant. Ricardo Wurmus
2021-04-13gnu: Remove python2-jupyter-console....* gnu/packages/python-xyz.scm (python2-jupyter-console): Remove variable. (python-jupyter-console)[properties]: Remove python2-variant. Ricardo Wurmus
2021-04-13gnu: Remove python2-jupyter-core....* gnu/packages/python-xyz.scm (python2-jupyter-core): Remove variable. Ricardo Wurmus
2021-04-13gnu: Remove python2-ipyparallel....* gnu/packages/python-xyz.scm (python2-ipyparallel): Remove variable. Ricardo Wurmus
2021-04-13gnu: Remove python2-matplotlib-documentation....* gnu/packages/python-xyz.scm (python2-matplotlib-documentation): Remove variable. Ricardo Wurmus
2021-04-13gnu: python-nbformat: Update to 5.1.3....* 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. Ricardo Wurmus
2021-04-13gnu: python-nbconvert: Update to 6.0.7....* 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. Ricardo Wurmus
2021-04-13gnu: Add python-nbclient....* gnu/packages/jupyter.scm (python-nbclient): New variable. Ricardo Wurmus
2021-04-13gnu: Add python-jupyterlab-pygments....* gnu/packages/jupyter.scm (python-jupyterlab-pygments): New variable. Ricardo Wurmus
2021-04-13gnu: Add python-nest-asyncio....* gnu/packages/python-xyz.scm (python-nest-asyncio): New variable. Ricardo Wurmus
2021-04-13gnu: python-notebook: Update inputs....* 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. Ricardo Wurmus
2021-04-13gnu: python-notebook: Update to 6.3.0....* gnu/packages/python-xyz.scm (python-notebook): Update to 6.3.0. Ricardo Wurmus
2021-04-13gnu: python-widgetsnbextension: Add missing inputs....* gnu/packages/python-xyz.scm (python-widgetsnbextension)[propagated-inputs]: Add python-argon2-cffi and python-terminado. Ricardo Wurmus
2021-04-13gnu: python-ipykernel: Update to 5.5.3....* gnu/packages/python-xyz.scm (python-ipykernel): Update to 5.5.3. Ricardo Wurmus
2021-04-13gnu: python-jupyter-client: Update to 6.1.12....* 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. Ricardo Wurmus
2021-04-13gnu: python-jupyter-core: Update to 4.7.1....* gnu/packages/python-xyz.scm (python-jupyter-core): Update to 4.7.1. Ricardo Wurmus
2021-04-13gnu: python-terminado: Update to 0.9.4....* 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. Ricardo Wurmus
2021-04-13gnu: esbuild: Update to 0.11.9....* gnu/packages/web.scm (esbuild): Update to 0.11.9. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Ryan Prior
2021-04-13gnu: visidata: Update to 2.4....* gnu/packages/visidata.scm (visidata): Update to 2.4. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Ryan Prior
2021-04-13gnu: gnu-standards: Update to 2020-11-25....* 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> Morgan Smith
2021-04-13gnu: Add texlive-xcharter....* gnu/packages/tex.scm: New variable. Paul Garlick
2021-04-13tests: halt: Fix it....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. Mathieu Othacehe
2021-04-12services: postgresql: Change service default socket directory....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> Christopher Baines
2021-04-12gnu: guile-picture-language: Update to 0.0.1-5.a1322bf....* gnu/packages/guile-xyz.scm (guile-picture-language): Update to 0.0.1-5.a1322bf. Ricardo Wurmus
2021-04-12services: ipfs: Tweak description....* gnu/services/networking.scm (ipfs-service-type)[description]: Avoid abbreviation. Ludovic Courtès
2021-04-12gnu: tests: Test basic funtionality of the IPFS service....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> Maxime Devos
2021-04-12tests: Support package extensions in the backdoor REPL....* 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> Maxime Devos
2021-04-12services: Add ipfs-service-type...* 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> Maxime Devos
2021-04-12gnu: racket: Don't inject store paths into Racket files....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> Philip McGrath
2021-04-12gnu: Add r-txdb-dmelanogaster-ucsc-dm6-ensgene....* gnu/packages/bioconductor.scm (r-txdb-dmelanogaster-ucsc-dm6-ensgene): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> hli
2021-04-12services: Support DELETE in MODIFY-SERVICES macro....* 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. Ricardo Wurmus
2021-04-12gnu: Add cl-bodge-queue....* 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> Adam Kandur
2021-04-12gnu: hydrogen: Update to 1.0.2....* gnu/packages/music.scm (hydrogen): Update to 1.0.2. Nicolas Goaziou
2021-04-12gnu: Add openvdb....* gnu/packages/graphics.scm (openvdb): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Ekaitz Zarraga
2021-04-12gnu: Add texlive-newtx....* gnu/packages/tex.scm: New variable. Paul Garlick
2021-04-12gnu: java-eclipse-jetty-util: Update to 9.4.39 [security fixes]....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. Julien Lepiller
2021-04-12gnu: hangups: Run test suite....* gnu/packages/messaging.scm (hangups)[arguments]: Use custom 'check phase. Efraim Flashner
2021-04-12gnu: hangups: Loosen version restrictions further....* gnu/packages/messaging.scm (hangups)[arguments]: Adjust custom 'relax-dependencies phase to allow more dependency versions. Efraim Flashner
2021-04-12gnu: python-mechanicalsoup: Update to 1.0.0....* 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> Ekaitz Zarraga
2021-04-12tests: docker: Increase VM building memory size to 1024MiB....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. Mathieu Othacehe
2021-04-12system: vm: Add a memory-size argument to system-docker-image....* gnu/system/vm.scm (system-docker-image): Add a memory-size argument and pass it to expression->derivation-in-linux-vm. Mathieu Othacehe
2021-04-12gnu: renpy: Update to 7.4.4....* gnu/packages/game-development.scm (python2-renpy): Update to 7.4.4. (python2-pygame-sdl2)[renpy-version]: Likewise. Leo Prikler
2021-04-12gnu: nginx: Enable stream module....* gnu/packages/web.scm (nginx)[arguments]: Add --with-stream option in the 'configure phase. Signed-off-by: Ludovic Courtès <ludo@gnu.org> methuselah-0
2021-04-12gnu: Add prips....gnu/packages/admin.scm (prips): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> methuselah-0
2021-04-12gnu: blis: Add deprecated aliases....Add deprecated aliases for packages removed in the parent commit. * gnu/packages/maths.scm (blis-sandybridge, blis-haswell, blis-knl): New variables. Ludovic Courtès