Commit graph

76952 commits

Author SHA1 Message Date
Ricardo Wurmus
c00996fdbe
gnu: Add python-deprecation.
* gnu/packages/python-xyz.scm (python-deprecation): New variable.
2021-04-13 13:41:18 +02:00
Ricardo Wurmus
5c89e2ac6f
gnu: python-testpath: Update to 0.4.4.
* gnu/packages/check.scm (python-testpath): Update to 0.4.4.
[arguments]: Build the package as intended with flit.
[native-inputs]: Add python-flit.
2021-04-13 13:41:18 +02:00
Ricardo Wurmus
636f4d5051
gnu: 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.
2021-04-13 13:41:18 +02:00
Ricardo Wurmus
a818a34f88
gnu: Add python-sphinxcontrib-github-alt.
* gnu/packages/sphinx.scm (python-sphinxcontrib-github-alt): New variable.
2021-04-13 13:41:18 +02:00
Ricardo Wurmus
f5acecdd46
gnu: Add python-requests-unixsocket.
* gnu/packages/python-web.scm (python-requests-unixsocket): New variable.
2021-04-13 13:41:18 +02:00
Ricardo Wurmus
2572bc8125
gnu: Add python-pygments-github-lexers.
* gnu/packages/python-xyz.scm (python-pygments-github-lexers): New variable.
2021-04-13 13:41:18 +02:00
Ricardo Wurmus
3bd962bc3c
gnu: Add python-pytoml.
* gnu/packages/python-build.scm (python-pytoml): New variable.
2021-04-13 13:41:18 +02:00
Ricardo Wurmus
5ce53a4d1c
gnu: Remove python2-ipykernel.
* gnu/packages/python-xyz.scm (python2-ipykernel): Remove variable.
(python-ipykernel)[properties]: Remove python2-variant.
2021-04-13 13:41:18 +02:00
Ricardo Wurmus
89f1a4a415
gnu: Remove python2-jupyter-console.
* gnu/packages/python-xyz.scm (python2-jupyter-console): Remove variable.
(python-jupyter-console)[properties]: Remove python2-variant.
2021-04-13 13:41:18 +02:00
Ricardo Wurmus
a0a8fdeaf2
gnu: Remove python2-jupyter-core.
* gnu/packages/python-xyz.scm (python2-jupyter-core): Remove variable.
2021-04-13 13:41:18 +02:00
Ricardo Wurmus
3a62614f32
gnu: Remove python2-ipyparallel.
* gnu/packages/python-xyz.scm (python2-ipyparallel): Remove variable.
2021-04-13 13:41:18 +02:00
Ricardo Wurmus
1388c166e7
gnu: Remove python2-matplotlib-documentation.
* gnu/packages/python-xyz.scm (python2-matplotlib-documentation): Remove variable.
2021-04-13 13:41:17 +02:00
Ricardo Wurmus
6b3872e871
gnu: 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.
2021-04-13 13:41:17 +02:00
Ricardo Wurmus
f4af353cb2
gnu: 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.
2021-04-13 13:41:17 +02:00
Ricardo Wurmus
74d2d7a322
gnu: Add python-nbclient.
* gnu/packages/jupyter.scm (python-nbclient): New variable.
2021-04-13 13:41:17 +02:00
Ricardo Wurmus
95456c2fc9
gnu: Add python-jupyterlab-pygments.
* gnu/packages/jupyter.scm (python-jupyterlab-pygments): New variable.
2021-04-13 13:41:17 +02:00
Ricardo Wurmus
2043e7bfc8
gnu: Add python-nest-asyncio.
* gnu/packages/python-xyz.scm (python-nest-asyncio): New variable.
2021-04-13 13:41:17 +02:00
Ricardo Wurmus
6d0a3dc4bc
gnu: 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.
2021-04-13 13:41:17 +02:00
Ricardo Wurmus
e9008a66ea
gnu: python-notebook: Update to 6.3.0.
* gnu/packages/python-xyz.scm (python-notebook): Update to 6.3.0.
2021-04-13 13:41:17 +02:00
Ricardo Wurmus
a7a92c00f4
gnu: python-widgetsnbextension: Add missing inputs.
* gnu/packages/python-xyz.scm (python-widgetsnbextension)[propagated-inputs]:
Add python-argon2-cffi and python-terminado.
2021-04-13 13:41:17 +02:00
Ricardo Wurmus
02746ead49
gnu: python-ipykernel: Update to 5.5.3.
* gnu/packages/python-xyz.scm (python-ipykernel): Update to 5.5.3.
2021-04-13 13:41:17 +02:00
Ricardo Wurmus
b1415bf089
gnu: 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.
2021-04-13 13:41:17 +02:00
Ricardo Wurmus
2a12cbaaab
gnu: python-jupyter-core: Update to 4.7.1.
* gnu/packages/python-xyz.scm (python-jupyter-core): Update to 4.7.1.
2021-04-13 13:41:16 +02:00
Ricardo Wurmus
95f25c9b13
gnu: 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.
2021-04-13 13:41:16 +02:00
Ryan Prior
85788dd64d
gnu: 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>
2021-04-13 14:23:47 +03:00
Ryan Prior
504a525d37
gnu: visidata: Update to 2.4.
* gnu/packages/visidata.scm (visidata): Update to 2.4.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-04-13 14:23:40 +03:00
Morgan Smith
bad0654d4f
gnu: 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>
2021-04-13 14:19:36 +03:00
Paul Garlick
995f685e4d
gnu: Add texlive-xcharter.
* gnu/packages/tex.scm: New variable.
2021-04-13 11:33:49 +01:00
Mathieu Othacehe
822eacc6bb
tests: 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.
2021-04-13 10:02:46 +02:00
Christopher Baines
c311147bd1
services: 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>
2021-04-12 19:12:46 -04:00
Ricardo Wurmus
1bbed20332
gnu: 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.
2021-04-12 21:51:38 +02:00
Morgan Smith
a6ac141ebb
etc/committer: Add missing newline.
* etc/committer.scm.in (main): Add newline to message.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2021-04-12 21:42:15 +02:00
Morgan Smith
d375eddda0
etc/committer: Use git plumbing instead of porcelain.
* 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>
2021-04-12 21:42:15 +02:00
Ludovic Courtès
d14f21389c
doc: Document 'gnu-build-system' keyword parameters.
* doc/guix.texi (Build Systems): Document keyword parameters of
'gnu-build-system'.
2021-04-12 18:44:09 +02:00
Ludovic Courtès
eb613eff58
doc: Move list of build phases to "Build Phases".
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.
2021-04-12 18:44:09 +02:00
Ludovic Courtès
a514b4ab19
channels: Build user channels with '-O1'.
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'.
2021-04-12 18:44:09 +02:00
Ludovic Courtès
4d0d6d8626
services: ipfs: Tweak description.
* gnu/services/networking.scm (ipfs-service-type)[description]: Avoid
abbreviation.
2021-04-12 18:44:09 +02:00
Maxime Devos
68c9e0a56e
gnu: 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>
2021-04-12 18:42:23 +02:00
Maxime Devos
3332f4365b
tests: 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>
2021-04-12 18:42:22 +02:00
Ludovic Courtès
b18f45c21f
Add (guix ipfs).
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>
2021-04-12 18:42:22 +02:00
Maxime Devos
2978832b92
services: 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>
2021-04-12 18:42:22 +02:00
Philip McGrath
834aa48504
gnu: 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>
2021-04-12 18:42:22 +02:00
hli
eb8da54170
gnu: 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>
2021-04-12 18:25:40 +02:00
Ricardo Wurmus
a247f5c753
services: 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.
2021-04-12 17:49:07 +02:00
Adam Kandur
c1ed3b048d
gnu: 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>
2021-04-12 17:06:31 +02:00
Nicolas Goaziou
7b04bdaba8
gnu: hydrogen: Update to 1.0.2.
* gnu/packages/music.scm (hydrogen): Update to 1.0.2.
2021-04-12 16:06:51 +02:00
Ekaitz Zarraga
f53ec9d99b
gnu: Add openvdb.
* gnu/packages/graphics.scm (openvdb): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2021-04-12 16:03:51 +02:00
Paul Garlick
e698843442
gnu: Add texlive-newtx.
* gnu/packages/tex.scm: New variable.
2021-04-12 14:21:23 +01:00
Julien Lepiller
ac3bf4e4da
gnu: 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.
2021-04-12 15:12:09 +02:00
Efraim Flashner
29f205f7e0
gnu: hangups: Run test suite.
* gnu/packages/messaging.scm (hangups)[arguments]: Use custom 'check
phase.
2021-04-12 15:16:58 +03:00