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65200 Commits

Author SHA1 Message Date
Mathieu Othacehe
5bc5371b34 gnu: cuirass: Update to 1.0.0-10.17e8759. 
* gnu/packages/ci.scm (cuirass): Update to 1.0.0-10.17e8759.
 2021-04-14 15:07:44 +02:00
Paul Garlick
9153e12d73 gnu: Add texlive-ly1. 
* gnu/packages/tex.scm: New package.
 2021-04-14 12:04:14 +01:00
Nicolas Goaziou
f181ee1f42 gnu: emacs-vertico: Update to 0.4. 
* gnu/packages/emacs-xyz.scm (emacs-vertico): Update to 0.4.
 2021-04-14 10:25:54 +02:00
Ricardo Wurmus
2aa03a99e7 gnu: Add srecord. 
* gnu/packages/flashing-tools.scm (srecord): New variable.
 2021-04-14 10:20:29 +02:00
Trevor Hass
c5e149a9d9 gnu: minetest: Fix absolute path to 'rm' command. 
* gnu/packages/games.scm (minetest)[patch-sources]: Substitute '/bin/rm' path.
[inputs]: Add coreutils.

Signed-off-by: Leo Prikler <leo.prikler@student.tugraz.at>
 2021-04-14 09:41:57 +02:00
Leo Famulari
a758a8a3c2 gnu: Guix: Update to 1.2.0-21.4dff6ec. 
Fixes <https://bugs.gnu.org/46829>.

* gnu/packages/package-management.scm (guix): Update to 1.2.0-21.4dff6ec.
 2021-04-13 19:24:31 -04:00
Ludovic Courtès
c2e83b7105 gnu: guile-git: Update to 0.5.0. 
* gnu/packages/guile.scm (guile-git): Update to 0.5.0.
 2021-04-13 22:08:01 +02:00
Xinglu Chen
82543e9649 gnu: emacs-git-link: Update to 0.8.3. 
* gnu/packages/emacs-xyz.scm (emacs-git-link): Update to 0.8.3.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2021-04-13 14:28:50 -04:00
Leo Famulari
15de49e60b gnu: le-certs: Update to new Let's Encrypt certificates. 
* gnu/packages/certs.scm (le-certs): Update the certificate store.
[inputs]: Add isrgrootx2.pem, letsencryptauthorityr3.pem,
letsencryptauthorityr4.pem, letsencryptauthoritye1.pem, and
letsencryptauthoritye2.pem. Remove letsencryptauthorityx3.pem and
letsencryptauthorityx4.pem.
[arguments]: Adjust the builder accordingly.
 2021-04-13 13:46:24 -04:00
Peter Lo
b5607d830c gnu: Add r-randomforestsrc. 
* gnu/packages/cran.scm (r-randomforestsrc): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2021-04-13 14:44:32 +02:00
Efraim Flashner
516a101dd4 gnu: openconnect-sso: Update to 0.7.2. 
* gnu/packages/vpn.scm (openconnect-sso): Update to 0.7.2.
[arguments]: Remove 'adjust-package-version-requirements phase.
 2021-04-13 15:21:32 +03:00
Roel Janssen
f0741f3efe gnu: Add r-hmm. 
* gnu/packages/cran.scm (r-hmm): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2021-04-13 13:55:01 +02:00
Ricardo Wurmus
9e7f09cbec gnu: python-tinycss2: Enable tests. 
* 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.
 2021-04-13 13:41:19 +02:00
Ricardo Wurmus
cf1517a1b7 gnu: python-ipywidgets: Update to 7.6.3. 
* 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.
 2021-04-13 13:41:19 +02:00
Ricardo Wurmus
7c4f9c17de gnu: python-widgetsnbextension: Remove unnecessary inputs. 
* 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.
 2021-04-13 13:41:19 +02:00
Ricardo Wurmus
4cb6120584 gnu: Add python-jupyterlab-widgets. 
* gnu/packages/jupyter.scm (python-jupyterlab-widgets): New variable.
 2021-04-13 13:41:18 +02:00
Ricardo Wurmus
a26dd2e282 gnu: Add python-jupyter-packaging. 
* gnu/packages/jupyter.scm (python-jupyter-packaging): New variable.
 2021-04-13 13:41:18 +02:00
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
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
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
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