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69497 Commits

Author SHA1 Message Date
Ricardo Wurmus
4590f8b338
gnu: r-glmmtmb: Update to 1.1.2. 
* gnu/packages/cran.scm (r-glmmtmb): Update to 1.1.2.
 2021-07-28 22:26:51 +02:00
Ricardo Wurmus
0af4e95b33
gnu: r-survey: Update to 4.1-1. 
* gnu/packages/cran.scm (r-survey): Update to 4.1-1.
 2021-07-28 22:26:51 +02:00
Ricardo Wurmus
dce011239f
gnu: r-doby: Update to 4.6.11. 
* gnu/packages/cran.scm (r-doby): Update to 4.6.11.
 2021-07-28 22:26:23 +02:00
Ricardo Wurmus
c633e5f40a
gnu: r-flextable: Update to 0.6.7. 
* gnu/packages/cran.scm (r-flextable): Update to 0.6.7.
 2021-07-28 22:26:23 +02:00
Ricardo Wurmus
8816d7e130
gnu: r-officer: Update to 0.3.19. 
* gnu/packages/cran.scm (r-officer): Update to 0.3.19.
 2021-07-28 22:26:23 +02:00
Ricardo Wurmus
3bc970802b
gnu: r-renv: Update to 0.14.0. 
* gnu/packages/cran.scm (r-renv): Update to 0.14.0.
 2021-07-28 22:26:23 +02:00
Ricardo Wurmus
db54fbe2b1
gnu: r-rastervis: Update to 0.50.3. 
* gnu/packages/cran.scm (r-rastervis): Update to 0.50.3.
 2021-07-28 22:26:23 +02:00
Ricardo Wurmus
1ba8c81f97
gnu: r-vim: Update to 6.1.1. 
* gnu/packages/cran.scm (r-vim): Update to 6.1.1.
 2021-07-28 22:26:23 +02:00
Ricardo Wurmus
76211cbc27
gnu: r-utf8: Update to 1.2.2. 
* gnu/packages/cran.scm (r-utf8): Update to 1.2.2.
[native-inputs]: Add r-rmarkdown.
 2021-07-28 22:26:23 +02:00
Ricardo Wurmus
165ecfb477
gnu: r-cli: Update to 3.0.1. 
* gnu/packages/cran.scm (r-cli): Update to 3.0.1.
 2021-07-28 22:26:23 +02:00
Ricardo Wurmus
57f04c64bc
gnu: r-laplacesdemon: Update to 16.1.6. 
* gnu/packages/cran.scm (r-laplacesdemon): Update to 16.1.6.
 2021-07-28 22:26:23 +02:00
Ricardo Wurmus
efaa549993
gnu: r-fastmatch: Update to 1.1-3. 
* gnu/packages/cran.scm (r-fastmatch): Update to 1.1-3.
 2021-07-28 22:26:23 +02:00
Ricardo Wurmus
e1a57fcdfa
gnu: r-jpeg: Update to 0.1-9. 
* gnu/packages/cran.scm (r-jpeg): Update to 0.1-9.
 2021-07-28 22:26:23 +02:00
Ricardo Wurmus
16c3ebaf14
gnu: r-rvest: Update to 1.0.1. 
* gnu/packages/cran.scm (r-rvest): Update to 1.0.1.
 2021-07-28 22:26:23 +02:00
Ricardo Wurmus
24ad9180fe
gnu: r-ggpp: Update to 0.4.1. 
* gnu/packages/cran.scm (r-ggpp): Update to 0.4.1.
[propagated-inputs]: Remove r-generics and r-plyr.
 2021-07-28 22:26:22 +02:00
Ricardo Wurmus
55a8d2f369
gnu: r-googlesheets4: Update to 1.0.0. 
* gnu/packages/cran.scm (r-googlesheets4): Update to 1.0.0.
[propagated-inputs]: Remove r-lifecycle; add r-cli.
 2021-07-28 22:26:22 +02:00
Ricardo Wurmus
6e27f274b2
gnu: Add r-lobstr. 
* gnu/packages/cran.scm (r-lobstr): New variable.
 2021-07-28 22:26:22 +02:00
Ricardo Wurmus
f39deacd21
gnu: Add r-datawizard. 
* gnu/packages/cran.scm (r-datawizard): New variable.
 2021-07-28 22:26:22 +02:00
Lars-Dominik Braun
9ac9bc6051
gnu: r-with-tests: Hardcode path to coreutils’ rm 
When running R in a container like this

	guix environment --no-cwd -C --ad-hoc r-minimal -- Rscript -e 'Sys.timezone()'

it would print an additional line

	sh: rm: command not found

before exiting.

* gnu/packages/statistics.scm (r-with-tests) [#:phases]: Add substitute*
to patch call to `rm` and rename phase to reflect what it does now.
 2021-07-28 22:26:19 +02:00
Ricardo Wurmus
042b6971d7
gnu: Add python-modin. 
* gnu/packages/python-science.scm (python-modin): New variable.
 2021-07-28 20:31:06 +02:00
Ricardo Wurmus
251bfbcfaa
gnu: Add python-distributed. 
* gnu/packages/python-science.scm (python-distributed): New variable.
 2021-07-28 20:31:06 +02:00
Ricardo Wurmus
41431282e2
gnu: Add python-zict. 
* gnu/packages/python-xyz.scm (python-zict): New variable.
 2021-07-28 20:31:06 +02:00
Ricardo Wurmus
45ee09dc96
gnu: Add python-heapdict. 
* gnu/packages/python-xyz.scm (python-heapdict): New variable.
 2021-07-28 20:31:06 +02:00
Ricardo Wurmus
532cfc5bd2
gnu: python-pyarrow: Fix parquet support. 
Co-authored-by: Phil Beadling <phil@beadling.co.uk>.

* gnu/packages/databases.scm (python-pyarrow)[arguments]: Add phases
patch-cmake-variables, patch-parquet-library, and set-PYARROW_WITH_PARQUET.
[propagated-inputs]: Add "include" output of apache-arrow package.
 2021-07-28 20:31:06 +02:00
Ricardo Wurmus
3a150e9f12
gnu: python-pandas: Update to 1.3.0. 
* gnu/packages/python-science.scm (python-pandas): Update to 1.3.0.
[arguments]: Adjust check phase.
 2021-07-28 20:31:06 +02:00
Ricardo Wurmus
242221e380
gnu: python-dask: Update to 2021.7.1. 
* gnu/packages/python-xyz.scm (python-dask): Update to 2021.7.1.
[arguments]: Do not skip test_shuffle.
 2021-07-28 20:31:05 +02:00
Ricardo Wurmus
f01d4b197a
gnu: python-partd: Update to 1.2.0. 
* gnu/packages/python-xyz.scm (python-partd): Update to 1.2.0.
 2021-07-28 20:31:05 +02:00
Ricardo Wurmus
27c6cab2c6
gnu: python-numexpr: Update to 2.7.3. 
* gnu/packages/python-xyz.scm (python-numexpr): Update to 2.7.3.
 2021-07-28 20:31:05 +02:00
Ricardo Wurmus
145296dbcb
gnu: python-cloudpickle: Update to 1.6.0. 
* gnu/packages/python-xyz.scm (python-cloudpickle-testpkg): New variable.
(python-cloudpickle): Update to 1.6.0; inherit from
python-cloudpickle-testpkg.
[source]: Fetch from git repository.
[native-inputs]: Add python-cloudpickle-testpkg; replace python-tornado with
python-tornado-6.
 2021-07-28 20:31:05 +02:00
Ricardo Wurmus
2422fbf6b2
gnu: python2-cloudpickle: Override version, source, and native-inputs. 
* gnu/packages/python-xyz.scm (python2-cloudpickle)[version]: Explicitly set
to 1.3.0.
[source]: Copy from base package.
[native-inputs]: Do not inherit; copy.
 2021-07-28 20:31:05 +02:00
Ricardo Wurmus
c486a61c27
gnu: cmake: Update to 3.21.1. 
* gnu/packages/cmake.scm (cmake): Update to 3.21.1.
[arguments]: Skip one more test.
 2021-07-28 20:31:05 +02:00
Efraim Flashner
c20c9e1685
gnu: julia-distances: Update flakey tests. 
* gnu/packages/julia-xyz.scm (julia-distances)[arguments]: Adjust the
custom 'skip-flakey-tests phase.
 2021-07-28 16:05:33 +03:00
Efraim Flashner
fcc900bd52
gnu: julia-docstringextensions: Skip tests. 
* gnu/packages/julia-xyz.scm (julia-docstringextensions)[arguments]:
Skip tests.
 2021-07-28 16:05:33 +03:00
Efraim Flashner
21747ffa87
gnu: julia-datavalues: Skip tests. 
* gnu/packages/julia-xyz.scm (julia-datavalues)[arguments]: Skip tests.
 2021-07-28 16:05:33 +03:00
Efraim Flashner
8832df0412
gnu: julia-compat: Update to 3.31.0. 
* gnu/packages/julia-xyz.scm (julia-compat): Update to 3.31.0.
 2021-07-28 16:05:33 +03:00
Efraim Flashner
a8977845cd
gnu: global: Update to 6.6.7. 
* gnu/packages/code.scm (global): Update to 6.6.7.
 2021-07-28 16:05:33 +03:00
Efraim Flashner
cbee534391
gnu: julia-jllwrappers: Add julia-preferences. 
* gnu/packages/julia-jll.scm (julia-jllwrappers)[propagated-inputs]: Add
julia-preferences.
 2021-07-28 16:05:33 +03:00
Efraim Flashner
f7eaa69dc2
gnu: Add julia-preferences. 
* gnu/packages/julia-xyz.scm (julia-preferences): New variable.
 2021-07-28 16:05:33 +03:00
Efraim Flashner
6886c4960d
gnu: julia: Skip tests on aarch64-linux. 
* gnu/packages/julia.scm (julia)[arguments]: Skip tests when building
for aarch64-linux.
 2021-07-28 16:05:32 +03:00
Efraim Flashner
cc85829fb9
gnu: llvm-julia: Overide build-type. 
* gnu/packages/julia.scm (llvm-julia)[arguments]: Move CMAKE_BUILD_TYPE
config from configure-flags to build-type.
 2021-07-28 16:05:32 +03:00
Efraim Flashner
6adea67cb0
gnu: libuv-julia: Clean up package definition. 
* gnu/packages/julia.scm (libuv-julia)[source]: Use git-file-name.
[build-system]: Remove field.
[arguments]: Remove field.
 2021-07-28 16:05:32 +03:00
Jean-Baptiste Volatier
55bb794248
gnu: julia: Update to 1.6.1. 
* gnu/packages/julia.scm (julia): Update to 1.6.1.
[arguments]: Adjust custom 'prepare-deps phase. Remove custom
'fix-precompile phase. Add new 'shared-objects-path phase to fix paths
to shared objects. Add new 'adjust-test-suite phase to adjust for
differences in bundled vs packaged libraries. Adjust custom
'disable-broken-tests phase for new version. Add symlinks to libs in
'symlink-libraries phase. In make-flags add more finegrained compilation
targets for x86_64-linux. Update make-flags for changes since last
version.
[inputs]: Add nghttp2:lib, gfortran:lib, curl-ssh. Remove arpack-ng,
curl. Sort alphabetically.
[native-inputs]: Add nss-certs. Sort alphabetically.

(libuv-julia): Update to newer revision.
(libunwind-julia)[source]: Add new patch.
(llvm-julia): Inherit from llvm-11.
[source]: Update patch list.
[arguments]: Apply minority of the Julia specific patches in
'julia-patches phase.
[inputs]: Add julia patches.

Co-Authored-By: Nicolò Balzarotti <nicolo@nixo.xyz>.
Co-Authored-By: zimoun <zimon.toutoune@gmail.com>.
Co-Authored-By: Efraim Flashner <efraim@flashner.co.il>.
 2021-07-28 16:05:32 +03:00
Jean-Baptiste Volatier
0faf5f1dd6
gnu: Add curl-ssh. 
* gnu/packages/curl.scm (curl-ssh): New hidden package.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-07-28 16:05:32 +03:00
Jean-Baptiste Volatier
2d4fa647b7
gnu: julia-staticarrays: Update to 1.2.5 
* gnu/packages/julia-xyz.scm (julia-staticarrays): Update to 1.2.5

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-07-28 16:05:32 +03:00
Jean-Baptiste Volatier
1978d716a9
gnu: openlibm: Fix cross-compiling. 
* gnu/packages/maths.scm (openlibm)[arguments]: Add configure-flag to
use cc-for-target.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-07-28 16:05:31 +03:00
Jean-Baptiste Volatier
4709b74bc8
gnu: openlibm: Update to 0.7.4. 
* gnu/packages/maths.scm (openlibm): Update to 0.7.4.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-07-28 16:05:31 +03:00
Jean-Baptiste Volatier
7db9573e86
gnu: Add pcre2-10.36. 
* gnu/packages/pcre.scm (pcre2-10.36): New variable.

Co-Authored-By: zimoun <zimoun.toutoune@gmail.com>.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-07-28 16:05:31 +03:00
Jean-Baptiste Volatier
2459cff9ae
gnu: Add utf8proc-2.6.1. 
* gnu/packages/textutils.scm (utf8proc-2.6.1): New variable.

Co-Authored-By: zimoun <zimon.toutoune@gmail.com>.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-07-28 16:05:31 +03:00
Franz Josef
7d93b21ab1
gnu: glibc-for-bootstrap: Update patch. 
There was/is something funny going on with the bootstrap glibc. The
symbol for posix_spawnp points to getopt_r. Which in turn leads to a
lot of crashed in tests later on. I extended the glibc-bootstrap patch
to work around this bug.

* gnu/packages/patches/glibc-bootstrap-system.patch: Adjust patch to
work correctly with new architectures.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-07-28 16:05:31 +03:00
Efraim Flashner
8afd85538a
gnu: global: Fix lisp install dir. 
* gnu/packages/code.scm (global)[arguments]: Adjust custom 'post-install
phase to move emacs files to the correct directory.
 2021-07-28 16:05:31 +03:00
Nicolas Goaziou
b07c7f0da6
gnu: python-pikepdf: Update to 2.16.0. 
* gnu/packages/python-xyz.scm (python-pikepdf): Update to 2.16.0.
 2021-07-27 21:35:52 +02:00
cage
d0ec73907c
gnu: telescope: Update to 0.4.1. 
* gnu/packages/web-browsers.scm (telescope): Update to 0.4.1.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-07-27 19:36:22 +02:00
Alexandr Vityazev
f87f60a8b5
gnu: emacs-link-hint: Update to 0.1-3.9fbf196. 
* gnu/packages/emacs-xyz.scm (emacs-link-hint): Update to 0.1-3.9fbf196.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-07-27 19:10:28 +02:00
Simon South
f62c140f47
gnu: emacs-elpher: Update to 2.10.3. 
* gnu/packages/emacs-xyz.scm (emacs-elpher): Update to 2.10.3.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-07-27 19:10:28 +02:00
Morgan Smith
4c4cf3d692
gnu: emacs-typit: Update to 0.2.1-2.fa125bf. 
* gnu/packages/emacs-xyz.scm (emacs-typit): Update to 0.2.1-2.fa125bf.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-07-27 19:10:28 +02:00
Morgan Smith
143d21fa95
gnu: emacs-typit: Fix dictionary location. 
Move the dictionary directory to be next to the lisp files, where it is
expected to be.

* gnu/packages/emacs-xyz.scm (emacs-typit)[arguments]
<#:phases>: Remove install-dictionaries phase.
<#:include>: Include dictionaries.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-07-27 19:10:27 +02:00
Vinicius Monego
3968134a4d
gnu: emacs-org-roam-bibtex: Update to 0.6.0. 
* gnu/packages/emacs-xyz.scm (emacs-org-roam-bibtex): Update to 0.6.0.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-07-27 19:10:27 +02:00
Vinicius Monego
3c76399745
gnu: emacs-org-roam: Update to 2.0.0. 
* gnu/packages/emacs-xyz.scm (emacs-org-roam): Update to 2.0.0.
[propagated-inputs]: Add emacs-magit.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-07-27 19:10:27 +02:00
Vinicius Monego
157f2f7f03
gnu: Add emacs-org-cv. 
* gnu/packages/emacs-xyz.scm (emacs-org-cv): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-07-27 19:10:26 +02:00
Ivan Gankevich
8cfd9ef831
gnu: mesa-opencl-icd: Use absolute path for the library. 
* gnu/packages/gl.scm (mesa-opencl-icd): Use absolute path for OpenCL
  platform library in "mesa.icd" file.  With this patch setting
  LD_LIBRARY_PATH=$LIBRARY_PATH is no longer needed to run OpenCL
  applications.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-07-27 18:36:34 +02:00
Tobias Geerinckx-Rice
5dc4fe1004
gnu: sudo: Update to 1.9.7p2. 
* gnu/packages/admin.scm (sudo): Update to 1.9.7p2.
 2021-07-27 18:10:15 +02:00
Leo Famulari
95c214e23d
gnu: WebKitGTK: Update to 2.32.3 [security fixes] 
Fixes CVE-2021-{21775,21779,30663,30665,30689,30724,30749,30795,30797,30799}.

https://webkitgtk.org/security/WSA-2021-0004.html

* gnu/packages/webkit.scm (webkitgtk): Update to 2.32.2.
 2021-07-27 11:02:08 -04:00
Nicolas Goaziou
87f6491e67
gnu: Remove rust-bat-0.17. 
* gnu/packages/crates-io.scm (rust-bat-0.17): Remove variable.
 2021-07-27 16:34:13 +02:00
Nicolas Goaziou
29ef6d0154
gnu: nushell: Update to 0.34.0. 
* gnu/packages/shells.scm (nushell):
(rust-nu-ansi-term-0.34):
(rust-nu-command-0.34):
(rust-nu-data-0.34):
(rust-nu-engine-0.34):
(rust-nu-errors-0.34):
(rust-nu-parser-0.34):
(rust-nu-plugin-0.34):
(rust-nu-plugin-binaryview-0.34):
(rust-nu-plugin-chart-0.34):
(rust-nu-plugin-fetch-0.34):
(rust-nu-plugin-from-bson-0.34):
(rust-nu-plugin-from-sqlite-0.34):
(rust-nu-plugin-inc-0.34):
(rust-nu-plugin-match-0.34):
(rust-nu-plugin-post-0.34):
(rust-nu-plugin-ps-0.34):
(rust-nu-plugin-query-json-0.34):
(rust-nu-plugin-sys-0.34):
(rust-nu-plugin-to-bson-0.34):
(rust-nu-plugin-to-sqlite-0.34):
(rust-nu-plugin-tree-0.34):
(rust-nu-plugin-xpath-0.34):
(rust-nu-pretty-hex-0.34):
(rust-nu-protocol-0.34):
(rust-nu-stream-0.34):
(rust-nu-test-support-0.34):
(rust-nu-value-ext-0.34): Update to 0.34.0.
(rust-nu-path-0.34):
(rust-nu-completion-0.34): New variable.
 2021-07-27 16:34:13 +02:00
Nicolas Goaziou
20e6b7ccd2
gnu: Add rust-mp4-0.8. 
* gnu/packages/crates-io.scm (rust-mp4-0.8): New variable.
 2021-07-27 16:34:12 +02:00
Nicolas Goaziou
9a38d56e3a
gnu: Add rust-calamine-0.18. 
* gnu/packages/crates-io.scm (rust-calamine-0.18): New variable.
(rust-calamine-0.17): Inherit from above.
 2021-07-27 16:34:12 +02:00
Nicolas Goaziou
88625b2424
gnu: rust-indexmap-1: Update to 1.7.0. 
* gnu/packages/crates-io.scm (rust-indexmap-1): Update to 1.7.0.
 2021-07-27 16:34:12 +02:00
Nicolas Goaziou
8eb20852dc
gnu: rust-minus-3: Update to 3.4.0. 
* gnu/packages/crates-io.scm (rust-minus-3): Update to 3.4.0.
 2021-07-27 16:34:11 +02:00
Nicolas Goaziou
5cbfd5c035
gnu: Add rust-ndarray-0.15. 
* gnu/packages/crates-io.scm (rust-ndarray-0.15): New variable.
(rust-ndarray-0.13): Inherit from above.
 2021-07-27 16:34:11 +02:00
Nicolas Goaziou
355ffee485
gnu: Add rust-matrixmultiply-0.3. 
* gnu/packages/crates-io.scm (rust-matrixmultiply-0.3): New variable.
(rust-matrixmultiply-0.2): Inherit from above.
 2021-07-27 16:34:10 +02:00
Nicolas Goaziou
240c73451a
gnu: Add rust-thread-tree-0.3. 
* gnu/packages/crates-io.scm (rust-thread-tree-0.3): New variable.
 2021-07-27 16:34:10 +02:00
Nicolas Goaziou
8df7c61944
gnu: Add rust-shadow-rs-0.6. 
* gnu/packages/crates-io.scm (rust-shadow-rs-0.6): New variable.
(rust-shadow-rs-0.5): Inherit from above.
 2021-07-27 16:34:10 +02:00
Nicolas Goaziou
0f32429a7a
gnu: rust-unicode-segmentation-1: Update to 1.8.0. 
* gnu/packages/crates-io.scm (rust-unicode-segmentation-1): Update to 1.8.0.
 2021-07-27 16:34:09 +02:00
Nicolas Goaziou
aadcdd2261
gnu: Add rust-tui-0.15. 
* gnu/packages/crates-io.scm (rust-tui-0.15): New variable.
(rust-tui-0.14): Inherit from above.
 2021-07-27 16:34:09 +02:00
Nicolas Goaziou
38a3cacca0
gnu: Add rust-s3handler-0.7. 
* gnu/packages/crates-io.scm (rust-s3handler-0.7): New variable.
(rust-s3handler-0.6): Inherit from above.
 2021-07-27 16:34:09 +02:00
Nicolas Goaziou
3aed641224
gnu: Add rust-rstest-0.10. 
* gnu/packages/crates-io.scm (rust-rstest-0.10): New variable.
 2021-07-27 16:34:08 +02:00
Nicolas Goaziou
afec299536
gnu: Add rust-polars-0.14. 
* gnu/packages/crates-io.scm (rust-polars-0.14): New variable.
(rust-polars-0.13): Inherit from above.
 2021-07-27 16:34:08 +02:00
Nicolas Goaziou
f686977bec
gnu: Add rust-polars-lazy-0.14. 
* gnu/packages/crates-io.scm (rust-polars-lazy-0.14): New variable.
(rust-polars-lazy-0.13): Inherit from above.
 2021-07-27 16:34:08 +02:00
Nicolas Goaziou
cd6a1e5f40
gnu: Add rust-polars-io-0.14. 
* gnu/packages/crates-io.scm (rust-polars-io-0.14): New variable.
(rust-polars-io-0.13): Inherit from above.
 2021-07-27 16:34:07 +02:00
Nicolas Goaziou
ed18419fe8
gnu: Add rust-simdutf8-0.1. 
* gnu/packages/crates-io.scm (rust-simdutf8-0.1): New variable.
 2021-07-27 16:34:07 +02:00
Nicolas Goaziou
08dfad9918
gnu: Add rust-polars-arrow-0.14. 
* gnu/packages/crates-io.scm (rust-polars-arrow-0.14): New variable.
(rust-polars-arrow-0.13): Inherit from above.
 2021-07-27 16:34:07 +02:00
Nicolas Goaziou
293d4064dc
gnu: Add rust-polars-core-0.14. 
* gnu/packages/crates-io.scm (rust-polars-core-0.14): New variable.
(rust-polars-core-0.13): Inherit from above.
 2021-07-27 16:34:06 +02:00
Nicolas Goaziou
f75044e780
gnu: rust-parquet-4: Update to 4.4.0. 
* gnu/packages/crates-io.scm (rust-parquet-4): Update to 4.4.0.
 2021-07-27 16:34:06 +02:00
Nicolas Goaziou
e376b00c31
gnu: Add rust-overload-0.1. 
* gnu/packages/crates-io.scm (rust-overload-0.1): New variable.
 2021-07-27 16:34:06 +02:00
Nicolas Goaziou
483e806865
gnu: rust-arrow-4: Update to 4.4.0. 
* gnu/packages/crates-io.scm (rust-arrow-4): Update to 4.4.0.
 2021-07-27 16:34:06 +02:00
Nicolas Goaziou
2c78572bd9
gnu: Add rust-is-executable-1. 
* gnu/packages/crates-io.scm (rust-is-executable-1): New variable.
(rust-is-executable): Remove variable.
 2021-07-27 16:34:05 +02:00
Nicolas Goaziou
daaa3ba07f
gnu: Add rust-sysinfo-0.18. 
* gnu/packages/crates-io.scm (rust-sysinfo-0.18): New variable.
(rust-sysinfo-0.16): Inherit from above.
 2021-07-27 16:34:05 +02:00
Matthew James Kraai
0ca6e13612
gnu: certbot, python-acme: Update to 1.17.0. 
* gnu/packages/tls.scm (certbot, python-acme): Update to 1.17.0.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2021-07-27 02:15:19 -04:00
Raghav Gururajan
e76423cd49
gnu: calibre: Update to 5.21.0. 
* gnu/packages/ebook.scm (calibre)[version]: Update to 5.21.0.
 2021-07-27 01:25:55 -04:00
Sarah Morgensen
e17f063627
gnu: gmnisrv: Fix configuration search path. 
Look in /etc for configuration files rather than
/gnu/store/...-gmnisrv-.../etc.

gnu/packages/web.scm (gmnisrv)[arguments]<#:configure-flags>: Set
--sysconfdir.

Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
 2021-07-27 02:42:39 +05:30
Sarah Morgensen
b459c39adb
gnu: gmnisrv: Remove dependency on /etc/mime.types. 
Remove the dependency on /etc/mime.types (fixes #49233).

gnu/packages/web.scm (gmnisrv)[arguments]<#:configure-flags>: Set
--with-mimedb to directly use mime.types from mailcap.
[propagated-inputs]: Move mailcap to...
[inputs]: ...here (/etc/mime.types no longer need in profiles).

Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
 2021-07-27 02:42:39 +05:30
Sarah Morgensen
3344f70e49
gnu: gmnisrv: Use #:make-flags, and cross-compile. 
gnu/packages/web.scm (gmnisrv)[arguments]<#:phases>{set-variables}: Move
'CC=' to...
<#:make-flags>: ...here, and support cross-compilation with (cc-for-target).

Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
 2021-07-27 02:42:38 +05:30
Sarah Morgensen
274fcfb251
gnu: gmnisrv: Disable tests using #:tests?. 
gnu/packages/web.scm (gmnisrv)[arguments]<#:phases>: Undelete check
phase, and...
<#:tests?>: ...disable tests here instead.

Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
 2021-07-27 02:42:38 +05:30
Leo Famulari
3314764193
gnu: Mutt: Update to 2.1.1. 
* gnu/packages/mail.scm (mutt): Update to 2.1.1.
 2021-07-26 17:04:49 -04:00
jgart
684259dfbc
gnu: Add python-flask-misaka. 
* gnu/packages/python-web.scm (python-flask-misaka): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-07-26 19:42:49 +02:00
Paul A. Patience
56de60cc27
gnu: interception-dual-function-keys: Minor fixes. 
* gnu/packages/linux.scm (interception-dual-function-keys)
[arguments]<#:make-flags>: Make use of cc-for-target, cxx-for-target and
%output.
<#:phases>{check}: Undelete phase. Disable tests instead with...
<#:tests?>: ...this. New field.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-07-26 19:42:49 +02:00
Paul A. Patience
3bbbb24f4c
gnu: interception-dual-function-keys: Update to 1.4.0. 
* gnu/packages/linux.scm (interception-dual-function-keys)
[version]: Update to 1.4.0.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-07-26 19:42:49 +02:00
Matthew James Kraai
0a1ea2b0fb
gnu: ghc-8.8: Update to 8.8.4. 
* gnu/packages/haskell.scm (ghc-8.8): Update to 8.8.4.
[arguments]: Add 'fix-cc-reference phase.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-07-26 19:42:49 +02:00
Ludovic Courtès
599b173b11
gnu: guix-jupyter: Update to 0.2.2. 
* gnu/packages/package-management.scm (guix-jupyter): Update to 0.2.2.
 2021-07-26 19:42:49 +02:00
Leo Famulari
456776e1ea
gnu: linux-libre 5.4: Update to 5.4.135. 
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.135.
(linux-libre-5.4-pristine-source): Update hash.
 2021-07-26 13:40:14 -04:00
Leo Famulari
1f6793f53e
gnu: linux-libre 5.10: Update to 5.10.53. 
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.53.
(deblob-scripts-5.10, linux-libre-5.10-pristine-source): Update hashes.
 2021-07-26 13:40:14 -04:00
Leo Famulari
559f80467d
gnu: linux-libre 5.13: Update to 5.13.5. 
* gnu/packages/linux.scm (linux-libre-5.13-version): Update to 5.13.5.
(deblob-scripts-5.13, linux-libre-5.13-pristine-source): Update hashes.
 2021-07-26 13:40:08 -04:00
Leo Famulari
93c6895910
gnu: linux-libre 4.4: Update to 4.4.276. 
* gnu/packages/linux.scm (linux-libre-4.4-version): Update to 4.4.276.
(linux-libre-4.4-pristine-source): Update hash.
 2021-07-26 09:34:39 -04:00
Leo Famulari
3a55b7a46e
gnu: linux-libre 4.9: Update to 4.9.276. 
* gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.276.
(linux-libre-4.9-pristine-source): Update hash.
 2021-07-26 09:34:39 -04:00
Leo Famulari
beb67e7098
gnu: linux-libre 4.14: Update to 4.14.240. 
* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.240.
(linux-libre-4.14-pristine-source): Update hash.
 2021-07-26 09:34:39 -04:00
Leo Famulari
b779450284
gnu: linux-libre 4.19: Update to 4.19.198. 
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.198.
(linux-libre-4.19-pristine-source): Update hash.
 2021-07-26 09:34:39 -04:00
Leo Famulari
75e647c884
gnu: linux-libre 5.4: Update to 5.4.134. 
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.134.
(linux-libre-5.4-pristine-source): Update hash.
 2021-07-26 09:34:39 -04:00
Leo Famulari
2c1382efd8
gnu: linux-libre 5.10: Update to 5.10.52. 
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.52.
(deblob-scripts-5.10, linux-libre-5.10-pristine-source): Update hashes.
 2021-07-26 09:34:38 -04:00
Leo Famulari
766d13721f
gnu: linux-libre: Update to 5.12.19. 
* gnu/packages/linux.scm (linux-libre-5.12-version): Update to 5.12.19.
(deblob-scripts-5.12, linux-libre-5.12-pristine-source): Update hashes.
 2021-07-26 09:34:38 -04:00
Leo Famulari
e286e16e75
gnu: linux-libre 5.13: Update to 5.13.4. 
* gnu/packages/linux.scm (linux-libre-5.13-version): Update to 5.13.4.
(deblob-scripts-5.13, linux-libre-5.13-pristine-source): Update hashes.
 2021-07-26 09:34:38 -04:00
qblade
151c54609b
gnu: uim: Enable 'uim-fep' to support the use of uim in text terminal. 
* gnu/packages/xorg.scm (uim)[inputs]: add ncurses.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2021-07-26 18:58:52 +08:00
Ricardo Wurmus
3e5eff8c30
gnu: Add seqan 3. 
* gnu/packages/bioinformatics.scm (seqan): Rename this variable...
(seqan-2): ...to this.
(seqan): New variable for seqan3.
(flexbar)[native-inputs]: Update name for seqan 2.
 2021-07-26 11:54:21 +02:00
Ricardo Wurmus
99ca1ae4f8
gnu: Add segemehl. 
* gnu/packages/bioinformatics.scm (segemehl): New variable.
 2021-07-26 11:08:13 +02:00
Nicolas Goaziou
d16694b546
gnu: bat: Update to 0.18.2. 
* gnu/packages/rust-apps.scm (bat): Update to 0.18.2.
 2021-07-26 10:51:43 +02:00
Nicolas Goaziou
088e9b5b1b
gnu: Add rust-nix-0.21. 
* gnu/packages/crates-io.scm (rust-nix-0.21): New variable.
(rust-nix-0.20): Inherit from above.
 2021-07-26 10:50:12 +02:00
Nicolas Goaziou
7b669da767
gnu: rust-memoffset-0.6: Update to 0.6.4. 
* gnu/packages/crates-io.scm (rust-memoffset-0.6): Update to 0.6.4.
 2021-07-26 10:49:06 +02:00
Nicolas Goaziou
69ce8f3ce1
gnu: xournalpp: Update to 1.1.0. 
* gnu/packages/pdf.scm (xournalpp): Update to 1.1.0.
 2021-07-26 10:42:44 +02:00
Tobias Geerinckx-Rice
4831f4e8c9
gnu: Update Zrythm Git URLs. 
* gnu/packages/audio.scm (libaudec, ztoolkit)[source, home-page]: Adjust to Gitea.
* gnu/packages/music.scm (zplugins)[source]: Likewise.
 2021-07-26 10:24:25 +02:00
Tobias Geerinckx-Rice
11d8a47bcf
gnu: Remove libgnomeprintui. 
* gnu/packages/gnome.scm (libgnomeprintui): Remove unused variable.
 2021-07-26 09:47:22 +02:00
Tobias Geerinckx-Rice
e8563962ee
gnu: Remove libgnomeprint. 
* gnu/packages/gnome.scm (libgnomeprint): Remove unused variable.
 2021-07-26 09:47:22 +02:00
Tobias Geerinckx-Rice
781a2befee
gnu: gsegrafix: Update to 1.0.7.2. 
This keeps this ancient package on life support for now.

* gnu/packages/maths.scm (gsegrafix): Update to 1.0.7.2.
[source]: Download from gsegrafix-experimental's Savannah.
[arguments]: Drop obsolete LDFLAGS.  Disable static library build.
[inputs]: Remove libgnomecanvas, libbonoboui, libgnomeui,
libgnomeprintui, and popt.  Add glib and gtk+.
 2021-07-26 09:47:22 +02:00
Nicolas Goaziou
1829e9d80f
gnu: wireshark: Update to 3.4.7. 
* gnu/packages/networking.scm (wireshark): Update to 3.4.7.
 2021-07-26 09:45:58 +02:00
Nicolas Goaziou
778af012ef
gnu: rosegarden: Update to 21.06.1. 
* gnu/packages/music.scm (rosegarden): Update to 21.06.1.
 2021-07-26 09:41:22 +02:00
Nicolas Goaziou
16f0bdf5f0
gnu: python-pikepdf: Update to 2.15.1. 
* gnu/packages/python-xyz.scm (python-pikepdf): Update to 2.15.1.
 2021-07-26 09:33:38 +02:00
Nicolas Goaziou
35b3c7c8eb
gnu: giac: Update to 1.7.0-21. 
* gnu/packages/algebra.scm (giac): Update to 1.7.0-21.
 2021-07-26 09:30:39 +02:00
Nicolas Goaziou
eb1a5dddda
gnu: mgba: Update to 0.9.2. 
* gnu/packages/emulators.scm (mgba): Update to 0.9.2.
 2021-07-26 09:22:05 +02:00
Tobias Geerinckx-Rice
11afd46519
gnu: ruby-stackprof: Build (more) reliably. 
* gnu/packages/ruby.scm (ruby-stackprof)[arguments]: Add a new
'skip-dubious-test phase.
 2021-07-26 02:52:34 +02:00
Tobias Geerinckx-Rice
900c2ca8f7
gnu: ruby-stackprof: Update to 0.2.17. 
* gnu/packages/ruby.scm (ruby-stackprof): Update to 0.2.17.
[arguments]: Add a new 'build-tests phase.
 2021-07-26 02:52:28 +02:00
Tobias Geerinckx-Rice
3e8537c146
gnu: java-commons-codec: Update to 1.15. 
* gnu/packages/java.scm (java-commons-codec): Update to 1.15.
 2021-07-25 23:14:48 +02:00
Tobias Geerinckx-Rice
94ec198506
gnu: java-commons-codec: Fix build on non-huge-memory machines. 
* gnu/packages/java.scm (java-commons-codec)[arguments]: Add a new
'skip-ravenous-test phase.
 2021-07-25 23:14:47 +02:00
Tobias Geerinckx-Rice
f91fceb920
gnu: java-commons-codec: Don't return #t from phases. 
* gnu/packages/java.scm (java-commons-codec)[arguments]: Don't return #t
from phases.
 2021-07-25 23:14:47 +02:00
Nicolas Goaziou
a3b6e90448
gnu: emacs-ebuild-mode: Update to 1.53. 
* gnu/packages/emacs-xyz.scm (emacs-ebuild-mode): Update to 1.53.
 2021-07-25 21:56:32 +02:00
Nicolas Goaziou
35d4bca2e9
gnu: emacs-counsel-etags: Update to 1.9.17. 
* gnu/packages/emacs-xyz.scm (emacs-counsel-etags): Update to 1.9.17.
[arguments]: Disable tests.
 2021-07-25 21:55:06 +02:00
Nicolas Goaziou
4755de6ed8
gnu: emacs-corfu: Update to 0.10. 
* gnu/packages/emacs-xyz.scm (emacs-corfu): Update to 0.10.
 2021-07-25 21:38:35 +02:00
Nicolas Goaziou
1d8521db83
gnu: emacs-modus-themes: Update to 1.5.0. 
* gnu/packages/emacs-xyz.scm (emacs-modus-themes): Update to 1.5.0.
 2021-07-25 21:35:25 +02:00
Nicolas Goaziou
1bcf2da570
gnu: emacs-flycheck-grammalecte: Update to 2.0. 
* gnu/packages/emacs-xyz.scm (emacs-flycheck-grammalecte): Update to 2.0.
 2021-07-25 21:31:40 +02:00
Nicolas Goaziou
b81ab18404
gnu: emacs-aggressive-indent: Update to 1.10.0. 
* gnu/packages/emacs-xyz.scm (emacs-aggressive-indent): Update to 1.10.0.
 2021-07-25 21:29:36 +02:00
Nicolas Goaziou
edca830c32
gnu: emacs-pyim: Update to 3.9.3. 
* gnu/packages/emacs-xyz.scm (emacs-pyim): Update to 3.9.3.
 2021-07-25 21:23:16 +02:00
Nicolas Goaziou
6fd2f881cf
gnu: emacs-ebdb: Update to 0.7. 
* gnu/packages/emacs-xyz.scm (emacs-ebdb): Update to 0.7.
 2021-07-25 21:22:38 +02:00
Tobias Geerinckx-Rice
cbeafb35e8
gnu: marble-qt: Fix source file name. 
* gnu/packages/geo.scm (marble-qt)[source]: Add a FILE-NAME field.
 2021-07-25 19:53:05 +02:00
Tobias Geerinckx-Rice
199f9e9170
gnu: marble-qt: Fix Git source URL. 
The package failed to build with:
fatal: remote error: Please use the https: protocol to connect to anongit

Fix the protocol & follow the subsequent HTTP redirection.

* gnu/packages/geo.scm (marble-qt)[source]: Fix upstream URL.
 2021-07-25 19:53:05 +02:00
Tobias Geerinckx-Rice
5079aa2afd
gnu: r-structuralvariantannotation: Update to 1.8.1. 
The previous 1.8.0 source tarball has vanished.

* gnu/packages/bioconductor.scm (r-structuralvariantannotation):
Update to 1.8.1.
[propagated-inputs]: Add r-genomicfeatures.
 2021-07-25 19:39:11 +02:00
Vinicius Monego
8854acd434
gnu: Add python-hyperopt. 
* gnu/packages/machine-learning.scm (python-hyperopt): New variable.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-07-25 17:56:58 +02:00
Vinicius Monego
aaf94ec750
gnu: Add emacs-ob-async. 
* gnu/packages/emacs-xyz.scm (emacs-ob-async): New variable.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-07-25 17:50:17 +02:00
Arun Isaac
ed9d146734
gnu: oil: Respect #:tests?. 
* gnu/packages/shells.scm (oil)[arguments]: Respect #:tests? in the custom
check phase.
 2021-07-25 20:08:27 +05:30
Felix Gruber
d1318cb4de
gnu: oil: Update to 0.9.0. 
* gnu/packages/shells.scm (oil): Update to 0.9.0.

Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
 2021-07-25 19:58:05 +05:30
Wiktor Żelazny
769326cf18
gnu: Add marble-qt. 
* gnu/packages/patches/marble-qt-add-qt-headers.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/geo.scm (marble-qt): New variable.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-07-25 13:51:45 +02:00
Sarah Morgensen
a92dfbce30
gnu: gmnisrv: Update to 0-2.32854b7. 
Update to latest commit. gmnisrv uses v3 X509 certificates now, and so
"requires fresh certificates, which could break clients with strict
trust-on-first-use policies."

gnu/packages/web.scm (gmnisrv): Update to 0-2.32854b7.

Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
 2021-07-25 15:56:02 +05:30
Morgan Smith
32b02fd99c
gnu: emacs-nov-el: Update to 0.3.4. 
* gnu/packages/emacs-xyz.scm (emacs-nov-el): Update to 0.3.4.
[arguments]<#:emacs>: Use emacs for libxml.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-07-25 12:13:01 +02:00
Raghav Gururajan
f703bef87a
gnu: weston: Enable some features. 
* gnu/packages/freedesktop.scm (weston)[inputs]: Add freerdp,
gstreamer and gst-plugins-base.
[configure-flags](backend-rdp,remoting): Remove flags.
(backend-default): New flag.
 2021-07-25 02:00:22 -04:00
Raghav Gururajan
dd3de0c475
gnu: freerdp: Propagate some inputs as per pkg-config files. 
* gnu/packages/rdesktop.scm (freerdp)[inputs]: Move libxkbcommon,
openssl and wayland to ...
[propagated-inputs]: ... here.
 2021-07-25 02:00:22 -04:00
Raghav Gururajan
e0fc091319
gnu: weston: Fix package inputs. 
The newly added inputs are referenced by the package but was missing in
the package definition. Some of these inputs might have been used
by the package indirectly via propagation from other inputs. The moved
inputs are referenced in pkg-config files.

* gnu/packages/freedesktop.scm (weston)[inputs]: Add glib, libdrm,
libpng, libx11 and libxcb. Move libxkbcommon and wayland to ...
[propagated-inputs]: ... here. Add pixman.
 2021-07-25 02:00:22 -04:00
Raghav Gururajan
17a8656bc7
gnu: weston: Update to 9.0.0 and adjust arguments+inputs accordingly. 
* gnu/packages/freedesktop.scm (weston)[version]: Update to 9.0.0.
[configure-flags](c_link_args): New flag.
(simple-dmabuf-drm): Remove flag.
[native-inputs]: Add mscgen.
[inputs]: Add pipewire.
 2021-07-25 01:59:49 -04:00
Tobias Geerinckx-Rice
45881ea747
gnu: perl-http-cookiejar: Update to 0.012. 
This fixes its build which had started to fail due to a time-bomb:

  Expires=Wed, 09 Jun 2021 10:18:14 GMT

in an examples.t test cookie.

* gnu/packages/web.scm (perl-http-cookiejar): Update to 0.012.
 2021-07-25 01:55:45 +02:00
Tobias Geerinckx-Rice
c7b51b799d
gnu: esmtp: Fix build with libesmtp >= 1.1.0. 
* gnu/packages/mail.scm (esmtp)[source]: Add patch.
* gnu/packages/patches/esmtp-add-lesmtp.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2021-07-24 23:59:07 +02:00
Pierre Neidhardt
fe0c3aee02
gnu: Add feeder. 
* gnu/packages/lisp-xyz.scm (cl-feeder, ecl-feeder, sbcl-feeder): New variables.
 2021-07-24 11:58:45 +02:00
Tobias Geerinckx-Rice
c3c003be69
gnu: java-xmlpull2: Use mirrored source and archived home page. 
* gnu/packages/xml.scm (java-xmlpull2)[source]: Download from a Gentoo
distfiles mirror.
[home-page]: Point to an archive.org snapshot.
 2021-07-23 23:29:34 +02:00
Marius Bakke
277f58040b
gnu: graphviz: Use HTTPS home page. 
* gnu/packages/graphviz.scm (graphviz)[home-page]: Use HTTPS.
 2021-07-23 17:29:34 +02:00
Marius Bakke
379bb236d4
gnu: php: Update to 7.4.21. 
* gnu/packages/php.scm (php): Update to 7.4.21.
[arguments]: Remove trailing #t's.
[native-inputs]: Remove INTLTOOL. Add GETTEXT-MINIMAL.
 2021-07-23 17:29:34 +02:00
Ludovic Courtès
c4918b54bb
gnu: tmux-themepack: Tweak description. 
* gnu/packages/tmux.scm (tmux-themepack)[description]: Tweak.
 2021-07-23 17:02:29 +02:00
Matthew James Kraai
efcd669c5a
gnu: tmux-themepack: Update to 1.1.0. 
* gnu/packages/tmux.scm (tmux-themepack): Update to 1.1.0.
[arguments]: Install only selected files.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-07-23 17:02:29 +02:00
Ludovic Courtès
7273b66945
gnu: modules: Avoid FHS file names in 'add.modules'. 
* gnu/packages/package-management.scm (modules)[arguments]: Add
'patch-add-modules' phase.
 2021-07-23 17:02:29 +02:00
Ivan Gankevich
8bcd920c71
gnu: Add modules. 
* gnu/packages/package-management.scm (modules): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-07-23 17:02:28 +02:00
Ludovic Courtès
1665bb0cec
gnu: hpcguix-web: Update to 0.1.0. 
* gnu/packages/web.scm (hpcguix-web): Update to 0.1.0.
[arguments]: In 'wrap-program' phase, change "/bin/run" to
"/bin/hpcguix-web".
[inputs]: Add BASH-MINIMAL.
* gnu/services/web.scm (hpcguix-web-shepherd-service): Run
"/bin/hpcguix-web".
 2021-07-23 17:02:28 +02:00
Andreas Enge
b48bc8953d
gnu: pari-gp: Update to 2.13.2. 
* gnu/packages/algebra.scm (pari-gp): Update to 2.13.2.
 2021-07-23 15:28:03 +02:00
Leo Prikler
4e19ad0fde
gnu: gnome-maps: Update to 3.38.5. 
* gnu/packages/geo.scm (gnome-maps): Update to 3.38.5.
 2021-07-23 12:41:01 +02:00
Guillaume Le Vaillant
785c96fbe1
gnu: Add radvd. 
* gnu/packages/admin.scm (radvd): New variable.
 2021-07-23 11:33:36 +02:00
宋文武
89ea0918a4
gnu: Add drawterm. 
* gnu/packages/plan9.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
 2021-07-22 19:52:53 +08:00
Pierre Neidhardt
d98fc80ffb
gnu: Add cl-libxml2. 
* gnu/packages/lisp-xyz.scm (cl-libxml2, ecl-cl-libxml2, sbcl-cl-libxml2): New
variables.
 2021-07-22 13:03:52 +02:00
Ricardo Wurmus
aa2686c368
gnu: r-opencpu: Update to 2.2.4. 
* gnu/packages/cran.scm (r-opencpu): Update to 2.2.4.
 2021-07-22 11:37:25 +02:00
Sharlatan Hellseher
9cfa6c3c58
gnu: Add r-opencpu 
* gnu/packages/cran.scm: (r-opencpu): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2021-07-22 11:37:25 +02:00
Sharlatan Hellseher
2b6dd1bde5
gnu: Add r-protolite 
* gnu/packages/cran.scm: (r-protolite): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2021-07-22 11:37:25 +02:00
Sharlatan Hellseher
c5baff1796
gnu: Add r-webutils 
* gnu/packages/cran.scm (r-webutils): New variable.
 2021-07-22 11:37:21 +02:00
Paul Garlick
b05a1eb5e3
gnu: Add python-dolfin-adjoint. 
* gnu/packages/simulation.scm (python-dolfin-adjoint): New variable.
 2021-07-22 10:03:53 +01:00
jgart
4c63efa5e3
gnu: Add abjad-ext-ipython. 
* gnu/packages/music.scm (abjad-ext-ipython): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-07-22 11:50:14 +03:00
jgart
ccfcbadd68
gnu: Add abjad-ext-nauert. 
* gnu/packages/music.scm (abjad-ext-nauert): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-07-22 11:48:45 +03:00
jgart
a909460099
gnu: Add abjad-ext-rmakers. 
* gnu/packages/music.scm (abjad-ext-rmakers): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-07-22 11:48:41 +03:00
Efraim Flashner
454460ca55
gnu: abjad: Remove obsolete phase. 
* gnu/packages/music.scm (abjad)[arguments]: Remove custom 'patch-source
phase.
 2021-07-22 11:14:33 +03:00
Efraim Flashner
91c42e4767
gnu: abjad: Move lilypond to inputs. 
* gnu/packages/music.scm (abjad)[native-inputs]: Move lilypond ...
[inputs]: ... to here.
 2021-07-22 11:13:57 +03:00
jgart
18f9e21b18
gnu: abjad: Improve description. 
* gnu/packages/music.scm (abjad)[description]: Improve abjad's
description.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-07-22 11:06:58 +03:00
jgart
dd7c2d2b1d
gnu: abjad: Move python-ply to propagated-inputs. 
* gnu/packages/music.scm (abjad)[ntaive-inputs]: Move python-ply ...
[propagated-inputs]: ... to here.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-07-22 11:05:41 +03:00
jgart
5535d5435e
gnu: python-abjad: Rename to abjad. 
* gnu/packages/music.scm (abjad): Rename from python-abjad.
(python-abjad): Keep as deprecated package.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-07-22 11:04:10 +03:00
Efraim Flashner
fd8aea010f
gnu: python-pysam: Make the check phase honor the tests? argument. 
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Adjust
custom 'check phase to skip tests when #:tests is #f.
 2021-07-22 10:58:22 +03:00
Efraim Flashner
877792a6a7
gnu: python-pysam: Update to 0.16.0.1. 
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.16.0.1.
[arguments]: Update custom 'check phase.
[propagated-inputs]: Replace htslib-1.9 with 1.10.
[native-inputs]: Add python-pytest. Replace samtools-1.9 with 1.10,
bcftools-1.9 with 1.10.
(bcftools-1.9): Replace with bcftools-1.10.
[native-inputs]: Replace htslib-1.9 with 1.10.
(samtools-1.9): Replace with samtools-1.10.
[inputs]: Replace htslib-1.9 with 1.10.
 2021-07-22 10:57:41 +03:00
Efraim Flashner
cc4906d13b
gnu: Add htslib-1.10. 
* gnu/packages/bioinformatics.scm (htslib-1.10): New variable.
 2021-07-22 10:50:58 +03:00
Efraim Flashner
309b38bed6
gnu: python-biopython: Update to 1.73. 
* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73.
 2021-07-22 09:14:12 +03:00
Eric Bavier
55db762b31
gnu: onionshare: Update to 2.3.2. 
* gnu/packages/tor.scm (onionshare-cli, onionshare): Update to 2.3.2.
(onionshare)[inputs]: Add python-colorama.
[arguments]: Insert "import pytest" for later "pytest.mark.skip".
 2021-07-21 23:08:14 -05:00
Joseph LaFreniere
e9d47ee718
gnu: Add emacs-seeing-is-believing. 
* gnu/packages/emacs-xyz.scm (emacs-seeing-is-believing): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-07-22 00:02:33 +02:00
Ludovic Courtès
de1ae96184
gnu: guile-git: Update to 0.5.2. 
Fixes <https://issues.guix.gnu.org/48855>.
Reported by Maxim Cournoyer <maxim.cournoyer@gmail.com>.

* gnu/packages/guile.scm (guile-git): Update to 0.5.2.
 2021-07-22 00:02:30 +02:00
Giacomo Leidi
1f07d4436c
gnu: extempore: Update to 0.8.9. 
* gnu/packages/music.scm (extempore): Update to 0.8.6.
[source]: Portaudio is no more in-tree.
[arguments]: Load external libraries through patched CMakeLists.txt.
[phases]: Symlink assets.
* gnu/packages/patches/extempore-unbundle-external-dependencies.patch:
Update accordingly.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2021-07-21 23:00:51 +02:00
Lars-Dominik Braun
403a689625
gnu: Add python-sparqlkernel. 
* gnu/packages/jupyter.scm (python-sparqlkernel): New variable.
 2021-07-21 13:36:09 +02:00
Lars-Dominik Braun
281808170a
gnu: Add python-sparqlwrapper. 
* gnu/packages/rdf.scm (python-sparqlwrapper): New variable.
 2021-07-21 13:36:09 +02:00
Lars-Dominik Braun
d57c34d26b
gnu: Add python-bash-kernel. 
* gnu/packages/jupyter.scm (python-bash-kernel): New variable.
 2021-07-21 13:36:08 +02:00
Lars-Dominik Braun
73830b5da3
gnu: Add r-battenberg. 
* gnu/packages/bioinformatics.scm (r-battenberg): New variable.
 2021-07-21 13:36:08 +02:00
Lars-Dominik Braun
ed636babfa
gnu: Add r-ascat. 
* gnu/packages/bioinformatics.scm (r-ascat): New variable.
 2021-07-21 13:36:08 +02:00
Lars-Dominik Braun
690df95d1a
gnu: Add nanosv. 
* gnu/packages/bioinformatics.scm (nanosv): New variable.
 2021-07-21 13:36:08 +02:00
Lars-Dominik Braun
2b665b8a49
gnu: Add python-pyvcf. 
* gnu/packages/bioinformatics.scm (python-pyvcf): New variable.
 2021-07-21 13:36:08 +02:00
Lars-Dominik Braun
086c6800cf
gnu: checkm: Rename and update to 1.1.3. 
Renamed from python2-checkm-genome to checkm to better reflect its
status as standalone-application and support for Python 3.

* gnu/packages/bioinformatics.scm (python2-checkm-genome): Redirect to…
(checkm): …here and update to 1.1.3.
[propagated-inputs]: Move to inputs.
[inputs]: Use Python 3 dependencies.
[home-page]: Point to real home-page.
 2021-07-21 13:36:08 +02:00
Lars-Dominik Braun
18a02fe7ca
gnu: Add tombo. 
* gnu/packages/bioinformatics.scm (tombo): New variable.
 2021-07-21 13:36:07 +02:00
Lars-Dominik Braun
117988b7ca
gnu: Add r-rmisc. 
* gnu/packages/cran.scm (r-rmisc): New variable.
 2021-07-21 13:36:07 +02:00