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Author SHA1 Message Date
Ricardo Wurmus
4d42fbd371
gnu: sleef: Adjust inputs. 
* gnu/packages/maths.scm (sleef)[inputs]: Replace openssl with openssl-1.1;
remove mpfr.
[arguments]: Remove custom phase 'make-git-checkout-writable; use G-expression
for configure-flags.
 2023-04-27 21:07:15 +02:00
Ricardo Wurmus
ecb4f4d015
gnu: gloo: Use OpenSSL 1.1. 
* gnu/packages/machine-learning.scm (gloo)[inputs]: Use openssl-1.1 instead of
openssl.
 2023-04-27 20:58:26 +02:00
Ricardo Wurmus
688d99282b
gnu: yubico-piv-tool: Update to 2.3.1. 
* gnu/packages/security-token.scm (yubico-piv-tool): Update to 2.3.1.
[source]: Fetch from Github repository.
[build-system]: Use cmake-build-system.
 2023-04-27 20:55:25 +02:00
Pierre Neidhardt
d59b4764f3
gnu: Add cl-prompter. 
* gnu/packages/lisp-xyz.scm (cl-prompter, ecl-prompter, sbcl-prompter): New variables.
 2023-04-27 17:50:38 +02:00
Ricardo Wurmus
297805b1f8
gnu: python-docutils-0.15: Add missing input. 
* gnu/packages/python-xyz.scm (python-docutils-0.15)[native-inputs]: Add
python-setuptools-57.
 2023-04-27 16:32:47 +02:00
Ricardo Wurmus
5775bbdd4b
gnu: gdcm: Disable dependent tests. 
* gnu/packages/bioinformatics.scm (gdcm)[arguments]: Disable tests that depend
on the output of a disabled test.
 2023-04-27 16:23:22 +02:00
Ricardo Wurmus
fa685c87ea
gnu: freebayes: Update to 1.3.7. 
* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.7.
[arguments]: Do not use "grep -P" in tests; drop trailing #T.
 2023-04-27 11:40:09 +02:00
Ricardo Wurmus
133957f7bb
gnu: vcflib: Use libwfa2.pc. 
* gnu/packages/bioinformatics.scm (vcflib)[source]: Use pkg-config to look for
libwfa2.
[inputs]: Move wfa2-lib from here...
[propagated-inputs]: ...to here.
[arguments]: Drop WFA_LINK_LIBRARIES option; fix typo in build phase name;
patch IntervalTree.h includes; add libwfa2 to pkg-config file.
 2023-04-27 11:38:16 +02:00
Ricardo Wurmus
479f2558fe
gnu: wfa2-lib: Install pkg-config file. 
* gnu/packages/bioinformatics.scm (wfa2-lib)[arguments]: Install libwfa2.pc.
 2023-04-27 11:37:36 +02:00
Ricardo Wurmus
9d82c475a3
gnu: express: Adjust bamtools location. 
* gnu/packages/bioinformatics.scm (express)[arguments]: Modify location of
libbamtools.so in 'use-shared-boost-libs-and-set-bamtools-paths; drop trailing
 #T.
 2023-04-27 09:25:26 +02:00
Ricardo Wurmus
f196b3b7a5
gnu: python-tinycss2: Simplify. 
* gnu/packages/python-web.scm (python-tinycss2)[build-system]: Use
pyproject-build-system.
[arguments]: Remove.
 2023-04-27 09:11:05 +02:00
Ricardo Wurmus
0dc7f773fd
gnu: python-openapi-core: Add missing input. 
* gnu/packages/python-web.scm (python-openapi-core)[build-system]: Use
pyproject-build-system.
[arguments]: Do not override 'check phase; specify #:test-flags.
[native-inputs]: Add python-mock.
 2023-04-27 08:43:29 +02:00
Ricardo Wurmus
d8fe2e4735
gnu: libwebsockets: Update to 4.3.2. 
* gnu/packages/web.scm (libwebsockets): Update to 4.3.2.
[arguments]: Remove.
[source]: Use GIT-FILE-NAME.
 2023-04-27 08:06:13 +02:00
Ricardo Wurmus
db19e30673
gnu: python-google-cloud-storage: Add missing input. 
* gnu/packages/python-web.scm (python-google-cloud-storage)[native-inputs]:
Add python-mock.
 2023-04-27 06:53:37 +02:00
Ricardo Wurmus
40451d0f2d
gnu: python-google-resumable-media: Add missing input. 
* gnu/packages/python-web.scm (python-google-resumable-media)[native-inputs]:
Add python-mock.
 2023-04-27 06:53:12 +02:00
Ricardo Wurmus
cec543e70f
gnu: python-aws-xray-sdk: Update to 2.12.0. 
* gnu/packages/python-web.scm (python-aws-xray-sdk): Update to 2.12.0.
[build-system]: Use pyproject-build-system.
[arguments]: Specify #:test-flags; do not override 'check phase; add
'pre-check phase.
[native-inputs]: Add python-httpx, python-mock, python-pytest-asyncio, and
python-pytest-benchmark.
 2023-04-27 06:48:27 +02:00
Ricardo Wurmus
e5619147d4
gnu: python-httpx: Update to 0.24.0. 
* gnu/packages/python-web.scm (python-httpx): Update to 0.24.0.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom check phase in favor of specifying #:test-flags.
[native-inputs]: Add python-hatchling and python-hatch-fancy-pypi-readme.
(python-httpx-bootstrap)[native-inputs]: Add python-hatchling and
python-hatch-fancy-pypi-readme.
 2023-04-27 06:37:23 +02:00
Ricardo Wurmus
3b19fc1801
gnu: python-httpcore: Update to 0.17.0. 
* gnu/packages/python-web.scm (python-httpcore): Update to 0.17.0.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom check phase; specify #:test-flags; disable broken
tests.
 2023-04-27 06:36:19 +02:00
Ricardo Wurmus
f95498c92e
gnu: python-h11: Update to 0.14.0. 
* gnu/packages/python-web.scm (python-h11): Update to 0.14.0.
[build-system]: Use pyproject-build-system.
[arguments]: Remove.
 2023-04-27 06:35:38 +02:00
Ricardo Wurmus
e1ca411852
gnu: python-wsproto: Update to 1.2.0. 
* gnu/packages/python-web.scm (python-wsproto): Update to 1.2.0.
[build-system]: Use pyproject-build-system.
[arguments]: Remove.
 2023-04-27 06:34:57 +02:00
Ricardo Wurmus
bb385f2472
gnu: python-dendropy: Fix build. 
* gnu/packages/bioinformatics.scm (python-dendropy)[native-inputs]: Add
python-pytest.
[arguments]: Add phase 'python-compatibility; remove 'skip-broken-tests; add
 #:test-flags; do not delete test files.
[build-system]: Use pyproject-build-system.
 2023-04-26 22:53:26 +02:00
Ricardo Wurmus
4ea332cd50
gnu: python-watchgod: Update to 0.8.1. 
* gnu/packages/python-xyz.scm (python-watchgod): Update to 0.8.1.
[build-system]: Use pyproject-build-system.
[arguments]: Specify #:test-flags instead of overwriting 'check phase.
[native-inputs]: Add python-anyio.
 2023-04-26 22:52:05 +02:00
Ricardo Wurmus
18786ae502
gnu: python-fastjsonschema: Use pyproject-build-system. 
* gnu/packages/python-xyz.scm (python-fastjsonschema): Reindent.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom check phase; update comment on why tests are
disabled.
 2023-04-26 22:12:32 +02:00
Ricardo Wurmus
182fbbb009
gnu: python-rapidjson: Update to 1.10. 
* gnu/packages/python-web.scm (python-rapidjson): Update to 1.10.
[source]: Simplify snippet.
[arguments]: Run tests conditionally; do not delete test files.
 2023-04-26 22:11:07 +02:00
Ricardo Wurmus
00cf71df80
gnu: rapidjson: Update to 1.1.0-1.949c771. 
* gnu/packages/patches/rapidjson-gcc-compat.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
* gnu/packages/web.scm (rapidjson): Update to 1.1.0-1.949c771.
[source]: Remove obsolete patch.
 2023-04-26 22:09:06 +02:00
Ricardo Wurmus
abda97b645
gnu: python-multiprocess: Update to 0.70.14. 
* gnu/packages/python-xyz.scm (python-multiprocess): Update to 0.70.14.
[build-system]: Use pyproject-build-system.
[arguments]: Adjust directory containing tests; disable two more tests;
replace check phase instead of deleting and adding it; run tests
conditionally.
 2023-04-26 21:33:02 +02:00
Ricardo Wurmus
95fdd862d0
gnu: python-dill: Update to 0.3.6. 
* gnu/packages/python-xyz.scm (python-dill): Update to 0.3.6.
[build-system]: Use pyproject-build-system.
[arguments]: Run tests conditionally; drop trailing #T from build phase.
 2023-04-26 21:33:02 +02:00
Ricardo Wurmus
d12ad4105a
gnu: python-jupyterlab-widgets: Update to 1.1.4. 
* gnu/packages/jupyter.scm (python-jupyterlab-widgets): Update to 1.1.4.
[build-system]: Use pyproject-build-system.
 2023-04-26 21:33:02 +02:00
Ricardo Wurmus
faa4485b52
gnu: python-fire: Add missing input. 
* gnu/packages/python-xyz.scm (python-fire)[native-inputs]: Add python-mock.
 2023-04-26 21:33:02 +02:00
Liliana Marie Prikler
d38bdca344
gnu: gitg: Fix build. 
* gnu/packages/patches/gitg-fix-positional-argument.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it here.
* gnu/packages/gnome.scm (gitg)[source]<patches>: Use it here.
 2023-04-26 20:52:33 +02:00
Liliana Marie Prikler
d7e489d6e0
gnu: gnome-2048: Fix build. 
* gnu/packages/patches/gnome-2048-fix-positional-argument.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it here.
* gnu/packages/games.scm (gnome-2048)[source]<patches>: Use it here.
 2023-04-26 20:52:32 +02:00
Ricardo Wurmus
e86851ccb3
gnu: python-umap-learn: Patch for sklearn/numpy compatibility. 
* gnu/packages/machine-learning.scm (python-umap-learn)[arguments]: Add phase
'numpy-compatibility.
 2023-04-26 18:34:46 +02:00
Ricardo Wurmus
5bfce83dc4
gnu: python-tables: Build cython files from source. 
* gnu/packages/python-xyz.scm (python-tables)[source]: Remove generated C
files.
[arguments]: Remove trailing #T from build phases; use G-expression; override
library directories.
[inputs]: Add c-blosc and lzo.
 2023-04-26 17:01:08 +02:00
Ricardo Wurmus
2d883cbd6d
gnu: python-bokeh: Add missing input. 
* gnu/packages/python-xyz.scm (python-bokeh)[native-inputs]: Add python-mock.
 2023-04-26 16:39:10 +02:00
Ricardo Wurmus
41ba9df6ba
gnu: python-tornado: Run a lot more tests and fix collections. 
* gnu/packages/python-web.scm (python-tornado)[arguments]: Do run tests; add
phase 'fix-collections.
 2023-04-26 16:11:11 +02:00
Andreas Enge
81ec8eba91
gnu: nikola: Add input. 
* gnu/packages/python-xyz.scm (nikola)[propagated-inputs]: Add python-toml.
 2023-04-26 15:56:30 +02:00
Sharlatan Hellseher
1f7d1125a3
gnu: cl-mock: Update to 1.1.0-0.01762fd. 
* gnu/packages/lisp-xyz.scm (sbcl-cl-mock): Update to 1.1.0-0.01762fd.
  [arguments]: Build cl-mock and cl-mock-basic systems.
  [inputs]: Add sbcl-bordeaux-threads.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2023-04-26 15:08:15 +02:00
Sharlatan Hellseher
8d217f1e22
gnu: cl-fast-ecs: Update to 0.2.2. 
* gnu/packages/lisp-xyz.scm (sbcl-cl-fast-ecs): Update to 0.2.2.
  [native-inputs]: Add sbcl-chlorophyll, sbcl-cl-mock.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2023-04-26 15:08:15 +02:00
Sharlatan Hellseher
870f2d40e0
gnu: Add cl-chlorophyll. 
* gnu/packages/lisp-xyz.scm (cl-chlorophyll, ecl-chlorophyll,
  sbcl-chlorophyll): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2023-04-26 15:08:15 +02:00
Artyom Bologov
e129321f13
gnu: cl-nclasses: Update to 0.4.0. 
gnu/packages/lisp-xyz.scm (sbcl-nclasses): Update to 0.4.0.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2023-04-26 15:08:15 +02:00
Guillaume Le Vaillant
62fed3b874
gnu: flwrap: Update to 1.3.6. 
* gnu/packages/radio.scm (flwrap): Update to 1.3.6.
 2023-04-26 15:08:15 +02:00
Guillaume Le Vaillant
bfbe2a518d
gnu: pdf2djvu: Update to 0.9.19. 
* gnu/packages/djvu.scm (pdf2djvu): Update to 0.9.19.
 2023-04-26 15:08:15 +02:00
jgart
f858704e7c
gnu: xonsh: Add missing input. 
Xonsh vim emulation mode/environment variable does not work without this.

* gnu/packages/shell.scm (xonsh)[inputs]: Add PYTHON-PROMPT-TOOLKIT.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2023-04-26 14:56:55 +02:00
kiasoc5
9d12ce6fa4
gnu: plocate: Update to 1.1.18. 
* gnu/packages/search.scm (plocate): Update to 1.1.18.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2023-04-26 14:49:08 +02:00
Nicolas Goaziou
2dc87d8dcf
gnu: emacs-vertico: Update to 1.3. 
* gnu/packages/emacs-xyz.scm (emacs-vertico): Update to 1.3.
 2023-04-26 14:49:08 +02:00
Christine Lemmer-Webber
3856ca96fc
gnu: Add emacs-lojban. 
* gnu/packages/emacs-xyz.scm (emacs-lojban): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2023-04-26 14:49:07 +02:00
zimoun
c3509c2148
gnu: valgrind: Update to 3.20.0. 
* gnu/packages/valgrind.scm (valgrind): Update to 3.20.0. Remove patch.
[arguments]<phases>: Remove trailing #t.
* gnu/packages/patches/valgrind-enable-arm.patch: Delete file.
* gnu/packages/valgrind.scm (dist_patch_DATA): Unregister patch.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2023-04-26 14:34:23 +02:00
zimoun
50dcd1acd7
gnu: lz4: Remove valgrind from native-inputs. 
* gnu/compression.scm (lz4)[native-inputs]: Remove valgrind.
[arguments]<phases>: Remove trailing #t.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2023-04-26 14:34:08 +02:00
Ricardo Wurmus
399e1b8e01
gnu: python-ipykernel: Fix build. 
* gnu/packages/python-xyz.scm (python-ipykernel)[build-system]: Use
pyproject-build-system.
[arguments]: Use pyproject-build-system modules; add build phase
'hide-zmq-deprecation-warnings.
 2023-04-26 13:33:30 +02:00
Ricardo Wurmus
4ef9fbcc35
gnu: python-jupyter-client: Disable one test. 
* gnu/packages/python-xyz.scm (python-jupyter-client)[arguments]: Begrudgingly
disable one failing test, because there is no information on why it fails.
 2023-04-26 11:44:45 +02:00
Ricardo Wurmus
cc79caccee
gnu: python-jupyter-client-bootstrap: Hide zmq deprecation warning. 
* gnu/packages/python-xyz.scm (python-jupyter-client-bootstrap)[arguments]:
Add phase 'hide-zmq-deprecation-warning.
 2023-04-26 11:44:45 +02:00
Ricardo Wurmus
358428c1ec
gnu: python-jupyter-client-bootstrap: Use pyproject-build-system. 
* gnu/packages/python-xyz.scm (python-jupyter-client-bootstrap)[build-system]:
Use pyproject-build-system.
 2023-04-26 11:44:45 +02:00
Ricardo Wurmus
5409ae48af
gnu: python-distributed: Fix build. 
* gnu/packages/python-science.scm (python-distributed)[build-system]: Use
pyproject-build-system.
[arguments]: Hide deprecation warnings from tornado, because they break almost
all tests; disable three more tests.
 2023-04-26 11:17:41 +02:00
Efraim Flashner
2bf96f2d9e
gnu: cppcheck: Update to 2.10.3. 
* gnu/packages/check.scm (cppcheck): Update to 2.10.3.
[home-page]: Update to new home-page.
 2023-04-26 10:51:52 +03:00
Efraim Flashner
8720e22fd0
gnu: cppcheck: Skip failing test. 
* gnu/packages/patches/check.scm (cppcheck)[source]: Add patch.
* gnu/packages/patches/cppcheck-disable-char-signedness-test.patch: New
file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2023-04-26 10:51:44 +03:00
Andreas Enge
ff4e463ddc
gnu: graphviz: Remove version 2.38. 
This is a follow-up to commit 370cb92eaa .

* gnu/packages/graphviz.scm: Drop imported modules.
(graphviz-2.38): Remove package.
 2023-04-26 09:40:16 +02:00
Ludovic Courtès
8093c6ba21
gnu: lcov: Update to 1.16. 
* gnu/packages/code.scm (lcov): Update to 1.16.
 2023-04-25 23:43:05 +02:00
Ludovic Courtès
9fcd51280f
gnu: perl-io-compress: Update to 2.204. 
* gnu/packages/perl-compression.scm (perl-io-compress): Update to 2.204.
 2023-04-25 23:43:05 +02:00
Ludovic Courtès
70acf8b23a
gnu: perl-compress-raw-bzip2: Update to 2.204. 
* gnu/packages/perl-compression.scm (perl-compress-raw-bzip2): Update to
2.204.
 2023-04-25 23:43:05 +02:00
Ludovic Courtès
6ea4228442
gnu: perl-compress-raw-zlib: Update to 2.204. 
* gnu/packages/perl-compression.scm (perl-compress-raw-zlib): Update to
2.204.
[arguments]: Remove.
 2023-04-25 23:43:05 +02:00
Efraim Flashner
e287a0e402
gnu: gnutls: Don't embed a phase inside another phase. 
* gnu/packages/tls.scm (gnutls)[arguments]: Adjust powerpc-linux phase
'increase-test-timeout to not be embedded inside another phase.
 2023-04-25 23:32:17 +03:00
Efraim Flashner
ccf64b6a8b
gnu: mpdevil: Add missing input. 
* gnu/packages/mpd.scm (mpdevil)[native-inputs]: Add gettext-minimal.
 2023-04-25 23:08:45 +03:00
Efraim Flashner
aeda325cf1
gnu: presage: Build with c++-14. 
* gnu/packages/fcitx.scm (presage)[arguments]: Adjust configure-flags to
use c++-14 cor CFLAGS and CXXFLAGS.
 2023-04-25 23:01:56 +03:00
Efraim Flashner
97323e5262
gnu: libpst: Fix python detection. 
* gnu/packages/mail.scm (libpst)[arguments]: Add a phase to detect newer
versions of python3.
[native-inputs]: Add autoconf, automake, gettext-minimal, libool.
 2023-04-25 22:52:29 +03:00
Ricardo Wurmus
72b1c9713b
gnu: perl-data-dumper: Update to 2.183. 
* gnu/packages/perl.scm (perl-data-dumper): Update to 2.183.
 2023-04-25 21:18:36 +02:00
Ricardo Wurmus
4598928a90
gnu: cwltool: Use pyproject-build-system. 
"setup.py install is deprecated. Use build and pip and other standards-based
tools."  It then falls back to attempting to install packages via pip.

* gnu/packages/bioinformatics.scm (cwltool)[build-system]: Use
pyproject-build-system.
 2023-04-25 21:18:36 +02:00
Ricardo Wurmus
92a903499b
gnu: python-schema-salad: Use pyproject-build-system. 
The python-build-system fails with "setuptools.installer is
deprecated. Requirements should be satisfied by a PEP 517 installer."  This,
in turn, causes all Python packages to be ignored and "pip install" to be
invoked for them.

* gnu/packages/bioinformatics.scm (python-schema-salad)[build-system]: Use
pyproject-build-system.
 2023-04-25 21:18:35 +02:00
Liliana Marie Prikler
2ec69787aa
gnu: gfeeds: Add missing gettext-minimal. 
* gnu/packages/syndication.scm (gfeeds)[inputs]: Add gettext-minimal.
 2023-04-25 21:09:13 +02:00
Liliana Marie Prikler
30a252760f
gnu: syndication-domination: Update to 1.0-1-7592032. 
* gnu/packages/syndication.scm (syndication-domination): Update to
1.0-1-7592032.
 2023-04-25 21:09:13 +02:00
Liliana Marie Prikler
ff777165cb
gnu: evolution: Update to 3.46.4. 
* gnu/packages/gnome.scm (evolution): Update to 3.46.4.
 2023-04-25 21:09:13 +02:00
Liliana Marie Prikler
916df2b9eb
gnu: evolution-data-server: Update to 3.46.4. 
* gnu/packages/gnome.scm (evolution-data-server): Update to 3.46.4.
 2023-04-25 21:09:12 +02:00
Ricardo Wurmus
5a1b246736
gnu: adapterremoval: Update to 2.3.3. 
* gnu/packages/bioinformatics.scm (adapterremoval): Update to 2.3.3.
[arguments]: Simplify.
[inputs]: Reformat.
 2023-04-25 19:46:29 +02:00
Efraim Flashner
d67b8788b3
gnu: ocaml-lwt: Add ocaml4.07 variant. 
* gnu/packages/ocaml.scm (ocaml-lwt)[properties]: New field.
(ocaml4.07-lwt): New variable.
 2023-04-25 20:42:22 +03:00
Efraim Flashner
52f6ccef82
gnu: perl-crypt-openssl-rsa: Update to 0.33. 
* gnu/packages/tls.scm (perl-crypt-openssl-rsa): Update to 0.33.
 2023-04-25 20:42:22 +03:00
Ricardo Wurmus
fc80efe1a0
gnu: bedtools-2.18: Fix build. 
* gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Fix operators in
'compatibility phase.
 2023-04-25 19:41:05 +02:00
Ricardo Wurmus
f2e90d6f43
gnu: hisat: Build with GCC 10. 
* gnu/packages/bioinformatics.scm (hisat)[native-inputs]: Add gcc-10.
 2023-04-25 19:30:43 +02:00
Ricardo Wurmus
0a4fa99b39
gnu: kallisto: Update to 0.48.0. 
* gnu/packages/bioinformatics.scm (kallisto): Update to 0.48.0.
[arguments]: Remove trailing #T from build phase.
 2023-04-25 19:28:42 +02:00
Ricardo Wurmus
7ae5325bf1
gnu: bpp-core: Build with GCC 10. 
* gnu/packages/bioinformatics.scm (bpp-core)[native-inputs]: Add gcc-10.
 2023-04-25 19:12:57 +02:00
Ricardo Wurmus
2c09cc19e6
gnu: vcflib: Update to 1.0.9. 
* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.9.
[source]: Update snippet.
[inputs]: Add curl, pybind11, and wfa2-lib.
[arguments]: Adjust and reformat.
 2023-04-25 19:10:19 +02:00
Ricardo Wurmus
4ad51f5914
gnu: tabixpp: Update to 1.1.2. 
* gnu/packages/bioinformatics.scm (tabixpp): Update to 1.1.2.
[source]: Simplify snippet.
[inputs]: Add curl.
[arguments]: Simplify and reformat.
 2023-04-25 19:10:19 +02:00
Ricardo Wurmus
8664c6230e
gnu: Add wfa2-lib. 
* gnu/packages/bioinformatics.scm (wfa2-lib): New variable.
 2023-04-25 19:10:18 +02:00
Josselin Poiret
8c5ba69d6e
gnu: biber: Fix build with new Perl. 
* gnu/packages/patches/biber-adapt-perl-5.36.patch: Backport patch from
upstream's 760e6e4ec08a3097f7e6136331541a7b8c1c9df7.
* gnu/packages/tex.scm (biber): Use it.
* gnu/local.mk (dist_patch_DATA): Register it.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2023-04-25 18:42:22 +02:00
Vivien Kraus
74038cf66e
gnu: gcc: Do not build gcov on MinGW. 
* gnu/packages/gcc.scm (gcc-configure-flags-for-triplet): Disable gcov when
targetting mingw.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2023-04-25 17:20:19 +02:00
Nicolas Graves
7f0fbd0463
gnu: nerd-dictation: Add package variants. 
* gnu/packages/machine-learning.scm (nerd-dictation)[inputs]: Remove.
(nerd-dictation-gexp): New procedure.
(nerd-dictation/xdotool, nerd-dictation/sox-xdotool)
(nerd-dictation/sox-ydotool, nerd-dictation/sox-wtype): New variables

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-04-25 17:19:21 +02:00
Bruno Victal
9be1ee6a49
services: tor: Deprecate 'tor-hidden-service' procedure. 
Due to (now renamed) 'hidden-service' record type not being exported, the only
way Onion services (formely hidden services) could have worked is through the
now deprecated 'tor-hidden-service' procedure.

This commit updates the Tor service documentation, corrects some inconsistently
named accessors in <tor-configuration> record-type, renames and refactors
tor-hidden-service-configuration to tor-onion-service-configuration using
define-configuration and also exports it, allowing Onion services to be
configured directly within a <tor-configuration> record.
Lastly, it also deprecates the 'tor-hidden-service' procedure.

* doc/guix.texi (Networking Services): Substitute mentions of “Hidden services”
with “Onion Services”. Add a Tor Onion service configuration example.
Document <tor-onion-service-configuration>. Remove mention of
'tor-hidden-service' procedure.
* gnu/services/networking.scm: Export tor-configuration-tor,
tor-configuration-config-file, tor-configuration-hidden-services,
tor-configuration-socks-socket-type, tor-configuration-control-socket-path,
tor-onion-service-configuration, tor-onion-service-configuration?,
tor-onion-service-configuration-name, tor-onion-service-configuration-mapping.
(<tor-configuration>)[control-socket?]: Rename accessor.
(<hidden-service>): Replace with …
(<tor-onion-service-configuration>): … this.
(tor-configuration->torrc): Update record-type name.
(tor-activation): Ditto.
(tor-hidden-service-type): Remove variable.
(tor-hidden-service): Deprecate procedure.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-04-25 17:19:21 +02:00
Lars-Dominik Braun
c354a345b9
gnu: ghc-8.10: Avoid testsuite timeouts on i686. 
* gnu/packages/haskell.scm (ghc-8.10)[arguments]: Add new phase
'skip-failing-tests-i686-cuirass.
 2023-04-25 16:54:57 +02:00
Ricardo Wurmus
3a37e3ecd8
gnu: lofreq: Set file timestamps to 1980s. 
This keeps Python from complaining: "ZIP does not support timestamps before
1980".

* gnu/packages/bioinformatics.scm (lofreq)[arguments]: Add build phase
'set-source-file-times-to-1980.
 2023-04-25 16:17:49 +02:00
Ricardo Wurmus
0ad4a4d155
gnu: lofreq: Drop input labels. 
* gnu/packages/bioinformatics.scm (lofreq)[inputs]: Drop package labels.
 2023-04-25 16:17:49 +02:00
Ricardo Wurmus
1fca85cd88
gnu: ivar: Update to 1.4.2. 
* gnu/packages/bioinformatics.scm (ivar): Update to 1.4.2.
[arguments]: Remove -Werror flag.
 2023-04-25 16:17:49 +02:00
Ricardo Wurmus
f69f346289
gnu: propeller-gcc-4: Use MODIFY-INPUTS. 
* gnu/packages/embedded.scm (propeller-gcc-4)[native-inputs]: Use
MODIFY-INPUTS and drop package label.
 2023-04-25 16:17:49 +02:00
Ricardo Wurmus
b9162199b3
gnu: propeller-gcc-4: Use G-expression. 
* gnu/packages/embedded.scm (propeller-gcc-4)[arguments]: Use G-expression
because the parent GCC package uses them too.
 2023-04-25 16:17:49 +02:00
Andreas Enge
b380fbca88
gnu: trurl: Correct inputs. 
* gnu/packages/curl.scm (trurl): Replace non-existant input curl-7.84.0 by
curl, which is version 7.85.0.
 2023-04-25 15:21:05 +02:00
Andreas Enge
c919bfefd9
Merge remote-tracking branch 'origin/master' into core-updates 2023-04-25 15:19:29 +02:00
Lars-Dominik Braun
472706ae2f
gnu: python-asyncssh: Update to 2.13.1. 
Includes fix for python-cryptography>=39 disallowing SHA-1 signatures,
which caused the testsuite to fail.

* gnu/packages/ssh.scm (python-asyncssh): Update to 2.13.1.
 2023-04-25 14:27:14 +02:00
Efraim Flashner
0daa747de2
gnu: alacritty: Patch reference to xdg-open. 
* gnu/packages/terminals.scm (alacritty)[arguments]: Add a phase to add
an absolute reference to xdg-open.
[inputs]: Add xdg-utils.
 2023-04-25 14:06:14 +03:00
Nicolas Goaziou
95787ffaa2
gnu: emacs-eshell-syntax-highlighting: Update to 0.5. 
* gnu/packages/emacs-xyz.scm (emacs-eshell-syntax-highlighting): Update to 0.5.
 2023-04-25 11:47:52 +02:00
Nicolas Goaziou
c9c4fea7c5
gnu: nethack: Update to 3.6.7. 
* gnu/packages/games.scm (nethack): Update to 3.6.7.
 2023-04-25 11:47:51 +02:00
Sharlatan Hellseher
11f078a1fb
gnu: Add trurl. 
* gnu/packages/curl.scm (trurl): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2023-04-25 11:47:51 +02:00
Nicolas Goaziou
26cdc7be84
gnu: emacs-auctex: Update to 13.2.0. 
* gnu/packages/emacs-xyz.scm (emacs-auctex): Update to 13.2.0.
 2023-04-25 11:47:51 +02:00
Joseph LaFreniere
af3daff5ea
gnu: Add emacs-xonsh-mode. 
* gnu/packages/emacs-xyz.scm (emacs-xonsh-mode): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2023-04-25 11:47:51 +02:00