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88844 commits

Author SHA1 Message Date
Ricardo Wurmus 0e09065460
gnu: bedtools: Remove reference to %outputs.
* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use a gexp instead of
referencing %outputs.
2021-12-03 23:36:18 +01:00
Ricardo Wurmus a5663a7c8a
gnu: qtltools: Replace references to %build-inputs.
* gnu/packages/bioinformatics.scm (qtltools)[arguments]: Use a gexp instead of
referencing %build-inputs.
2021-12-03 23:26:48 +01:00
Ricardo Wurmus ce9bfcddb5
gnu: imp: Update to 2.15.0.
* gnu/packages/bioinformatics.scm (imp): Update to 2.15.0.
[arguments]: Disable one more test.
2021-12-03 22:29:52 +01:00
Ricardo Wurmus dcf857e486
gnu: Add r-fpeek.
* gnu/packages/cran.scm (r-fpeek): New variable.
2021-12-03 22:29:40 +01:00
Liliana Marie Prikler 15404ff19b
gnu: emacs: Load package descriptors from packages referenced by subdirs.el
* gnu/packages/aux-files/emacs/guix-emacs.el
(guix-emacs--non-core-load-path): New procedure.
(guix-emacs-autoload-packages): Use it here.
(guix-emacs-load-package-descriptors): New procedure.
* gnu/packages/emacs.scm (emacs)[install-site-start]: Install advice to run
‘guix-emacs-load-package-descriptors’.
2021-12-03 21:39:50 +01:00
Liliana Marie Prikler 98cec36957
build-system: emacs: Keep -pkg.el files.
Partly fixes <https://bugs.gnu.org/48331> -- package descriptions can now be
found in the install directory.

* guix/build/emacs-build-system.scm (%default-exclude): Remove "-pkg\\.el$".
2021-12-03 21:39:50 +01:00
Liliana Marie Prikler 4baeb72717
gnu: emacs: Make DocView PDF work out of the box.
* gnu/packages/emacs.scm (emacs)[patch-program-file-names]: Add patches for
the programs “gs”, “dvipdf”, “ps2pdf” and “pdftotext”.
[inputs]: Add ghostscript and poppler.
2021-12-03 21:39:49 +01:00
Liliana Marie Prikler f725279cdd
gnu: emacs: Find real GVFS processes.
* gnu/packages/emacs.scm (emacs)[#:phases]<patch-program-file-names>: Expand
calls to “tramp-compat-process-running-p” so that Guix wrappers are also
matched.
2021-12-03 21:39:49 +01:00
phodina 269baba919
gnu: Add valeronoi.
* gnu/packages/engineering.scm (valeronoi): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-12-03 21:38:30 +01:00
jgart 19528e39bb
gnu: st: Install terminfo files.
* gnu/packages/suckless.scm (st)[native-inputs]: Add ncurses.
[make-flags](TERMINFO): New flag.
[phases](inhibit-terminfo-install): Remove phase.

Signed-off-by: Raghav Gururajan <rg@raghavgururajan.name>
2021-12-03 15:27:41 -05:00
Morgan Smith 170cb4c881
gnu: emacs-org: Preserve version information.
* gnu/packages/emacs-xyz.scm (emacs-org)[#:phases]: Prevent install phase from
deleting the version information.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-12-03 21:14:25 +01:00
Nicolas Goaziou 85ed37c170
gnu: emacs-consult-notmuch: Update to 0.6.
* gnu/packages/emacs-xyz.scm (emacs-consult-notmuch): Update to 0.6.
2021-12-03 19:43:12 +01:00
Nicolas Goaziou 6557f17000
gnu: emacs-helm: Update to 3.8.2.
* gnu/packages/emacs-xyz.scm (emacs-helm): Update to 3.8.2.
2021-12-03 19:41:27 +01:00
Nicolas Goaziou a7776d5ac0
gnu: emacs-vertico: Update to 0.17.
* gnu/packages/emacs-xyz.scm (emacs-vertico): Update to 0.17.
2021-12-03 19:36:35 +01:00
Ricardo Wurmus b8d6e77476
gnu: python-ont-fast5-api: Update to 4.0.0.
* gnu/packages/bioinformatics.scm (python-ont-fast5-api): Update to 4.0.0.
[source]: Remove bundled plugin binaries.
[arguments]: Install plugin from inputs.
[inputs]: Add vbz-compression.
[propagated-inputs]: Remove python-six; add python-packaging.
2021-12-03 14:55:38 +01:00
Ricardo Wurmus d0aa14a43d
gnu: Add vbz-compression.
* gnu/packages/bioinformatics.scm (vbz-compression): New variable.
2021-12-03 14:55:38 +01:00
Mathieu Othacehe 3354e41c1e
system: vm: Remove the vga argument.
* gnu/system/vm.scm (common-qemu-options): Remove the "-vga std" argument that
is the default since QEMU 2.2.

Suggested-by: Attila Lendvai <attila@lendvai.name>
2021-12-03 14:25:57 +01:00
Attila Lendvai b42bfbdfe5
guix system vm: Add --no-graphic CLI argument.
It configures QEMU to use the tty it was started in for IO (as opposed to
opening a separate graphical window).  This enables copy-pasting and
scrollback.  Exit QEMU with C-a x.

* gnu/system/vm.scm (system-qemu-image/shared-store-script): Also add the
'-nographic' QEMU argument when called with #:graphic? #false.
* guix/scripts/system.scm (system-derivation-for-action): Propagate
the #:graphic? keyword arg.
(perform-action): Add and propagate the #:graphic? keyword arg.
(show-help): Add --no-graphic CLI arg.
(%options): Process the new --no-graphic CLI arg.
(process-action): Feed in the CLI arg through the #:graphic? keyword arg.
* doc/guix.texi (Invoking guix system): Add example to combine guix system and
invoking the vm start script into one command.  Split the description of the
various options into separate paragraphs.  Add a paragraph to describe
--no-graphic.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-12-03 14:18:32 +01:00
Charles 5a18cf3604
gnu: cl-coalton: Update to 0.0.1-2.012f6c8.
* gnu/packages/lisp-xyz.scm (sbcl-coalton): Update to 0.0.1-2.012f6c8.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2021-12-03 14:08:14 +01:00
Charles 6e0c4a28b9
gnu: cl-float-features: Update to 1.0.0-2.c1f86ae.
* gnu/packages/lisp-xyz.scm (sbcl-float-features): Update to 1.0.0-2.c1f86ae.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2021-12-03 13:59:46 +01:00
Ricardo Wurmus 6d4f260166
gnu: bamutils: Update to 1.0.14.
* gnu/packages/bioinformatics.scm (bamutils): Update to 1.0.14.
[arguments]: Patch DATE for reproducibility; prepare sources of libstatgen.
[native-inputs]: Add sources of libstatgen.
2021-12-03 13:56:02 +01:00
Ricardo Wurmus 673cc29908
gnu: bamutils: Remove reference to %outputs.
* gnu/packages/bioinformatics.scm (bamutils)[arguments]: Use gexp.
2021-12-03 13:56:01 +01:00
Ricardo Wurmus 361e0d9f27
gnu: bamm: Remove reference to %build-inputs.
* gnu/packages/bioinformatics.scm (bamm)[arguments]: Use gexp instead of
%build-inputs.
2021-12-03 13:56:01 +01:00
Ricardo Wurmus 4f536c4607
gnu: python2-openpyxl: Explicitly build with Python 2.
* gnu/packages/python-xyz.scm (python2-openpyxl)[arguments]: Add value
for #:python field.
2021-12-03 13:56:01 +01:00
Ricardo Wurmus 7fb5bfc54f
gnu: python-plastid: Update to 0.5.1.
* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.5.1.
2021-12-03 13:56:01 +01:00
Ricardo Wurmus b7aaf6c418
gnu: ivar: Disable parallel tests.
* gnu/packages/bioinformatics.scm (ivar)[arguments]: Disable parallel tests.
2021-12-03 13:48:41 +01:00
Ricardo Wurmus aa2d5ca02e
gnu: Remove python2-biom-format.
There are no users of this variant, and the current version of biom-format
does not support Python 2.

* gnu/packages/bioinformatics.scm (python2-biom-format): Remove variable.
(python-biom-format)[properties]: Remove field.
2021-12-03 13:31:32 +01:00
Ricardo Wurmus 8fa7de386c
gnu: r-flowclust: Add gsl.
* gnu/packages/bioconductor.scm (r-flowclust)[inputs]: Remove accidentally
committed comment character.
2021-12-03 13:31:32 +01:00
Mark H Weaver 3e9dc2754e
gnu: icecat: Remove vestigial icecat-78-makeicecat.patch.
This is a followup to commit a63231003e.

* gnu/packages/patches/icecat-78-makeicecat.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2021-12-03 04:45:15 -05:00
Mathieu Othacehe c0d9ba22d0
gnu: cuirass: Update to 1.1.0-6.df8837c.
* gnu/packages/ci.scm (cuirass): Update to 1.1.0-6.df8837c.
2021-12-03 10:41:37 +01:00
jgart fcf7e6513c
gnu: python-pandocfilters: Update to 1.5.0.
* gnu/packages/textutils.scm (python-pandocfilters): Update to 1.5.0.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-12-03 10:41:37 +01:00
Mark H Weaver d49e7a592f
gnu: icecat: Fix CVE-2021-43527.
* gnu/packages/patches/icecat-CVE-2021-43527.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gnuzilla.scm (icecat-source): Apply it.
2021-12-03 04:37:42 -05:00
Mark H Weaver 080a5de2ee
gnu: nss: Fix CVE-2021-43527 via graft.
* gnu/packages/patches/nss-CVE-2021-43527.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/nss.scm (nss/fixed): New variable
(nss)[replacement]: New field.
2021-12-03 04:37:21 -05:00
Ricardo Wurmus 345b341919
gnu: openjdk16: Use MAKE-FILE-WRITABLE.
* gnu/packages/java.scm (openjdk16)[arguments]: Do not shell out to "chmod".
2021-12-02 23:58:56 +01:00
Arne Babenhauserheide 68e71fbb17
gnu: Add openjdk17.
* gnu/packages/java.scm (openjdk17): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2021-12-02 23:58:53 +01:00
Leo Famulari f697fc267c
doc: Give more details about generating patches with base commit information.
* doc/contributing.texi (Submitting Patches): Talk more about '--base'.
2021-12-02 14:31:13 -05:00
Ricardo Wurmus 1f5c1bc024
gnu: python2-decorator: Downgrade to 4.3.0
* gnu/packages/python-xyz.scm (python2-decorator): Keep at 4.3.0.
(python-decorator)[properties]: Add python2-variant.
2021-12-02 18:56:29 +01:00
Ricardo Wurmus a2423c0ca4
gnu: ribodiff: Remove trailing #T.
* gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Remove trailing #T
from build phase.
2021-12-02 18:32:33 +01:00
Ricardo Wurmus 1123d25830
gnu: ribodiff: Disable broken test.
* gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Add build phase
'disable-plot-test.
2021-12-02 18:32:10 +01:00
Ricardo Wurmus f28f5be11d
gnu: python2-statsmodels: Downgrade to 0.9.0.
* gnu/packages/statistics.scm (python2-statsmodels): Downgrade to 0.9.0.
2021-12-02 18:31:38 +01:00
Ricardo Wurmus 31d372cd8a
gnu: khmer: Fix build with Python 3.8.
* gnu/packages/bioinformatics.scm (khmer)[source]: Remove trailing #T.
[arguments]: Remove trailing #T from build phases; add build phase
'python-3.8-compatibility.
2021-12-02 18:24:31 +01:00
Ricardo Wurmus 32d5fb01f8
gnu: python-biom-format: Update to 2.1.10.
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.10.
[source]: Simplify snippet.
[arguments]: Add phase 'relax; remove trailing #T from other build phases.
[propagated-inputs]: Add python-anndata; replace python-pandas-0.25 with
python-pandas.
2021-12-02 18:02:07 +01:00
jgart fab80c3672
gnu: Add trayer-srg.
* gnu/packages/wm.scm (trayer-srg): New variable.

Co-authored-by: Disseminate Dissent <disseminatedissent@protonmail.com>
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-12-02 15:44:31 +01:00
Ricardo Wurmus 28ad55a59d
gnu: pardre: Update to 2.2.5.
* gnu/packages/bioinformatics.scm (pardre): Update to 2.2.5.
[arguments]: Remove trailing #T and update comment about tests.
2021-12-02 15:40:46 +01:00
Ricardo Wurmus fc20fad6f7
gnu: pardre: Use C++ bindings for MPI.
* gnu/packages/bioinformatics.scm (pardre)[inputs]: Replace openmpi with
openmpi-c++.
2021-12-02 15:40:46 +01:00
Ricardo Wurmus 2d6be35ea2
gnu: Add openmpi-c++.
* gnu/packages/mpi.scm (openmpi-c++): New variable.
2021-12-02 15:40:45 +01:00
Liliana Marie Prikler df4f960cb8
gnu: Add libconfini.
* gnu/packages/cpp.scm (libconfini): New variable.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-12-02 15:38:17 +01:00
Vinicius Monego 2d92b3bbb6
gnu: shotcut: Update to 21.10.31.
* gnu/packages/video.scm (shotcut): Update to 21.10.31.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-12-02 15:29:33 +01:00
Vinicius Monego 82e5a1b4c3
gnu: kdenlive: Update to 21.08.3.
* gnu/packages/kde.scm (kdenlive): Update to 21.08.3.
[arguments]: Pass "-DBUILD_TESTING=off" to #:configure-flags as tests are
currently disabled.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-12-02 15:29:33 +01:00
Vinicius Monego 6fc0cfe1b5
gnu: mlt: Update to 7.2.0.
* gnu/packages/video.scm (mlt): Update to 7.2.0.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-12-02 15:29:33 +01:00