21e2be5968
gnu: emacs-peg: Update to 0.10.3.
...
* gnu/packages/emacs-xyz.scm (emacs-peg): Update to 0.10.3.
2021-12-05 14:20:16 +01:00
bf9a1dfd59
gnu: Add imppg
...
* gnu/packages/astronomy.scm: (imppg): New variable.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-12-05 12:35:55 +01:00
c663d037aa
gnu: Add pqiv.
...
* gnu/packages/image-viewers.scm (pqiv): New variable.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-12-05 12:27:02 +01:00
66a2d3830c
gnu: Add pudb.
...
* gnu/packages/python-xyz.scm (pudb): New variable.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-12-05 12:18:24 +01:00
53afb3cf2a
gnu: leo: Use GIT-VERSION.
...
* gnu/packages/web-browsers.scm (leo)[source]: Use `git-version' instead of
crafting version string. Also fix indentation.
2021-12-05 12:08:16 +01:00
2149515808
gnu: Add leo.
...
* gnu/packages/web-browsers.scm (leo): New variable.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-12-05 11:03:14 +01:00
e70e26423b
gnu: minimap2: Update to 2.23.
...
* gnu/packages/bioinformatics.scm (minimap2): Update to 2.23.
2021-12-05 11:51:10 +02:00
030d9b261f
gnu: Add guile-ini.
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* gnu/packages/guile-xyz.scm (guile-ini): New variable.
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-12-05 09:53:59 +01:00
20d525a842
gnu: Add libphonenumber
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* gnu/package/messaging.scm (libphonenumber): New variable
Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2021-12-04 23:03:54 +01:00
ac872546fc
gnu: Add guile-smc
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* gnu/packages/guile-xyz.scm (guile-smc): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-12-04 22:45:27 +01:00
f044ffc1c4
gnu: ocaml4.07-ppx-let: Make 'properties' an alist.
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The incorrect 'properties' value was introduced in
3649c56a5f
2021-12-04 21:57:27 +01:00
7fcb20a8fa
nls: Update translations.
2021-12-04 19:40:52 +01:00
f199427c1b
gnu: emacs-org-roam-bibtex: Update to 0.6.1.
...
* gnu/packages/emacs-xyz.scm (emacs-org-roam-bibtex): Update to 0.6.1.
2021-12-04 16:17:58 +01:00
1e5656e7bd
news: Add copyright line for myself.
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* etc/news.scm: Add myself to the copyright headers.
2021-12-04 15:10:29 +01:00
da70132ee9
gnu: janet: Update to 1.19.0.
...
* gnu/packages/lisp.scm (janet): Update to 1.19.0.
Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2021-12-04 13:51:49 +01:00
612fe425b4
gnu: tinmop: Update to 0.9.2.
...
* gnu/packages/web-browsers.scm (tinmop): Update to 0.9.2.
[inputs]: Move nano, openssl and xdg-utils to...
[native-inputs]: ... here. Add automake, autoconf and mandoc. Remove curl
and gnupg.
[arguments]: Add 'fix-configure.ac' phase.
Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2021-12-04 13:44:17 +01:00
18a85213ae
gnu: pigx-sars-cov2-ww: Update to 0.0.4.
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* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.4.
[inputs]: Add bbmap, bedtools, fastp, ivar, and r-r-utils.
2021-12-04 12:42:51 +01:00
ce9bfcddb5
gnu: imp: Update to 2.15.0.
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* gnu/packages/bioinformatics.scm (imp): Update to 2.15.0.
[arguments]: Disable one more test.
2021-12-03 22:29:52 +01:00
dcf857e486
gnu: Add r-fpeek.
...
* gnu/packages/cran.scm (r-fpeek): New variable.
2021-12-03 22:29:40 +01:00
15404ff19b
gnu: emacs: Load package descriptors from packages referenced by subdirs.el
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* 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
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
4baeb72717
gnu: emacs: Make DocView PDF work out of the box.
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* 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
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
269baba919
gnu: Add valeronoi.
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* gnu/packages/engineering.scm (valeronoi): New variable.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-12-03 21:38:30 +01:00
19528e39bb
gnu: st: Install terminfo files.
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* 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
170cb4c881
gnu: emacs-org: Preserve version information.
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* 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
85ed37c170
gnu: emacs-consult-notmuch: Update to 0.6.
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* gnu/packages/emacs-xyz.scm (emacs-consult-notmuch): Update to 0.6.
2021-12-03 19:43:12 +01:00
6557f17000
gnu: emacs-helm: Update to 3.8.2.
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* gnu/packages/emacs-xyz.scm (emacs-helm): Update to 3.8.2.
2021-12-03 19:41:27 +01:00
a7776d5ac0
gnu: emacs-vertico: Update to 0.17.
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* gnu/packages/emacs-xyz.scm (emacs-vertico): Update to 0.17.
2021-12-03 19:36:35 +01:00
b8d6e77476
gnu: python-ont-fast5-api: Update to 4.0.0.
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* 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
d0aa14a43d
gnu: Add vbz-compression.
...
* gnu/packages/bioinformatics.scm (vbz-compression): New variable.
2021-12-03 14:55:38 +01:00
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
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
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
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
b7aaf6c418
gnu: ivar: Disable parallel tests.
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* gnu/packages/bioinformatics.scm (ivar)[arguments]: Disable parallel tests.
2021-12-03 13:48:41 +01:00
aa2d5ca02e
gnu: Remove python2-biom-format.
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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
8fa7de386c
gnu: r-flowclust: Add gsl.
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* gnu/packages/bioconductor.scm (r-flowclust)[inputs]: Remove accidentally
committed comment character.
2021-12-03 13:31:32 +01:00
3e9dc2754e
gnu: icecat: Remove vestigial icecat-78-makeicecat.patch.
...
This is a followup to commit a63231003e
2021-12-03 04:45:15 -05:00
c0d9ba22d0
gnu: cuirass: Update to 1.1.0-6.df8837c.
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* gnu/packages/ci.scm (cuirass): Update to 1.1.0-6.df8837c.
2021-12-03 10:41:37 +01:00
fcf7e6513c
gnu: python-pandocfilters: Update to 1.5.0.
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* 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
d49e7a592f
gnu: icecat: Fix CVE-2021-43527.
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* 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
080a5de2ee
gnu: nss: Fix CVE-2021-43527 via graft.
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* 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
345b341919
gnu: openjdk16: Use MAKE-FILE-WRITABLE.
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* gnu/packages/java.scm (openjdk16)[arguments]: Do not shell out to "chmod".
2021-12-02 23:58:56 +01:00
68e71fbb17
gnu: Add openjdk17.
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* gnu/packages/java.scm (openjdk17): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2021-12-02 23:58:53 +01:00
f697fc267c
doc: Give more details about generating patches with base commit information.
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* doc/contributing.texi (Submitting Patches): Talk more about '--base'.
2021-12-02 14:31:13 -05:00
1f5c1bc024
gnu: python2-decorator: Downgrade to 4.3.0
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* 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
a2423c0ca4
gnu: ribodiff: Remove trailing #T.
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* gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Remove trailing #T
from build phase.
2021-12-02 18:32:33 +01:00
1123d25830
gnu: ribodiff: Disable broken test.
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* gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Add build phase
'disable-plot-test.
2021-12-02 18:32:10 +01:00
f28f5be11d
gnu: python2-statsmodels: Downgrade to 0.9.0.
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* gnu/packages/statistics.scm (python2-statsmodels): Downgrade to 0.9.0.
2021-12-02 18:31:38 +01:00
Nicolas Goaziou
Sharlatan Hellseher
dissent
jgart
Efraim Flashner
Artyom V. Poptsov
Ryan Desfosses
Ludovic Courtès
Julien Lepiller
Jonathan Brielmaier
cage
Ricardo Wurmus
Liliana Marie Prikler
phodina
Morgan Smith
Mathieu Othacehe
Attila Lendvai
Charles
Mark H Weaver
Arne Babenhauserheide
Leo Famulari