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* gnu: python-django-netfields: Update to 1.2.4.•••* gnu/packages/django.scm (python-django-netfields): Update to 1.2.4. Marius Bakke2021-12-051-2/+2
* gnu: python-django: Update to 3.2.9.•••* gnu/packages/django.scm (python-django): Update to 3.2.9. Marius Bakke2021-12-051-2/+2
* gnu: drbd-utils: Update to 9.19.1.•••* gnu/packages/cluster.scm (drbd-utils): Update to 9.19.1. Marius Bakke2021-12-051-2/+2
* gnu: emacs-peg: Update to 0.10.3.•••* gnu/packages/emacs-xyz.scm (emacs-peg): Update to 0.10.3. Nicolas Goaziou2021-12-051-2/+2
* gnu: Add imppg•••* gnu/packages/astronomy.scm: (imppg): New variable. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr> Sharlatan Hellseher2021-12-051-0/+53
* gnu: Add pqiv.•••* gnu/packages/image-viewers.scm (pqiv): New variable. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr> dissent2021-12-051-0/+46
* gnu: Add pudb.•••* gnu/packages/python-xyz.scm (pudb): New variable. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr> jgart2021-12-051-0/+39
* gnu: leo: Use GIT-VERSION.•••* gnu/packages/web-browsers.scm (leo)[source]: Use `git-version' instead of crafting version string. Also fix indentation. Nicolas Goaziou2021-12-051-6/+6
* gnu: Add leo.•••* gnu/packages/web-browsers.scm (leo): New variable. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr> jgart2021-12-051-0/+26
* gnu: minimap2: Update to 2.23.•••* gnu/packages/bioinformatics.scm (minimap2): Update to 2.23. Efraim Flashner2021-12-051-2/+2
* gnu: Add guile-ini.•••* gnu/packages/guile-xyz.scm (guile-ini): New variable. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org> Artyom V. Poptsov2021-12-051-0/+36
* gnu: Add libphonenumber•••* gnu/package/messaging.scm (libphonenumber): New variable Co-authored-by: Ludovic Courtès <ludo@gnu.org> Ryan Desfosses2021-12-041-0/+35
* gnu: Add guile-smc•••* gnu/packages/guile-xyz.scm (guile-smc): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Artyom V. Poptsov2021-12-041-0/+88
* gnu: ocaml4.07-ppx-let: Make 'properties' an alist.•••The incorrect 'properties' value was introduced in 3649c56a5f23501a5bb3418dc6047b71d494f0fa. * gnu/packages/ocaml.scm (ocaml4.07-ppx-let)[properties]: Turn into an alist. Ludovic Courtès2021-12-041-1/+1
* gnu: emacs-org-roam-bibtex: Update to 0.6.1.•••* gnu/packages/emacs-xyz.scm (emacs-org-roam-bibtex): Update to 0.6.1. Nicolas Goaziou2021-12-041-2/+2
* 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> jgart2021-12-041-2/+2
* 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> cage2021-12-041-10/+24
* gnu: pigx-sars-cov2-ww: Update to 0.0.4.•••* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.4. [inputs]: Add bbmap, bedtools, fastp, ivar, and r-r-utils. Ricardo Wurmus2021-12-041-2/+7
* gnu: imp: Update to 2.15.0.•••* gnu/packages/bioinformatics.scm (imp): Update to 2.15.0. [arguments]: Disable one more test. Ricardo Wurmus2021-12-031-3/+5
* gnu: Add r-fpeek.•••* gnu/packages/cran.scm (r-fpeek): New variable. Ricardo Wurmus2021-12-031-0/+22
* 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’. Liliana Marie Prikler2021-12-032-10/+31
* 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. Liliana Marie Prikler2021-12-031-2/+17
* 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. Liliana Marie Prikler2021-12-031-0/+6
* gnu: Add valeronoi.•••* gnu/packages/engineering.scm (valeronoi): New variable. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr> phodina2021-12-031-0/+40
* 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> jgart2021-12-031-7/+6
* 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> Morgan Smith2021-12-031-0/+4
* gnu: emacs-consult-notmuch: Update to 0.6.•••* gnu/packages/emacs-xyz.scm (emacs-consult-notmuch): Update to 0.6. Nicolas Goaziou2021-12-031-2/+2
* gnu: emacs-helm: Update to 3.8.2.•••* gnu/packages/emacs-xyz.scm (emacs-helm): Update to 3.8.2. Nicolas Goaziou2021-12-031-2/+2
* gnu: emacs-vertico: Update to 0.17.•••* gnu/packages/emacs-xyz.scm (emacs-vertico): Update to 0.17. Nicolas Goaziou2021-12-031-2/+2
* 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. Ricardo Wurmus2021-12-031-3/+18
* gnu: Add vbz-compression.•••* gnu/packages/bioinformatics.scm (vbz-compression): New variable. Ricardo Wurmus2021-12-031-0/+37
* 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> Mathieu Othacehe2021-12-031-1/+0
* 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> Attila Lendvai2021-12-031-0/+2
* 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> Charles2021-12-031-10/+12
* 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> Charles2021-12-031-23/+24
* gnu: ivar: Disable parallel tests.•••* gnu/packages/bioinformatics.scm (ivar)[arguments]: Disable parallel tests. Ricardo Wurmus2021-12-031-0/+1
* 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. Ricardo Wurmus2021-12-031-17/+1
* gnu: r-flowclust: Add gsl.•••* gnu/packages/bioconductor.scm (r-flowclust)[inputs]: Remove accidentally committed comment character. Ricardo Wurmus2021-12-031-1/+0
* gnu: icecat: Remove vestigial icecat-78-makeicecat.patch.•••This is a followup to commit a63231003e7bbeafb0110b077788e47e78685f20. * gnu/packages/patches/icecat-78-makeicecat.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. Mark H Weaver2021-12-032-111/+0
* gnu: cuirass: Update to 1.1.0-6.df8837c.•••* gnu/packages/ci.scm (cuirass): Update to 1.1.0-6.df8837c. Mathieu Othacehe2021-12-031-3/+3
* 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> jgart2021-12-031-2/+2
* 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. Mark H Weaver2021-12-033-0/+356
* 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. Mark H Weaver2021-12-033-1/+360
* gnu: openjdk16: Use MAKE-FILE-WRITABLE.•••* gnu/packages/java.scm (openjdk16)[arguments]: Do not shell out to "chmod". Ricardo Wurmus2021-12-021-5/+2
* gnu: Add openjdk17.•••* gnu/packages/java.scm (openjdk17): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Arne Babenhauserheide2021-12-021-0/+33
* 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. Ricardo Wurmus2021-12-021-2/+13
* gnu: ribodiff: Remove trailing #T.•••* gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Remove trailing #T from build phase. Ricardo Wurmus2021-12-021-2/+1
* gnu: ribodiff: Disable broken test.•••* gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Add build phase 'disable-plot-test. Ricardo Wurmus2021-12-021-0/+5
* gnu: python2-statsmodels: Downgrade to 0.9.0.•••* gnu/packages/statistics.scm (python2-statsmodels): Downgrade to 0.9.0. Ricardo Wurmus2021-12-021-0/+10
* 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. Ricardo Wurmus2021-12-021-6/+9
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