gnu: trealla: Update to 2.83.8.

* gnu/packages/prolog.scm (trealla): Update to 2.83.8.

Change-Id: I190612b48e6a69e31384bb12d81465a668f2de59

gnu: git-lfs: Fix build.

This change is to bypass combination of go-build-system and custom make
targets where the import path is set manually, see discussion in
guix/guix#2133.

* gnu/packages/version-control.scm (git-lfs): Rename binary and home page

Change-Id: Ic87627412f715ebed07cf79ddd298e777746975f
Reviewed-by: Nicolas Graves <ngraves@ngraves.fr>
Reviewed-by: Maxim Cournoyer <maxim@guixotic.coop>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: guile-emacs: Fix build with gcc-14.

* gnu/packages/guile.scm (guile-for-guile-emacs)[arguments]: Replace
emacs-minimal's CFLAGS in #:configure-flags with specific and extra flags to
relax gcc-14's strictness.

Change-Id: I6b3f871695eb25fbf84a2334525e1d0e15e36b92

gnu: Add python-six-bootstrap.

* gnu/packages/python-xyz.scm (python-six-bootstrap): New variable.

Fixes: guix-science/guix-past#20.
Reported-by: @gabor-udvari
Change-Id: I15b993e39c76dd39d1871179fc899e963d411d45

gnu: mallard-ducktype: Move to documentation.

* gnu/packages/python-xyz.scm (mallard-ducktype): Move from here ...
* gnu/packages/documentation.scm: ... to here.

Fixes: guix/guix#1200.
Change-Id: I05895a56626a0416c4c7710c48f06b62538b4622

gnu: toot: Update to 0.50.1.

* gnu/packages/fediverse.scm (toot): Update to 0.50.1.
[arguments]: Remove field.
[inputs]: Remove python-urwid and python-urwidgets; add python-dateutil
and python-urwid-3.
[native-inputs]: Remove python-psycopg2-binary, python-pyyaml, and
python-typing-extensions; add python-pillow and python-setuptools-scm.

Change-Id: I06a39646b1ffac130a42a1d1d10bbdcfc625ab94

services: mumi: Raise maximum duration of indexing job.

Indexing all Debbugs issues from scratch can take more than an hour.

* gnu/services/web.scm (mumi-shepherd-services): Raise #:max-duration to 2
hours.

gnu: dbxfs: Fix build.

* gnu/packages/file-systems.scm (dbxfs)[build-system]: Switch to the
pyproject-build-system.
[native-inputs]: Add python-setuptools.

Change-Id: I79dfd9e7092aaf0b5078900c6b2ecbbe9137b44f

gnu: vmware-open-vm-tools: Update to 13.0.0.

* gnu/packages/virtualization.scm (vmware-open-vm-tools): Update to
 13.0.0.

Change-Id: I503b9202db82992442a76af3c6b2ce8ffe017e4a
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: neovim: Add support for guix neovim packages.

Enables the use of guix as a package manager for neovim, compatible with
the outputs of `vim-build-system`.

* gnu/packages/vim.scm (neovim)[arguments]: Added another phase to
install the system init file to the correct place.
* gnu/packages/aux-files/guix-nvim.vim: New file.
* Makefile.am (AUX_FILES): Register file.

Change-Id: I375e3e0d051da27d065dff5456cb298a01bc90b1
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

teams: Add entry for Rutherther.

Add myself to release team.

* etc/teams.scm (Rutherther): New member.

Change-Id: Ied242919f54abe05e429fb8e658bdc9e0ffc0cb1
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: python-quadpy: Adjust inputs.

* gnu/packages/maths.scm (python-quadpy)[inputs]: Add python-matplotlib.
[native-inputs]: Remove python-wheel.

Change-Id: I72f2d7daafebd98f96245697aecb60c176981336

gnu: python-scikit-fem: Update to 11.0.0.

* gnu/packages/python-science.scm (python-scikit-fem): Update to 11.0.0.
[propagated-inputs]: Add python-matplotlib.
[native-inputs]: Remove python-wheel.

Change-Id: I52ac1f1125f7d5849b8a90f5db74aeabc08fd6ef

gnu: python-plotly: Fix tests.

* gnu/packages/python-science.scm (python-plotly) [native-inputs]:
Remove python-wheel; add python-nbformat.

Change-Id: I257a9b06343b37e95428bfa46f4b5547b7adb876

gnu: python-textdistance: Limit concurrent tests.

* gnu/packages/python-xyz.scm (python-textdistance)[arguments]
<test-flags>: Limit parallel tests up to 4 threads.

Change-Id: Id70320f528a0618e3058ccabaec5675180b06b74

gnu: python-poppy: Fix tests.

* gnu/packages/astronomy.scm (python-poppy)[arguments] <test-flags>:
Avoid "docs/ext/numfig.py".

Change-Id: If0ab442d6e5ab93ef59f602be4fa3cf37ce23422

gnu: python-pygtrie: Fix and run tests.

* gnu/packages/python-xyz.scm (python-pygtrie)
[source]: Switch to git-fetch.
[arguments]<#:test-backend>: Set it.
<#:phases>: Add phase 'set-version.
[native-inputs]: Remove python-wheel.

Change-Id: Ib3da3430340077624410e334d7846b75b6928471
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-distance: Update to 0.1.3-0.ad7f9dc.

* gnu/packages/python-xyz.scm (python-distance): Update to 0.1.3-0.ad7f9dc.
[source]: Switch to git-fetch.
[arguments]: Set <#:test-backend> and <#:test-flags>.
[native-inputs]: Remove python-wheel.

Change-Id: I76fdce7caa7cff779ef6df60dd3969aea57be5d5
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-pyxdameraulevenshtein: Run and fix tests.

* gnu/packages/python-xyz.scm (python-pyxdameraulevenshtein)
[source]: Switch to git-fetch.
[native-inputs]: Add python-pytest, remove python-wheel.

Change-Id: I5835d0367438a3f3cc017b1dc37fd5d6f2f3c120
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-matrix-nio: Disable failing tests.

* gnu/packages/matrix.scm (python-matrix-nio)
[arguments]<#:test-flags>: Disable failing tests.
<#:phases>: Improve style ; add phase 'relax-requirements.
[native-inputs]: Remove python-mypy, python-mypy-extensions,
python-poetry-core, python-pytest-cov, python-pytest-flake8,
python-wheel.

Change-Id: I45ddc6ca02333eb5384f310cfd6cdb9091626334
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>