gnu: python-contourpy: Update to 1.3.2.

* gnu/packages/python-xyz.scm (python-contourpy): Update to 1.3.2.

Change-Id: I3e8517805d1c45f8738f6326c484604315f6b1f3

gnu: Add python-narwhals.

* gnu/packages/python-science.scm (python-narwhals): New variable.

Change-Id: Iae0e6a3260ffb066172377c464a645bcb126b17b

gnu: python-scikit-image: Fix tests.

In some cases there could be an issue to test compiled Cython library
which is not available in local checkout working directory.  This change
is inspired by the way NixOS packages scikit-image and run tests from
the output with "--pyargs" option where compiled library is available.

See: <https://github.com/NixOS/nixpkgs/blob/nixos-25.05/\
pkgs/development/python-modules/scikit-image/default.nix>.

* gnu/packages/python-science.scm (python-scikit-image) [arguments]
<test-flags>: Run tests from {#$output}, add "--pyargs" option and skip
one more problematic test.
<phases>: Use default 'check; add 'pre-check and post-check.

Change-Id: I60f58359f59b371854f4963e2f7c65c9221a0924

gnu: python-distributed: Update to 2024.12.1.

* gnu/packages/python-science.scm (python-distributed): Update to 2024.12.1.

Change-Id: Ia557e7d87e48a709298bf7024ee01b08098f5842
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-dask-expr: Update to 1.1.21.

* gnu/packages/python-science.scm (python-dask-expr): Update to 1.1.21.

Change-Id: Iaee50368ffafc473164865249e2a51732b1ea54f
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-dask: Update to 2024.12.1.

* gnu/packages/python-xyz.scm (python-dask): Update to 2024.12.1.

Change-Id: I776e9dd3d4a12d33e89e4d48a5e637cb9d6f465e
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: rlwrap: Update to 0.46.2.

* gnu/packages/readline.scm (rlwrap): Update to 0.46.2.

Change-Id: I1e5a34caec94519f59777557231ccbf623aa61df
Signed-off-by: Andreas Enge <andreas@enge.fr>

gnu: python-sip-4: Make compatible with python 3.11.

The package used an internal python API that was removed in
python 3.11, causing a compiler error. This commit replaces
the internal call with the official replacement API.

* gnu/packages/qt.scm (python-sip-4): Make compatible with python@3.11.

Change-Id: Ifbf888bcdaab314cb7ec5a5908656cbb1b2a52d2
Signed-off-by: Andreas Enge <andreas@enge.fr>

gnu: python-zeroc-ice-3.6: Register patch.

This is a follow-up to commit
03c4dc54a72f787da597972b43ff6ae9309ebad8 .

* gnu/local.mk (dist_patch_DATA): Register
python-zeroc-ice-3.6.5-python-3.11-support.patch.

Change-Id: I3c55994539422eac053449b9a28b7d7111c83888

gnu: chez-nanopass: Fix failed document build.

Fixes guix/guix#890.

* gnu/packages/chez.scm (chez-nanopass)[arguments]<#:phases>: Add new
phase 'fix-user-guide-date', pin the date of PDF document to the release
date.
In phase 'build-doc', set environment 'XDG_CACHE_HOME' before invoking
'make'.

Change-Id: I91e5f5efd08c3f5d2d94fbc9754f922df492a9ef

gnu: recoll: Update to 1.43.2.

* gnu/packages/search.scm (recoll): Update to 1.43.2.
  [build-system]: Switch to meson-build-system.
  [arguments]{configured-flags}: Switch to meson-build-system.
  {phases}: Replace phase 'set-LDFLAGS by 'patchelf (LDFLAGS doesn't
  seem to have any influence in this setup, only patchelf seems to fix
  the rpath) ; refresh phase 'wrap-filters in a more modern and
  readable style.
  {imported-modules, modules}: Add required ones.
  [native-inputs]: Add patchelf, remove which.

gnu: python-graph-tool: Use G-expressions.

* gnu/packages/graph.scm (python-graph-tool): Apply G-expressions.
  [arguments]: Drop import of SITE-PACKAGES procedure from
  python-build-system by replacing it with equivalent construction.

Change-Id: Ia2e4263ef08858fc910bf5142379978fa70ae664

gnu: python-leidenalg: Improve package, enable tests.

* gnu/packages/graph.scm (python-leidenalg):
  [source]: Switch to git-fetch containing tests.
  [build-system]: Use pyproject.
  [arguments] <tests?>: Enable them.
  <phases>: Remove absolute 'fix-requirements; add 'pretend-version.
  [native-inputs]: Add python-ddt, python-pytest, python-setuptools, and
  python-wheel.

Change-Id: I3fe5249b2c2947fb676b3347bd25a76d470aec17

gnu: python-plotly: Move to python-science.

This package is not related to Graph at all and imported by
bioinformatics and astronomy modules only which are Science disciplines.
This change moves it closer to related packages and preserves copyright
header records extracted from git log.

* gnu/packages/graph.scm (python-plotly): Move from here ...
* gnu/packages/python-science.scm: ... to here.

Change-Id: I5544ebdf1f545b2d7740dd56cab2d04bbe9d7715

gnu: python-plotly: Improve package.

* gnu/packages/graph.scm (python-plotly): Simplify and improve package.
  [build-system]: Use pyproject.
  [arguments] <test-flags>: Utilize it and skip only problematic tests
  which miss some packages, requiring networking or fail abnormaly.
  <phases>: Use default 'check.
  [propagated-inputs]: Remove python-six; add python-scikit-image and
  python-vaex-core.
  [native-inputs]: Add python-setuptools and python-wheel.

Change-Id: I4fefedbbf3e9180b07b40252fb8fb89f49983dbd

gnu: Remove python-plotly-2.4.1.

This variant is not in use any longer.

* gnu/packages/graph.scm (python-plotly-2.4.1): Delete variable.

Change-Id: Ibbead973b266c113a38d6e85d6ecd56d7e644e4b

gnu: packages/graph: Sort use-module alphabetically.

* gnu/packages/graph.scm: Sort use-module alphabetically.

Change-Id: I7f8f6a26d0607cc7c3946891b425747370081989

gnu: Add qvge.

* gnu/packages/graph.scm (qvge): New variable.

Change-Id: Ia4765de13caea2f576f247c459113f9babc31ef6
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: nethogs: Fix cross-compiling.

* gnu/packages/networking.scm (nethogs): Fix cross-compiling.
[arguments]<#:make-flags>: Set "CXX" variable.

Change-Id: I891ad4c9d2e8670e4d70a722f8d799d61a93fba7

gnu: nethogs: Modernize the package.

* gnu/packages/networking.scm (nethogs): Modernize the package.
[arguments]: Use GEXPs.

Change-Id: I552fc343f9125f38601588a01bcfe04e534bf5ea