gnu: pigx-rnaseq: Add missing input.

* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Add r-genomeinfodb.

Change-Id: I358d6dca2acde401eaf6cdd370109cd9aa0b558d

gnu: primesieve: Update to 12.10

* gnu/packages/maths.scm(primesieve): Update to 12.10.

Change-Id: I1ba241afbba68d974570694d044ec3e14f58a425
Signed-off-by: Andreas Enge <andreas@enge.fr>

gnu: primecount: Update to 7.20.

* gnu/packages/maths.scm(primecount): Update to 7.20.

Change-Id: I018f5e61cb7a6f2ad27d03124208ac5950bc5ead
Signed-off-by: Andreas Enge <andreas@enge.fr>

gnu: primesieve: Reformat.

* gnu/packages/maths.scm (primesieve): Reformat.
[source, arguments]: Indent.
[description]: Fill column limit.
[home-page]: Put right before license.

Change-Id: I9a94d6dc043ff934d29800d05c48ea7a5e137f54
Signed-off-by: Andreas Enge <andreas@enge.fr>

gnu: primecount: Reformat.

* gnu/packages/maths.scm(primecount): Reformat.
[source, arguments]: Indent.
[description]: Fill column limit.
[home-page]: Put right before license.

Change-Id: I7630dc994166664bf96a7da262062c2b292f0073
Signed-off-by: Andreas Enge <andreas@enge.fr>

gnu: crun: Update to 1.25.1.

* gnu/packages/containers.scm (crun): Update to 1.25.1.

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

gnu: ikiwiki: Replace deprecated input.

* gnu/packages/web.scm (ikiwiki)[native-inputs]: Remove bazaar; add breezy.

Change-Id: Iebaaea0088bbfe60b101774fde6204e3effb1256

gnu: mcy: Update to 0.60.

* gnu/packages/electronics.scm (mcy): Update to 0.60.

Change-Id: I6499b4381b064967aada2f3f880c9c00859a5e61

gnu: eqy: Update to 0.60.

* gnu/packages/electronics.scm (eqy): Update to 0.60.

Change-Id: I5830309c613becbf92051bdcaa3ba36a40e0dc83

gnu: sby: Update to 0.60.

* gnu/packages/electronics.scm (sby): Update to 0.60.

Change-Id: I14633f778eaed74fc6af059ac1d37cdb5c6c88ef

gnu: yosys: Update to 0.60.

* gnu/packages/electronics.scm (yosys): Update to 0.60.
[inputs]: Add editline.
[native-inputs]: Remove python and tcl.
[arguments]: Enable libyosys in ’configure-makefile #:phase.
[synopsys]: Update.
[description]: Update.

Change-Id: I295961abf7d4bfa9dc9ce1b2e8bd68b0950e96f0

gnu: abc-yosyshq: Update to 0.60.

* gnu/packages/electronics.scm (abc-yosyshq): Update to 0.60.

Change-Id: I496352f70b03fe39618e64e02b3ecc98f3dcd0df

gnu: perl-sdl: Fix build with gcc@14.

* gnu/packages/perl.scm (perl-sdl)[arguments]<#:phases>{gcc-14}:
New phase to set CFLAGS.

Fixes: guix/guix#4630
Change-Id: I8bc422b6867e0c49586797b57ef49df2881fcbba
Signed-off-by: Andreas Enge <andreas@enge.fr>

gnu: openfoam-com: Update to 2506.

* gnu/packages/simulation.scm (openfoam-com): Update to 2506.
[source]: Switch to git-fetch. Remove snippets.
[arguments]: Add parent variable to replace version for inherited package.

Change-Id: I2c79e98e621516dfe0e950a41b9abb515da43af3
Signed-off-by: Andreas Enge <andreas@enge.fr>

gnu: openfoam-org: Update to 13.

* gnu/packages/simulation.scm (openfoam-org): Update to 13.
[source]: Switch to git-fetch. Move snippets to phases.
[native-inputs, inputs]: Move runtime dependencies from native-inputs
to inputs. Add dependencies for paraview to build plugin. Switch to Qt6.
[arguments]: Reorder phases, use configure phase for configuration.
Add version suffix to OpenFOAM install folder.
Add phase to patch version. Add phase to patch paraview.
Wrap the binaries with the environment variables sourced from bashrc.

Change-Id: I26a313fa3aab22bff5a743890c6ffb0d56857f0b
Signed-off-by: Andreas Enge <andreas@enge.fr>

gnu: python-clf: Switch to pyproject.

* gnu/packages/web.scm (python-clf):
[build-system]: Switch to pyproject-build-system.
[arguments]: Relocate field, improve style.
[propagated-inputs]: Remove python-nose, python-lxml, python-pyaml.
[native-inputs]: Add python-pynose, python-setuptools.

Change-Id: I975f1db21afbfa5af283a0f409e1d6b4259d3575
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-jupyter-console: Switch to pyproject.

* gnu/packages/python-xyz.scm (python-jupyter-console):
[build-system]: Switch to pyproject-build-system.
[arguments]<#:test-backend>: Set it.
[native-inputs]: Add python-setuptools.  Remove python-nose.

Change-Id: Ida809559b38d65e03be9fb25d244eb2550b0c353
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-pdf2image: Replace python-nose by python-pynose.

* gnu/packages/python-xyz.scm (python-pdf2image)
[arguments]: Improve style.
[native-inputs]: Remove python-wheel.  Replace python-nose by
python-pynose.

Change-Id: I2a7f607931144c6858efc95f4845f2866be0224d
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-colorspacious: Disable tests.

python-nose runs 0 tests, let's remove it and disable tests instead.

* gnu/packages/python-xyz.scm (python-colorspacious)
[arguments]<#:tests?>: Disable them.
[native-inputs]: Remove python-nose, python-wheel.
[description]: Improve style.

Change-Id: I6a2a58ea8f5183e4933b1dca227e8086640cd11d
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-restructuredtext-lint: Remove python-nose native-inputs.

* gnu/packages/python-xyz.scm (python-restructuredtext-lint)
[arguments]<#:test-backend>: Switch to unittest.
[native-inputs]: Remove python-nose.

Change-Id: I1d59f2012ff939b5856c3cc482d40391f0d2fb5e
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>