gnu: binutils-boot0: Refactor arguments.

When the inherited binutils package had a #:phases argument, it would replace
that fo binutils-boot0 (being appended), and causing breakage.

* gnu/packages/commencement.scm (binutils-boot0): Do not append the inherited
binutils arguments; modify them with a chained ensure-keyword-arguments and
substitute-keyword-arguments.

Suggested-by: Rutherther <rutherther@ditigal.xyz>
Change-Id: If1245556e363b9a1da2e2bb65c83e3b3aa4ff6de

gnu: binutils: Enable zstd compression.

* gnu/packages/base.scm (binutils) [native-inputs]: Add pkg-config.
[inputs]: Add zstd:lib.
(binutils-gold) [#:phases] {set-LD_LIBRARY_PATH}: New phase.

Change-Id: I344242724b5978c98dd20d8309de02702e78cf9a

gnu: binutils: Do not compress debug sections.

This is in preparation to a new phase which will deduplicate debug symbols
with dwz (and compress them after via objcopy).

* gnu/packages/base.scm (binutils) [#:configure-flags]: Remove
--enable-compressed-debug-sections=all.

Change-Id: I992bc680f3e5f7bb6b7aae81e9311352745402cf

gnu: binutils: Fix indentation.

* gnu/packages/base.scm (binutils): Fix indentation.

Change-Id: Icd8d298e00ae6c826aaef5f4e59688b6d8374b9e

gnu: binutils-final: Enable zstd support.

* gnu/packages/commencement.scm (binutils-final)
[#:allowed-references]: Add zstd-final:lib.
[native-inputs]: Add pkg-config-final.
[inputs]: Add zstd-final:lib.

Change-Id: I2c57f376f79ab866bce4456a41e752fcfa5c9826

gnu: Add pkg-config-final.

* gnu/packages/commencement.scm (pkg-config-final): New package.
(make-gnu-make-final): Use it.

Change-Id: I1452a09e765de863ac9725ac7924a0a97d3010ca

gnu: %final-inputs: Use zstd-final.

* gnu/packages/commencement.scm (%final-inputs): Use zstd-final instead of
computing it, now that there's a binding for it.

Change-Id: I3d28538b56f2480397d827cd4dac1275f0d27d66

gnu: Add zstd-final.

* gnu/packages/commencement.scm (zstd-final): New variable.

Change-Id: Ic6bef892f35a4bca809ff80dd279190b0f4902bd

gnu: python-parabam: Update to 3.0.1-0.be5bd35, fix build.

* gnu/packages/bioinformatics.scm (python-parabam): Update to
be5bd35012d37df8cfa88771325a0273519c8c98 commit.
[source]: Switch to git-fetch.
[arguments] <tests?>: No tests.
<phases>: Add 'cythonize.
[native-inputs]: Remove python-wheel; add python-cython.

Change-Id: I56e2dbeac106f2942289e2b751520b3bf1abb60f

gnu: python-schema-0.5: Deprecate in favor of python-schema.

There is no any users in Guix main channel, keeping the symbol for one
month.

* gnu/packages/python-xyz.scm (python-schema-0.5): Deprecate variable.

Change-Id: I099b91df49448eae5f38b066eca0ae6f61f80a5c

gnu: python-usbrelay: Fix build.

* gnu/packages/hardware.scm (python-usbrelay): Fix build.
[arguments] <#:phases>: Replace 'check phase.
[native-inputs]: Remove python-wheel.

Change-Id: I8b1de9158c277e83775fad4cab9ce56f87a8caab

gnu: python-paho-mqtt: Update to 2.1.0.

* gnu/packages/messaging.scm (python-paho-mqtt): Update to 2.1.0.
[build-system]: Switch to pyproject-build system.
[arguments] <#:phases>: Add 'patch-tests phase, remove replaced 'check
phase.
[native-inputs]: Add python-hatchling.

Change-Id: I150e2854bd92c66abc751ef8f9b9923d9e90dee4

gnu: python-ws4py: Update to 0.6.0.

* gnu/packages/python-web.scm (python-ws4py): Update to 0.6.0.
[build-system]: Switch to pyproject-build-system.
[arguments]: Use gexps.
<#:phases>: remove 'python3.7-compatibility phase.
[native-inputs]: Add python-setuptools and python-pytest.

Change-Id: Ia1c4d66f329ca0acd32d2b934836347b19cb711a

gnu: python-gipc: Enable tests.

* gnu/packages/python-xyz.scm (python-gipc)
[arguments] <tests?>: Enable them.
<phases>: Add 'adjust-for-pytest-8 phase.

Change-Id: Ib118dfd8f6cff1400e19880f1a96460fbac343b9

gnu: python-asprin: Fix build.

* gnu/packages/potassco.scm (python-asprin): Fix build.
[arguments] <#:phases>: Replace 'check phase.
[native-inputs]: Remove python-wheel.

Change-Id: I1f5b6418e50812bef5ba565877e8cdf4cd04d632

Revert "gnu: python-fenics-ufl: Update to 2025.1.0."

This reverts commit 5c522a1abff0b60d3a3d526605ef41bbf354162e.

The update breaks depending packages.

gnu: Add python-aiohttp-retry.

* gnu/packages/python-web.scm (python-aiohttp-retry): New variable.

Change-Id: I46f42d0f6a205a264eb1e9c9d00e3cd792dbfe3c
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

CODEOWNERS: Really order files alphabetically.

This is a follow-up to commit fe59616ba01e027cfdd81f0edc32788f9fcdcb73
and necessary to keep the file as-is through autogeneration.

* CODEOWNERS: Regenerate file.

Change-Id: I273b0d4142e3cb7ea55351ca46f64001588f7548

gnu: python-slepc4py: Update to 3.24.0.

* gnu/packages/maths.scm (python-slepc4py): Update to 3.24.0.

Change-Id: I23786bf36ed8dbbdad7f4b18e5985075487c4bcd

gnu: python-petsc4py: Update to 3.24.0.

* gnu/packages/maths.scm (python-petsc4py): Update to 3.24.0.

Change-Id: I8c530eadc777bfb26e7539594355f11c03c0f062