gnu: hdf4-alt: Disinherit from hdf4.

* gnu/packages/maths.scm (hdf4-alt)[inherit]: Remove field.
[version, source, build-system, native-inputs, inputs, home-page,
synopsis, description, license]: Copy and paste from hdf4.
[arguments]: Adapt from hdf4 without changing the derivation.

Change-Id: I37cb97d7d97ea4426158b6970b98695d4f514332
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Remove python-pyhdf.

* gnu/packages/python-xyz.scm (python-pyhdf): Delete variable.

Change-Id: I74811a533b603524f44805078b6a57babe44f63f
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Remove python-hdf4.

* gnu/packages/python-xyz.scm (python-hdf4): Delete variable.

Change-Id: I763ef2f0aa528b36f933a02dddcfd8d5fbf51147
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Remove gctp.

* gnu/packages/maths.scm (gctp): Delete variable.

Fixes: guix/guix#4761
Change-Id: If04e27063eb68dcfbe1d0057f1b4e097c8de153f
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Remove hdf-eos5.

* gnu/packages/maths.scm (hdf-eos5): Delete variable.

Change-Id: Id4dbf13e73df2cbeadc6944a6a05711ef7a427cf
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Remove hdf-eos2.

* gnu/packages/maths.scm (hdf-eos2): Delete variable.

Change-Id: I71e3ba4106b2d800439e4affc7b65d7b428bb160
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-sphinx-autoapi: Update to 3.6.1.

* gnu/packages/sphinx.scm (python-sphinx-autoapi): Update to 3.6.1.
[source]: Switch to git-fetch.
[arguments]<#:test-flags>: Disable test that requires network.
[propagated-inputs]: Remove python-unidecode.
[native-inputs]: Remove python-setuptools, python-sphinx, and python-wheel; add
nss-certs-for-test, python-beautifulsoup4, python-flit-core, and
python-pytest.

Change-Id: I7e3d71a71b2316953559cdd9cdc4ac8d157571f7
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-brian2tools: Fix build.

* gnu/packages/machine-learning.scm (python-brian2tools): Add missing input.
[propagated-inputs]: Add python-tables.

Change-Id: I974d3a4e1101272710e791ab92b9bc793d17f28e
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-scanrbp: Include data in package.

* gnu/packages/bioinformatics.scm (python-scanrbp): Fix build and include data.
[native-inputs]: Remove python-wheel.
<#:phases>: Add 'patchpath and 'copy-data phases. Replace 'check phase.

Change-Id: Ie61792f696f59383789cac89bf9f354f0ce1d188
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-domain-connect: Remove unused inputs.

* gnu/packages/python-web.scm (python-domain-connect):
[native-inputs]: Remove python-wheel.
[propagated-inputs]: Remove python-publicsuffix.

Change-Id: I959e6239149c51a25d44ffc18ddad0b6ce9f9b63
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: nml: Switch to pyproject.

* gnu/packages/game-development.scm (nml):
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:phases>: Use tests? for 'check phase.
[native-inputs]: Add python-setuptools.

Change-Id: I4bcc1e586e0fd9e0cec749e85502661532485975
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: grokmirror: Update to 2.0.12.

* gnu/packages/version-control.scm (grokmirror): Update to 2.0.12.
[source]<file-name>: Refresh it.
[build-system]: Switch to pyproject-build-system.
[arguments]: Improve style.
<#:phases>: Refresh phase 'install-manpages.
[native-inputs]: Add python-setuptools.

Change-Id: I9ccec338eda46227b44d5f5435e648978e7820fb
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: shirah: Switch to pyproject.

* gnu/packages/ebook.scm (shirah):
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:tests?>: Disable them.
[native-inputs]: Add python-setuptools.

Change-Id: I349bd87b45debaf61c1b3cbbd9e5b9e7202710d0
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-biothings-client: Update to 0.4.1.

* gnu/packages/bioinformatics.scm (python-biothings-client): Update to 0.4.1.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-setuptools.
[propagated-inputs]: Add python-httpx.

Change-Id: I3d5c9ea79fd23a8291074f32d37adfede4e0e238
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: patatt: Switch to pyproject.

* gnu/packages/version-control.scm (patatt):
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]: Improve comment.
[native-inputs]: Add python-setuptools.

Change-Id: Id46c10a5e93c727b3ba58e940d6f4463ccde7cd7
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: temper-exporter: Switch to pyproject.

* gnu/packages/monitoring.scm (temper-exporter):
[arguments]<#:tests?>: Enable them.
<#:test-flags>: Ignore failing test.
<#:phases>: Refresh them.
[native-inputs]: Add python-setuptools.  Remove python-pytest-runner.

Change-Id: I5880ca3700cf40e876e42b95410d5c76668c5806
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pyinotify: Reduce package closure size.

This Python package can be used both as a library and as a standalone
command line application.  It does so by adding a shebang to the library
code. Dropping this shebang prevents the build system from adding
python-wrapper as an input, reducing package closure size from
~200 MiB to ~0.2 MiB.  A new python-pyinotify-cli package is added to
allow users who desire so to use the CLI application.

* gnu/packages/python-xyz.scm (python-pyinotify)[phases]{drop-shebang}:
New phase.
(python-pyinotify-cli): New variable.

Change-Id: Ifb796d26fc6a7bedec69093f7c9bd43ada8bebac
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: gnome-plots: Switch to pyproject.

* gnu/packages/gnome-xyz.scm (gnome-plots):
[build-system]: Switch to pyproject-build-system.
[arguments]: Relocate field.
<#:imported-modules, #:modules, #:phases>: Switch to pyproject-build-system.
[native-inputs]: Add python-setuptools.

Change-Id: I8bb462e4b67b2f692949540e91c4d4498b9d17aa
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-libevdev: Update to 0.13.1.

* gnu/packages/freedesktop.scm (python-libevdev): Update to 0.13.1.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:phases>: Remove 'check phase replacement.
[native-inputs]: Add python-setuptools.
[description]: Improve style.

Change-Id: I3fe76e0923e3606c027cc98e6aadc6ca63be3a26
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: mkbootimg: Switch to copy-build-system.

* gnu/packages/android.scm (mkbootimg):
[arguments]: Drop them.
<#:install-plan>: Set it.
[build-system]: Switch to copy-build-system.
[inputs]: Add python-wrapper.
[source, description]: Improve style.

Change-Id: I72c80fea6bd7120f70302a927ae7fa67b5bb5030
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>