gnu: seqmagick: Fix build and remove python-nose.

* gnu/packages/bioinformatics.scm (seqmagick)
[arguments]<#:phases>: Add phase 'set-version.
[native-inputs]: Remove python-wheel.  Replace python-nose by
python-pynose.

Change-Id: I5a10d7702d59c6f837761ff96e11f0ff470e0626
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: rseqc: Disable tests.

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

* gnu/packages/bioinformatics.scm (rseqc)
[arguments]<#:tests?>: Disable them.
[native-inputs]: Remove python-nose.
[propagated-inputs]: Remove python-wheel.

Change-Id: I5be4019f6093478b5ab28f07a52319c7cfbd7cd8
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: crossmap: Disable tests.

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

* gnu/packages/bioinformatics.scm (crossmap)
[arguments]<#:tests?>: Disable them.
[native-inputs]: Remove python-nose, python-wheel.

Change-Id: I2fbbefac935901c4bafea3b8c941b81d3e404a23
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: clipper-peak: Adjust native-inputs.

* gnu/packages/bioinformatics.scm (clipper-peak)[native-inputs]:
Remove python-wheel; replace python-nose by python-pynose; sort a->z.

Change-Id: Id8fa425960c4d8675f3e863e0576dc407c383d8f
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: ciri-long: Replace python-nose by python-pynose.

* gnu/packages/bioinformatics.scm (ciri-long)
[arguments]: Run guix style -S arguments.
[native-inputs]: Replace python-nose by python-pynose.

Change-Id: If028b5e1eb3915019aa6f4798aaf73d4cd13797f
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-benchexec: Adjust native-inputs.

* gnu/packages/benchmark.scm (python-benchexec)[native-inputs]:
Remove python-wheel; replace python-nose by python-pynose.

Change-Id: I2c6a250c249b88c0bc62975956c0660405477ef8
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

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

* gnu/packages/admin.scm (hungrycat)[native-inputs]: Improve style,
replace python-nose by python-pynose.

Change-Id: I922c0ca7d4c24d546e0510e182abc9f584ec3c69
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: hydrus-network: Switch to pyproject.

* gnu/packages/image-viewers.scm (hydrus-network):
[build-system]: Switch to pyproject-build-system.
[arguments]<#:phases>: Rewrite 'check phase replacement.
[native-inputs]: Add python-setuptools.  Remove python-nose.

Change-Id: Ibf6c4e5beacb220c66ede6991ae7b47d873c5c9a
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-pynose: Improve package.

* gnu/packages/python-check.scm (python-pynose):
[arguments] <phases>: Use custom 'check.
[native-inputs]: Remove python-wheel.
[synopsis]: Adjust it to reflect the logic.
[description]: Add more details from proejct's README and mention that
it may be used as Nose replacement.

Change-Id: Ib5b35803d8e5240433a86f57423d28691ec696e8

image: Fix bootloader-uses-grub-efi logic.

* gnu/system/image.scm (bootloader-uses-grub-efi?):
Check by symbol names, not by bounded symbols.

Change-Id: Ia50b07a160ca9c081c9e4cb5e3d6ebdabc89ad4c
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

image: Supply grub-efi from esp partition initializer.

Instead of passing down grub-efi in system-disk-image,
pass it down only where it's necessary - in esp partitions.

Since the esp partitions are only for grub, I renamed them
so that it's more clear to future users of them. They
do not check the bootloader of os at all, they always
initialize grub.

Followup of 1dfe1ebdf6399256b5ed9f2d6e77722aceaae07d,
fixing regression for mbr-hybrid images.

Fixes: #4538.

* guix/system/image.scm
(esp-partition/grub): Rename from esp-partition; Pass grub-efi to
initialize-efi-partition.
(esp32-partition/grub): Rename from esp32-partition; Pass grub32-efi to
initialize-efi-partition.
(esp-partition, (esp32-partition): Deprecate.
(system-disk-image): Do not supply grub-efi arguments.

Change-Id: I336c3144e8efc3ce872031e631d64d3708546ff8
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: Add open-logic.

* gnu/packages/electronics.scm (open-logic): New variable.

Change-Id: Icb4619170339d678d7769de09a4ca36ff87b1221
Signed-off-by: Gabriel Wicki <gabriel@erlikon.ch>

gnu: Add python-sounddevice.

* gnu/packages/audio.scm (python-sounddevice): New variable.

Change-Id: Ia4bb0b52aab812232f82ca299b29e429d07007ce
Signed-off-by: Gabriel Wicki <gabriel@erlikon.ch>

gnu: emacs-gptel-prompts: Update to 1.0-2.f1c2920.

* gnu/packages/emacs-xyz.scm (emacs-gptel-prompts): Update to
1.0-2.f1c2920.

Change-Id: If4a077419a9729bd9767481cb2ef719ddc6c1ddc

gnu: emacs-gptel: Update to 0.9.9.3.

* gnu/packages/emacs-xyz.scm (emacs-gptel): Update to 0.9.9.3.
[arguments]: Add #:test-command.
<#:phases>: Add ’unpack-tests, ’rename-pkg, ’rename-pkg-back and updated
’use-appropriate-curl.
[native-inputs]: Add emacs-gptel-test-files.

Change-Id: I4cbdba248a108d87f9c4b43d36de5ec912fa4d5e

gnu: ocaml-4.07: Fix build with gcc@14.

* gnu/packages/ocaml.scm (ocaml-4.07)[arguments]:
   <#:phases>{patch-cflags}: Add CFLAGS
  `-Wno-incompatible-pointer-types` and
  `-Wno-implicit-function-declaration` to configure and build scripts.
  Also remove `-Werror` to avoid failure on macro redefinition.

Change-Id: I2defd11fc2741856cd48f853706fe37b165a16c0
Signed-off-by: Julien Lepiller <julien@lepiller.eu>

gnu: camlboot: Fix build with gcc@14.

* gnu/packages/ocaml.scm (camlboot)[arguments]:
  <#:phases>{patch-makefile}: Make configure errors more visible.
  <#:phases>{patch-cflags}: Add CFLAGS
  `-Wno-incompatible-pointer-types` and
  `-Wno-implicit-function-declaration` to configure and build scripts.
  Also remove `-Werror` to avoid failure on macro redefinition.

Change-Id: I132ae6af1360f63cccfa6dd3afcb643c92726487
Signed-off-by: Julien Lepiller <julien@lepiller.eu>

gnu: ocaml-guile: Fix build with gcc@14.

* gnu/packages/ocaml.scm (ocaml-guile)[arguments]: Modify Dune
  configurator script to add CFLAG `-Wno-int-conversion`.

Change-Id: I9eab10fc7e10904e46346bfeb207eae3a58ca300
Signed-off-by: Julien Lepiller <julien@lepiller.eu>

gnu: podman: Update to 5.7.0.

* gnu/packages/containers.scm (podman): Update to 5.7.0.
[arguments]<#:phases>{fix-hardcoded-paths}: Update file name.
[native-inputs]: Use go-1.24.

Closes: https://issues.guix.gnu.org/79919
Change-Id: I4193174311eee928a98a653e16d6be4a5deb2624
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: go-github-com-cpuguy83-go-md2man-v2: Update to 2.0.7.

* gnu/packages/golang-xyz.scm (go-github-com-cpuguy83-go-md2man-v2): Update to
2.0.7.

Change-Id: I91a88f88c3ee974eb0a1191bc1c87ed438200530
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>