python-pyhmmer: Update python-pyhmmer PKGBUILD

[althonos]

Involved packages

• python-pyhmmer

Details

• Tested in the local machine (largest 16G RAM) and it is passed without any issue
• Provide New Package
• Fix the Packages
  • PKGBUILD
  • lilac.yaml
  • lilac.py
• Would like to continue to work with us

Additional Note

This PR updates the python-pyhmmer PKGBUILD to the latest version. The last release (v0.11.0) changed the build system from setuptools to CMake and scikit-build-core, so the build dependencies and process had to be updated.

[starsareintherose]

Is git still nedded in make depends as the source is a git url

[kbipinkumar]

git is needed for initialising submodules present in the vendor folder. without git as makedepends the build will fail in clean chroot

additionally while attempting to build with modified `PKGBUILD' after adding git as dependency the build process fails at check() stage with following output

*** Making wheel...
*** Created pyhmmer-0.11.0-cp313-cp313-linux_x86_64.whl
Successfully built pyhmmer-0.11.0-cp313-cp313-linux_x86_64.whl
==> Starting check()...
Traceback (most recent call last):
  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "/usr/lib/python3.13/site-packages/installer/__main__.py", line 98, in <module>
    _main(sys.argv[1:], "python -m installer")
    ~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.13/site-packages/installer/__main__.py", line 86, in _main
    with WheelFile.open(args.wheel) as source:
         ~~~~~~~~~~~~~~^^^^^^^^^^^^
  File "/usr/lib/python3.13/contextlib.py", line 141, in __enter__
    return next(self.gen)
  File "/usr/lib/python3.13/site-packages/installer/sources.py", line 162, in open
    with zipfile.ZipFile(path) as f:
         ~~~~~~~~~~~~~~~^^^^^^
  File "/usr/lib/python3.13/zipfile/__init__.py", line 1362, in __init__
    self.fp = io.open(file, filemode)
              ~~~~~~~^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/build/python-pyhmmer/src/pyhmmer-0.11.0/dist/pyhmmer-0.11.0-cp313-cp313-linux_x86_64.whl'
==> ERROR: A failure occurred in check().
    Aborting...

[sukanka]

Thanks for your contribution, could you please fix these minor problems?

[althonos]

@sukanka @starsareintherose @kbipinkumar : Good catch, thanks. I tested this locally on a computer with git installed and didn't realize I removed it.

[kbipinkumar]

running namcap on final package archive shows following missing dependencies

> namcap python-pyhmmer-0.11.0-1-x86_64.pkg.tar.zst | less | grep "E:"
python-pyhmmer E: Dependency python-typing_extensions detected and not included (python modules ['typing_extensions.Literal', 'typing_extensions.TypedDict', 'typing_extensions.Unpack'] needed in files ['usr/lib/python3.13/site-packages/pyhmmer/hmmer/_base.py', 'usr/lib/python3.13/site-packages/pyhmmer/hmmer/_jackhmmer.py'])
python-pyhmmer E: Dependency python-numpy detected and not included (python modules ['numpy'] needed in files ['usr/lib/python3.13/site-packages/pyhmmer/tests/test_doctest.py'])

python-numpy is probably for running tests during build process but python-typing_extensions seems to be imported by main pyhmmer package itself.

[althonos]

python-typing_extensions is also not required, it's only ever needed for Python versions older than 3.11, and only used in type checking, so the package will work just fine without it as the imports are gated:

if typing.TYPE_CHECKING:

    if sys.version_info >= (3, 8):
        from typing import Literal, TypedDict
    else:
        from typing_extensions import Literal, TypedDict  # type: ignore

[kbipinkumar]

python-typing_extensions is also not required, it's only ever needed for Python versions older than 3.11, and only used in type checking, so the package will work just fine without it as the imports are gated:

if typing.TYPE_CHECKING:

    if sys.version_info >= (3, 8):
        from typing import Literal, TypedDict
    else:
        from typing_extensions import Literal, TypedDict  # type: ignore

Okay. So we can ignore the errors.

[starsareintherose]

@sukanka Can this PR be merged?

[kbipinkumar]

@sukanka Can this PR be merged?

the license install line in package () section needs to be modified as install -Dm644 ${srcdir}/${_name}/COPYING "$pkgdir/usr/share/licenses/$pkgname/COPYING" to call proper build directory. everything else is fine

[kbipinkumar]

install -Dm644 ${srcdir}/${_name}-${pkgver}/COPYING "$pkgdir/usr/share/licenses/$pkgname/COPYING" should be changed to install -Dm644 ${srcdir}/${_name}/COPYING "$pkgdir/usr/share/licenses/$pkgname/COPYING" as well for calling the correct build directory