ci: Check PRs for semantic labels

[flying-sheep]

… and adapts towncrier fragments to match the labels

Also:

• cleans up CI (remove useless options, update actions)
• adds dependabot for automatic GH actions updates
• uploads test results to codecov

Does not:

• check if PR title matches fragment (TODO? how to deal with breaking vs “!”)?

[codecov]

❌ 1 Tests Failed:

Tests completed	Failed	Passed	Skipped
6526	1	6525	1163

View the top 1 failed test(s) by shortest run time

src.anndata.experimental.merge::anndata.experimental.merge.concat_on_disk

Stack Traces | 0.349s run time

518 ...     sc.settings.datasetdir.mkdir(parents=True, exist_ok=True)
519 ...     out_path.write_bytes(httpx.get(file_url).content)
520 ...     return out_path
521 >>> path_b_cells = get_cellxgene_data('a93eab58-3d82-4b61-8a2f-d7666dcdb7c4')
522 >>> path_fetal = get_cellxgene_data('d170ff04-6da0-4156-a719-f8e1bbefbf53')
523 
524 Now we can concatenate them on-disk:
525 
526 >>> import anndata as ad
527 >>> ad.experimental.concat_on_disk(
UNEXPECTED EXCEPTION: OSError('Unable to synchronously open file (truncated file: eof = 10682368, sblock->base_addr = 0, stored_eof = 22528845)')
Traceback (most recent call last):
  File "............/home/runner/.local.../uv/python/cpython-3.13.7-linux-x86_64-gnu/lib/python3.13/doctest.py", line 1398, in __run
    exec(compile(example.source, filename, "single",
    ~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                 compileflags, True), test.globs)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<doctest anndata.experimental.merge.concat_on_disk[7]>", line 1, in <module>
  File ".../anndata/experimental/merge.py", line 581, in concat_on_disk
    groups = [as_group(f, mode="r") for f in in_files]
              ~~~~~~~~^^^^^^^^^^^^^
  File "............/home/runner/.local.../uv/python/cpython-3.13.7-linux-x86_64-gnu/lib/python3.13/functools.py", line 934, in wrapper
    return dispatch(args[0].__class__)(*args, **kw)
           ~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
  File ".../anndata/experimental/merge.py", line 115, in _
    return h5py.File(store, mode=mode)
           ~~~~~~~~~^^^^^^^^^^^^^^^^^^
  File "............/home/runner/.local.../anndata/88DSKUwu/hatch-test.pre/lib/python3.13.../h5py/_hl/files.py", line 564, in __init__
    fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)
  File "............/home/runner/.local.../anndata/88DSKUwu/hatch-test.pre/lib/python3.13.../h5py/_hl/files.py", line 238, in make_fid
    fid = h5f.open(name, flags, fapl=fapl)
  File "h5py/_objects.pyx", line 56, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 57, in h5py._objects.with_phil.wrapper
  File "h5py/h5f.pyx", line 102, in h5py.h5f.open
OSError: Unable to synchronously open file (truncated file: eof = 10682368, sblock->base_addr = 0, stored_eof = 22528845)
#x1B[1m#x1B[31m.../anndata/experimental/merge.py#x1B[0m:527: UnexpectedException

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[flying-sheep]

please double-check if I got them all right. I didn’t add a test, but these don’t change so it should be fine.