How to generate test coverage report?

[szabgab]

Question

I ran

hatch test --cover

on the cloned repository.

It started out running the tests, but after 24 minutes I got a bunch of errors.

I copied a few:

ERROR tests/test_readwrite.py::test_forward_slash_key[False-h5ad-layers] - OSError: could not create numbered dir with prefix test_forward_slash_key_False_h in /tmp/pytest-of-gabor/pytest-4 after 10 tries
ERROR tests/test_readwrite.py::test_write_elem_version_mismatch - OSError: could not create numbered dir with prefix test_write_elem_version_mismat in /tmp/pytest-of-gabor/pytest-4 after 10 tries
ERROR tests/test_x.py::test_io_missing_X[zarr2] - OSError: could not create numbered dir with prefix test_io_missing_X_zarr2_ in /tmp/pytest-of-gabor/pytest-4 after 10 tries
==== 23 failed, 5487 passed, 938 skipped, 183 xfailed, 3896 warnings, 1791 errors in 1432.47s (0:23:52) ====

$ python3 -V
Python 3.13.7

$ df -h /tmp/
Filesystem      Size  Used Avail Use% Mounted on
tmpfs            14G  3.4G   11G  25% /tmp

$ du -hs /tmp/pytest-of-gabor/pytest-4/
202M	/tmp/pytest-of-gabor/pytest-4/

[szabgab]

I ran it again. This time it ran for 30 minutes.

It seems to have mad a lot more progress. This is the end of the test report:

tests/test_x.py ................................................................................x....x....x....x..................FF..                                                                       [ 99%]
tests/test_xarray.py ................................                                                                                                                                                        [ 99%]
ci/scripts/min-deps.py E                                                                                                                                                                                     [ 99%]
docs/concatenation.rst E                                                                                                                                                                                     [100%]

==== ERRORS ====
___ ERROR at setup of [doctest] ci.scripts.min-deps.min_dep ___

Then errors and th the summary looks like this:

=== short test summary info ===
FAILED tests/test_x.py::test_io_missing_X[zarr2] - OSError: [Errno 28] No space left on device: '/tmp/pytest-of-gabor/pytest-5/test_io_missing_X_zarr2_0/x_none_adata.zarr/obsm/df/.zgroup.e654f00b7e7b4ffe95e9c41a243f1713.partial'
FAILED tests/test_x.py::test_io_missing_X[zarr3] - OSError: [Errno 28] No space left on device: '/tmp/pytest-of-gabor/pytest-5/test_io_missing_X_zarr3_0/x_none_adata.zarr/zarr.85c145902dd544d88d41a7fab09e4263.partial'
ERROR ci/scripts/min-deps.py::ci.scripts.min-deps.min_dep - OSError: could not create numbered dir with prefix ci_scripts_min_deps_min_dep in /tmp/pytest-of-gabor/pytest-5 after 10 tries
ERROR docs/concatenation.rst::concatenation.rst - OSError: could not create numbered dir with prefix concatenation_rst in /tmp/pytest-of-gabor/pytest-5 after 10 tries
=== 2 failed, 7285 passed, 948 skipped, 185 xfailed, 5164 warnings, 2 errors in 1838.45s (0:30:38) ====

So here I can see it complain about "No space left on device:", but when I check it:

$ du -hs /tmp/pytest-of-gabor/pytest-5
1.6G	/tmp/pytest-of-gabor/pytest-5

and

$ df -h /tmp/
Filesystem      Size  Used Avail Use% Mounted on
tmpfs            14G  3.4G   11G  25% /tmp

So it seems I have space on the disk and yet this seems to be the reported problem.

[flying-sheep]

Your Linux distribution has mounted /tmp/ as tmpfs, i.e. it’s a file system that lives in your memory instead of on disk.

This means that your memory needs to not only fit your system’s memory requiremens and the tests’, but also the temporary files created while testing. I assume you ran out of memory, so your system started swapping, which slowed everything down.

I didn’t check, but you might be able to use pytest’s --basetemp option:

hatch test --basetemp=/home/$USER/.cache

Aon’t forget to delete ~/.cache/pytest-* after you’re done!

And please report back! anndata’s tests do some funky things with the tempdir, so changing it should work, but isn’t guaranteed.

I hope that clears everything up, but please check back if you still have problems! It should be possible to contribute to AnnData without 32GB of RAM for sure!