This request goes along with #100812 and #100814 that also update all related dependencies to have a consistent version (1.11)

Can any of you test if the current commit succeeds on your end?
I applied the changes suggested above and I started getting:

    import pysam
pysam/__init__.py:5: in <module>
    from pysam.libchtslib import *
E   ModuleNotFoundError: No module named 'pysam.libchtslib'

I also got this failure while reviewing #100654 but @jonringer reported success there.
The build also includes pysam in pythonImportCheck so I don't understand why it worked. I assumed it was some misconfiguration on my side. This was also the reason why I decided to try to enable the tests here.

I now also made pysam use the nixpkgs htslib instead of the bundled one, but the error was already present before this change.

I also got this failure while reviewing #100654 but @jonringer reported success there.
The build also includes pysam in pythonImportCheck so I don't understand why it worked. I assumed it was some misconfiguration on my side. This was also the reason why I decided to try to enable the tests here.

sometimes if you have a local directory with the module name, ./pysam/, python will prefer to attempt to import from there, however, that's generally not what you want.

usually I do something like:

  preCheck = ''
    rm -r pysam
  '';

  preCheck = ''
    rm -r pysam
  '';

Added this and pytest stopped finding any test.

============================= test session starts ==============================
platform linux -- Python 3.8.6, pytest-5.4.3, py-1.9.0, pluggy-0.13.1 -- /nix/store/346skv0d24rqnf4npknbp9h5bs14j8zy-python3-3.8.6/bin/python3.8
cachedir: .pytest_cache
rootdir: /build/source, inifile: setup.cfg, testpaths: pysam, tests
collected 0 items                                                              

============================ no tests ran in 0.00s =============================
ERROR: file not found: pysam

Then adding pytestFlagsArray = [ "tests/" ]; fails with:

Traceback:
tests/test_samtools_python.py:1: in <module>
    import pysam
pysam.py:1: in <module>
    raise ImportError('''calling "import pysam" from the source directory is not supported - please import pysam from somewhere else.''')
E   ImportError: calling "import pysam" from the source directory is not supported - please import pysam from somewhere else.

This happens because tests are launched with ../python -m pytest ... and pysam seems to not like to be loaded this way.
Oddly enough running the exact same command with pytest ... instead of python -m pytest works.

I feel I'm getting deeper and deeper into rabbit holes with this... Can I somehow tell nix to use the pytest command instead of python -m pytest without overriding pytestCheckPhase and losing the benefits of disabledTests ?

Ok, I'm reverting the use of pytestCheckHook due to the two issues above:

• pysam detecting how its loaded and raising an exception when loaded by pytest launched with python -m pytest.
• disableTests ignoring more tests than the failing ones (52 instead of 11).

I'll revisit this in the future if pytestCheckHook adds additional mechanisms to customize how tests are executed.

Thanks everyone and in particular @jonringer for detailed reviewing and lots of feedback and guidance.