file not found error in abspath

[martinschorb]

Hi,

in just one CI environment I run into a file not found error in os.path.abspath:

/opt/conda/lib/python3.7/site-packages/mobie/image_data.py:87: in add_bdv_image
    data_path = bdv_metadata.get_data_path(xml_path, return_absolute_path=True)
/opt/conda/lib/python3.7/site-packages/pybdv/metadata.py:845: in get_data_path
    path = os.path.abspath(os.path.relpath(path))
/opt/conda/lib/python3.7/posixpath.py:475: in relpath
    start_list = [x for x in abspath(start).split(sep) if x]
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
path = '.'
    def abspath(path):
        """Return an absolute path."""
        path = os.fspath(path)
        if not isabs(path):
            if isinstance(path, bytes):
                cwd = os.getcwdb()
            else:
>               cwd = os.getcwd()
E               FileNotFoundError: [Errno 2] No such file or directory
/opt/conda/lib/python3.7/posixpath.py:383: FileNotFoundError

Doing some research, I found that if CWD is deleted during the call, it can cause this behaviour in certain combinations in a python environment.

conda/conda#6584
pytest-dev/pytest-cov#306

I cannot really understand what is going on, because the error does NOT show up neither in my dev environment nor in my docker that I use to mimic the CI scenario. There, the tests run just fine.
Only on the Gitlab CI, I run into this error.
I also tried forcing certain conda or pytest versions without success.

Do you think that there is potential confusion for CWD by some cd calls somewhere in mobie or pybdv.metadata that we could change to avoid running into this scenario?

[constantinpape]

Do you think that there is potential confusion for CWD by some cd calls somewhere in mobie or pybdv.metadata that we could change to avoid running into this scenario?

No, neither mobie nor pybdv.metadata do any os.chdir or similar directory changing. This looks like an issue with your CI set-up that's not connected to pybdv. I would recommend to either deactivate that setting or mark the corresponding test as expected failure for it.

[martinschorb]

OK, that's what I expected. I really have no idea what's going on.
Unfortunately the mobie.add_image call is the core of the procedure I like to test.
Fingers crossed that there is some solution on the CI side for this.