Pytest picking up tests in wrong location?

[LiterallyUniqueLogin]

• a detailed description of the bug or suggestion

I have two copies of a package on my computer: one which is installed (at /storage/conda/lib/python3.7/site-packages/trtools) and one which has been cloned from git (at /tmp/trtools_data_download/trtools). I'm doing this because I want to test the installed package but some of the test data only exists in the repo and not in the installation.

I want to test the installed package with pytest, but when I run it it is picking up the python test files from the cloned git repo and not the installation, even though I've cd'd to the root of the installation. Any idea why this is happening?

Here is the relevant output. Note the location of test_compareSTR.py file that is being run is not the copy in my current subdirectory.

The --datadir argument is something my tests pick up via the instructions here. It's the only thing I can think of that could be mucking with test discovery. But I don't see how it would do that.

(temp_pip_install) $ ls /storage/conda/lib/python3.7/site-packages/trtools/compareSTR/tests/
__init__.py  __pycache__  test_compareSTR.py
(temp_pip_install) $ pwd
/storage/conda/lib/python3.7/site-packages/trtools
(temp_pip_install) $ python -m pytest . -p trtools.testsupport.dataloader --datadir /tmp/trtools_data_download/trtools/testsupport
========================================== test session starts ==========================================
platform linux -- Python 3.7.6, pytest-5.4.2, py-1.8.1, pluggy-0.13.1
rootdir: /tmp/trtools_data_download, inifile: pytest.ini
collected 72 items

../../../../../../../tmp/trtools_data_download/compareSTR/tests/test_compareSTR.py ..             [  2%]

• output of pip list from the virtual environment you are using

(temp_pip_install) $ pip list
Package                Version
---------------------- -------------------
attrs                  19.3.0
certifi                2020.4.5.1
cffi                   1.14.0
chardet                3.0.4
conda                  4.8.3
conda-package-handling 1.7.0
cryptography           2.9.2
cycler                 0.10.0
idna                   2.9
importlib-metadata     1.6.0
kiwisolver             1.2.0
matplotlib             3.2.1
more-itertools         8.3.0
numpy                  1.18.4
packaging              20.4
pandas                 1.0.4
pip                    20.0.2pluggy                 0.13.1
py                     1.8.1
pybedtools             0.8.1
pycosat                0.6.3
pycparser              2.20
pyOpenSSL              19.1.0
pyparsing              2.4.7
pysam                  0.15.4
PySocks                1.7.1
pytest                 5.4.2
python-dateutil        2.8.1
pytz                   2020.1
PyVCF                  0.6.8
requests               2.23.0
ruamel-yaml            0.15.87
scipy                  1.4.1
setuptools             46.4.0.post20200518
six                    1.14.0
tqdm                   4.46.0
trtools                2.0.18
urllib3                1.25.8
wcwidth                0.1.9
wheel                  0.34.2
zipp                   3.1.0

• pytest and operating system versions

(temp_pip_install) $ pytest --version
This is pytest version 5.4.2, imported from /storage/conda/lib/python3.7/site-packages/pytest/__init__.py

(temp_pip_install) $ cat /etc/os-releaseNAME="CentOS Linux"VERSION="7 (Core)"ID="centos"ID_LIKE="rhel fedora"

Thanks for the help!

[RonnyPfannschmidt]

this is a bug as pytest suport for packages is second class, and the insertion of the path in the arguments messes with the combination of the test folder finding

[gdhameeja]

I'd like to work on this.

[nicoddemus]

@RonnyPfannschmidt perhaps this was fixed in #7040?

[RonnyPfannschmidt]

Seems possible, but we have validate

[nicoddemus]

@LiterallyUniqueLogin is it possible for you to test that with the latest master? Or provide a minimal reproducible example so we can try it out?

[bluetech]

Closing per above.