tests don't run from pycharm

[cmungall]

/Users/cjm/Library/Caches/pypoetry/virtualenvs/semsim-UokXyP9h-py3.9/bin/python /Applications/PyCharm.app/Contents/plugins/python/helpers/pycharm/_jb_unittest_runner.py --path /Users/cjm/repos/semsim/tests/test_get_phenodigm_pairs.py 
Testing started at 3:40 PM ...
Launching unittests with arguments python -m unittest /Users/cjm/repos/semsim/tests/test_get_phenodigm_pairs.py in /Users/cjm/repos/semsim/tests


Error
Traceback (most recent call last):
  File "/Users/cjm/repos/semsim/tests/test_get_phenodigm_pairs.py", line 40, in test_make_filtered_map
    map_df = pd.read_csv(
  File "/Users/cjm/Library/Caches/pypoetry/virtualenvs/semsim-UokXyP9h-py3.9/lib/python3.9/site-packages/pandas/util/_decorators.py", line 311, in wrapper
    return func(*args, **kwargs)
  File "/Users/cjm/Library/Caches/pypoetry/virtualenvs/semsim-UokXyP9h-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 680, in read_csv
    return _read(filepath_or_buffer, kwds)
  File "/Users/cjm/Library/Caches/pypoetry/virtualenvs/semsim-UokXyP9h-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 575, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
  File "/Users/cjm/Library/Caches/pypoetry/virtualenvs/semsim-UokXyP9h-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 934, in __init__
    self._engine = self._make_engine(f, self.engine)
  File "/Users/cjm/Library/Caches/pypoetry/virtualenvs/semsim-UokXyP9h-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1218, in _make_engine
    self.handles = get_handle(  # type: ignore[call-overload]
  File "/Users/cjm/Library/Caches/pypoetry/virtualenvs/semsim-UokXyP9h-py3.9/lib/python3.9/site-packages/pandas/io/common.py", line 786, in get_handle
    handle = open(
FileNotFoundError: [Errno 2] No such file or directory: 'tests/resources/test_mapping.csv'





Ran 2 tests in 0.011s

FAILED (errors=2)

Error
Traceback (most recent call last):
  File "/Users/cjm/repos/semsim/tests/test_get_phenodigm_pairs.py", line 27, in test_make_phenodigm
    make_phenodigm(
  File "/Users/cjm/repos/semsim/semsim/get_phenodigm_pairs.py", line 46, in make_phenodigm
    raise FileNotFoundError(f"Cannot find {filepath}!")
FileNotFoundError: Cannot find tests/resources/test_jaccard!

I recommend not constructing strings with "/"s, it's not very portable. Older code uses os.path.join but I recommend doing with Path, see:

https://github.com/INCATools/ontology-access-kit/blob/56778858b271838ce2db6cd6a4f87287952c68fa/tests/__init__.py#L1-L8

[justaddcoffee]

One thing to check here in PyCharm is the working directory in your runtime configuration - PyCharm automatically sets this to the test/ directory, and breaks these tests with hardcoded paths to test fixtures

I recommend not constructing strings with "/"s, it's not very portable. Older code uses os.path.join but I recommend doing with Path, see:
https://github.com/INCATools/ontology-access-kit/blob/56778858b271838ce2db6cd6a4f87287952c68fa/tests/__init__.py#L1-L8

+1