Fix ResourceWarning due to unclosed file

[kkovary]

Changelogs

closes #211

• enumerate the changes of that PR. This PR addresses a ResourceWarning that was being raised due to an unclosed file in datamol/mol.py. The warning was triggered by the following line of code:

  SALT_SOLVENT_PATH = datamol.data.open_datamol_data_file("salts_solvents.smi").name

This line opens a file but does not close it, which is why the ResourceWarning was being raised. To resolve this issue, I've modified the line to use a with block, which ensures that the file is properly closed after its name is retrieved:

with datamol.data.open_datamol_data_file("salts_solvents.smi") as file_obj:
    SALT_SOLVENT_PATH = file_obj.name

This change should prevent the ResourceWarning from being raised in the future. I've tested the change locally and confirmed that it resolves the warning without causing any other issues.

---

Checklist:

• [ ] Was this PR discussed in an issue? It is recommended to first discuss a new feature into a GitHub issue before opening a PR.
• [ ] Add tests to cover the fixed bug(s) or the new introduced feature(s) (if appropriate).
• [ ] Update the API documentation is a new function is added, or an existing one is deleted.
• [ ] Write concise and explanatory changelogs below.
• [x] If possible, assign one of the following labels to the PR: feature, fix or test (or ask a maintainer to do it for you).

---

discussion related to that PR

[codecov[bot]]

Codecov Report

Merging #212 (4bf712c) into main (22b5bb0) will decrease coverage by 0.04%. The diff coverage is 77.77%.

@@            Coverage Diff             @@
##             main     #212      +/-   ##
==========================================
- Coverage   91.95%   91.91%   -0.04%     
==========================================
  Files          46       46              
  Lines        3827     3835       +8     
==========================================
+ Hits         3519     3525       +6     
- Misses        308      310       +2     

Flag	Coverage Δ
unittests	91.91% <77.77%> (-0.04%)	:arrow_down:

Flags with carried forward coverage won't be shown. Click here to find out more.

Files Changed	Coverage Δ
datamol/data/__init__.py	78.07% <75.00%> (-0.24%)	:arrow_down:
datamol/mol.py	97.00% <100.00%> (ø)

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[hadim]

Thank you for the catch! This is indeed a bug, but I don't think we should even open that file to get its path. Instead we should simply retrieve the path.

In datamol/data/__init__.py, can you add the below function and use it in mol.py with SALT_SOLVENT_PATH = datamol_data_file_path("salts_solvents.smi")?

@functools.lru_cache()
def datamol_data_file_path(filename: str, dm_module: str = "datamol.data"):
    if sys.version_info < (3, 9, 0):
        with importlib_resources.path("datamol.data", filename) as p:
            data_path = p
    else:
        data_path = importlib_resources.files(dm_module).joinpath(filename)

    return str(data_path)

[kkovary]

Thanks for the suggestion @hadim, that's definitely a much better way of handling things. I'll push an update a little later today.

[kkovary]

@hadim I just pushed a commit with the requested changes.

[hadim]

Thank you, @kkovary, for your contribution!

[kkovary]

Thank you @hadim for the wonderful tools, hope to make more contributions in the future 😄