patch to pass Python pytest checks (applies only to Linux) #96
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With the advent of Python 3.13, this no longer yields only a syntax warning but is a syntax error (label F632 by flake8, version 7.1.1). Edit based on discussion.[1] [1] mcs07#92 Signed-off-by: Norwid Behrnd <nbehrnd@yahoo.com>
Matthew Swan left a considerable test bench of Pytest checks. Coupled to a GitHub action, this could be used to check the state of the package. Based on `datawarrior_clustersort`,[1] the scope is constrained to Linux (GitHub's runner of Ubuntu 24.04) with Python 3.13 because PubChemPy's work in Windows is known to (currently) present difficulties.[2] [1] https://github.com/nbehrnd/datawarrior_clustersort [2] mcs07#89 Signed-off-by: Norwid Behrnd <nbehrnd@yahoo.com>
The PubChem database limits the number of queries per unit of time. The threshold appears to be lower, than the GitHub runners normally launch pytest checks which eventually may yield to a refusal by PubChem's interface, and hence a failure of a pytest check. This is now addressed with a throttle on pytest's side. Signed-off-by: Norwid Behrnd <nbehrnd@yahoo.com>
Previously, the Python wheel likely was build with bdist and the `setup.py`. A build with `python -m build` and organization with a `pyproject.toml` file can be set up independent to this as an additional workflow which independent to the former. Signed-off-by: Norwid Behrnd <nbehrnd@yahoo.com>
At present, the bioassay of PubChem AID 490 is of status "revoked".[1] This contrasts e.g., to AID 1490 of current status "live".[2] By edit of the test script, instead of "1 failure 3 errors" pytest now reports "1 failure 3 passes" indicative some problems of the automated checks indeed are due to changes on the side of the database accessed. [1] https://pubchem.ncbi.nlm.nih.gov/bioassay/490 [2] https://pubchem.ncbi.nlm.nih.gov/bioassay/1490 Signed-off-by: Norwid Behrnd <nbehrnd@yahoo.com>
Manual tests on pubchem's website reveal AID 3490 is a record which fits the criterion of "Project Category == Literature, Extracted" (section 8.4 on the current web site layout).[1] This edit eventually renders all assertions of the pytest script `test_assay.py` True. [1] https://pubchem.ncbi.nlm.nih.gov/bioassay/3490#section=Project-Category Signed-off-by: Norwid Behrnd <nbehrnd@yahoo.com>
As by today CID 150194 is pubchem's record[1] about dichloro- tetrakis(dimethylsulfoxide)ruthenium II (date of creation 2005-08-01, last modification: 2025-03-29). Thus the identifier is removed from function `test_no_identifiers` which in turn renders all other assertions of pytest `test_identifiers.py` True. [1] https://pubchem.ncbi.nlm.nih.gov/compound/150194 Signed-off-by: Norwid Behrnd <nbehrnd@yahoo.com>
There are read-outs of data (for instance `molecular_weight`) from the database which should be processed as floats. As an additional safety layer to process them well (includes checks as defined for instance in file `test_compound.py`), explicit datatype conversions were added. Signed-off-by: Norwid Behrnd <nbehrnd@yahoo.com>
Function `mmff94_energy_3d` is commented out because reference compound 241 (benzene) does not reports this value on its record page[1] (last revision by 2025-03-29) and it appears possible pytest fails (equally) for looking up this in vain. Signed-off-by: Norwid Behrnd <nbehrnd@yahoo.com>
Because the main function doesn't return mmff94_energy_3d`, the check on this by the test function equally is muted. Signed-off-by: Norwid Behrnd <nbehrnd@yahoo.com>
Apparently it isn't presence/absence of column values, but the sequence of these list elements vs the reference which let the check fail. Signed-off-by: Norwid Behrnd <nbehrnd@yahoo.com>
The edits allowing PubChemPy to pass again most of Matthew Swain's test bank actually are a patch and hence should increment the version count. This however acknowledges "working" is constrained to Linux as operating system. Signed-off-by: Norwid Behrnd <nbehrnd@yahoo.com>
In the setup provided by Matthew Swain, versioning is managed from one place. The commit thus establishes again synchronicity, adds the pyproject.toml file (and extends its information about the project). Signed-off-by: Norwid Behrnd <nbehrnd@yahoo.com>
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Changes on side of the PubChem database and Python's syntax broke some of the checks with pytest defined until April 2017. Except for probing the readout of
mmff94_energy_3dnow commented out, each of them pass again in GitHub's runner image of Ubuntu 24.04 with Python 3.13.2 and pytest 8.3.5. The additionalpyproject.tomlfile includes a constraining classifieras a brief reminder about the difficulties to run
pubchempy.pyin Windows.