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Standardize toolkit I/O #1006

Merged
merged 43 commits into from
Jul 7, 2021
Merged

Standardize toolkit I/O #1006

merged 43 commits into from
Jul 7, 2021

Commits on Jul 1, 2021

  1. normalize format name to upper-case

    @adalke
    adalke committed Jul 1, 2021
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  2. normalize file format in from_file_obj(). Move .upper() to a common f… 

    …unction
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  3. raise an exception when the format isn't supported, rather than retur… 

    …ning mols = []
    @adalke
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  4. use a common helper function to map file_format to the OEFormat_*; ra… 

    …ise ValueError if not found.
    @adalke
    adalke committed Jul 1, 2021
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  5. OpenEye wrapper from_file() now listens to file_format

    @adalke
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  6. in RDKit.from_file_obj(file_format="SMI") save to a local file and us… 

    …e SmilesMolSupplier instead of writing a new SMILES parser
    @adalke
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  7. the RDKit API allows "MOL" as an alias for "SDF" so do the same here.

    @adalke
    adalke committed Jul 1, 2021
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  8. forward RDKit's from_file_obj(allow_undefined_stereo) for SDF

    @adalke
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  9. properly change if/elif in format_name test. If from_file_obj(format_… 

    …name) doesn't exist, raise ValueError
    @adalke
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  10. test the OEChem and RDKit toolkit wrappers have the same file I/O beh… 

    …avior
    @adalke
    adalke committed Jul 1, 2021
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Commits on Jul 2, 2021

  1. check fileobj coordinate handling. Check _cls handling in from_file/f… 

    …rom_file_obj
    @adalke
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  2. pulled the SDF parsing into its own method so from_file_obj() could u… 

    …se the same code as from_file()
    @adalke
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  3. add tests for the "smi" to_file()/to_file_obj(), change toolkits to u… 

    …se the same SMILES as to_smiles(); don't include a header line in RDKit
    @adalke
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  4. added more informative error messages when the file_obj is in binary … 

    …instead of text mode
    @adalke
    adalke committed Jul 2, 2021
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  5. normalize the error message when the output format isn't supported

    @adalke
    adalke committed Jul 2, 2021
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  6. check for SMILES parse error

    @adalke
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  7. add some basic SMILES tests

    @adalke
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  8. fixed bug where the RDKit SMILES file output didn't include the molec… 

    …ule name
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  9. check for "ethanol" in the SMILES output line. Check that stereochemi… 

    …stry testing works in from_smiles()
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  10. added atom_map test from test_toolkits.py

    @adalke
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  11. black and isort

    @adalke
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  12. the change I made support OEChem to_file() means I don't need tempora… 

    …ry_cd()
    @adalke
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  13. add requires_{rdkit,openeye} guards

    @adalke
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  14. improve comments for data file managers. Using "file_obj_manager" ins… 

    …tead of "fileobj_manager" for consistency
    @adalke
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  15. added test that the SDF parser could handle two molecules

    @adalke
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  16. test reading two molecules from a SMILES file

    @adalke
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  17. handle RDKit parse failures in SMILES file lines instead of raise an … 

    …odd exception with the None molecule
    @adalke
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  18. tests for reading multiple structure SDF/SMI files, including skippin… 

    …g error records
    @adalke
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  19. use Chem.ForwardSDMolSuppler instead of Chem.SupplierFromFilename bec… 

    …ause the format is specified; no need to guess from the filename.
    @adalke
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  20. Added OEChem ifs(filename).IsValid() test to see if the open failed. … 

    …Raise error if it fails.
    @adalke
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  21. added test that file_format overrides any default guess the toolkit m… 

    …ight have
    @adalke
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  22. check OEChem oeofstream(filename).IsValid() and raise OEError on failure

    @adalke
    adalke committed Jul 2, 2021
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  23. black cleanup

    @adalke
    adalke committed Jul 2, 2021
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  24. added ParseError to toolkit.utils.__all__

    @adalke
    adalke committed Jul 2, 2021
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  25. I should learn to run the tests before committing. They work again.

    @adalke
    adalke committed Jul 2, 2021
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  26. added information about issue #1005 / PR #1006

    @adalke
    adalke committed Jul 2, 2021
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Commits on Jul 3, 2021

  1. improved documentation on RDKit SMILES from_file_obj() backwards comp… 

    …ability support for 't'ext mode files
    @adalke
    adalke committed Jul 3, 2021
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  2. Put information about the changed to_file(file_format="SMI") behavior… 

    …s: explicit [H]:s for both toolkits, no header line for RDKit
    @adalke
    adalke committed Jul 3, 2021
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  3. improved the text (hopefully) concerning the SMILES to_file() changes… 

    … from PR #1006.
    @adalke
    adalke committed Jul 3, 2021
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Commits on Jul 7, 2021

  1. comment the toolkit wrapper fixture based on feedback at #1006 (comment)

    @adalke
    adalke committed Jul 7, 2021
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  2. fixed copy&paste error resulting in two tests with the same name. 

    Fixed the test case that wasn't actually being tested.
    @adalke
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  3. fixed two more cases where copy&paste'd method names weren't updated,… 

    … shadowing other tests
    @adalke
    adalke committed Jul 7, 2021
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  4. black

    @adalke
    adalke committed Jul 7, 2021
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