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[v2]: CI Overhaul (and make v2 actually _pass_ the CI) #714

Merged
merged 18 commits into from
Apr 1, 2024
Merged

[v2]: CI Overhaul (and make v2 actually _pass_ the CI) #714

merged 18 commits into from
Apr 1, 2024

Commits on Apr 1, 2024

  1. overhaul the continuous integration file 

    see inline comments and PR description for more details
    @JacksonBurns
    JacksonBurns committed Apr 1, 2024
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  2. update .flake8 for the new filepaths post-v2rc1

    @JacksonBurns
    JacksonBurns committed Apr 1, 2024
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  3. huge code churn for compliance with pep8, see extended 

     - removed unused imports
 - change tests with unused variables to instead use said variables
 - update the `pyproject.toml` specification for pep8 checking to match what we were doing in the CI
 - replaced star imports with explicit imports
 - add explicit exports in `__init__.py`'s
 - generic formatting changes i.e. trailing spaces, newlines, etc.
    @JacksonBurns
    JacksonBurns committed Apr 1, 2024
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  4. make CI build test actually use builld instead of install

    @JacksonBurns
    JacksonBurns committed Apr 1, 2024
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  5. black check in ci verbose

    @JacksonBurns
    JacksonBurns committed Apr 1, 2024
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  6. fix the required version of black in pyproject and ci 

    otherwise it can pass locally and fail on GHA
    @JacksonBurns
    JacksonBurns committed Apr 1, 2024
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  7. fix erroneous imports in the utils init file

    @JacksonBurns
    JacksonBurns committed Apr 1, 2024
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  8. fix missing import for featurizers

    @JacksonBurns
    JacksonBurns committed Apr 1, 2024
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  9. fix typo in class name

    @JacksonBurns
    JacksonBurns committed Apr 1, 2024
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  10. replace pytorch_scatter with native pytorch scatter calls 

     - simplifies installation process throughout as well
    @JacksonBurns
    JacksonBurns committed Apr 1, 2024
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  11. remove unused dependency from optional test installation

    @JacksonBurns
    JacksonBurns committed Apr 1, 2024
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  12. set default num_workers in CLI to match docstring of dataloader class 

    this resolves the hanging issue on windows and for some reason mac
    @JacksonBurns
    JacksonBurns committed Apr 1, 2024
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  13. review comment - clarify inline comment

    @JacksonBurns
    JacksonBurns committed Apr 1, 2024
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  14. remove unused dependencies from test CI step

    @JacksonBurns
    JacksonBurns committed Apr 1, 2024
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  15. whitepsace fixes for checkpoint loading fix 

    linter was not run on chemprop#741
    @JacksonBurns
    JacksonBurns committed Apr 1, 2024
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  16. review comment - change line length in ci.yml 

    see chemprop#714 (comment)
    @JacksonBurns
    JacksonBurns committed Apr 1, 2024
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  17. review comment - check individual elements are none to comply with pep8 

    see chemprop#714 (comment)
    @JacksonBurns
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  18. review comment - fix re-implementation of scatter_softmax 

    see chemprop#714 (comment)
    @JacksonBurns
    JacksonBurns committed Apr 1, 2024
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