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Code Cleanup #28

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Code Cleanup #28

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This PR is mainly to resolve a number of potential issues and code quality concerns in the current state of the repository. In particular, this PR aims to fix the following (among other minor fixes):

  • Over-reliance on the os package, which can be unsafe (or, at least, less safe than pathlib for what its being used for)
  • Output fails to work as expected, often crashing out in common use cases (i.e. relative output paths, see Designating where to place output fails in many cases #26)
  • Many hard-coded variables in the code itself, rather than in separate configuration files, making the code overly specific to only out use-case
  • Inefficient use of Pandas utilities (making code take much longer than it could, or being harder to debug/generalize)
  • Overzealous imports, which could result in global variable pollution (and by extension, the potential for nightmare bugs)

Once this pass is completed, the next step will be implementing automated testing to help ensure that further refactors/tests don't break existing functionality (which I am currently testing manually). Cheers!

kalum.ost added 12 commits January 14, 2025 17:41
…ion types; it will now process all available types when this occurs.
…io.test.docx") and be placed in directories that do not initially exist at runtime, through the power of PathLib!
…for the NeuroPoly wiki) is now placed in the same place as everything else.
…ueries doesn't exist; it will now just notify the user with a warning instead + fix for user requesting 0 publication types
…ollution in preparation for future refactoring
…now you can mix both files and raw identifiers if you want! This is part of an overall CLI refactor, to preparation for automated testing.
…tions can be called *without* needing a shell to call them!
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