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cucapra / pollen

generating hardware accelerators for pangenomic graph queries
MIT License
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Redundancies in `pollen-py`? #90

Closed anshumanmohan closed 11 months ago

anshumanmohan commented 1 year ago

Running the Black formatter on all our Python files caused me to take an unplanned tour of pollen_py. I'm just wondering if there has maybe been a mistake in committing files after a planned rename/restructure. The structure looks like

pollen
|
+- pollen/                   // here be all the new Rust stuff, great!!
+- pollen_py/
     |
     +- depth/
     +- pollen/
          |
          +- depth/

and I'm a bit confused. The two depth/ directories look the same, or at least very similar. Sorry if I'm missing something!

anshumanmohan commented 1 year ago

It seems MyPy also thinks this is an issue.

mypy $(git ls-files '*.py')
pollen_py/pollen/depth/processing-elements/calyx_depth_simple.py: error: Duplicate module named "calyx_depth_simple" (also at "pollen_py/depth/processing-elements/calyx_depth_simple.py")
pollen_py/pollen/depth/processing-elements/calyx_depth_simple.py: note: See https://mypy.readthedocs.io/en/stable/running_mypy.html#mapping-file-paths-to-modules for more info
pollen_py/pollen/depth/processing-elements/calyx_depth_simple.py: note: Common resolutions include: a) using `--exclude` to avoid checking one of them, b) adding `__init__.py` somewhere, c) using `--explicit-package-bases` or adjusting MYPYPATH
Found 1 error in 1 file (errors prevented further checking)
sampsyo commented 1 year ago

To crystallize the question for @susan-garry: it looks like the stuff in this directory: https://github.com/cucapra/pollen/tree/main/pollen_py/pollen

is also duplicated in this directory (alongside project metadata) in this directory: https://github.com/cucapra/pollen/tree/main/pollen_py

and we should almost certainly delete the latter, keeping the former.