Nikolaos integration #35
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I updated several parts of the `CTAInterface` class. First of all, I made requirements into a variable that is simply set in each implementation of the class to increase clarity and simplicity. Then, I modified the outputs of the `convert` method to also allow for returning a `pandas.DataFrame` to allow for more output variety. Since a `DataFrame` cannot be comprised of `DataFrame` columns, I had to change the output of the `annotate` function to a `dict[str, Series | DataFrame]` The celltypist interface needed some minor tweaks to increase its functionality to at least match that of Nikolaos' code. Some minor refactoring was also required to work with the modified requirements module. I also added some more documentation for the sake of clarity. I added one more extra/testenv called `torch38` housing the packages that require Python 3.8 and torch. This is because torch and SCANVI take ~5GB for requirements for every virtual environment it is installed on, so it makes sense to only install it in one place. I created a `NotNoneRequirement` to require certain parameters to not be a `None` value. Also, I updated the versions of certain used GitHub actions. Finally, I ran `isort` on the `src` and `tests` directories to organize the downloads.
It's possible that the new versions of actions/checkout and actions/setup-python are breaking the GitHub actions.
The new NotNoneRequirement imported from the `requirements` module it's in, which caused the error. I had to wrap all tool interface imports inside try-except-ImportError clauses to make the modules work when the proper extras are installed. Also, I increased the versions of the CI back to the latest ones.
Moved configuration from `setup.cfg` to `pyproject.toml` and `.flake8`
This was probably a necessary file
Removing the top-level `__init__.py` did not fix the issue. Trying to remove package caching to see if this is the issue.
In the main branch where the tests still work, this file is empty, while the main `__init__.py` is not.
I suspect the error suppression might be interfering with something in the GitHub actions.
I think the program might be failing to include submodules without this *.
Some part of `scvi-tools` is not working on windows, and since this program will most likely be running on a linux machine or container, we can just remove Windows support.
AleksBekker
added
enhancement
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Does #1 #2