graphein [fix] change progressbar for pdb download

[fix] change progressbar for pdb download

Open kierandidi opened this issue 1 year ago • 1 comments

What does this implement/fix? Explain your changes

When using the download_pdb_multiprocessing function, a progress bar for each individual download would be created. This was quite confusing since the progress bars change to quickly to see anything; at the same time one does not know how far the download process is in practice

https://github.com/a-r-j/graphein/assets/58345129/b4dacaef-de0b-4e38-ae90-1f0670c17a1e

In this MR, this is changed so that the process instead is monitored by one overall progress bar that gives more informative information about the progress. It does this via the imap_unordered function that returns the requests async; every download request that returns increments the bar so that we have a more realistic idea of how far the download process is.

What testing did you do to verify the changes in this PR?

I downloaded several pdbs, either just a few or a few thousand.

Pull Request Checklist

[x] Added a note about the modification or contribution to the ./CHANGELOG.md file (if applicable)
[ ] Added appropriate unit test functions in the ./graphein/tests/* directories (if applicable)
[ ] Modify documentation in the corresponding Jupyter Notebook under ./notebooks/ (if applicable)
[ ] Ran python -m py.test tests/ and make sure that all unit tests pass (for small modifications, it might be sufficient to only run the specific test file, e.g., python -m py.test tests/protein/test_graphs.py)
[ ] Checked for style issues by running black . and isort .