OpenFreeEnergy / OpenFreeEnergy/openfe
Discuss: gzip PDB files where we can
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- Dominant language
- Python
- Stars
- 332
- Forks
- 56
- Avg merge
- 3d 9h
- Merged PRs (30d)
- 13
Description
Recently we added a PDB file to our test data that we couldn't import from the RSCB website (I'm not sure why that would be, but separate issue).
In any case, that file is only used to be loaded into an MDAnalysis universe, which reads gzipped files naturally. Indeed a lot of our stack can actually handle this (or if it doesn't, it should!).
This issue is to discuss us always trying to gzip PDB files (and other data files), when storing them (anywhere, either in the repo or zenodo, etc...).
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
No files, tests, or entry points are named. Review how PDB and other data files are currently stored and loaded, check which parts of the stack support gzip, and define a repository- and Zenodo-wide policy with representative validation before proposing the change.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100