RosettaCommons / RosettaCommons/atomworks
Include `inplace` argument for all `Transforms`
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- Dominant language
- Python
- Stars
- 446
- Forks
- 52
- PR merge metrics
- No merged PRs in 30d
Description
Many Transforms both modify the AtomArray in-place and return the modified AtomArray, which is an anti-pattern.
We should unify the codebase to support an inplace argument to control this behavior, where we can conduct a shallow copy.
For efficiency, Transforms, should use the inplace=True option to avoid unnecessary copy operations.
Contributor guide
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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
Start by locating the Transforms that modify and return an AtomArray, then review how each currently handles copying and returns. The issue names no files or tests; done means the affected Transforms consistently support the requested inplace behavior and use it where avoiding copies is intended.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Refactor
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 40/100