feat(alphafold): add custom jackhmmer save directory option (#49)#234
Draft
Elarwei001 wants to merge 2 commits into
Draft
feat(alphafold): add custom jackhmmer save directory option (#49)#234Elarwei001 wants to merge 2 commits into
Elarwei001 wants to merge 2 commits into
Conversation
Add a jackhmmer_savedir parameter (Python) / -jhd, --jackhmmer_savedir flag (CLI) to gget alphafold so users can choose where the temporary jackhmmer files (~2 GB) are stored instead of the hardcoded ~/tmp/jackhmmer/ folder in the home directory. The new get_jackhmmer_dir() helper centralizes the path resolution and clean_up() now operates on the resolved directory. Default behavior is unchanged (backward compatible). Resolves scverse#49. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## dev #234 +/- ##
==========================================
+ Coverage 56.14% 56.50% +0.36%
==========================================
Files 29 29
Lines 9244 9252 +8
==========================================
+ Hits 5190 5228 +38
+ Misses 4054 4024 -30 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
|
Add a network-free test for the clean_up(None) default-directory branch: it patches get_jackhmmer_dir so the None default resolves to a temporary folder (never the real ~/tmp) and asserts clean_up() resolves and removes it. Covers the previously-uncovered default-resolution line. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Resolves #49
Summary
gget alphafold: Added a newjackhmmer_savedirargument (-jhd/--jackhmmer_savediron the command line) that lets you choose where the temporary jackhmmer files are stored. By default,gget alphafoldstill creates a~/tmp/jackhmmer/folder in your home directory (which can take up to ~2 GB of disk space); the new argument lets you redirect these files elsewhere, e.g. to a disk with more free space. Resolves issue 49.Testing
Unit tests in
tests/test_alphafold.py(argument/path-handling level, since AlphaFold's heavy deps are unavailable in CI); run with pytest.