Move config and indices to persistent user data directory#5
Merged
Conversation
Reference genomes and HCRconfig.yaml were previously stored inside the package directory, which meant they were lost on `pip install -U`. This moves all mutable data to ~/.hcrprobedesign/ (overridable via HCRPROBEDESIGN_DATA_DIR env var) so indices and configuration persist across upgrades. Key changes: - New _datadir.py module manages the data directory lifecycle - Auto-migration from old package-relative locations on first run - All modules (genomeMask, referenceGenome, listReferences) updated to read/write from the user data directory - listReferences now shows the data directory path in output - Version bump: 0.3.0 -> 0.3.1 - 10 new tests for _datadir, all 39 tests passing https://claude.ai/code/session_01L9BrYriTeA72fsqqTvgdxy
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Summary
HCRconfig.yamland Bowtie2 indices from the package directory to a persistent user data directory (~/.hcrprobedesign/), so reference genomes survivepip install -UupgradesHCRPROBEDESIGN_DATA_DIRenvironment variable to override the data directory locationTest plan
_datadirtests + 29 existing, updated for isolation)listReferencesshows data directory path and registered speciesfetchMouseIndex/buildGenomeIndexwrite to~/.hcrprobedesign/HCRPROBEDESIGN_DATA_DIRoverride workshttps://claude.ai/code/session_01L9BrYriTeA72fsqqTvgdxy