Fix #219: Database cache dir defaults to download cache, not GTF directory#340
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When a Genome is constructed with a local GTF and no explicit cache_directory_path, the sqlite Database (and SequenceData caches) now write into the resolved download cache directory rather than the GTF's parent directory. This unblocks users pointing pyensembl at GTFs in read-only locations who previously hit a PermissionError on index(). Database's standalone fallback (cache next to GTF when no path provided) is unchanged so direct Database(...) callers behave as before. Bump version to 2.6.13.
Now that Genome hands the resolved download-cache dir (rather than the
FASTA's parent dir) to SequenceData, the target directory may not exist
yet when no remote files have been downloaded. Mirror Database.create's
ensure_dir call before dump_pickle.
Fixes test_missing_genome_sources.{test_transcript_fasta_only,test_protein_fasta_only}.
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coverage: 83.547% (-0.1%) from 83.649% — fix-219-database-default-cache-dir into main |
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Summary
Genomeis built from a local GTF without an explicitcache_directory_path, the sqliteDatabase(and protein/transcriptSequenceDatacaches) are now created under the resolved download-cache directory instead of next to the source GTF. Closes Database path should not default to gtf path #219.Database's standalone fallback (write next to the GTF when nocache_directory_pathis passed) is unchanged, so callers constructingDatabasedirectly behave as before.Test plan
tests/test_database_cache_dir.pycovers both the fallback path (viaPYENSEMBL_CACHE_DIR) and the explicit-path casetests/test_ucsc_gtf.py(which exercisesgenome.index()with an explicit cache dir) still passes./lint.sh