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Build # 25711484616

Build Type

push

github

Committed by web-flow

Commit Message

Fix #219: Database cache dir defaults to download cache, not GTF directory (#340)

* Fix #219: Genome's Database uses download cache dir instead of GTF dir

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.

* SequenceData ensures cache directory exists before pickling

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}.

Coverage Stats

4 of 4 new or added lines in 2 files covered. (100.0%)

2 existing lines in 2 files now uncovered.

1371 of 1641 relevant lines covered (83.55%)

3.34 hits per line