Massive PR to merge all the clodius changes#164
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pkerpedjiev merged 37 commits intodevelopfrom Mar 25, 2026
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Replace the get_test_data.sh download script with Git LFS-tracked test fixtures committed directly to the repository. This fixes the CI failure caused by inaccessible S3 URLs (wget exit code 8). - Add .gitattributes with LFS tracking rules for binary genomics formats (.cool, .mv5, .h5, .hdf5, .bam, .bai, .beddb, .bb, .bigWig, etc.) - Commit 24 test fixture files (~450 MB) via LFS - Update .gitignore: replace blanket data/ exclusion with explicit per-file allowlist so generated outputs remain ignored - Update CI workflow: add lfs: true to checkout, remove the Cache Fixtures and Download Fixtures steps - Remove get_test_data.sh Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
The script was re-introduced by the rebase; test fixtures are now in LFS. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Add data/regions.valid.bed.gz to LFS and data/regions.spaces.bed to git - Update .gitignore to allow both files - Add "Test Fixtures (Git LFS)" section to README explaining how to clone with LFS and how to add new test fixture files Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- parse_cigar_string: return empty list when cigar is null/None (oxbow 0.6+ returns null for unmapped reads instead of "*") - abs2genomic: use Series.iloc[cid] instead of Series[cid] to avoid KeyError in pandas 3.x where integer indexing on string-keyed Series no longer falls back to positional access Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
The new oxbow DataSource API (from_bam, from_gff, etc.) requires 3.12+. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Replace raw_tabix_fetcher's internal read_gff (with deprecated attr_defs param) with ox.from_gff public API using attribute_defs, mirroring the dataframe_tabix_fetcher pattern used for BED files - Fix None safety bug in single_indexed_tile when max_results is set but no data was fetched (ret_vals could be None) - Handle None raw_data in gff.py tiles() before calling parse_gff_to_models Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Description
What was changed in this pull request?
Bringing clodius up to date with rhodius.
Why is it necessary?
To maintain one repo instad of two.
Fixes #___
Checklist
black .