Release v3.1.0 - #19
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A minor rather than a patch: COTTAS gained a working query engine, validation gained a SHACL shape layer, and the census oracle learned two things it had been getting wrong on real data. COTTAS is queried through comunica over DuckDB instead of pycottas' rdflib Store. The old path could not answer a genotype query at benchmark scale -- 12.7 s for LIMIT 1 on a 39 MB artifact, and 41 hours on q05_sample_genotype_counts without finishing. The same cell now completes in 99.8 minutes with every engine agreeing. A query is also finally interruptible: run_query_process existed with no callers, and no engine ever emitted the exit 124 the query loop keys on, so --validation-query-timeout could not stop anything. The oracle counted value items for INFO only, while the emitter decomposes positional FORMAT keys too. Any file with AD or PL -- most real VCFs -- failed validation with the whole item layer reported as unexpected. It also scored every run against a structured expectation because the representation was never passed across the container boundary, so --info-representation raw could not pass at all. Also: the SHACL profile bundled and applied by default below 512 MiB, severity- aware pyshacl parsing, QLever as the validation default, a cohort-scale refusal before the volume fills, and TSV intermediates freed at the last reader. Conda sha256 returns to its placeholder until the tag exists; populate it with `python3 scripts/release.py 3.1.0 --fetch-conda-sha256` after pushing v3.1.0. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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Version markers only —
pyproject.toml,CITATION.cff,README.md,conda-recipe/.A minor rather than a patch, because three things changed behaviour rather than fixing it in place:
COTTAS is queryable. Through comunica over DuckDB instead of pycottas' rdflib Store. The old path took 12.7 s for
LIMIT 1on a 39 MB artifact and ran 41 h onq05_sample_genotype_countswithout finishing; the same cell now completes in 99.8 min with all four engines agreeing. Queries are also interruptible for the first time —run_query_processexisted with no callers, and no engine emitted the exit 124 the query loop keys on, so--validation-query-timeoutcould not stop anything.The oracle matches the emitter. It counted value items for INFO only while the emitter also decomposes positional FORMAT keys, so any file with
ADorPLfailed validation. And it never learned which representation produced the graph, so--info-representation rawcould not pass at all.Validation gained a SHACL layer, bundled and applied by default below 512 MiB, with severity-aware pyshacl parsing.
The conda sha256 is back to its placeholder: the v3.1.0 source archive does not exist until the tag is pushed. Populate it after tagging with
python3 scripts/release.py 3.1.0 --fetch-conda-sha256.Known, pre-existing and not from this release: the vendored
vcf-core-vocabulary.bundle.ttlis at 2.1.2 while the vocabulary checkout is at 2.1.3. The drift check skips without a sibling checkout, so CI does not see it — worth a decision, but it predates this branch.🤖 Generated with Claude Code