Changelog

Install or upgrade with python -m pip install --upgrade osteosarc, and check your version with osteosarc --version. Pin both the package version and your snapshot (by name or download date) for reproducible analyses. Full release notes are on GitHub.

0.6.0 (2026-09-24)

  • RecoveryPolicy(on_timeout="incomplete") keeps the verified seed reads and partners already matched when a later partner query times out, instead of failing. The receipt says status="incomplete" and names the failed query; a later call retries it and resumes from verified extractions. Fixture recipes can request this through a source's acquisition, and bundles record the incomplete acquisition (#28).

0.5.0 (2026-09-24)

  • The CLI is easier to explore with (#38):
  • samples and specimens show sequencing with the filter names, such as rna-seq; wes; wgs; scrna-seq (ont, pacbio).
  • samples --assay scrna-seq --platform ont lists the samples with that sequencing; describe_samples() takes the same filters.
  • assets prints a table with complete file keys and a hint when rows are cut off; --json prints the full records.
  • Explorer tables never truncate file keys, and sizes read as KB, MB or GB.
  • An assay, platform or tissue filter that no file uses raises an error listing the valid values, instead of an empty selection. A registry label such as scRNA_ONT names the filters to use instead.

0.4.0 (2026-09-24)

  • Removed the CLI's positional snapshot argument (osteosarc samples baseline); choose a snapshot with --snapshot. Removed the empty [reads] install extra.
  • The explorer's assets command accepts sample=, as in assets sample=T1_tumor.

0.3.0 (2026-09-24)

  • Snapshots are indexed by download date, and the most recent is the default (#35). Dataset.sync() and osteosarc sync need no name: they save a snapshot named by the UTC date and reopen it for the rest of that day. Dataset.open() and every CLI command use the newest snapshot. Dataset.snapshots() and osteosarc snapshots list them. Dataset.open(date="2026-09") or --snapshot 2026-09 picks the newest from a download date, month or year, and Dataset.open(name) or --snapshot NAME picks one exactly by name or ID prefix. Offline, sync() builds a snapshot from sources already in the cache.
  • Named snapshots keep working. The CLI's leading snapshot argument (osteosarc samples baseline) is deprecated in favor of --snapshot.
  • The documentation no longer uses a baseline snapshot name.

0.2.6 (2026-09-24)

  • Reorganized documentation with key concepts, a command-line guide, a complete API reference and this changelog. The README is a shorter landing page that lists the main features (#32).
  • The documentation example checker covers every published page and the strict build validates anchors (#31).

0.2.5 (2026-09-24)

  • The SV interest catalogue: 637 structural-variant nominations with original calls, breakend geometry, Ensembl 115 annotation, T2 expression and scoped RNA evidence. It loads offline with load_sv_interest() or load_panel("sv-interest-v1") (#29).
  • The command line can now run the whole quickstart: assets --sample, reads --variant ID --padding N and --version (#33).

0.2.4 (2026-09-23)

  • Partner recovery selects seed query names with samtools view -N before applying its record cap, so unrelated reads at dense loci can't exhaust it. Adds ReadFilter(query_names=...) (#26).

0.2.3 (2026-09-23)

  • Shared historical fixture adapters for Isovar, Topiary and Vaxrank, and the additional SV research panel. See OpenVax fixture adoption (#15).
  • Python 3.9 support.

0.2.2 (2026-09-23)

  • Portable fixture bundles: generate, pack, verify, list and export (#14).

0.2.1 (2026-09-23)

  • Bounded mate and SA partner recovery with explicit receipts (#13).

0.2.0 (2026-09-23)

  • Versioned fixture recipes and one selection executor shared by the Python API, Dataset and CLI (#12).

0.1.4 (2026-09-22)

  • Reconciled eight corrections after upstream source changes; historical snapshots keep their original IDs and corrections (#10).

0.1.3 (2026-09-21)

  • to_varcode() converts chrM and M to Ensembl's MT and keeps the original contig name (#8).

0.1.2 (2026-09-21)

  • Verified GRCh38 alleles for FAM157A and COL3A1, with explicit outcomes for MUC3A, OTUD4 and USH2A (#5).
  • Clearer sample, timepoint and assay documentation.

0.1.1 (2026-09-20)

  • Downloads use datacache; pysam is a standard dependency.
  • Adds describe_samples(), assets_for_sample() and extract_reads(variants=...).
  • SAMtools capabilities are checked before acquisition (#3); malformed count rows no longer hide valid entries (#4).

0.1.0 (2026-09-19)

  • First release: pinned metadata snapshots, file discovery, variants and vaccines, indexed read extraction, source corrections, the clinical timeline and the interactive explorer.