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Recent Releases of https://github.com/biocommons/anyvar

https://github.com/biocommons/anyvar - 0.9.0

What's Changed

  • Fixes so I can build and run the anyvar docker container. by @naomifox-invitae in https://github.com/biocommons/anyvar/pull/6
  • Fix #8- SeqRepoDataProxy by @jarbesfeld in https://github.com/biocommons/anyvar/pull/9
  • added postgres data store, fix #10 by @jarbesfeld in https://github.com/biocommons/anyvar/pull/11
  • docs: update readme for postgres setup by @korikuzma in https://github.com/biocommons/anyvar/pull/14
  • feat #13: get statistics about variation content by @jarbesfeld in https://github.com/biocommons/anyvar/pull/16
  • feat: add endpoint for querying alleles in one genomic region by @korikuzma in https://github.com/biocommons/anyvar/pull/15
  • fix: use VRS-Python for translate call by @jsstevenson in https://github.com/biocommons/anyvar/pull/18
  • test: basic route coverage by @jsstevenson in https://github.com/biocommons/anyvar/pull/31
  • test: add coverage reporting by @jsstevenson in https://github.com/biocommons/anyvar/pull/32
  • feat: use Variation Normalizer for translation by @jsstevenson in https://github.com/biocommons/anyvar/pull/33
  • style: add new linting checks by @jsstevenson in https://github.com/biocommons/anyvar/pull/34
  • feat: use FastAPI for endpoint service by @jsstevenson in https://github.com/biocommons/anyvar/pull/43
  • fix: don't create redundant DB entries by @jsstevenson in https://github.com/biocommons/anyvar/pull/46
  • feat: add vcf endpoint by @jsstevenson in https://github.com/biocommons/anyvar/pull/48
  • Enable batched insert by @jsstevenson in https://github.com/biocommons/anyvar/pull/50
  • fix: don't expose stack in error response by @jsstevenson in https://github.com/biocommons/anyvar/pull/57
  • merge hackathon work by @jsstevenson in https://github.com/biocommons/anyvar/pull/60
  • feat!: use vrs 2-alpha1 by @korikuzma in https://github.com/biocommons/anyvar/pull/61
  • chore: remove unused code by @korikuzma in https://github.com/biocommons/anyvar/pull/63
  • Added 'dependencies' and 'optional-dependencies' to dynamic list by @ehclark in https://github.com/biocommons/anyvar/pull/69
  • Snowflake database storage integration by @ehclark in https://github.com/biocommons/anyvar/pull/70
  • Add parameter to the /vcf endpoint to control whether VRS IDs are generated for REF alleles by @ehclark in https://github.com/biocommons/anyvar/pull/74
  • Cleanup storage integration and write pending batches on shutdown by @ehclark in https://github.com/biocommons/anyvar/pull/76
  • Improve performance of AnyVar.put_object() by eliminating unnecessary digest computation by @ehclark in https://github.com/biocommons/anyvar/pull/73
  • Add parameter to /vcf endpoint to force async writes to complete before returning response by @ehclark in https://github.com/biocommons/anyvar/pull/75
  • Add support for GRCh37 to /vcf endpoint by @ehclark in https://github.com/biocommons/anyvar/pull/77
  • Apply formatting and specify version by @theferrit32 in https://github.com/biocommons/anyvar/pull/82
  • Update README-pg.md by @larrybabb in https://github.com/biocommons/anyvar/pull/79
  • Fix postgres connection issue and typo in postgres readme by @theferrit32 in https://github.com/biocommons/anyvar/pull/83
  • Update VCF annotator code to be compatible with superclass in vrs-python by @ehclark in https://github.com/biocommons/anyvar/pull/86
  • Snowflake storage integration updates for collation and private key auth by @ehclark in https://github.com/biocommons/anyvar/pull/90
  • Update unit tests to match the new VRS 2.0 digests by @ehclark in https://github.com/biocommons/anyvar/pull/92
  • Integrate SQLAlchemy for db conn management and introduce new SqlStorage abstraction by @ehclark in https://github.com/biocommons/anyvar/pull/93
  • docs: update readme + postgres_init.sql commands by @korikuzma in https://github.com/biocommons/anyvar/pull/96
  • fix: update ga4gh.vrs version + add back VRS type anno in models by @korikuzma in https://github.com/biocommons/anyvar/pull/95
  • feat!: update configs and core template stuff by @jsstevenson in https://github.com/biocommons/anyvar/pull/97
  • Fix problems introduced by project configuration changes and dependency upgrades by @ehclark in https://github.com/biocommons/anyvar/pull/101
  • Convert ANYVARSQLSTOREFLUSHONBATCHCTXEXIT env value to boolean explicitly by @ehclark in https://github.com/biocommons/anyvar/pull/105
  • Add feature to allow logging configuration to be specified at runtime by @ehclark in https://github.com/biocommons/anyvar/pull/106
  • VCF annotation via asynchronous request-response pattern by @ehclark in https://github.com/biocommons/anyvar/pull/108
  • Suppress Pydantic warnings by default by @ehclark in https://github.com/biocommons/anyvar/pull/110
  • build: pin VRS-Python 2.0a12 by @jsstevenson in https://github.com/biocommons/anyvar/pull/114

New Contributors

  • @naomifox-invitae made their first contribution in https://github.com/biocommons/anyvar/pull/6
  • @jarbesfeld made their first contribution in https://github.com/biocommons/anyvar/pull/9
  • @ehclark made their first contribution in https://github.com/biocommons/anyvar/pull/69
  • @theferrit32 made their first contribution in https://github.com/biocommons/anyvar/pull/82
  • @larrybabb made their first contribution in https://github.com/biocommons/anyvar/pull/79

Full Changelog: https://github.com/biocommons/anyvar/compare/0.1.1...0.9.0

- Python
Published by jsstevenson about 1 year ago