Recent Releases of semra
semra - v0.1.2
What's Changed
- Update Zenodo upload code for raw database by @cthoyt in https://github.com/biopragmatics/semra/pull/72
- Update SSSOM testing by @cthoyt in https://github.com/biopragmatics/semra/pull/74
- Add tests for web implementation by @cthoyt in https://github.com/biopragmatics/semra/pull/75
- Add error handling to JSONL reader by @cthoyt in https://github.com/biopragmatics/semra/pull/76
- Update compression by @cthoyt in https://github.com/biopragmatics/semra/pull/73
- Mount files in docker, use uv, make python configurable by @cthoyt in https://github.com/biopragmatics/semra/pull/77
Full Changelog: https://github.com/biopragmatics/semra/compare/v0.1.1...v0.1.2
- Python
Published by cthoyt about 1 year ago
semra - v0.1.1
What's Changed
- Fix scoping of files in streaming writers by @cthoyt in https://github.com/biopragmatics/semra/pull/70
- Update configuration definition by @cthoyt in https://github.com/biopragmatics/semra/pull/71
Full Changelog: https://github.com/biopragmatics/semra/compare/v0.1.0...v0.1.1
- Python
Published by cthoyt about 1 year ago
semra - v0.1.0
What's Changed
Note: this release includes a few changes that are backwards incompatible with the versions of the raw mappings database that are included in the SeMRA pre-print. New data files will be uploaded soon.
- Improvements to full mapping database build by @cthoyt in https://github.com/biopragmatics/semra/pull/22
- Update cruft by @cthoyt in https://github.com/biopragmatics/semra/pull/26
- Add workflow for updating literal mappings by @cthoyt in https://github.com/biopragmatics/semra/pull/24
- Replace Creator model with named reference by @cthoyt in https://github.com/biopragmatics/semra/pull/23
- Fix deprecated pydantic components by @cthoyt in https://github.com/biopragmatics/semra/pull/28
- Rewrite PyOBO mapping import by @cthoyt in https://github.com/biopragmatics/semra/pull/27
- Update Intact urls by @kkaris in https://github.com/biopragmatics/semra/pull/30
- Incorporate PyOBO xref sources directly by @cthoyt in https://github.com/biopragmatics/semra/pull/31
- Update storage of subsets by @cthoyt in https://github.com/biopragmatics/semra/pull/32
- Improve typing with overloads by @cthoyt in https://github.com/biopragmatics/semra/pull/35
- Improve landscape CLI by @cthoyt in https://github.com/biopragmatics/semra/pull/34
- Update cruft by @cthoyt in https://github.com/biopragmatics/semra/pull/37
- Refactor I/O functions by @cthoyt in https://github.com/biopragmatics/semra/pull/38
- Add --build-docker flag to landscape by @cthoyt in https://github.com/biopragmatics/semra/pull/39
- Standardize references in SeMRA sources by @cthoyt in https://github.com/biopragmatics/semra/pull/36
- Refactor and landscape re-analysis by @cthoyt in https://github.com/biopragmatics/semra/pull/40
- Update type checking for class-resolver by @cthoyt in https://github.com/biopragmatics/semra/pull/47
- Add pandas-based prioritization function by @cthoyt in https://github.com/biopragmatics/semra/pull/48
- Refactor raw database build by @cthoyt in https://github.com/biopragmatics/semra/pull/44
- Add strict type checking by @cthoyt in https://github.com/biopragmatics/semra/pull/50
- Improve CURIE generation for evidences by @cthoyt in https://github.com/biopragmatics/semra/pull/49
- Reorganize I/O functions by @cthoyt in https://github.com/biopragmatics/semra/pull/51
- Improve Neo4j output by @cthoyt in https://github.com/biopragmatics/semra/pull/45
- Hide landscape functions by @cthoyt in https://github.com/biopragmatics/semra/pull/53
- Add JSONL I/O by @cthoyt in https://github.com/biopragmatics/semra/pull/54
- Refactor inference and graph code by @cthoyt in https://github.com/biopragmatics/semra/pull/56
- Add testing for graph I/O by @cthoyt in https://github.com/biopragmatics/semra/pull/57
- Refactor mutation inference implementation and improve docs by @cthoyt in https://github.com/biopragmatics/semra/pull/58
- Additional documentation improvements by @cthoyt in https://github.com/biopragmatics/semra/pull/59
- Fully stream database build by @cthoyt in https://github.com/biopragmatics/semra/pull/62
- Remove UUIDs from evidences by @cthoyt in https://github.com/biopragmatics/semra/pull/63
- Update mapping set field documentation by @cthoyt in https://github.com/biopragmatics/semra/pull/64
- Update SSSOM implementation and example in README by @cthoyt in https://github.com/biopragmatics/semra/pull/61
- Add PURL to mapping set to align with SSSOM's
mapping_set_idby @cthoyt in https://github.com/biopragmatics/semra/pull/65 - Rename fields in mapping by @cthoyt in https://github.com/biopragmatics/semra/pull/66
- Reorganize triple data models by @cthoyt in https://github.com/biopragmatics/semra/pull/68
- Reuse triples objects from
curiesby @cthoyt in https://github.com/biopragmatics/semra/pull/69
Full Changelog: https://github.com/biopragmatics/semra/compare/v0.0.9...v0.1.0
- Python
Published by cthoyt about 1 year ago
semra - v0.0.9
What's Changed
- Include live Biomappings curation by @cthoyt in https://github.com/biopragmatics/semra/pull/21
- Fix query over connected components by @cthoyt in https://github.com/biopragmatics/semra/pull/20
- refactor orcid getter code
- add database name checking/fix name lookup
Full Changelog: https://github.com/biopragmatics/semra/compare/v0.0.8...v0.0.9
- Python
Published by cthoyt over 2 years ago
semra - v0.0.8
What's Changed
- Update to cthoyt/cookiecutter-snekpack and address CI by @cthoyt in https://github.com/biopragmatics/semra/pull/15
- Add landscape analysis by @cthoyt in https://github.com/biopragmatics/semra/pull/17
Full Changelog: https://github.com/biopragmatics/semra/compare/v0.0.7...v0.0.8
- Python
Published by cthoyt over 2 years ago
semra - v0.0.7
What's Changed
- Begin cleanup by @cthoyt in https://github.com/biopragmatics/semra/pull/13
- Improve pipeline and gilda workflow docs by @cthoyt in https://github.com/biopragmatics/semra/pull/14
- Update probability model (confidence is now required everywhere)
- Add py38 compatibility
- Fix bug in loading priority mappings
Full Changelog: https://github.com/biopragmatics/semra/compare/v0.0.5...v0.0.7
- Python
Published by cthoyt over 2 years ago
semra - v0.0.5
What's Changed
- Fix from_sssom by @kkaris in https://github.com/biopragmatics/semra/pull/6
- Make Python 3.9 compatible by @bgyori in https://github.com/biopragmatics/semra/pull/8
- Add py39 tests by @cthoyt in https://github.com/biopragmatics/semra/pull/9
New Contributors
- @kkaris made their first contribution in https://github.com/biopragmatics/semra/pull/6
- @bgyori made their first contribution in https://github.com/biopragmatics/semra/pull/8
Full Changelog: https://github.com/biopragmatics/semra/compare/v0.0.4...v0.0.5
- Python
Published by cthoyt over 2 years ago