Release v1.8.0

New Features

• new list in genes.py - get_therapeutic_associated_genes
• constants.py - expanded with commonly used GKB return properties.
• GraphKBConnection login on init if given username and password.
• typing_extensions>=3.7.4.2,<4.4

Improvements

• new test - match TERT:c.-124C>T
• skipped test GERO-299 - test_missense_is_not_nonsense - not yet fixed. (Intercepted by pori_ipr_python).
• Refactor - simplify init.py - move GraphKBConnection to util.py
• Refactor - simplify - remove custom VERBOSE logging level.
• update tests - fix test_known_fusion_single_gene_no_match

What's Changed

• increase typing_extension version; remove failing test by @mattdoug604 in #66
• Bugfix/gero 299 hgvs cds hgvs genomic matching misssense to nonsense by @dustinbleile in #67
• Refactor - group constants into constants.py by @dustinbleile in #68
• GERO-295 - add STATEMENT_RETURN_PROPERTIES constant from pori_ipr_python by @dustinbleile in #70
• Feature/sdev 3256 gene list updates by @dustinbleile in #71
• Release/v1.8.0 constants usablity by @dustinbleile in #73

New Contributors

• @mattdoug604 made their first contribution in #66

Full Changelog: v1.7.0...v1.8.0

v1.7.0

New Features:

• new RELEVANCE_BASE_TERMS 'pharmacogenomic': ['metabolism', 'toxicity', 'dosage'] and 'cancer predisposition': ['pathogenic'] (GERO-272)
• setup update - use pyproject.toml and setup.cfg (DEVSU-1697)

v1.6.0

New Features

• #39: Support arbitrary base queries

Improvements

• Use parameterize to clean up tests
• Add build support for python versions: 3.9, 3.10

BugFixes

• GERO-217: Ignore null positions

v1.5.4

Improvements

• Update documentation to include Graph Theory notation for the matching algorithm
• Rename examples to usage examples

v1.5.3

Improvements

• new utility function for converting 3-letter AA notation to 1-letter AA notation
• Additional documentation for tutorials and scripts

v1.5.2

Improvements

• Add additional documentation for matching algorithm

v1.5.1

Improvements

• Default ignore_cache argument to False
• pass-through ignore_cache from top-level API functions to allow users to turn off caching if desired

v1.5.0

New Features

• Move the statement categorization logic from the IPR adapter to the graphkb adapter

v1.4.0

Improvements

• Infer record is gene Id based on pattern
• use global cache so it is shared when creating multiple reports
• remove type from docstrings since types are annotated

New Features

• support searching features by a source + sourceId if given

v1.3.7

Improvements

• allow features to be matched outside the match function and the record Id passed in separately instead of as part of the variant string. This will avoid gene name issues