Releases · biocommons/hgvs

Bug Fixes

Ensure hgvs seqrepo dir is unset during testing by @ccaitlingo in #669
#652 - Fix for Error: AttributeError: 'UTA_postgresql' object has no attribute '_pool' by @davmlaw in #666
Fix typo in formatted string by @ecalifornica in #680
#670 - Gene Symbol support dash and underscore by @davmlaw in #683
Fix for issue 704 - pass on prevalidation_level by @davmlaw in #746
fix: projection issue for stop retained insertion (#707) by @holtgrewe in #708
fix(cicd): add cache-apt-pkgs-action to install zsh by @korikuzma in #754
fix(test): add vcr_config for cassette management and re-run cassettes by @korikuzma in #755
Fix exception in g_to_c mapping by @b0d0nne11 in #765
Fix variant region for ins and dup on intron-exon boundary by @b0d0nne11 in #748
fix(#712): This fixes the broken make develop install by @andreasprlic in #713
#730 - Fix single letter amino acid bug by @jPleyte in #731
#722 Babelfish VCF bugs by @davmlaw in #723

New Features

#447 - implement babelfish for VCF by @davmlaw in #660
#661 - Improve Parser startup time by storing generated Python code by @davmlaw in #664
feat: update default data version config by @jsstevenson in #734
feat(#741): Pretty print by @andreasprlic in #742
Add variant region condition for dups ending in UTR by @b0d0nne11 in #716
#744 - babelfish vcf conversion accept contig accessions as chrom names by @davmlaw in #745

Other Changes

Updated instructions for hgvs readme by @ccaitlingo in #656

Internal and Developer Changes

Remove unused variables by @ecalifornica in #681
Remove unused string format argument by @ecalifornica in #678
Remove superfluous import by @ecalifornica in #677
Add inline ignore for line too long errors by @ecalifornica in #674
Remove unused imports by @ecalifornica in #675
Add isort profile configuration to match black by @ecalifornica in #672
Fix undefined names by @ecalifornica in #679
Fix linter complaint about ambiguous variable name by @ecalifornica in #676
Explicitly define test imports by @ecalifornica in #686
Remove unused variables by @ecalifornica in #685
#689 - undo circular import introduced from linting fix by @davmlaw in #690
Remove top level code environment script by @ecalifornica in #696
updates to documentation by @katiestahl in #694
Remove unused imports by @ecalifornica in #684
Remove test HTTP network calls by @ecalifornica in #697
#688 - remove future usage by @davmlaw in #726
#695 - Remove top level code environment scripts from modules by @davmlaw in #728
#178 - use abc for Edit class to ensure method definition by @davmlaw in #729
chore: remove trailing whitespace by @jsstevenson in #737
refactor: use importlib instead of pkg_resources by @jsstevenson in #738
build: require python >= 3.10 by @jsstevenson in #739
Update authors for 2024 (last updated 4 years ago) by @davmlaw in #752
Remove python2 legacy by @davmlaw in #753
Update test cache by @reece in #756
Resolve testing warnings by @reece in #763
update project config to pyproject.toml and drop krufty config by @reece in #769
fix typo. Sentence about g -> r stated g -> c by @brechtmann in #772