Tidy up: delete unused target variants module #47
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## fix-nonadditive #47 +/- ##
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+ Coverage 89.18% 89.19% +0.01%
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Files 40 39 -1
Lines 2320 2249 -71
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- Hits 2069 2006 -63
+ Misses 251 243 -8
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nebfield
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Oct 7, 2024
* add pydantic dependency * implement pydantic model drafts * split models into CatalogScoreVariant and ScoreVariant * fix doctests * refactor to use a DictWriter * fix doctest imports * refactor classes into separate files * add non-additive error checking * skip non-additive scores * add non-additive CLI tests * export EffectTypeError * fix missing CatalogError * tidy up: put reusable pydantic models in models.py and export them * simplify n_finished check * set all effect weight fields to str with coerce_numbers_to_str * add rsid field validator * fix field validator field name o_o * Update score log structure (#49) * include example of validating a scoring file header * update header models * integrate ScoreLog and ScoreLogs * fix doctest imports * add log warning re: missing variants * test log output with incompatible effect type * make ScoreLogs a RootModel to act as a json list * refactor weight types from enum to string * prevent revalidation of ScoreVariants during ScoreLog instantiation * prevent checking position for complex variants * fix log creation with missing variants * update is_non_additive check to support mixed column types * Tidy up: delete unused target variants module (#47) * remove targetvariants class * fix deleted imports * fix imports * Gradually introduce type checking (#50) * set up type checking pre-commit * set up type checks for pgscatalog.core * add mypy action * don't use poetry for mypy * fix is_complex check * delete redundant functions * drop unused NormalisedScoringFile * rename variants -> variant_sources in ScoreLog * add support for ancestry specific allele frequencies * fix writing out * hm_match_chr and hm_match_pos: treat empty strings as None * set up a ProcessPoolExecutor skeleton * fix multiprocessing coverage * convert empty strings to None: is_haplotype and is_diplotype * fix TypeError -> ValueError for pydantic * fix doctest * add support for variant_type field * add complex variant tests * improve model documentation * bump minor version * simplify effect_weight_must_float again * Revert "simplify effect_weight_must_float again" This reverts commit 0d5c6e5. * document and improve effect_weight_must_float * docs: stop being confusing * cache computed fields in model * add more CLI logging messages * add has_complex_alleles computed field * set up annotated types in models and VariantLog model * add package mypy config * ignore typing when reading ScoreVariants as dicts of strings * clarify log messages when writing out
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These library classes and functions are no longer imported or used anywhere, so should probably be deleted
The last time they were called was prior to #22 being merged