Merge dev #5
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Merge dev #5
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This reverts commit 0776f31.
* Update README.md fix link * merge matchlib and matchapp (#2) * add exceptions * add QueryError * add InvalidAccessionErrors * refactor to include normalise() and private modules * add functions for normalise * add combine CLI * add test combineapp * Update README.md * use threadpoolexecutor * migrate to relative imports, add liftover * export genomebuild * update lockfile * update lockfile * fix import * add liftover to combine cli * fix test * improve dunder methods * fix test * add coverage * move read_header * Revert "add coverage" This reverts commit 0776f31. * add progress bar * add autoapi and docs * ignore autoapi * add targetvariants class * simplfy reading zstd/gz with xopen and add ID to TargetVariant * set up pyarrow support for TargetVariants * add tqdm * add pyarrow and exports * fix test * export NormalisedScoringFile * add dataframe classes * improve context managers * update matchlib * add tests * write out scorefiles * refactor writing out scorefiles * make plinkframes internal * add PlinkScoreFiles * fix labelling * use labelled df to write scoring files * fix tests * extract plinkscorefiles * fix tests * check log counts * fix test * add matchlib to docs * update exports * add matchlib pytest * install all extras for tests * add match cli * add matchapp tests * update pytest action * sort test output to get consistent results * bump dependency for node 20 * add merge cli * fix test * add support for writing --split and --combined * update docs and tests * fix cache * update lockfile * add polygenicscore to calclib * add calclib to docs * add calcapp * more ancestry stuff * update lockfiles * make pytest strict: fail on warnings * add PrincipalComponents class * fix test * start adjust method * fix test * add adjust() doctest * add writing adjusted scores * bump poetry * add export to __all__ * add ancestry CLI and test * fix futurewarning error * update autoapi docs * update docs * fix script path
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