[pull] main from AlphaGenes:main #3
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* Update tinyhouse referenc * Update .gitignore * Updated submodule reference to 65456ea #16 * Undo update * Fixing outputkey for writekey * Updated submodule reference to 0add4b8 AlphaGenes/AlphaPeel#118 * Add tests.yml * Update workflow actions versions * Add pre-commit configuration file * Reformatting * Modify distribution version * Modify distribution name * Skip tests in workflow * Bugfix in Heuristic_Peeling.py #40 Pointed out by @XingerTang in #40 * Add seg output and Fix bugs - Add segregation output feature, further improvement can be made with modifications in tinyhouse - Fix edge case bug of no known loci in forward imputation discovered by the PIC group - Fix the edge case of the imputation of heterozygous loci described in #46 - Modify the genotype error rate from 0.01 to 0.0001in fillPointEstimates to reflect a more realistic error rate and therefore a better accuracy - Remove commit hash and date info in version.py, as the correct version should be able to indicate both - Automate the generation of version info in version.py based on the version info in the package metadata - Fix the deprecation of the file referencing of the license in the pyproject.toml - Discard outdated zip file - Update gitignore * Run pre-commit & Update documentation * Fix #27 Fix #30 Fix #31 Fix #36 Fix #41 Fix #43 Add a sample test * Fix wheel file name * Include pytest in the test pipeline --------- Co-authored-by: Gregor Gorjanc <gregor.gorjanc@gmail.com> Co-authored-by: yqiqichen <s2459130@ed.ac.uk>
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