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Make release 0.3.0 #246

Merged
merged 65 commits into from
Sep 4, 2024
Merged

Make release 0.3.0 #246

merged 65 commits into from
Sep 4, 2024

Commits on Aug 27, 2024

  1. Allow to wrap a scoring funcion and produce PhenotypeScorer.

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  2. Create DeVriesPhenotypeScorer stub.

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    ielis committed Aug 27, 2024
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  3. Check genotype categories in boxplot function.

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    ielis committed Aug 27, 2024
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  4. Fix bug in the check.

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    ielis committed Aug 27, 2024
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  5. Next development iteration v0.2.1.dev0.

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  6. Merge remote-tracking branch 'origin/develop' into ielis/issue217

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  7. Improve the MTC user guide section.

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  8. Merge pull request #234 from monarch-initiative/update-mtc-section 

    Improve the MTC user guide section
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  9. Merge remote-tracking branch 'origin/develop' into ielis/issue217

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  10. Made updates to all the notebooks to reflect the rebrand

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    lnrekerle committed Aug 27, 2024
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  11. Configure the protein metadata service in the preprocessing module.

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Commits on Aug 28, 2024

  1. Add KaryotypicSex.

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  2. Merge pull request #235 from monarch-initiative/gpsea_notebook_updates 

    Made updates to all the notebooks to reflect the rebrand
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  3. Merge remote-tracking branch 'origin/develop' into handle-inheritance… 

    …-modes
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  4. Added an error if there were multiple of the same patient_ids

    @lnrekerle
    lnrekerle committed Aug 28, 2024
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  5. Updated so it will check every patient before incase there is more th… 

    …an one.
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  6. Fixed error

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  7. Add Sex to Patient.

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Commits on Aug 29, 2024

  1. WIP, de Vries score and documentation

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  2. de Vries score and documentation and unit tests

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  3. Merge branch 'develop' into ielis/issue217

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  4. Implement ModeOfInheritanceParedicate.

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  5. Fix typos, rearrange few things.

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  6. foxing documentation

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  7. Merge remote-tracking branch 'origin/ielis/issue217' into ielis/issue217

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  8. Revert the way of testing for hypertelorism.

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  9. Merge pull request #232 from monarch-initiative/ielis/issue217 

    Create de Vries scorer, support wrapping phenotype scoring function
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  10. Made changes to the cohort creator - duplicate patient ID verifier an… 

    …d added test
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  11. Merge branch 'develop' into duplicate_patient_id

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  12. Sorting so we get same output every time

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  13. sort didn't work in line.

    @lnrekerle
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  14. Minor test enhancements.

    @ielis
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  15. Rename variable from list (Python keyword) to something else.

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Commits on Aug 30, 2024

  1. Merge branch 'develop' into handle-inheritance-modes

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  2. Move DeVriesScorer test elsewhere.

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  3. Fine tune the inheritance mode assignment.

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  4. Improve documentation for predicates.

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    ielis committed Aug 30, 2024
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Commits on Sep 1, 2024

  1. Check compatibility between the predicates and the count statistic.

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Commits on Sep 2, 2024

  1. Add docs to ModeOfInheritancePredicate.

    @ielis
    ielis committed Sep 2, 2024
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  2. Fix compatibility checking bug.

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    ielis committed Sep 2, 2024
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Commits on Sep 3, 2024

  1. Remove the obsolete PhenotypeMtcFilter.filter_terms_to_test method.

    @ielis
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  2. Add PhenotypePolyPredicate.present_phenotype_categorization property.

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    ielis committed Sep 3, 2024
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  3. Improve PhenotypeMtcFilter tests.

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  4. Implement filtering genotype predicate for choosing the genotype cate… 

    …gories of interest.
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  5. Improve generating the polypredicate question.

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  6. Improve docs for filtering_predicate.

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  7. Merge pull request #239 from monarch-initiative/handle-inheritance-modes 

    Handle inheritance modes
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Commits on Sep 4, 2024

  1. Allow loading of a bunch of file paths.

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    ielis committed Sep 4, 2024
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  2. Describe new loading in the docs.

    @ielis
    ielis committed Sep 4, 2024
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  3. Add missing exports.

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  4. Merge branch 'develop' into duplicate_patient_id

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  5. Merge pull request #238 from monarch-initiative/duplicate_patient_id 

    Duplicate patient
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  6. Merge branch 'develop' into tweak-pp-loading

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  7. Merge pull request #242 from monarch-initiative/tweak-pp-loading 

    Simplify phenopacket loading functions
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  8. Add TTestStatistic.

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  9. Mention the pscore.stats module in the docs.

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  10. Merge pull request #243 from monarch-initiative/ielis/issue240 

    Add T test
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  11. Remove obsolete analysis code.

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  12. Update README.md.

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  13. Merge pull request #244 from monarch-initiative/remove-obsoleted-anal… 

    …ysis-code

Remove obsolete analysis code
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  14. Allow using Sex as a genotype predicate.

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  15. Allow using disease diagnosis as a genotype predicate.

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  16. Merge pull request #245 from monarch-initiative/ielis/issue236 

    Allow using `Sex` and disease diagnosis as a genotype predicate
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  17. Update SUOX notebook.

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  18. Make release 0.3.0.

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