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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

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ielis
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@ielis ielis commented Sep 4, 2024

Make release 0.3.0.

ielis and others added 30 commits August 27, 2024 14:39
@ielis
Allow to wrap a scoring funcion and produce PhenotypeScorer.
c6b8178
@ielis
Create DeVriesPhenotypeScorer stub.
e0c70b6
@ielis
Check genotype categories in boxplot function.
303858f
@ielis
Fix bug in the check.
92800cb
@ielis
Next development iteration v0.2.1.dev0.
5e81498
@ielis
Merge remote-tracking branch 'origin/develop' into ielis/issue217
52c6213
@ielis
Improve the MTC user guide section.
d4e6ffa
@ielis
Merge pull request #234 from monarch-initiative/update-mtc-section
493a24c 
Improve the MTC user guide section
@ielis
Merge remote-tracking branch 'origin/develop' into ielis/issue217
8ba4237
@lnrekerle
Made updates to all the notebooks to reflect the rebrand
abd5545
@ielis
Configure the protein metadata service in the preprocessing module.
3f38f15
@ielis
Add KaryotypicSex.
d641c08
@pnrobinson
Merge pull request #235 from monarch-initiative/gpsea_notebook_updates
e9228fb 
Made updates to all the notebooks to reflect the rebrand
@ielis
Merge remote-tracking branch 'origin/develop' into handle-inheritance…
a8defa6 
…-modes
@lnrekerle
Added an error if there were multiple of the same patient_ids
30f0521
@lnrekerle
Updated so it will check every patient before incase there is more th…
8277991 
…an one.
@lnrekerle
Fixed error
566f80f
@ielis
Add Sex to Patient.
9613f94
@pnrobinson
WIP, de Vries score and documentation
1e3c463
@pnrobinson
de Vries score and documentation and unit tests
57a2a7d
@pnrobinson
Merge branch 'develop' into ielis/issue217
98f4b0c
@ielis
Implement ModeOfInheritanceParedicate.
202be91
@ielis
Fix typos, rearrange few things.
1b9ed11
@pnrobinson
foxing documentation
eb08b30
@pnrobinson
Merge remote-tracking branch 'origin/ielis/issue217' into ielis/issue217
a64d579
@ielis
Revert the way of testing for hypertelorism.
900922f
@pnrobinson
Merge pull request #232 from monarch-initiative/ielis/issue217
946c606 
Create de Vries scorer, support wrapping phenotype scoring function
@lnrekerle
Made changes to the cohort creator - duplicate patient ID verifier an…
600955d 
…d added test
@lnrekerle
Merge branch 'develop' into duplicate_patient_id
1758888
@lnrekerle
Sorting so we get same output every time
1ca62b1
@ielis
Check compatibility between the predicates and the count statistic.
7acfc72
@ielis
Add docs to ModeOfInheritancePredicate.
ae2e8d0
@ielis
Fix compatibility checking bug.
304df63
@ielis
Remove the obsolete PhenotypeMtcFilter.filter_terms_to_test method.
ade5d5c
@ielis
Add PhenotypePolyPredicate.present_phenotype_categorization property.
ab0a116
@ielis
Improve PhenotypeMtcFilter tests.
b35790b
@ielis
Implement filtering genotype predicate for choosing the genotype cate…
af302c0 
…gories of interest.
@ielis
Improve generating the polypredicate question.
21caddc
@ielis
Improve docs for filtering_predicate.
8ba618e
@ielis
Merge pull request #239 from monarch-initiative/handle-inheritance-modes
cf42c4e 
Handle inheritance modes
@ielis
Allow loading of a bunch of file paths.
b65a69d
@ielis
Describe new loading in the docs.
7136a1c
@ielis
Add missing exports.
e4533eb
@ielis
Merge branch 'develop' into duplicate_patient_id
7ecd5c3
@ielis
Merge pull request #238 from monarch-initiative/duplicate_patient_id
61e92ad 
Duplicate patient
@ielis
Merge branch 'develop' into tweak-pp-loading
b522972
@ielis
Merge pull request #242 from monarch-initiative/tweak-pp-loading
532e611 
Simplify phenopacket loading functions
@ielis
Add TTestStatistic.
a9f66b2
@ielis
Mention the pscore.stats module in the docs.
cda263f
@ielis
Merge pull request #243 from monarch-initiative/ielis/issue240
0c06174 
Add T test
@ielis
Remove obsolete analysis code.
7241b08
@ielis
Update README.md.
e9ff7d4
@ielis
Merge pull request #244 from monarch-initiative/remove-obsoleted-anal…
0a4ebc2 
…ysis-code

Remove obsolete analysis code
@ielis
Allow using Sex as a genotype predicate.
53653e5
@ielis
Allow using disease diagnosis as a genotype predicate.
c61b087
@ielis
Merge pull request #245 from monarch-initiative/ielis/issue236
f8be8ea 
Allow using `Sex` and disease diagnosis as a genotype predicate
@ielis
Update SUOX notebook.
620bd86
@ielis
Make release 0.3.0.
140a8f0
@ielis ielis merged commit f23741a into main Sep 4, 2024
3 checks passed
@ielis ielis deleted the release-0.3.0 branch September 4, 2024 14:05
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3 participants
@ielis @lnrekerle @pnrobinson