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update main to show latest docs #223

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wants to merge 858 commits into from
Closed

update main to show latest docs #223

wants to merge 858 commits into from

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pnrobinson
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frehburg and others added 30 commits July 9, 2024 15:31
@frehburg
moved drawing of variant marker to class
9d7c108
@frehburg
made bottom of protein track look like top (visual bug)
7b72af5
@frehburg
corrected spelling of variant types to be correct in legend 2
5df1ffa
@frehburg
added x axis label, changed typo in comment
8118d7f
@frehburg
plotting legend1 correctly
ca017f3
@frehburg
removed unnecessary print
5a2ee56
@lnrekerle
Merge branch 'develop' into Feature_counts
9239823
@lnrekerle
added new dependency
dfd716d
@lnrekerle
Removed "Homozygous_reference" for AlleleCounter.
492ec46
@lnrekerle
Removed changes that would affect PR #184
b1a87a8
@lnrekerle
Moved titles to top
819fa82
@ielis
Merge remote-tracking branch 'origin/develop' into variant-predicate
0b28d3c
@ielis
Add get_question to VariantPredicate, implement `GenotypeBooleanP…
6832727 
…redicate` and `GroupingPredicate` using `AlleleCounter`s.
@ielis
Mark classes targeted for removal with TODO markers.
ec411b1
@ielis
Remove obsolete cohort analysis implementation.
4f7d0a1
@ielis
Remove boolean and grouping predicate implementations from the public…
e91049a 
… API.
@frehburg
changed dataclass code to be compatible with python 3.8
7cafaf3
@frehburg
removed unnecessary prints
c91cdce
@ielis
Fix incorrect kw argument.
4818e98
@ielis
Elaborate on building the predicate.
55e172d
@ielis
Prepare for removing CohortAnalysis convenience methods in favor of…
d639310 
… `VariantPredicate` builder.
@ielis
Update the tutorial.rst.
f77a801
@ielis
Revert missing CohortAnalysisConfiguration setter.
a34d0a1
@ielis
Add the new compare methods to the API.
bb89ed1
@ielis
Add config for default protein metadata service.
7796890
@lnrekerle
Made requested changes for the PR
4755cf3
@ielis
Simplify parts of variant predicates.
22091bd
@ielis
overlapping_exons is in fact nullable.
3370f7a
@ielis
Fix typo.
df7750c
@ielis
Use private random number generator.
fb6a4f5
ielis added 28 commits August 22, 2024 16:24
@ielis
Update tests.
acb8e55
@ielis
Merge pull request #225 from monarch-initiative/update-tutorial
b8d7b7b 
Update tutorial
@ielis
We will not run the notebooks anymore. The docs are the source of truth.
50372a4
@ielis
Revert back to the editable install.
da21a17
@ielis
Merge pull request #229 from monarch-initiative/do-not-run-the-notebo…
15e7179 
…oks-in-ci

Do not run notebooks in CI
@ielis
Rebrand the project files.
5577dd1
@ielis
Rebrand code and tests.
211c795
@ielis
The final touch.
9b3d356
@ielis
Consider environment variable when creating the cache directory.
ea029d1
@ielis
Keep track of the responses used in tests.
ee15848
@ielis
Fix the input-data.rst chapter.
8aab653
@ielis
Fixe the predicates.rst chapter.
b3f51c1
@ielis
Skip testing qc_results for now.
07fcd07
@ielis
Merge pull request #230 from monarch-initiative/rebrand-to-gpsea
1c12f31 
Change the project name to GPSEA
@ielis
Move GenotypePolyPredicate and GenotypeBooleanPredicate to `gpsea…
3b8a9ae 
….analysis.predicate.genotype` #218
@ielis
Update Genotypes pydoc.
b04f7ec
@ielis
Break the gpsea.analysis into smaller modules.
505f7e2
@ielis
Fix test_stats.
42f6c02
@ielis
Add a comment.
207a1c7
@ielis
Fix spurious test failures.
e6a4d17
@ielis
Improve user-guide/stats.
1ce0cfb
@ielis
Move category code into pcats.
649f61d
@ielis
Delete GenotypeBooleanPredicate.
cf95937
@ielis
Create gpsea.analysis.pscore.PhenotypeScorer API.
dce50c3
@ielis
Implement phenotype score testing.
426dcb1
@ielis
Delete inheritance checker stubs.
c4060ea
@ielis
Add removal markers.
6dfebf4
@ielis
Merge pull request #231 from monarch-initiative/form-statistical-tests
0ac0df9 
Split `analysis` package into analysis types
@ielis
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ielis commented Aug 27, 2024

I'll update main elsewhere.

@ielis ielis closed this Aug 27, 2024
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4 participants
@pnrobinson @ielis @frehburg @lnrekerle