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Release v0.8.0 #380

Merged
merged 91 commits into from
Dec 11, 2024
Merged

Release v0.8.0 #380

merged 91 commits into from
Dec 11, 2024

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ielis
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@ielis ielis commented Dec 11, 2024 •
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Release v0.8.0.

ielis and others added 30 commits November 4, 2024 18:41
@ielis
Update typing annotations in genome.
5a5a6a9
@ielis
Improve index and setup.
b016b85
@ielis
Merge remote-tracking branch 'origin/develop' into improve-docs
20e723a
@ielis
Include CYP21A2 cohort in the tests.
16f4eaa
@ielis
Show HPO info in it's section.
0c808cd
@ielis
Improve Cohort report styling.
ec49ece
@ielis
Setup colors and base template.
595cbe0
@ielis
Improve layout.
c5f2da2
@ielis
Simplify MtcStatsViewer.
6aadca5
@ielis
Update variant viewer.
8f171a4
@ielis
Revise ProteinVariantViewer.
7d6c1ba
@ielis
Regenerate doc materials.
f3977e2
@ielis
Skip manual tests.
48fb146
@ielis
Add missing super().__init__() call.
54f3c0e
@ielis
Centralize flag for controlling generation of embedded doc elements.
0f4851f
@ielis
Remove _report package.
f936a4a
@ielis
Group viewers into a single module.
7389277
@ielis
Next development iteration 0.7.2.dev0.
d7e5e96
@ielis
Merge branch 'develop' into ielis/issue353
f531496
@ielis
Add dark mode, apply the style solely to the report.
54e8b51
@ielis
Merge pull request #354 from monarch-initiative/ielis/issue353
05e6492 
Revise reports
@pnrobinson
also return t statistic (not just the p value)
7f596b1
@ielis
Disable dark mode.
f328f17
@pnrobinson
Adding TRANSMEMBRANE and TOPOLOGICAL DOMAIN to protein types for disp…
c1f7102 
…lay in protein metadata etc.
@pnrobinson
updating documentation for CountingPhenotypeScorer
7adadce
@ielis
Wrap p value in a container and include an optional statistic for all…
59c7b1a 
… currently used statistical tests.
@ielis
Merge branch 'develop' into t_stat
fa4c3fb
@ielis
Keep track of both statistic and the result.
7106f22
@ielis
Merge pull request #357 from monarch-initiative/t_stat
218e35b 
Fixes #356
@ielis
Harmonize caching. Cache in JSON format instead of pickle. Update tes…
f6cb5b5 
…t caches.
ielis added 25 commits December 8, 2024 22:21
@ielis
Add figures to genotype predicates.
3b15214
@ielis
Add a config file.
9ab215e
@ielis
Ignore ruff cache.
59ada8d
@ielis
Remove .flake8.
1c1dc32
@ielis
Remove case study notebooks
c7228eb
@ielis
Merge pull request #374 from monarch-initiative/reformat-with-ruff
8cfbceb 
Use Ruff to lint and format
@ielis
Merge branch 'develop' into remove-case-studies
3c8d7db
@ielis
Merge pull request #375 from monarch-initiative/remove-case-studies
48529e9 
Remove case study notebooks
@ielis
Merge branch 'develop' into improve-docs
8bfad1f
@ielis
Remove dev files.
13fd8cf
@ielis
Merge pull request #376 from monarch-initiative/remove-dev-files
4c51d03 
Remove `dev` files
@ielis
Merge remote-tracking branch 'origin/develop' into improve-docs
212f4e1
@ielis
Add figures to mono- and biallelic predicates.
6118a9c
@ielis
Add figures to allele count predicate section.
981b1bd
@ielis
Revise variant predicates text.
ca6f1f6
@ielis
Minor update.
7234800
@ielis
Add pronounciation.
d07f31d
@ielis
Fix documentation lints.
88d15f4
@ielis
Merge pull request #348 from monarch-initiative/improve-docs
e127ec6 
Improve `index` and `setup` doc sections
@ielis
Improve the docs for specified terms MT filter.
996a0ec
@ielis
Merge pull request #378 from monarch-initiative/ielis/issue373
c36810a 
Improve the docs for specified terms MT filter
@ielis
Ignore transcripts with errors when parsing multiple.
d4e075c
@ielis
Test parsing tx coordinates for a gene.
2d17cd9
@ielis
Fix coordinate system-related bug.
b984620
@ielis
Merge pull request #379 from monarch-initiative/ielis/issue345
ba6464d 
Ignore the inconsistent transcripts when getting transcripts for a gene from Variant Validator
@ielis ielis changed the title Release v0.7.2 Release v0.8.0 Dec 11, 2024
@ielis ielis merged commit f9fe293 into main Dec 11, 2024
3 checks passed
@ielis ielis deleted the release-0.x branch December 11, 2024 13:43
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2 participants
@ielis @pnrobinson