Code

Release v0.8.0#380

Code

Merged

ielis merged 91 commits intomainmonarch-initiative/gpsea:mainfrom release-0.xmonarch-initiative/gpsea:release-0.xCopy head branch name to clipboardDec 11, 2024

+41,469-10,988

Commits

Commits on Nov 4, 2024

• Update typing annotations in genome.

  ielis

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  5a5a6a9

• Improve index and setup.

  ielis

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  b016b85

Commits on Nov 12, 2024

• Merge remote-tracking branch 'origin/develop' into improve-docs

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  20e723a

Commits on Nov 14, 2024

• Include CYP21A2 cohort in the tests.

  ielis

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  16f4eaa

• Show HPO info in it's section.

  ielis

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  0c808cd

• Improve Cohort report styling.

  ielis

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  ec49ece

• Setup colors and base template.

  ielis

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  595cbe0

• Improve layout.

  ielis

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  c5f2da2

• Simplify MtcStatsViewer.

  ielis

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  6aadca5

• Update variant viewer.

  ielis

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  8f171a4

• Revise ProteinVariantViewer.

  ielis

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  7d6c1ba

• Regenerate doc materials.

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  f3977e2

• Skip manual tests.

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  48fb146

• Add missing super().__init__() call.

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  54f3c0e

Commits on Nov 15, 2024

• Centralize flag for controlling generation of embedded doc elements.

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  0f4851f

• Remove _report package.

  ielis

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  f936a4a

• Group viewers into a single module.

  ielis

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  7389277

• Next development iteration 0.7.2.dev0.

  ielis

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  d7e5e96

• Merge branch 'develop' into ielis/issue353

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  f531496

• Add dark mode, apply the style solely to the report.

  ielis

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  54e8b51

• Merge pull request #354 from monarch-initiative/ielis/issue353

  Show description for 05e6492
  ielis

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  05e6492

• also return t statistic (not just the p value)

  pnrobinson

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  7f596b1

• Disable dark mode.

  ielis

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  f328f17

Commits on Nov 18, 2024

• Adding TRANSMEMBRANE and TOPOLOGICAL DOMAIN to protein types for display in protein metadata etc.

  pnrobinson

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  c1f7102

• updating documentation for CountingPhenotypeScorer

  pnrobinson

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  7adadce

Commits on Nov 21, 2024

• Wrap p value in a container and include an optional statistic for all currently used statistical tests.

  ielis

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  59c7b1a

• Merge branch 'develop' into t_stat

  ielis

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  fa4c3fb

• Keep track of both statistic and the result.

  ielis

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  7106f22

• Merge pull request #357 from monarch-initiative/t_stat

  Show description for 218e35b
  ielis

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  218e35b

Commits on Nov 22, 2024

• Harmonize caching. Cache in JSON format instead of pickle. Update test caches.

  ielis

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  f6cb5b5

• Use default protein metadata service in tutorial.

  ielis

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  ecbcb95

• Merge pull request #361 from monarch-initiative/serialize-our-stuff

  Show description for d453d40
  ielis

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  d453d40

• Merge remote-tracking branch 'origin/develop' into topological_domain

  ielis

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  bea106e

Commits on Nov 25, 2024

• MInor doc tweaks.

  ielis

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  8809f75

Commits on Nov 26, 2024

• Merge remote-tracking branch 'origin/develop' into u-score-documentation

  ielis

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  190d6e1

• Merge remote-tracking branch 'origin/develop' into topological_domain

  ielis

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  e57df42

• Merge pull request #359 from monarch-initiative/topological_domain

  Show description for be10016
  ielis

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  be10016

Commits on Nov 28, 2024

• Remove test protein service.

  ielis

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  9837ea7

• Merge branch 'develop' into disable-dark-mode

  ielis

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  d242628

• Merge pull request #358 from monarch-initiative/disable-dark-mode

  Show description for 37fa338
  ielis

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  37fa338

• Merge branch 'develop' into improve-docs

  ielis

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  817e3f7

• Wordsmith the tutorial.

  ielis

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  02b263c

Commits on Nov 29, 2024

• Update index.

  ielis

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  7ad268b

• Update setup & tutorial.

  ielis

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  1f5cdb8

• Improve input-data docs.

  ielis

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  9f34cbe

Commits on Dec 2, 2024

• Fetch a few more feature types from Uniprot.

  ielis

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  b5f4dd7

• Update test cache.

  ielis

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  27eb22f

• Use a proper variant key for caching.

  ielis

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  a7104e1

Commits on Dec 4, 2024

• Simplify CI script.

  ielis

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  3a7a945

• Simplify config checks.

  ielis

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  c878d54

• Update test cache.

  ielis

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  cedcefa

• Use str instead of a gpsea.model.FeatureType.

  ielis

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  d86055c

• Merge pull request #369 from monarch-initiative/improve-uniprot-response-parsing

  Show description for edf3306
  ielis

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  edf3306

• Transcript id is a must for CohortViewer.

  ielis

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  346780a

• Merge pull request #370 from monarch-initiative/require-tx-id-in-cohort-viewer

  Show description for e234924
  ielis

  authored
  e234924

Commits on Dec 5, 2024

• P val can be NaN in StatisticResult.

  ielis

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  21e565c

• Raise AnalysisException for weird datasets along with data computed so far to simplify troubleshooting.

  ielis

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  41ec006

• Merge pull request #372 from monarch-initiative/ielis/issue371

  Show description for 6f65cdd
  ielis

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  6f65cdd

• Merge branch 'develop' into improve-docs

  ielis

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  b938fa8

• Fix lints.

  ielis

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  ce684fb

• Refine user-guide/index.

  ielis

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  555c628

• Update input data section.

  ielis

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  4c225af

• Update exploratory section.

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  c948964

Commits on Dec 6, 2024

• Restructure the user guide into three sections.

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  4f6be93

Commits on Dec 8, 2024

• Add figures to genotype predicates.

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  3b15214

• Add a config file.

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  9ab215e

Commits on Dec 9, 2024

• Ignore ruff cache.

  ielis

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  59ada8d

• Remove .flake8.

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  1c1dc32

• Remove case study notebooks

  ielis

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  c7228eb

• Merge pull request #374 from monarch-initiative/reformat-with-ruff

  Show description for 8cfbceb
  ielis

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  8cfbceb

• Merge branch 'develop' into remove-case-studies

  ielis

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  3c8d7db

• Merge pull request #375 from monarch-initiative/remove-case-studies

  Show description for 48529e9
  ielis

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  48529e9

• Merge branch 'develop' into improve-docs

  ielis

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  8bfad1f

• Remove dev files.

  ielis

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  13fd8cf

• Merge pull request #376 from monarch-initiative/remove-dev-files

  Show description for 4c51d03
  ielis

  authored
  4c51d03

• Merge remote-tracking branch 'origin/develop' into improve-docs

  ielis

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  212f4e1

• Add figures to mono- and biallelic predicates.

  ielis

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  6118a9c

• Add figures to allele count predicate section.

  ielis

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  981b1bd

• Revise variant predicates text.

  ielis

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  ca6f1f6

• Minor update.

  ielis

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  7234800

Commits on Dec 10, 2024

• Add pronounciation.

  ielis

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  d07f31d

• Fix documentation lints.

  ielis

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  88d15f4

• Merge pull request #348 from monarch-initiative/improve-docs

  Show description for e127ec6
  ielis

  authored
  e127ec6

• Improve the docs for specified terms MT filter.

  ielis

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  996a0ec

• Merge pull request #378 from monarch-initiative/ielis/issue373

  Show description for c36810a
  ielis

  authored
  c36810a

Commits on Dec 11, 2024

• Ignore transcripts with errors when parsing multiple.

  ielis

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  d4e075c

• Test parsing tx coordinates for a gene.

  ielis

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  2d17cd9

• Fix coordinate system-related bug.

  ielis

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  b984620

• Merge pull request #379 from monarch-initiative/ielis/issue345

  Show description for ba6464d
  ielis

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  ba6464d

• Remove phonetics.

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  4d2c393

• Make release 0.8.0.

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  dcb6d04