Code

Deploy to prod#635

Code

Merged

amstilp merged 169 commits intodeploy/productionUW-GAC/primed-django:deploy/productionfrom deploy/stageUW-GAC/primed-django:deploy/stageCopy head branch name to clipboardJul 1, 2024

+12,719-2,252

Commits

Commits on Jun 6, 2024

• Allow a dbGaP PI to view their dbGaP application detail view

  Show description for 0215478
  amstilp

  committed
  0215478

• Allow dbGaP PIs to see DAR snapshots for their application

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  amstilp

  committed
  e8eaae0

• Reduce database queries in dbGaP Detail views

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  amstilp

  committed
  014e538

• Allow dbGaP PIs to see the DAR history page

  Show description for f4bbec4
  amstilp

  committed
  f4bbec4

Commits on Jun 7, 2024

• Show PI name instead of username in dbGaP application

  amstilp

  committed
  31a6873

• Add link to PI user profile on dbGaP application page

  amstilp

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  2721588

• Track collaborators associated with a dbGaP application

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  amstilp

  committed
  1a53c66

• Switch dbGaPApplicationDetail view to use MultiTableMixin

  Show description for 1f1b58e
  amstilp

  committed
  1f1b58e

• Add a table to show User, account, and group membership

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  amstilp

  committed
  1d99d30

• Add a table of collaborators to the dbGaPApplicationDetail page

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  amstilp

  committed
  8c8e4dc

• Add form and view to update dbGaP application collaborators

  amstilp

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  03a5879

• Change collaborators widget to autocomplete selector

  amstilp

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  19cd56c

Commits on Jun 9, 2024

• Bump responses from 0.25.0 to 0.25.2

  Show description for e444517
  dependabot[bot]

  authored
  e444517

• Bump pytest from 8.2.1 to 8.2.2

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  dependabot[bot]

  authored
  46c11a5

• Bump ruff from 0.4.7 to 0.4.8

  Show description for 536b787
  dependabot[bot]

  authored
  536b787

Commits on Jun 10, 2024

• Merge dependabot/pip/ruff-0.4.8 into combined-prs-branch

  github-actions[bot]

  authored
  266c719

• Merge dependabot/pip/pytest-8.2.2 into combined-prs-branch

  github-actions[bot]

  authored
  ec69ed8

• Merge dependabot/pip/responses-0.25.2 into combined-prs-branch

  github-actions[bot]

  authored
  a2d4ea6

• Merge branch 'main' into combined-prs-branch

  github-actions[bot]

  authored
  80cc20b

• Merge pull request #603 from UW-GAC/combined-prs-branch

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  amstilp

  authored
  c2e4b8d

• Bump tornado from 6.4 to 6.4.1 in /requirements

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  dependabot[bot]

  authored
  7053c1e

• Add full relative path back to requirements files

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  amstilp

  committed
  fc1250e

• Fix path to dev-requirements.txt in compiled file

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  amstilp

  committed
  6b058db

• Fix extension for dev-requirements in compiled file

  amstilp

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  0794480

• Merge pull request #598 from UW-GAC/dependabot/pip/requirements/tornado-6.4.1

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  amstilp

  authored
  9f4729a

• Start reworking audit namespaces

  Show description for 7edb105
  amstilp

  committed
  7edb105

Commits on Jun 11, 2024

• Move dbGaP audit code into its own subdirectory

  Show description for 0c93614
  amstilp

  committed
  0c93614

Commits on Jun 12, 2024

• Add skeleton classes for collaborator audits

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  amstilp

  committed
  fa255f4

• Add initial auditing classes for dbGaPCollaboratorAudit

  Show description for 068e138
  amstilp

  committed
  068e138

• Rename access audit templates for clarity

  amstilp

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  9900d19

Commits on Jun 13, 2024

• Change collaborator to user in audit result classes

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  amstilp

  committed
  b79340c

• Add definition and tests for dbGaPCollaboratorAudit view

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  amstilp

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  9339fee

• Add a method to audit an application and a group

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  amstilp

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  12095a8

• Dispatch audit based on object type using an internal method

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  amstilp

  committed
  7e2268a

• Use case-insensitive strings when looking up objects by email

  amstilp

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  15455fa

• Add view to resolve collaborator audits

  Show description for 7a112a1
  amstilp

  committed
  7a112a1

• Use admins group in settings file in audits

  Show description for 90df70b
  amstilp

  committed
  90df70b

• Add tests for collaborator audit result classes

  amstilp

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  8130caa

Commits on Jun 14, 2024

• Limit the number of pytest-xdist workers to 4

  Show description for 4c9b194
  amstilp

  committed
  4c9b194

• Add tests for the dbGaPCollaboratorAuditTable

  amstilp

  committed
  e2a3eab

• Run the collaborator audit as part of the run_dbgap_audit command

  amstilp

  committed
  cbd3f05

• Clean up test coverage

  amstilp

  committed
  e72ccc6

• Allow collaborators on dbGaP applications to see info

  Show description for d2cc1da
  amstilp

  committed
  d2cc1da

• Update language on templates

  amstilp

  committed
  3f608b5

• Add collaborator audit to navbar

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  amstilp

  committed
  0c0ec2d

• Add phenotype inventory link to navbar

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  amstilp

  committed
  31331f3

• Add tests for collaborator links on dbGaPApplicationDetail view

  amstilp

  committed
  216c78f

Commits on Jun 16, 2024

• Bump ruff from 0.4.8 to 0.4.9

  Show description for 4fab3e5
  dependabot[bot]

  authored
  4fab3e5

• Bump django-crispy-forms from 2.1 to 2.2

  Show description for 2882aad
  dependabot[bot]

  authored
  2882aad

• Bump responses from 0.25.2 to 0.25.3

  Show description for 54375dd
  dependabot[bot]

  authored
  54375dd

Commits on Jun 17, 2024

• Merge dependabot/pip/responses-0.25.3 into combined-prs-branch

  github-actions[bot]

  authored
  e906402

• Merge dependabot/pip/django-crispy-forms-2.2 into combined-prs-branch

  github-actions[bot]

  authored
  c6393e2

• Merge dependabot/pip/ruff-0.4.9 into combined-prs-branch

  github-actions[bot]

  authored
  21fd3f4

• Merge branch 'main' into combined-prs-branch

  github-actions[bot]

  authored
  db118eb

• [pre-commit.ci] pre-commit autoupdate

  Show description for d5f9617
  pre-commit-ci[bot]

  authored
  d5f9617

• Merge pull request #609 from UW-GAC/combined-prs-branch

  Show description for 64ecffb
  amstilp

  authored
  64ecffb

• Require numpy<2.0

  Show description for 1ae5ede
  amstilp

  committed
  1ae5ede

• Compile requirements files

  

  amstilp

  authored and

  github-actions[bot]

  committed
  9260fde

• Merge pull request #611 from UW-GAC/pip-tools/update-requirements-files/610

  Show description for 0a8c9c3
  amstilp

  authored
  0a8c9c3

• Also put a limit on the pandas version

  Show description for 7b9fe1e
  amstilp

  committed
  7b9fe1e

• Pass verbose flag to pip-compile

  Show description for 14948fd
  amstilp

  committed
  14948fd

• Remove both numpy and pandas requirements temporarily

  Show description for 4b3e9fb
  amstilp

  committed
  4b3e9fb

• Compile requirements files

  

  amstilp

  authored and

  github-actions[bot]

  committed
  bcd98c3

• Add numpy<2.0 back to requriements file

  amstilp

  committed
  9a6954e

• Try just specifying pandas requirement

  Show description for c6b12ab
  amstilp

  committed
  c6b12ab

• Merge pull request #612 from UW-GAC/pip-tools/update-requirements-files/610

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  amstilp

  authored
  8e17d29

• Remove pandas pinned version requirement

  Show description for cf12a8d
  amstilp

  committed
  cf12a8d

• Specify more verbosity for pip-compile

  amstilp

  committed
  96ae985

• Try silencing any warning from a third-party package

  Show description for d23a904
  amstilp

  committed
  d23a904

• Fix syntax errors in pytest config file

  amstilp

  committed
  157ff82

• Undo pytest config changes

  Show description for 6a37070
  amstilp

  committed
  6a37070

• Try using an environment marker in requirements file

  amstilp

  committed
  4a76ed5

• Fix environment marker specification for numpy

  amstilp

  committed
  c286bd6

• Fix numpy version for python 3.12

  amstilp

  committed
  2021025

• Change verbosity back to single v for pip-compile

  amstilp

  committed
  59b1fe4

• Merge pull request #610 from UW-GAC/maint/numpy-version

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  amstilp

  authored
  8fc12cc

• Merge pull request #604 from UW-GAC/pre-commit-ci-update-config

  Show description for 1d369cc
  amstilp

  authored
  1d369cc

Commits on Jun 18, 2024

• Add dbGaP application info to user profile

  amstilp

  committed
  fecded2

• Clean up test coverage

  amstilp

  committed
  746736a

• Fix url in run_collaborative_analysis_audit

  Show description for 308e988
  amstilp

  committed
  308e988

• Fix accordion ids and collapse targets

  amstilp

  committed
  6619790

• Add statement when there are no associated dbGaP apps

  Show description for 9edcecc
  amstilp

  committed
  9edcecc

• Allow staff view users to see data access mechanisms

  Show description for 4e4d9d2
  amstilp

  committed
  4e4d9d2

• Add CDSA "coming soon" to profile page

  Show description for d96949e
  amstilp

  committed
  d96949e

• Merge pull request #599 from UW-GAC/feature/dbgap-application-views-for-pis

  Show description for 175ef59
  amstilp

  authored
  175ef59

• Add accessors and uploaders to CDSA models

  Show description for e326d2f
  amstilp

  committed
  e326d2f

• Add accessors and uploaders to CDSA forms

  amstilp

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  f21b8e4

• Allow CDSA reps, accessors, and uploaders to see detail page

  Show description for 3ea744e
  amstilp

  committed
  3ea744e

Commits on Jun 19, 2024

• Show the list of accessors and uploaders on the detail view

  Show description for 66fdd39
  amstilp

  committed
  66fdd39

Commits on Jun 20, 2024

• Add forms for updating accessors and uploaders

  amstilp

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  0e524aa

• Rearrange CDSA update urls

  Show description for 4022a3a
  amstilp

  committed
  4022a3a

• Add views to update accessors and uploaders

  Show description for 5a8a5e4
  amstilp

  committed
  5a8a5e4

• Rework tests for SignedAgreementDetail view links

  amstilp

  committed
  969cd5b

• Add links to accessor/uploader update views on detail pages

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  amstilp

  committed
  5ed5f57

• Remove signed_agremeent field from uploader update form

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  amstilp

  committed
  1d000d0

• Add classes to audit accessors for SignedAgreements

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  a758f76

• Rework CDSA audit url namespaces

  Show description for f4d4f86
  amstilp

  committed
  f4d4f86

• Set uploaders and accessors in test data script

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  amstilp

  committed
  d4e6223

• Add a view to run the SignedAgreementAccessorAudit

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  committed
  62696a5

• Use the UserFactory when creating accounts for test data

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  committed
  db21e2e

Commits on Jun 21, 2024

• Add view to resolve SignedAgreement Accessor audit results

  Show description for a341a6e
  amstilp

  committed
  a341a6e

• Add action button to accessor audit table

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  amstilp

  committed
  6c50e46

• Set min value in random_int factories

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  amstilp

  committed
  a12e0ab

• Add classes for auditing CDSA uploaders

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  6f6a016

• Fix language in template

  amstilp

  committed
  4375c70

• Add view to show DataAffiliateUploaderAudit results

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  f51a55b

• Add view to resolve a DataAgreementUploaderAudit result

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  187901c

• Add action column with template to DataAffiliateUploaderAuditTable

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  6c8d08f

• Add uploader audit link to navbar

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  0d50327

• Add tests for other Accessor/Uploader audit classes

  Show description for 8a06af4
  amstilp

  committed
  8a06af4

• Update test data for better CDSA audit examples

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  4b2468c

• Rename audit classes to have shorter names

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  87fabaf

• Rename templates to match audit classes and views

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  31ff6d0

• Shorten template names to match audit classes

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  8b3c369

Commits on Jun 22, 2024

• Show accessor or uploader CDSAs on user detail

  amstilp

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  28e3e9e

• Fix duplicate data access mechanisms on user profile

  Show description for 3dd5587
  amstilp

  committed
  3dd5587

Commits on Jun 23, 2024

• Bump types-requests from 2.32.0.20240602 to 2.32.0.20240622

  Show description for 3f51e9f
  dependabot[bot]

  authored
  3f51e9f

• Bump whitenoise from 6.6.0 to 6.7.0

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  dependabot[bot]

  authored
  e6763cf

• Bump ruff from 0.4.9 to 0.4.10

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  dependabot[bot]

  authored
  3c8619a

• Bump django-htmx from 1.17.3 to 1.18.0

  Show description for c0f647b
  dependabot[bot]

  authored
  c0f647b

Commits on Jun 24, 2024

• Merge dependabot/pip/django-htmx-1.18.0 into combined-prs-branch

  github-actions[bot]

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• Merge dependabot/pip/ruff-0.4.10 into combined-prs-branch

  github-actions[bot]

  authored
  55853ab

• Merge dependabot/pip/whitenoise-6.7.0 into combined-prs-branch

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  f3d77ac

• Merge dependabot/pip/types-requests-2.32.0.20240622 into combined-prs-branch

  github-actions[bot]

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  0739de3

• Merge branch 'main' into combined-prs-branch

  github-actions[bot]

  authored
  24d3369

• [pre-commit.ci] pre-commit autoupdate

  Show description for 197c22f
  pre-commit-ci[bot]

  authored
  197c22f

• Clean up coverage

  amstilp

  committed
  c16b3a9

• Remove stray prints statement

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  c134e86

• Add accessor audits to the run_cdsa_audit management command

  amstilp

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  ded77d2

• Add uploader audits to run_cdsa_audit management command

  amstilp

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  e87096a

• Merge pull request #614 from UW-GAC/feature/cdsa-views-for-investigators

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  amstilp

  authored
  bc1d927

• Merge pull request #619 from UW-GAC/combined-prs-branch

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  amstilp

  authored
  5427d85

• Merge pull request #620 from UW-GAC/pre-commit-ci-update-config

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  amstilp

  authored
  71cf7b2

• Update urllib to >=2.2.2 to fix security update

  amstilp

  committed
  f7d290e

• Compile requirements files

  

  amstilp

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  github-actions[bot]

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  cab0f72

• Merge pull request #623 from UW-GAC/pip-tools/update-requirements-files/622

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  amstilp

  authored
  958f768

• Update requests to fix security alert

  amstilp

  committed
  36be49d

• Compile requirements files

  

  amstilp

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  github-actions[bot]

  committed
  3f146e2

• Merge pull request #624 from UW-GAC/pip-tools/update-requirements-files/622

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  amstilp

  authored
  7e35b4b

Commits on Jun 25, 2024

• Update idna to fix security alert

  amstilp

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  1d5f6a3

• Compile requirements files

  

  amstilp

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  github-actions[bot]

  committed
  de42f87

• Merge pull request #625 from UW-GAC/pip-tools/update-requirements-files/622

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  amstilp

  authored
  7910014

• Merge pull request #622 from UW-GAC/maint/security-updates

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  amstilp

  authored
  c17254d

• Merge pull request #626 from UW-GAC/main

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  amstilp

  authored
  8e6d416

• Add button to update dbGaPApplication collaborators

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  amstilp

  committed
  85ae464

• Update example data scripts so both CDSA and dbGaP ones can be added

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  amstilp

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  ca73be3

• Add collaborators in example data to get dbGaP auditing

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  2f9e1d1

• Add new template for dbGaP collaborator update

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  fd807d5

• Fix title and remove some details from template

  amstilp

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Commits on Jun 27, 2024

• Define filter for StudyList

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  wkirdp

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  f4e4813

• Remove get_queryset(). It is not needed.

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  b12dcca

Commits on Jun 28, 2024

• Show representative CDSAs on user detail page

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  amstilp

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  d609778

• Update templates for investigator viewers

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  amstilp

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  cec812a

• Whitespace changes to get pre-commit.ci to run again

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  amstilp

  committed
  f6059c7

• Add order by short_name to queryset

  wkirdp

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  9db27d8

• Update tests for definition list format change

  amstilp

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  6dbdc89

• Fix additional definition list test

  amstilp

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  267deec

• Merge pull request #627 from UW-GAC/feature/harmonize-dbgap-cdsa-updates

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  amstilp

  authored
  cf38e3b

Commits on Jun 30, 2024

• Bump ruff from 0.4.10 to 0.5.0

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  dependabot[bot]

  authored
  4d8edd3

• Bump mypy from 1.10.0 to 1.10.1

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  dependabot[bot]

  authored
  4f031aa

Commits on Jul 1, 2024

• Merge dependabot/pip/mypy-1.10.1 into combined-prs-branch

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  e5db17c

• Merge dependabot/pip/ruff-0.5.0 into combined-prs-branch

  github-actions[bot]

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  e48d79a

• Merge branch 'main' into combined-prs-branch

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  17d4685

• Update CI to run ubuntu 22.04 defaults

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  cbf0030

• Use quotes around python version

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  a2c9d1e

• Merge pull request #633 from UW-GAC/maint/ci/ubuntu-22.04

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  amstilp

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  5fb30e3

• Merge pull request #631 from UW-GAC/combined-prs-branch

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  amstilp

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  1e212d8

• Merge pull request #628 from UW-GAC/feature/add-search-to-study-list

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  amstilp

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  ddecf59

• Merge pull request #634 from UW-GAC/main

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