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Release/v0.1.0 #24

Merged
merged 180 commits into from
Aug 12, 2024
Merged

Release/v0.1.0 #24

merged 180 commits into from
Aug 12, 2024

Commits on Jun 18, 2024

  1. fix pytest, quick-pytest

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  2. lint with black

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    elewis2 committed Jun 18, 2024
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  3. add skip

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    elewis2 committed Jun 18, 2024
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  4. add todos

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  5. lint with black

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    elewis2 committed Jun 18, 2024
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Commits on Jun 19, 2024

  1. fix retvals remove comments

    @elewis2
    elewis2 committed Jun 19, 2024
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  2. fix version

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    elewis2 committed Jun 19, 2024
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  3. Merge branch 'develop' of https://github.com/bcgsc/pori_python into b… 

    …ugfix/fix-gh-workflows
    @elewis2
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  4. Merge branch 'develop' of https://github.com/bcgsc/pori_python into b… 

    …ugfix/DEVSU-2348-add-gene-assoc-to-pharmacogenelist
    @elewis2
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  5. bump min python version to 3.9

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Commits on Jun 20, 2024

  1. Merge pull request #1 from bcgsc/bugfix/fix-gh-workflows 

    Bugfix/fix gh workflows
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  2. Merge branch 'develop' into bugfix/DEVSU-2348-add-gene-assoc-to-pharm… 

    …acogenelist
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Commits on Jul 1, 2024

  1. get url from env first if possible

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Commits on Jul 2, 2024

  1. use name for preferred gene source

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  2. get rid of source from name

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  3. skip some bcgsc-specific tests

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  4. check for any ensg version

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  5. skip db-dependent test in test_statement

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  6. skip db-dependent test in test_util

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  7. fix errors

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Commits on Jul 4, 2024

  1. add exceptions

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Commits on Jul 8, 2024

  1. Merge pull request #2 from bcgsc/bugfix/DEVSU-2348-add-gene-assoc-to-… 

    …pharmacogenelist

Bugfix/devsu 2348 add gene assoc to pharmacogenelist
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  2. update readme

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  3. Merge branch 'develop' of https://github.com/bcgsc/pori_python into f… 

    …eat/update-readme
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  4. fix period

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  5. add async loading option for reports

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  6. cleanup

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  7. Merge branch 'develop' of https://github.com/bcgsc/pori_python into f… 

    …eature/DEVSU-2349-add-async-report-loading
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  8. lint with black

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Commits on Jul 9, 2024

  1. handle other possible states, add return

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  2. handle waiting

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  3. Merge pull request #3 from bcgsc/feat/update-readme 

    Feat/update readme
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  4. Merge branch 'develop' into feature/DEVSU-2349-add-async-report-loading

    @elewis2
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  5. reformat, fix bug

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  6. Merge branch 'feature/DEVSU-2349-add-async-report-loading' of https:/… 

    …/github.com/bcgsc/pori_python into feature/DEVSU-2349-add-async-report-loading
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  7. log failedReason

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  8. lint with black

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  9. Merge pull request #4 from bcgsc/feature/DEVSU-2349-add-async-report-… 

    …loading

Feature/devsu 2349 add async report loading
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  10. remove old docs, update versions

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  11. remove package version ceilings

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  12. add testpypi workflow

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  13. use test credentials in test workflow

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  14. disable test workflow; working

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  15. set to manual trigger

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  16. update docs workflow

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  17. updates

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  18. SDEV-4409 - replace PHARMACOGENOMIC_SOURCE_EXCLUDE_LIST with GSC_PHAR… 

    …MACOGENOMIC_SOURCE_DISPLAYNAME_EXCLUDE_LIST
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  19. SDEV-4409 - GSC_PHARMACOGENOMIC_SOURCE_EXCLUDE_LIST and GSC_PHARMACOG… 

    …ENOMIC_SOURCE_DISPLAYNAME_EXCLUDE_LIST
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  20. SDEV-4409 - allow typing_extension>4.4; remove max version on requests

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  21. Merge branch 'SDEV-4409_add_constants' of https://github.com/bcgsc/po… 

    …ri_python into SDEV-4409_remove_import_maximums
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Commits on Jul 10, 2024

  1. Merge pull request #5 from bcgsc/feat/update-gh-workflows 

    Feat/update gh workflows
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  2. Merge branch 'develop' into SDEV-4409_add_constants

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  3. Merge branch 'develop' into SDEV-4409_remove_import_maximums

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  4. Merge pull request #7 from bcgsc/SDEV-4409_remove_import_maximums 

    SDEV-4409 - allow typing_extension>4.4; remove max version on requests
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  5. Merge pull request #6 from bcgsc/SDEV-4409_add_constants 

    SDEV-4409 - replace PHARMACOGENOMIC_SOURCE_EXCLUDE_LIST with GSC_PHAR…
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  6. Merge branch 'develop' of https://github.com/bcgsc/pori_python into S… 

    …DEV-4409_remove_import_maximums
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  7. SDEV-4409 - bugfix - replace progressbar2 with tqdm to display progre… 

    …ss in long matching.
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  8. Merge branch 'main' of https://github.com/bcgsc/pori_python into SDEV… 

    …-4409_remove_import_maximums
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Commits on Jul 11, 2024

  1. check for presence of ident instead of state

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  2. minor cleanup

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  3. lint with black

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Commits on Jul 12, 2024

  1. Merge pull request #8 from bcgsc/bugfix/SDEV-4409_progressbar_error 

    Bugfix/sdev 4409 progressbar error
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  2. add bcgsc skips

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  3. resolve merge

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  4. Merge branch 'develop' into bugfix/unexpected-state-on-success

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  5. Merge pull request #9 from bcgsc/bugfix/unexpected-state-on-success 

    Bugfix/unexpected state on success
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  6. linting - isort and black

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  7. lint - isort black - line-len 100

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  8. add optional async-related args to entrypt

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  9. lint

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  10. commit to merge

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Commits on Jul 13, 2024

  1. Merge pull request #11 from bcgsc/feat/DEVSU-2349-add-async-option-to… 

    …-command-interface

add optional async-related args to entrypt
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  2. merge

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  3. Merge branch 'develop' of https://github.com/bcgsc/pori_python into i… 

    …mprovement/lint_isort_black_linelen
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  4. lint black

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  5. add gkb settings options to ipr main

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  6. make gkb settable, add optional skips

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  7. add skips

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  8. add gkb connection options

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  9. add skip and gkb options

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Commits on Jul 14, 2024

  1. add e2e upload tests with civic data

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  2. add test instructions

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Commits on Jul 15, 2024

  1. Merge pull request #10 from bcgsc/improvement/lint_isort_black_linelen 

    Improvement/lint isort black linelen
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  2. lint - remove unused variables

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  3. Merge branch 'develop' of https://github.com/bcgsc/pori_python into i… 

    …mprovement/lint_typing
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  4. lint - import warning error - pytest fixtures cannot be imported.

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  5. lint - silence F401 error from import in __init__.py

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  6. bugfix - mins_to_wait and async_upload variables are reversed

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  7. merge

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  8. linting - import urllib3 directly, instead of through requests, to ge… 

    …t typing hints.
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  9. lint - simplify TypedDict import - drop support for old python versions.

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  10. lint

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  11. lint - fix expected type str error in util.py

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  12. lint - fix expected type str error in therapeutic_options.py

    @dustinbleile
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  13. refactor - replace graphkb/types.py and ipr/types.py with a single po… 

    …ri_python/types.py
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  14. refactor - remove OntologyLinks and reduce typing errors.

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  15. lint - fix alterations redeclared

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  16. lint - fix filters redeclared

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  17. refactor - remove redundant types - replace GkbStatement with Statement.

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Commits on Jul 18, 2024

  1. update to match current report-asnc return value

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  2. improve async upload check; add test

    @elewis2
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  3. lint

    @elewis2
    elewis2 committed Jul 18, 2024
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  4. typing errors - add 'name' as a field for records

    @dustinbleile
    dustinbleile committed Jul 18, 2024
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  5. typing fixes - remove ontologyTermRepr - feature is unused.

    @dustinbleile
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  6. Merge branch 'feat/DEVSU-2349-match-async-report-return' of https://g… 

    …ithub.com/bcgsc/pori_python into refactor/lint_unify_types
    @dustinbleile
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  7. Merge pull request #14 from bcgsc/feat/DEVSU-2349-match-async-report-… 

    …return

improve async upload check; add test
    @dustinbleile
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  8. SDEV-4409 - remove TestOntologyTermRepr - no longer used.

    @dustinbleile
    dustinbleile committed Jul 18, 2024
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  9. SDEV-4409 - merge - fix import after refactor.

    @dustinbleile
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  10. lint - isort, black linelen=100

    @dustinbleile
    dustinbleile committed Jul 18, 2024
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  11. fix F541 f-string is missing placeholders

    @dustinbleile
    dustinbleile committed Jul 18, 2024
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  12. remove unused import

    @dustinbleile
    dustinbleile committed Jul 18, 2024
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  13. Merge branch 'develop' of https://github.com/bcgsc/pori_python into r… 

    …efactor/lint_unify_types
    @dustinbleile
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Commits on Jul 19, 2024

  1. add sync and async upload test

    @elewis2
    elewis2 committed Jul 19, 2024
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  2. lint and fix arg order

    @elewis2
    elewis2 committed Jul 19, 2024
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  3. Merge branch 'develop' into feat/DEVSU-2349-add-async-and-sync-upload… 

    …-test
    @elewis2
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  4. Merge branch 'develop' into improvement/lint_typing

    @elewis2
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  5. Merge pull request #12 from bcgsc/improvement/lint_typing 

    Improvement/lint typing
    @elewis2
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  6. Merge branch 'develop' into improvement/lint_typing_fixes_TypedDict

    @elewis2
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  7. Merge branch 'develop' into feat/DEVSU-2349-add-async-and-sync-upload… 

    …-test
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  8. Merge branch 'develop' of https://github.com/bcgsc/pori_python into r… 

    …efactor/lint_unify_types
    @dustinbleile
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  9. Merge branch 'improvement/lint_typing_fixes_TypedDict' of https://git… 

    …hub.com/bcgsc/pori_python into refactor/lint_unify_types
    @dustinbleile
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  10. Merge branch 'develop' of https://github.com/bcgsc/pori_python into i… 

    …mprovement/lint_typing_fixes_TypedDict
    @dustinbleile
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  11. SDEV-4409 - merge - fix import after refactor.

    @dustinbleile
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  12. Merge branch 'improvement/lint_typing_fixes_TypedDict' of https://git… 

    …hub.com/bcgsc/pori_python into improvement/lint_typing_fixes_TypedDict
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  13. Merge branch 'improvement/lint_typing_fixes_TypedDict' of https://git… 

    …hub.com/bcgsc/pori_python into refactor/lint_unify_types
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  14. Merge branch 'feat/DEVSU-2349-add-async-and-sync-upload-test' of http… 

    …s://github.com/bcgsc/pori_python into refactor/lint_unify_types
    @dustinbleile
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  15. lint - remove unused imports. black --line-len 100 -C

    @dustinbleile
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  16. SDEV-4431 - bugfix - error message tries to use non-existant key

    @dustinbleile
    dustinbleile committed Jul 19, 2024
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  17. Merge branch 'bugfix/SDEV-4431_failed_message_err' of https://github.… 

    …com/bcgsc/pori_python into improvement/SDEV-4431_migration_to_pori_python
    @dustinbleile
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  18. Merge pull request #13 from bcgsc/improvement/lint_typing_fixes_Typed… 

    …Dict

Improvement/lint typing fixes typed dict
    @elewis2
    elewis2 authored Jul 19, 2024
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  19. Merge branch 'develop' into feat/DEVSU-2349-add-async-and-sync-upload… 

    …-test
    @elewis2
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  20. change master->main, reduce num suites run

    @elewis2
    elewis2 committed Jul 19, 2024
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  21. restore quicktest on push for all branches

    @elewis2
    elewis2 committed Jul 19, 2024
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  22. use diff on syntax

    @elewis2
    elewis2 committed Jul 19, 2024
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  23. Merge branch 'develop' into bugfix/SDEV-4431_failed_message_err

    @dustinbleile
    dustinbleile authored Jul 19, 2024
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  24. SDEV-4431 - typing errors - variant types only as str

    @dustinbleile
    dustinbleile committed Jul 19, 2024
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  25. Merge pull request #15 from bcgsc/feat/DEVSU-2349-add-async-and-sync-… 

    …upload-test

Feat/devsu 2349 add async and sync upload test
    @elewis2
    elewis2 authored Jul 19, 2024
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  26. Merge branch 'develop' into bugfix/gh-actions-branch-exclusions

    @elewis2
    elewis2 authored Jul 19, 2024
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  27. Merge pull request #19 from bcgsc/bugfix/gh-actions-branch-exclusions 

    Bugfix/gh actions branch exclusions
    @elewis2
    elewis2 authored Jul 19, 2024
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  28. Merge branch 'develop' into bugfix/SDEV-4431_failed_message_err

    @elewis2
    elewis2 authored Jul 19, 2024
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Commits on Jul 20, 2024

  1. Merge branch 'develop' of https://github.com/bcgsc/pori_python into i… 

    …mprovement/SDEV-4431_migration_to_pori_python
    @dustinbleile
    dustinbleile committed Jul 20, 2024
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Commits on Jul 22, 2024

  1. Merge pull request #17 from bcgsc/bugfix/SDEV-4431_failed_message_err 

    SDEV-4431 - bugfix - error message tries to use non-existant key
    @dustinbleile
    dustinbleile authored Jul 22, 2024
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  2. SDEV-4431 - typing - casting and silencing of typing errors from mypy.

    @dustinbleile
    dustinbleile committed Jul 22, 2024
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  3. Merge branch 'develop' of https://github.com/bcgsc/pori_python into i… 

    …mprovement/SDEV-4431_migration_to_pori_python
    @dustinbleile
    dustinbleile committed Jul 22, 2024
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  4. SDEV-4431 - bugfix match.py - comparison brackets misplaced.

    @dustinbleile
    dustinbleile committed Jul 22, 2024
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Commits on Jul 23, 2024

  1. SDEV-4431 - refactor - remove typing errors from annotate.py - using … 

    …cast and Hashable dict types.
    @dustinbleile
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  2. SDEV-4431 - refactor typing errors - use HashableDict types in to red… 

    …uce typing errors. Make HashableDict a type.
    @dustinbleile
    dustinbleile committed Jul 23, 2024
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  3. SDEV-4431 - refactor - remove typing issues from summary.py

    @dustinbleile
    dustinbleile committed Jul 23, 2024
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  4. SDEV-4431 - refactor - remove typing errors from inputs.py

    @dustinbleile
    dustinbleile committed Jul 23, 2024
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  5. SDEV-4431 - refactor - remove remaining typing errors from genes.py

    @dustinbleile
    dustinbleile committed Jul 23, 2024
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  6. SDEV-4431 - bugfix - typo displayname -> displayName and move function

    @dustinbleile
    dustinbleile committed Jul 23, 2024
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  7. SDEV-4431 - bugfix - python3.9 compatibility use from __future__ impo… 

    …rt annotations
    @dustinbleile
    dustinbleile committed Jul 23, 2024
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  8. SDEV-4431 - python3.9 types compatibility - use from __future__ impor… 

    …t annotations for typing.
    @dustinbleile
    dustinbleile committed Jul 23, 2024
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Commits on Jul 24, 2024

  1. merge

    @elewis2
    elewis2 committed Jul 24, 2024
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  2. skip tests of bcgsc data

    @elewis2
    elewis2 committed Jul 24, 2024
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  3. check sync/async report diff

    @elewis2
    elewis2 committed Jul 24, 2024
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Commits on Jul 25, 2024

  1. add sampleinfo test

    @elewis2
    elewis2 committed Jul 25, 2024
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  2. lint

    @elewis2
    elewis2 committed Jul 25, 2024
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  3. fix undefined

    @elewis2
    elewis2 committed Jul 25, 2024
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  4. remove debugging code

    @elewis2
    elewis2 committed Jul 25, 2024
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  5. fix headers param

    @elewis2
    elewis2 committed Jul 25, 2024
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  6. lint without -S

    @elewis2
    elewis2 committed Jul 25, 2024
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  7. Merge pull request #16 from bcgsc/improvement/SDEV-4431_migration_to_… 

    …pori_python

Improvement/sdev 4431 migration to pori python
    @elewis2
    elewis2 authored Jul 25, 2024
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  8. Merge branch 'develop' into feat/external-deployment

    @dustinbleile
    dustinbleile authored Jul 25, 2024
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  9. black, isort fixes

    @dustinbleile
    dustinbleile committed Jul 25, 2024
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  10. Merge pull request #20 from bcgsc/feat/external-deployment 

    Feat/external deployment
    @elewis2
    elewis2 authored Jul 25, 2024
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Commits on Jul 26, 2024

  1. typing fix - mypy type error removed from test_upload.py

    @dustinbleile
    dustinbleile committed Jul 26, 2024
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  2. KBDEV-1231 - add test_wt_not_matched - TP53:p.E285K should not match … 

    …to statements of 'TP53 wildtype'
    @dustinbleile
    dustinbleile committed Jul 26, 2024
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  3. remove typing error

    @dustinbleile
    dustinbleile committed Jul 26, 2024
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  4. remove unused import

    @dustinbleile
    dustinbleile committed Jul 26, 2024
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  5. black formatting

    @dustinbleile
    dustinbleile committed Jul 26, 2024
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Commits on Jul 29, 2024

  1. add list sorting to equality check

    @elewis2
    elewis2 committed Jul 29, 2024
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  2. lint

    @elewis2
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Commits on Jul 30, 2024

  1. Merge pull request #21 from bcgsc/bugfix/fix-variably-ordered-list-tests 

    add list sorting to equality check
    @dustinbleile
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  2. Merge branch 'develop' of https://github.com/bcgsc/pori_python into b… 

    …ugfix/KBDEV-1231_wildtype_mismatch
    @dustinbleile
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  3. add additional sorting to result comparison

    @elewis2
    elewis2 committed Jul 30, 2024
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Commits on Jul 31, 2024

  1. Merge pull request #22 from bcgsc/bugfix/sorting-errors-in-test-upload 

    add additional sorting to result comparison
    @dustinbleile
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  2. Merge branch 'develop' of https://github.com/bcgsc/pori_python into b… 

    …ugfix/KBDEV-1231_wildtype_mismatch
    @dustinbleile
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Commits on Aug 2, 2024

  1. Merge pull request #23 from bcgsc/bugfix/KBDEV-1231_wildtype_mismatch 

    Bugfix/kbdev 1231 wildtype mismatch
    @dustinbleile
    dustinbleile authored Aug 2, 2024
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Commits on Aug 6, 2024

  1. major version

    @elewis2
    elewis2 committed Aug 6, 2024
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