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Feature/python typing/components command.py #2223

Merged
merged 63 commits into from
Oct 17, 2023
Merged

Feature/python typing/components command.py #2223

merged 63 commits into from
Oct 17, 2023

Commits on Mar 28, 2023

  1. my repo test

    @NovakApis
    NovakApis committed Mar 28, 2023
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  2. Merge branch 'dev' into feature/python-typing/components_command.py

    @NovakApis
    NovakApis committed Mar 28, 2023
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  3. black + isort

    @NovakApis
    NovakApis committed Mar 28, 2023
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  4. first test

    @NovakApis
    NovakApis committed Mar 28, 2023
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  5. python-typing/components_command.py 

    Ready for nf-core pr
    @NovakApis
    NovakApis committed Mar 28, 2023
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  6. add mypy ci check

    @fabianegli
    fabianegli authored Mar 28, 2023
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Commits on Mar 29, 2023

  1. made some variable types depend on function return value 

    Changed components_utils->get_repo_info to return a tuple of three concrete types instead of a list of three Any types.
Implemented suggestion to include self.dir as None. This was done in the __init__ argument typing
    @NovakApis
    NovakApis committed Mar 29, 2023
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  2. updated __init__ keyword arguments

    @NovakApis
    NovakApis committed Mar 29, 2023
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  3. Merge branch 'dev' into feature/python-typing/components_command.py

    @fabianegli
    fabianegli authored Mar 29, 2023
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  4. make mypy ignore missing imports

    @fabianegli
    fabianegli authored Mar 29, 2023
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  5. mypy configuration edit 

    fixed syntax error for ingroe_missing_imports and added follow_imports="skip"
    @NovakApis
    NovakApis committed Mar 29, 2023
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Commits on Apr 3, 2023

  1. use mypy without pre-built action

    @fabianegli
    fabianegli authored Apr 3, 2023
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  2. fix typo in mypy target directory

    @fabianegli
    fabianegli authored Apr 3, 2023
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  3. install missing type annotations for mypy

    @fabianegli
    fabianegli authored Apr 3, 2023
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  4. install types non-interactive and with a target

    @fabianegli
    fabianegli authored Apr 3, 2023
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  5. install mypy check requirements explicitly

    @fabianegli
    fabianegli authored Apr 3, 2023
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  6. install tools dependencies for mypy checks

    @fabianegli
    fabianegli authored Apr 3, 2023
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  7. allow redefinition in mypy checks

    @fabianegli
    fabianegli authored Apr 3, 2023
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  8. ignore redefinitions in mypy checks

    @fabianegli
    fabianegli authored Apr 3, 2023
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  9. use tool prefix for mypy section

    @fabianegli
    fabianegli authored Apr 3, 2023
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  10. make disable error code a string

    @fabianegli
    fabianegli authored Apr 3, 2023
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Commits on Oct 16, 2023

  1. Merge branch 'dev' into feature/python-typing/components_command.py

    @kedhammar
    kedhammar authored Oct 16, 2023
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  2. Update nf_core/components/components_command.py 

    Remove superfluous type hinting

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
    @kedhammar @mirpedrol
    kedhammar and mirpedrol authored Oct 16, 2023
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  3. Update nf_core/components/components_command.py 

    Remove superfluous type hinting

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
    @kedhammar @mirpedrol
    kedhammar and mirpedrol authored Oct 16, 2023
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  4. Update nf_core/components/components_command.py 

    Remove superfluous type hinting

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
    @kedhammar @mirpedrol
    kedhammar and mirpedrol authored Oct 16, 2023
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  5. Update nf_core/components/components_command.py 

    Remove superfluous type hinting

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
    @kedhammar @mirpedrol
    kedhammar and mirpedrol authored Oct 16, 2023
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  6. Update nf_core/components/components_command.py 

    Remove superfluous type hinting

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
    @kedhammar @mirpedrol
    kedhammar and mirpedrol authored Oct 16, 2023
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  7. Update nf_core/components/components_command.py 

    Remove superfluous type hinting

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
    @kedhammar @mirpedrol
    kedhammar and mirpedrol authored Oct 16, 2023
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  8. Update nf_core/components/components_command.py 

    Remove superfluous type hinting

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
    @kedhammar @mirpedrol
    kedhammar and mirpedrol authored Oct 16, 2023
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  9. Try adding mypy to pre-commit config

    @kedhammar
    kedhammar committed Oct 16, 2023
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  10. Fix invalid pre-commit config

    @kedhammar
    kedhammar committed Oct 16, 2023
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  11. Revert pre-commit change for now

    @kedhammar
    kedhammar committed Oct 16, 2023
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  12. Try changing CI to only run mypy on changed files

    @kedhammar
    kedhammar committed Oct 16, 2023
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  13. Differentiate dir arg (optional) from dir path

    @kedhammar
    kedhammar committed Oct 16, 2023
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  14. Declare type within func

    @kedhammar
    kedhammar committed Oct 16, 2023
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Commits on Oct 17, 2023

  1. Try installing MyPy stubs

    @kedhammar
    kedhammar committed Oct 17, 2023
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  2. Specify missing stubs

    @kedhammar
    kedhammar committed Oct 17, 2023
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  3. try passing mypy

    @kedhammar
    kedhammar committed Oct 17, 2023
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  4. prettier

    @kedhammar
    kedhammar committed Oct 17, 2023
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  5. bump python version

    @kedhammar
    kedhammar committed Oct 17, 2023
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  6. bugfix

    @kedhammar
    kedhammar committed Oct 17, 2023
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  7. try reverting variable differentiation and instead adapt initial typi… 

    …ng of variable to downstream expected function inputs
    @kedhammar
    kedhammar committed Oct 17, 2023
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  8. Don't combine typing square bracket syntax with non-subscriptable abc… 

    … object os.PathLike
    @kedhammar
    kedhammar committed Oct 17, 2023
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  9. Try further simplifying typing to prevent pytest suite from trying to… 

    … interpret os.PathLike as subscriptable object
    @kedhammar
    kedhammar committed Oct 17, 2023
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  10. extend last commit to this file

    @kedhammar
    kedhammar committed Oct 17, 2023
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  11. Supplement typing and remove superfluous code

    @kedhammar
    kedhammar committed Oct 17, 2023
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  12. isort

    @kedhammar
    kedhammar committed Oct 17, 2023
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  13. supplement typing, 2 errors left

    @kedhammar
    kedhammar committed Oct 17, 2023
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  14. 1 error left

    @kedhammar
    kedhammar committed Oct 17, 2023
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  15. Try fixing typing error by clarifying list-of-dicts parsing

    @kedhammar
    kedhammar committed Oct 17, 2023
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  16. Fix mypy complaints across entire repo

    @kedhammar
    kedhammar committed Oct 17, 2023
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  17. add stubs

    @kedhammar
    kedhammar committed Oct 17, 2023
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  18. isort

    @kedhammar
    kedhammar committed Oct 17, 2023
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  19. try reading custom config in GHA

    @kedhammar
    kedhammar committed Oct 17, 2023
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  20. Revert last 4 commits

    @kedhammar
    kedhammar committed Oct 17, 2023
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  21. Update .github/workflows/lint-code.yml 

    "because we can"

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
    @kedhammar @mashehu
    kedhammar and mashehu authored Oct 17, 2023
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  22. Update .github/workflows/lint-code.yml 

    Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
    @kedhammar @mashehu
    kedhammar and mashehu authored Oct 17, 2023
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  23. Update nf_core/components/components_command.py 

    no context for this arg ever being undefined

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
    @kedhammar @mashehu
    kedhammar and mashehu authored Oct 17, 2023
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  24. Update nf_core/components/components_utils.py 

    Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
    @kedhammar @mashehu
    kedhammar and mashehu authored Oct 17, 2023
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  25. Update nf_core/components/components_utils.py 

    Change typing based on nf_core.utils.determine_base_dir() outputs. A bit messy, but let's not increase the scope further.

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
    @kedhammar @mashehu
    kedhammar and mashehu authored Oct 17, 2023
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  26. import missing typing obj

    @kedhammar
    kedhammar committed Oct 17, 2023
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  27. black

    @kedhammar
    kedhammar committed Oct 17, 2023
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  28. revert minor tweak to prevent breaking

    @kedhammar
    kedhammar committed Oct 17, 2023
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