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Split script into 2 commands: 1 to extract, 1 to filter tools #18

Merged
merged 21 commits into from
Nov 1, 2023
Merged

Split script into 2 commands: 1 to extract, 1 to filter tools #18

merged 21 commits into from
Nov 1, 2023

Commits on Oct 31, 2023

  1. Split script into 2 commands: 1 to extract, 1 to filter tools

    @bebatut
    bebatut committed Oct 31, 2023
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  2. Update README and bash scripts

    @bebatut
    bebatut committed Oct 31, 2023
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  3. Merge branch 'main' of github.com:bebatut/galaxy_tool_extractor into … 

    …split_commands
    @bebatut
    bebatut committed Oct 31, 2023
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  4. Fix a function call and verify to False for bio.tools API

    @bebatut
    bebatut committed Oct 31, 2023
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  5. Fix linting

    @bebatut
    bebatut committed Oct 31, 2023
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  6. Fix filtering by categories

    @bebatut
    bebatut committed Oct 31, 2023
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  7. Apply suggestions from code review 

    Co-authored-by: Nicola Soranzo <[email protected]>
    @bebatut @nsoranzo
    bebatut and nsoranzo authored Oct 31, 2023
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  8. Restructure check_categories function 

    Co-authored-by: Nicola Soranzo <[email protected]>
    @bebatut @nsoranzo
    bebatut and nsoranzo authored Oct 31, 2023
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  9. Apply suggestions from code review 

    Co-authored-by: Nicola Soranzo <[email protected]>
    @bebatut @nsoranzo
    bebatut and nsoranzo authored Oct 31, 2023
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  10. Update extract_galaxy_tools.py

    @bebatut
    bebatut authored Oct 31, 2023
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  11. Update extract_galaxy_tools.py

    @bebatut
    bebatut authored Oct 31, 2023
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  12. Update bin/extract_galaxy_tools.py 

    Co-authored-by: Nicola Soranzo <[email protected]>
    @bebatut @nsoranzo
    bebatut and nsoranzo authored Oct 31, 2023
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  13. Fix type annotations + add .isort.cfg

    @nsoranzo
    nsoranzo committed Oct 31, 2023
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  14. Fix format col

    @bebatut
    bebatut committed Oct 31, 2023
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  15. Change CSV to TSV

    @bebatut
    bebatut committed Oct 31, 2023
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  16. Fix format col

    @bebatut
    bebatut committed Oct 31, 2023
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  17. bio.tools DNS entry is back

    @nsoranzo
    nsoranzo committed Oct 31, 2023
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  18. Add missing type annotations

    @nsoranzo
    nsoranzo committed Oct 31, 2023
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  19. Exclude broken pandas-stubs version for Python 3.8 mypy

    @nsoranzo
    nsoranzo committed Oct 31, 2023
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Commits on Nov 1, 2023

  1. Write extracted tools only once 

    Also:
- Use `.extend()` instead of `+=` (slightly faster)
- Write error messages to `sys.stderr`
    @nsoranzo
    nsoranzo committed Nov 1, 2023
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  2. create the folder if needed

    @paulzierep
    paulzierep committed Nov 1, 2023
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