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Add integration test #27

Merged
merged 34 commits into from
Feb 27, 2024
Merged

Add integration test #27

merged 34 commits into from
Feb 27, 2024

Commits on Feb 27, 2024

  1. docs: update conda command

    @BioGeek
    BioGeek committed Feb 27, 2024
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  2. test: add integration test

    @BioGeek
    BioGeek committed Feb 27, 2024
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  3. test: add requirements-dev.txt

    @BioGeek
    BioGeek committed Feb 27, 2024
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  4. ci: remove default_language_version from .pre-commit-config.yaml

    @BioGeek
    BioGeek committed Feb 27, 2024
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  5. Merge branch 'main' into tests

    @BioGeek
    BioGeek committed Feb 27, 2024
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  6. ci: lint pytest-multiversion.yml

    @BioGeek
    BioGeek committed Feb 27, 2024
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  7. ci: update pyopenms version (to install in python 3.10+)

    @BioGeek
    BioGeek committed Feb 27, 2024
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  8. ci: allow pyopenms to be installed in python 3.8+

    @BioGeek
    BioGeek committed Feb 27, 2024
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  9. ci: remove deepspeed from requirements.txt

    @BioGeek
    BioGeek committed Feb 27, 2024
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  10. ci: use environment markers for pyopenms and scikit-learn 

    See: https://peps.python.org/pep-0508/#environment-markers
    @BioGeek
    BioGeek committed Feb 27, 2024
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  11. ci: remove torchaudio and torchvision

    @BioGeek
    BioGeek committed Feb 27, 2024
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  12. docs: Publish docs via GitHub Pages

    @BioGeek
    BioGeek committed Feb 27, 2024
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  13. ci: install ninja-build

    @BioGeek
    BioGeek committed Feb 27, 2024
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  14. ci: Setup Ninja for Python 3.11

    @BioGeek
    BioGeek committed Feb 27, 2024
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  15. ci: move install of ninja-build before installing requirements

    @BioGeek
    BioGeek committed Feb 27, 2024
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  16. ci: use newer version of Levenstein on Python 3.11

    @BioGeek
    BioGeek committed Feb 27, 2024
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  17. ci: update pyarrow version due to security vurnability 

    See: https://github.com/instadeepai/InstaNovo/security/dependabot/2
    @BioGeek
    BioGeek committed Feb 27, 2024
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  18. ci: upgeade jiwer version and remove specific levensthein version for… 

    … python 3.11
    @BioGeek
    BioGeek committed Feb 27, 2024
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  19. ci: installing ninja-build no longer needed

    @BioGeek
    BioGeek committed Feb 27, 2024
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  20. ci: update actions/setup-python to v5

    @BioGeek
    BioGeek committed Feb 27, 2024
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  21. docs: upgrade pip before building docs

    @BioGeek
    BioGeek committed Feb 27, 2024
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  22. ci: upgrade pytorch to be able to run tests on python 3.11

    @BioGeek
    BioGeek committed Feb 27, 2024
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  23. docs: switch to latest mkdocs-material docker image

    @BioGeek
    BioGeek committed Feb 27, 2024
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  24. ci: upgrade actions/checkout to v4

    @BioGeek
    BioGeek committed Feb 27, 2024
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  25. docs: upgrade pip before building docs (via forked GitHub Action)

    @BioGeek
    BioGeek committed Feb 27, 2024
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  26. ci: pin version of libCST

    @BioGeek
    BioGeek committed Feb 27, 2024
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  27. docs: split out requirements for docs

    @BioGeek
    BioGeek committed Feb 27, 2024
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  28. docs: add mkdocs.yml

    @BioGeek
    BioGeek committed Feb 27, 2024
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  29. docs: change gitlab to github url

    @BioGeek
    BioGeek committed Feb 27, 2024
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  30. docs: add assets and index page

    @BioGeek
    BioGeek committed Feb 27, 2024
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  31. ci: replace gitlab with github

    @BioGeek
    BioGeek committed Feb 27, 2024
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  32. ci: cache pip dependencies

    @BioGeek
    BioGeek committed Feb 27, 2024
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  33. ci: add cache-dependency-path

    @BioGeek
    BioGeek committed Feb 27, 2024
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  34. feat: add environment.yml file

    @BioGeek
    BioGeek committed Feb 27, 2024
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