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toml install / requirements version boost #1242

Merged
merged 77 commits into from
Aug 28, 2023
Merged

toml install / requirements version boost #1242

merged 77 commits into from
Aug 28, 2023

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WardDeb
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@WardDeb WardDeb commented Aug 21, 2023

Welcome to deepTools GitHub repository! Please check the following regarding
your pull request :

  • Does the PR contain new feature?
  • Does the PR contain bugfix?
  • Does the PR contain documentation changes?
  • Does the PR contain changes to the galaxy wrapper?

This PR tries to update requirements / python setup to more recent versions (>=3.7).

  1. pyproject.toml file
    • dependencies and metadata are defined in the toml file (setup.py & requirements deprecated)
    • scripts / entrypoints are defined here as well (bin folder deprecated)
    • wheels are built setuptools / toml file now (python >= 3.7)
    • deeptools' version is defined in the toml file as well (no more _version.py, keep importlib as a requirement until we drop python 3.7 support).
    • --version flags have been changed to use importlib in all executables.
    • matplotlib version pin has been removed, some changes in the cm.py for newer version.
  2. CI / github actions
    • nosetests are deprecated and ported to pytests
    • pytests now run on proposed wheel with version 3.7 - 3.11
    • dependency on the custom typescript action (https://github.com/deeptools/github-actions) has been deprecated in favor of micromamba/python/miniconda-setup actions
    • planemo tests and pytests use conda environment(.github/test_and_build.yml), historical 'foo' name is dropped.
    • planemo tests expected pngs are slightly changed (due to mpl updates)
    • expected qual metrics in plotfingerprint changed, not 100% where exactly the rounding difference comes from
    • planemo tests run on galaxy 23.1

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WardDeb commented Aug 21, 2023

@bgruening Do you mind having a look ?
I'm not sure if the change to 3.10 will bring some difficulties especially with the galaxy version ?

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Cool, a few comments inline :)

Thanks @WardDeb

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@@ -27,7 +40,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ['3.7']
python-version: ['3.10']
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we could test multiple versions if we like.
Historically we tested for the lower bound. But we could test for lower and upper-supported python versions.

3.8 and 3.11?

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I've included 3.7 & 3.11, though I'm not sure how relevant it is at this stage (planemo_combine_outputs): The tests have already ran at that time, right ?

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@WardDeb WardDeb changed the title python 3.10 toml install / requirements version boost Aug 25, 2023
@WardDeb WardDeb requested a review from bgruening August 25, 2023 13:58
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Very nice. Thanks a lot @WardDeb

@WardDeb WardDeb merged commit 3f8010c into deeptools:develop Aug 28, 2023
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2 participants