Update python dependencies and other minor fixes #1405
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The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, conda-incubator/setup-miniconda@v2, actions/cache@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
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