Fix deprecation-related errors and warnings #878
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CI: fix the same R installation line -- HTTPS required now Dockerfile: remove unused command. Installing R and DNAcopy by apt seems fine.
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- Remove 3.10-MacOS test in favor of 3.11-MacOS - Check types on 3.11 instead of 3.10
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Python 3.12 drops distutils from stdlib, which breaks the setuptools configuration for package installation. Need to deal with that separately.
Remove networkx and dateutil; these seem to be pulled in automatically by other packages automatically at the right versions now.
Use --break-system-packages as required (sort of) by Py3.11+
This results in both a shorter Dockerfile and a smaller final image. The conda environment matches the existing conda packaging in devtools/.
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