Update Python versions

[victorlin]

Description of proposed changes

Drop support for end of life Python versions 3.8 and 3.9; add explicit support for 3.14.

I'll try to break the first commit into multiple to follow the pattern in #325.

Related issue(s)

• Closes Python 3.8 deprecation warning from cryptography #522

Checklist

• Revert 8987cfd
• Checks pass
• Update changelog

[victorlin]

test-standalone is failing with ModuleNotFoundError: No module named 'importlib_resources' after changing setup-integration-tests to use Python 3.10. I expected the module to be available from Augur's bioconda recipe, but it is indeed not listed as a dependency:

$ micromamba repoquery depends augur=33.1.0 -c conda-forge -c bioconda --json \
  | jq -r '.result.pkgs[] | select(.name == "augur") | .depends[]'
pyyaml
mafft
iqtree
fasttree
seqkit
raxml
vcftools
python >=3.10
packaging >=19.2
cvxopt >=1.1.9,<2
scipy >=1.0.0,<2
biopython >=1.80,<2
pyfastx >=1.0.0,<3
treetime >=0.11.2,<0.12
bcbio-gff >=0.7.1,<0.8
networkx >=2.5,<4
python-calamine >=0.2.0
sqlite >=3.39,<4
jsonschema >=4.18.0,<5
xopen >=2.0.0,<3
pandas >=1.4.0,<3
referencing >=0.29.1,<1
isodate >=0.6.0,<0.8
numpy >=1.0.0,<3

This is because the augur package is noarch and does not respect selectors such as [py<311]. From conda-forge docs on noarch:

The noarch: python directive, in the build section, makes pure-Python packages that only need to be built once.
In order to qualify as a noarch python package, all of the following criteria must be fulfilled:

• No python version specific requirements
• …

It had previously worked with <3.10 because importlib-resources was pulled in by another dependency.

I'll make a PR to fix this in the bioconda recipe.

[victorlin]

bioconda/bioconda-recipes#64995