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victorlin
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Apr 30, 2026
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| - uses: ./src/.github/actions/setup-integration-tests | ||
| with: | ||
| python-version: '3.9' | ||
| python-version: '3.10' |
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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: pythondirective, in thebuildsection, 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.
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Update python_requires in setup.py, PyPI classifiers, and documentation to reflect the new minimum version of Python 3.10. Subsequent commits will remove the 3.8 and 3.9-specific workarounds.
Removed two now-unnecessary ignore markers. Also added an explicit flush() method to LinePrefixer (reasoning in comment).
Both TypeAlias and EllipsisType are available in the standard library as of Python 3.10, which is now our minimum supported version.
urllib3 isn't used directly by the code so I'm not sure why these were added. Removing them to get rid of the Python 3.8 and 3.9 specific dependencies.
pytest 7.0.0 had a bug on Python 3.9; since 3.9 is no longer supported this workaround is no longer needed.
Path.is_relative_to() is now always available with a minimum Python version of 3.10.
Replace the runtime version check with a constant "options" string. Python 3.10 changed the default argument group title from "optional arguments" to "options" (cpython#23858). Since 3.10 is now our minimum, the version guard is no longer needed.
Remove the reference to 3.9 which is no longer supported.
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This reverts "Suppress warning from cryptography about deprecated Python 3.8 support" (8987cfd) since 3.8 is no longer supported.
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Description of proposed changes
Drop support for end of life Python versions 3.8 and 3.9.
Changes broken into multiple to follow the pattern in #325.
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