8000 ete3 cannot be used with Python 3.13 due to the deprecation of the cgi module · Issue #780 · etetoolkit/ete · GitHub
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ete3 cannot be used with Python 3.13 due to the deprecation of the cgi module #780

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terrycojones opened this issue May 6, 2025 · 0 comments
Open

ete3 cannot be used with Python 3.13 due to the deprecation of the cgi module #780

terrycojones opened this issue May 6, 2025 · 0 comments

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@terrycojones
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The cgi module, used in ete3/webplugin/webapp.py was deprecated in Python 3.11 and removed in 3.13 (see https://docs.python.org/3.13/whatsnew/3.13.html). So trying from ete3 import Tree results in an import exception:

Traceback:
../../.local/share/uv/python/cpython-3.13.1-macos-aarch64-none/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
test/test_trees.py:2: in <module>
    from ete3 import Tree
.venv/lib/python3.13/site-packages/ete3/__init__.py:56: in <module>
    from .webplugin.webapp import *
.venv/lib/python3.13/site-packages/ete3/webplugin/webapp.py:44: in <module>
    import cgi
E   ModuleNotFoundError: No module named 'cgi'

This can be fixed by using urllib.parse.parse_qs. Pull request coming up.
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