Python 3.11-14 deprecations

[nsoranzo]

List of deprecated stuff we are currently using:

• [x] PEP 594 led to the deprecations of the following modules slated for removal in Python 3.13: imghdr
• [ ] datetime.datetime’s utcnow() and utcfromtimestamp() are deprecated and will be removed in a future version. Instead, use timezone-aware objects to represent datetimes in UTC: respectively, call now() and fromtimestamp() with the tz parameter set to datetime.UTC.
• [x] Deprecated the importlib.abc.Traversable class, scheduled for removal in Python 3.14. Use importlib.resources.abc.Traversable class instead.
• [x] The lib2to3 package and 2to3 tool are now deprecated and slated for removal in Python 3.13. Also they may not be able to parse Python 3.10 or newer. See PEP 617, introducing the new PEG parser, for details.
• [ ] tarfile: Extracting tar archives without specifying filter is deprecated until Python 3.14, when 'data' filter will become the default. See Extraction filters for details.
• [ ] The argparse.FileType type converter is deprecated in Python 3.14. Anything with resource management should be done downstream after the arguments are parsed.

Others we may be using:

• [x] Remove the filename attribute of gzip’s gzip.GzipFile, deprecated since Python 2.6, use the name attribute instead. In write mode, the filename attribute added '.gz' file extension if it was not present.

More are listed at https://docs.python.org/3/whatsnew/3.11.html#deprecated , https://docs.python.org/3/whatsnew/3.12.html#deprecated , https://docs.python.org/3.13/whatsnew/3.13.html#removed-modules-and-apis and https://docs.python.org/3.13/whatsnew/3.13.html#new-deprecations

[cat-bro]

The version of tensorflow in optional dependencies is too low to be compatible with python 3.11

[nsoranzo]

@cat-bro This is now tracked separately at https://github.com/galaxyproject/galaxy/issues/17857 .