SyntaxWarning:

Hi,

I'm using the Biocontainer Docker image of planemo.

It seems to work well but there are some ugly warning when I run any planemo command.

```bash
$ docker run --rm -v $PWD:/data/ -w /data quay.io/biocontainers/planemo:0.75.33--pyhdfd78af_0 planemo --version

/usr/local/lib/python3.14/site-packages/pydantic/_internal/_generate_schema.py:2249: UnsupportedFieldAttributeWarning: The 'default' attribute with value None was provided to the `Field()` function, which has no effect in the context it was used. 'default' is field-specific metadata, and can only be attached to a model field using `Annotated` metadata or by assignment. This may have happened because an `Annotated` type alias using the `type` statement was used, or if the `Field()` function was attached to a single member of a union type.
warnings.warn(
/usr/local/lib/python3.14/site-packages/Cheetah/SettingsManager.py:19: SyntaxWarning: "\(" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\("? A raw string is also an option.
'[\(]*' + Number + r'[ \t]*\+[ \t]*' + Number + '[\)]*')
/usr/local/lib/python3.14/site-packages/Cheetah/SettingsManager.py:19: SyntaxWarning: "\)" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\)"? A raw string is also an option.
'[\(]*' + Number + r'[ \t]*\+[ \t]*' + Number + '[\)]*')
/usr/local/lib/python3.14/site-packages/Cheetah/Parser.py:464: SyntaxWarning: "\*" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\*"? A raw string is also an option.
+ r'(?P\*' + interval + '\*)'
/usr/local/lib/python3.14/site-packages/Cheetah/Parser.py:557: SyntaxWarning: "\$" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\$"? A raw string is also an option.
"""Unescape any escaped Cheetah \$vars in the string.
/usr/local/lib/python3.14/site-packages/Cheetah/SourceReader.py:8: SyntaxWarning: "\s" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\s"? A raw string is also an option.
ENCODINGsearch = re.compile("coding[=:]\s*([-\w.]+)").search
/usr/local/lib/python3.14/site-packages/Cheetah/Template.py:147: SyntaxWarning: "\*" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\*"? A raw string is also an option.
\*\* Preprocessors are an advanced topic \*\*
/usr/local/lib/python3.14/site-packages/Cheetah/Template.py:1620: SyntaxWarning: "\*" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\*"? A raw string is also an option.
USERS SHOULD \*NEVER\* CALL THIS METHOD THEMSELVES.
/usr/local/lib/python3.14/site-packages/Cheetah/Template.py:1774: SyntaxWarning: "\*" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\*"? A raw string is also an option.
\*\*\* KLUDGE: 'debug' is supposed to insert into the template output,
/usr/local/lib/python3.14/site-packages/Cheetah/Template.py:1984: SyntaxWarning: "\d" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\d"? A raw string is also an option.
re.search('[ \t]*File.*line (\d+)', formatedExc).group(1))
/usr/local/lib/python3.14/site-packages/Cheetah/Template.py:2025: SyntaxWarning: "\d" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\d"? A raw string is also an option.
cheetahPosMatch = re.search('line (\d+), col (\d+)', formatedExc)
/usr/local/lib/python3.14/site-packages/Cheetah/Template.py:2035: SyntaxWarning: "\d" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\d"? A raw string is also an option.
cheetahPosMatch = re.search('line (\d+), col (\d+)',
planemo, version 0.75.33
```

There are less with older version.

```bash
$ docker run --rm -v $PWD:/data/ -w /data quay.io/biocontainers/planemo:0.75.31--pyhdfd78af_0 planemo --version

/usr/local/lib/python3.10/site-packages/galaxy/tool_util/cwl/cwltool_deps.py:16: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
from cwltool import (
```

Start by reproducing the issue with the two Biocontainer planemo images and their planemo --version commands. Compare the warnings and trace them to the reported Python dependencies, including pydantic, Cheetah, and pkg_resources. Done means the relevant planemo command no longer emits these warnings, or the issue clearly documents which upstream dependency warnings remain.

Written by the indexing model from the issue text.