Restrict shapely version

[ekatef]

A quick fix to resolve the recent environment issues, discussed in #1009.

Checklist

• I consent to the release of this PR's code under the AGPLv3 license and non-code contributions under CC0-1.0 and CC-BY-4.0.
• I tested my contribution locally and it seems to work fine.
• Code and workflow changes are sufficiently documented.
• Newly introduced dependencies are added to envs/environment.yaml and doc/requirements.txt.
• Changes in configuration options are added in all of config.default.yaml and config.tutorial.yaml.
• Add a test config or line additions to test/ (note tests are changing the config.tutorial.yaml)
• Changes in configuration options are also documented in doc/configtables/*.csv and line references are adjusted in doc/configuration.rst and doc/tutorial.rst.
• A note for the release notes doc/release_notes.rst is amended in the format of previous release notes, including reference to the requested PR.