Stacking and align/TMalign update, small updates to docs

[gezmi]

Code of Conduct

OK

Description

• Added support for writing mmCIF files
• Added support to read some CIF files while missing some columns
• Added stacking - a collection of structures to streamline filtering and other operations (with tutorial)
• Added CIF file support in stack module
• Added extendable alignment module and implemented TMalign functionality (with tutorial)
• Updated tests and documentation (AF database version, erronous linking and API markdown format)

Related issues or pull requests

There was an older pull request that I now canceled

Pull Request Checklist

• Added a note about the modification or contribution to the ./docs/sources/CHANGELOG.md file (if applicable)
• Added appropriate unit test functions in the ./biopandas/*/tests directories (if applicable)
• Modify documentation in the corresponding Jupyter Notebook under biopandas/docs/sources/ (if applicable)
• Ran PYTHONPATH='.' pytest ./biopandas -sv and make sure that all unit tests pass (for small modifications, it might be sufficient to only run the specific test file, e.g., PYTHONPATH='.' pytest ./biopandas/classifier/tests/test_stacking_cv_classifier.py -sv)
• Checked for style issues by running flake8 ./biopandas

[gezmi]

I needed to changes things also for appveyor for the tests to pass - it complained python3.11 not being available for win-32