Alphapulldown

Bugs fixed:

1. Fixed the incorrectly installed alphafold submodule 232 many thanks for the help from aokosinska
2. Fixed the import issue from biopython 234 and 231 Thanks for the help from aokosinska and grandrea
3. Fixed the create_notebook.py issue 211

Bugs fixed:

1. Fixed the incorrectly installed AlphaLink2 submodule 224
2. removed jax dependency when saving results pickles. credits to DimaMolod 06461b8

- Fix feature generation with mmseqs2 and the new ColabFold API. Added tokens, print ColabFold citation when --mmseqs2=True.
- Fix a bug when removing clashes and low plddt residues from the template.
- Added corresponding tests.
- Don't import run_alphafold if already imported (credits to gchojnowski)

- Fix for generating features with multimeric mmCIF templates. Correctly map sequence from entity_poly_seq table with Biopython structure when auth_seq_id is different from label_seq_id in atom_site table.

What's Changed
* Update Python version and jax version. Please be aware that the singularity image was updated as well. There are now 2 singularity images, one for the results generated by AlphaPulldown prior than version 1.0.0 and the other for the predictions generated by AlphaPulldown after version 1.0.0. Please check the details in Section 3 in [example_1.md](https://github.com/KosinskiLab/AlphaPulldown/blob/main/manuals/example_1.md) or [example_2.md](https://github.com/KosinskiLab/AlphaPulldown/blob/main/manuals/example_2.md)
* Allow the users to integrate cross-link mass spec data with AlphaFold predictions via AlphaLink2. Please refer to [run_with_AlphaLink2.md](https://github.com/KosinskiLab/AlphaPulldown/blob/main/manuals/run_with_AlphaLink2.md) for the details.

* Can use multimeric templates for guiding AlphaFold predictions, please refer to [example_3.md](https://github.com/KosinskiLab/AlphaPulldown/blob/main/manuals/example_3.md) for details. Credits to DimaMolod
* Added options to compress or remove pickle files in the results directories so that the output directories take much smaller space. Thanks to the advice from joshtburdick

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