Alphapulldown

New features added:
1. Added calculation of average PAE value of interface residues to analysis_pipeline
2. Added calculation of average plDDT value of interface residues to analysis_pipeline
3. Added calculation of binding energy via pyRosetta value of interfaces to analysis_pipeline
4. Updated pyTest thanks for the help from DimaMolod

Bugs fixed:
1. Fixed crashes caused by monomer 312
2. Fixed wrong contents in the plotted PAE images 312
3. Fixed wrong calculation of iptm-ptm and iptm scores when using padding mode 312

Notice:
Apart from installing the beta version of alphapulldown from pypi, using pip install alphapulldown==2.0.0b2, please re-download the alpha-analysis singularity images again this time.
If your results are from AlphaPulldown prior to version 1.0.0, please use the link: [`alpha-analysis_jax_0.3.sif`](https://www.embl-hamburg.de/AlphaPulldown/downloads/alpha-analysis_jax_0.3.sif).
If your results are from AlphaPulldown with version >=1.0.0, please use the link: [`alpha-analysis_jax_0.4.sif`](https://www.embl-hamburg.de/AlphaPulldown/downloads/alpha-analysis_jax_0.4.sif).

New features added:
1. Refactorised the codes; introduced folding_backend 303 thanks for the help from maurerv and DimaMolod
2. Allow the user to pad input matrices to desired number of MSAs and desired number of residues to speed up overall modelling process and avoid unnecessary re-compiling of AlphaFold neural network.
3. New way of modelling with customised structure templates without the need of recalculating the features again. 268
4. Separated post-modelling processes from prediction process 297 by DimaMolod
5. Supports full mmseqs2 mode i.e. without the need of local structural template database when using mmseqs mode 233

Bugs fixed:
1. Fixed incorrect colour scheme when ploting structures in jupyter-notebook 304 thanks for the help from gchojnowski and report from gilep
2. Fixed operands broadcast error when the features are created by mmseqs2 287 thanks for the report from Qrouger
3. Updated alpha-analysis.sif to avoid crashes when no model satisfies the cutoff value 307
4. Fix the config.cfg to avoid installing tensorflow versions that are not compatible with GPUs without latest CUDA. 298 Thanks for the help from kashyapchhatbar

Notice:
Apart from installing the beta version of alphapulldown from pypi, using pip install alphapulldown==2.0.0b1, please re-download the alpha-analysis singularity images again.
If your results are from AlphaPulldown prior to version 1.0.0, please use the link: [`alpha-analysis_jax_0.3.sif`](https://www.embl-hamburg.de/AlphaPulldown/downloads/alpha-analysis_jax_0.3.sif).
If your results are from AlphaPulldown with version >=1.0.0, please use the link: [`alpha-analysis_jax_0.4.sif`](https://www.embl-hamburg.de/AlphaPulldown/downloads/alpha-analysis_jax_0.4.sif).

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