Revamp documentation

[padix-key]

This PR completely revamps the documentation to make the structure clearer and give the user (almost) all information they need to use PLINDER.

The previous Makefile is gone. Instead everything necessary is done with sphinx-build docs <output_dir>

• Important missing pieces added soon:
  • Annotation table is not searchable, filterable and is not paginated
  • The dataset reference misses some subdirectories and some table elements are missing
  • API tutorial and reference is completely work in progress

[github-actions[bot]]

Coverage report

Click to see where and how coverage changed

File	Statements	Missing	Coverage	Coverage (new stmts)	Lines missing
src/plinder/core
__init__.py
src/plinder/data
__init__.py
final_structure_qc.py
get_system_annotations.py
splits.py					256
src/plinder/data/pipeline
config.py
io.py
utils.py
src/plinder/data/structure
atoms.py
src/plinder/data/utils/annotations
aggregate_annotations.py					425-427, 436, 1080
get_ligand_validation.py					69
interaction_utils.py
ligand_utils.py
protein_utils.py					104
rdkit_utils.py					297-298, 347-352, 358, 514-541
save_utils.py
src/plinder/eval/docking
utils.py
Project Total

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