Pytorch dataloader example

[danielkovtun]

Breaking changes

• PinderLoader has been overhauled to play better with torch Dataset/DataLoader APIs. There are some breaking changes to the PinderLoader API, but the PPIDataset has been adapted to use the new PinderLoader interface without breaking changes

Changed

• PinderSystem to defer loading of {holo/apo/pred}_{receptor/ligand} structures until they are requested via cached_property

Added

• Ability to sample mixes of different monomers when working with PinderLoader
• New example dataset+dataloader implementation (PinderDataset) targeting the vanilla torch Dataset and DataLoader APIs
• Helper methods for collating items in a batch (pad_and_stack and collate_batch)
• New base classes for filters and transforms that operate on a Structure-level rather than PinderSystem level

Documentation

• Revamped API docs with pydata-sphinx theme
• Extended pinder-loader tutorial to capture:
  • More extensive documentation of PinderLoader
  • Examples of how to use the new PinderDataset torch dataset
  • Applied tutorial for constructing custom torch datasets/dataloaders for arbitrary ML pipelines

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 80.62016% with 50 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
src/pinder-core/pinder/core/loader/loader.py	77.51%	23 Missing and 15 partials :warning:
src/pinder-core/pinder/core/loader/structure.py	0.00%	4 Missing and 1 partial :warning:
src/pinder-core/pinder/core/loader/transforms.py	76.92%	3 Missing :warning:
src/pinder-core/pinder/core/index/system.py	96.42%	1 Missing and 1 partial :warning:
src/pinder-core/pinder/core/loader/filters.py	83.33%	2 Missing :warning:

Files with missing lines	Coverage Δ
src/pinder-core/pinder/core/loader/geodata.py	78.31% <100.00%> (ø)
src/pinder-core/pinder/core/index/system.py	82.18% <96.42%> (+0.70%)	:arrow_up:
src/pinder-core/pinder/core/loader/filters.py	82.13% <83.33%> (+0.04%)	:arrow_up:
src/pinder-core/pinder/core/loader/transforms.py	81.39% <76.92%> (ø)
src/pinder-core/pinder/core/loader/structure.py	81.39% <0.00%> (-2.98%)	:arrow_down:
src/pinder-core/pinder/core/loader/loader.py	77.00% <77.51%> (+3.37%)	:arrow_up:

... and 7 files with indirect coverage changes