Add compatibility layer for PackedGraph

[cthoyt]

Summary

This PR adds a compatibility layer for the packed graph class from torch drug while we're waiting for an upstream fix (DeepGraphLearning/torchdrug#70). This layer makes sure there's a to() function that takes a device, as we usually expect torch stuff to do.

• Unit tests provided for these changes
• Documentation and docstrings added for these changes using the sphinx style

Changes

• Add a new module chemicalx.compat
• Implement a subclass of torchdrug.data.PackedGraph that implements the to() function
• Implement subclass of torchdrug.data.Graph that uses the monkey patched PackedGraph when called in chemicalx.data.drugfeatureset

[codecov-commenter]

Codecov Report

Merging #84 (081a117) into main (040fc7b) will decrease coverage by 0.83%.
The diff coverage is 58.06%.

@@            Coverage Diff             @@
##             main      #84      +/-   ##
==========================================
- Coverage   95.84%   95.00%   -0.84%     
==========================================
  Files          32       33       +1     
  Lines        1419     1441      +22     
==========================================
+ Hits         1360     1369       +9     
- Misses         59       72      +13     

Impacted Files	Coverage Δ
chemicalx/compat.py	38.09% <38.09%> (ø)
chemicalx/data/batchgenerator.py	98.30% <100.00%> (ø)
chemicalx/data/drugfeatureset.py	100.00% <100.00%> (ø)
chemicalx/data/drugpairbatch.py	100.00% <100.00%> (ø)
chemicalx/models/deepdds.py	97.43% <100.00%> (ø)
chemicalx/models/deepdrug.py	96.77% <100.00%> (ø)
chemicalx/models/epgcnds.py	100.00% <100.00%> (ø)
chemicalx/models/gcnbmp.py	97.61% <100.00%> (ø)
chemicalx/models/mrgnn.py	100.00% <100.00%> (ø)
chemicalx/models/ssiddi.py	98.73% <100.00%> (ø)

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[benedekrozemberczki]

A GPU equipped dedicated runner could work, let us look into this.

[cthoyt]

@benedekrozemberczki I just added a unit test that should demonstrate that the transfer to GPU works (but it only runs if a GPU is available, so the tests will pass on the current runner regardless)

[cthoyt]

Good news! I tested the following on a google colab notebook with GPU embedded:

!python -m pip install torch
!python -m pip install "torch-scatter>=2.0.8"
!python -m pip install git+https://github.com/cthoyt/chemicalx.git@packed-graph-compat

import torch.cuda
from torchdrug.data import Molecule

from chemicalx.compat import Graph, PackedGraph

assert torch.cuda.is_available(), "can not test compatibility layer without a GPU available"

gpu_device = torch.device("cuda")

structures = ["C(=O)O", "CCO"]
molecules = [Molecule.from_smiles(smiles) for smiles in structures]
packed_graph = Graph.pack(molecules)
assert isinstance(packed_graph, PackedGraph)

assert "cpu" == packed_graph.edge_list.device.type
assert -1 == packed_graph.edge_list.get_device(), "Device should be -1 to represent it's on the CPU"

gpu_packed_graph = packed_graph.to(gpu_device)
assert "cuda" == gpu_packed_graph.edge_list.device.type
assert 0 <= gpu_packed_graph.edge_list.get_device(), "Device should 0 or higher for a cuda device"


assert packed_graph is not gpu_packed_graph, "The PackedGraph.cuda() creates a new object. There is no in-place versions of this, unfortunately"

so I am confident that this PR does what's intended.

[benedekrozemberczki]

@cthoyt this is amazing!

[benedekrozemberczki]

@cthoyt Feel free to merge this!