FoldComp ML Datasets (#284)

* add foldcomp dataset util

* clean up

* add import warnings

* add foldcomp dataset extra dependencies

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* exclude foldcomp from notebook tests. download too big :(

* update changelog

* add lightning datamodule wrapper

* add transform functionality

* docs: add new module to API reference

* update notebook

* fix: fix paths issue on setup

* add foldcomp dataset tutorial to docs

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* add stage param to setup

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/workflows/build.yaml

@@ -80,4 +80,4 @@ jobs:
       - name: Run unit tests and generate coverage report
         run: pytest .
       - name: Test notebook execution
-        run: pytest --nbval-lax notebooks/ --current-env --ignore-glob="notebooks/dataloader_tutorial.ipynb" --ignore-glob="notebooks/datasets_and_dataloaders.ipynb"
+        run: pytest --nbval-lax notebooks/ --current-env --ignore-glob="notebooks/dataloader_tutorial.ipynb" --ignore-glob="notebooks/datasets_and_dataloaders.ipynb" --ignore-glob="notebooks/foldcomp.ipynb"

.github/workflows/minimal__install.yaml

@@ -47,4 +47,4 @@ jobs:
       - name: Run unit tests and generate coverage report
         run: pytest . --ignore-glob="tests/protein/tensor"
       - name: Test notebook execution
-        run: pytest --nbval-lax notebooks/ --current-env --ignore-glob="notebooks/dataloader_tutorial.ipynb" --ignore-glob="notebooks/higher_order_graphs.ipynb" --ignore-glob="notebooks/protein_graph_analytics.ipynb" --ignore-glob="notebooks/subgraphing_tutorial.ipynb" --ignore-glob="notebooks/splitting_a_dataset.ipynb" --ignore-glob="notebooks/protein_tensors.ipynb" --ignore-glob="notebooks/datasets_and_dataloaders.ipynb"
+        run: pytest --nbval-lax notebooks/ --current-env --ignore-glob="notebooks/dataloader_tutorial.ipynb" --ignore-glob="notebooks/higher_order_graphs.ipynb" --ignore-glob="notebooks/protein_graph_analytics.ipynb" --ignore-glob="notebooks/subgraphing_tutorial.ipynb" --ignore-glob="notebooks/splitting_a_dataset.ipynb" --ignore-glob="notebooks/protein_tensors.ipynb" --ignore-glob="notebooks/datasets_and_dataloaders.ipynb" --ignore-glob="notebooks/foldcomp.ipynb"

.requirements/extras.in

@@ -6,3 +6,5 @@ rdkit
 selfies
 smilite
 einops
+foldcomp
+nest_asyncio

CHANGELOG.md

@@ -1,3 +1,9 @@
+### 1.6.1 - UNRELEASED
+
+#### New Features
+* [FoldComp Dataset] - [#284](https://github.com/a-r-j/graphein/pull/284) - Create ML datasets from FoldComp databases.
+
+
 ### 1.6.0dev - UNRELEASED
 
 #### New Features

docs/source/datasets.rst

@@ -12,6 +12,7 @@ Summaries
    :glob:
 
    notebooks/dataloader_tutorial.nblink
+   notebooks/foldcomp.nblink
    datasets/pscdb
    notebooks/pscdb_processing.nblink
    notebooks/pscdb_baselines.nblink

docs/source/modules/graphein.ml.rst

@@ -16,6 +16,9 @@ Datasets
 .. automodule:: graphein.ml.datasets.torch_geometric_dataset
     :members:
 
+.. automodule:: graphein.ml.datasets.foldcomp_dataset
+    :members:
+
 Dataset Splitting
 -----------------
 .. automodule:: graphein.ml.clustering

docs/source/notebooks/foldcomp.nblink

@@ -0,0 +1,3 @@
+{
+    "path": "../../../notebooks/foldcomp.ipynb"
+}