Merge pull request #3 from basf/implement_chemprop_regression

adapt to chemprop 2.0.0 structure and implement remaining predictors

.github/workflows/linting.yml

@@ -30,7 +30,6 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install $(find . -name "requirement*" -type f -printf ' -r %p')
         pip install mypy
         mypy . || exit_code=$?
         mypy --install-types --non-interactive
@@ -148,3 +147,69 @@ jobs:
       - name: Analysing the code with isort
         run: |
           isort --profile black .
+
+  test_basis:
+    needs:
+        - pylint
+        - mypy
+        - pydocstyle
+        - docsig
+        - black
+        - flake8
+        - interrogate
+        - bandit
+        - isort
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install package
+        run: |
+          python -m pip install --upgrade pip
+          pip install .
+      - name: Run unit-tests
+        run: |
+          python -m unittest discover -v -s tests -t .
+
+  test_chemprop:
+    needs:
+      - test_basis
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.11"
+      - name: Install package
+        run: |
+          python -m pip install --upgrade pip
+          pip install torch
+          pip install .[chemprop]
+      - name: Run unit-tests for chemprop
+        run: |
+          python -m unittest discover -v -s test_extras/test_chemprop -t .
+
+  test_notebooks:
+    needs:
+      - test_basis
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.11"
+      - name: Install package
+        run: |
+          python -m pip install --upgrade pip
+          pip install .[notebooks]
+      - name: Run unit-tests for notebooks
+        run: |
+          python test_extras/test_notebooks/test_notebooks.py  --continue-on-failure

molpipeline/estimators/chemprop/__init__.py

@@ -1,11 +1,18 @@
 """Initialize Chemprop module."""
 
-import pkgutil
+try:
+    from molpipeline.estimators.chemprop.models import (  # noqa: F401
+        ChempropClassifier,
+        ChempropModel,
+        ChempropNeuralFP,
+        ChempropRegressor,
+    )
 
-installed_packages = {pkg.name for pkg in pkgutil.iter_modules()}
-if "chemprop" in installed_packages:
-    from molpipeline.estimators.chemprop.models import ChempropModel  # noqa
-
-    __all__ = ["ChempropModel"]
-else:
+    __all__ = [
+        "ChempropClassifier",
+        "ChempropModel",
+        "ChempropNeuralFP",
+        "ChempropRegressor",
+    ]
+except ImportError:
     __all__ = []

molpipeline/estimators/chemprop/abstract.py

@@ -13,7 +13,7 @@
 import numpy.typing as npt
 
 try:
-    from chemprop.data import MoleculeDataset, MolGraphDataLoader
+    from chemprop.data import MoleculeDataset, build_dataloader
     from chemprop.models.model import MPNN
     from lightning import pytorch as pl
 except ImportError:
@@ -90,7 +90,7 @@ def fit(
         if y.ndim == 1:
             y = y.reshape(-1, 1)
         X.Y = y
-        training_data = MolGraphDataLoader(
+        training_data = build_dataloader(
             X, batch_size=self.batch_size, num_workers=self.n_jobs
         )
         self.lightning_trainer.fit(self.model, training_data)