Fixing GitHub CI and tests.

.github/workflows/build.yaml

@@ -1,4 +1,4 @@
-name: build
+name: Build GAUCHE and run unit tests.
 
 on:
   push:
@@ -15,31 +15,30 @@ on:
       - "CONTRIBUTING.md"
       - "imgs/"
 
+permissions:
+  contents: read
+
 jobs:
-  build_cpu:
-    runs-on: ubuntu-18.04
+  build:
+
+    runs-on: ubuntu-latest
+
     strategy:
+      fail-fast: true
       matrix:
-        python-version: [3.7, 3.8, 3.9, 3.11]
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v2
-        # See: https://github.com/marketplace/actions/setup-conda
-      - name: Setup anaconda
-        uses: s-weigand/setup-conda@v1
-        with:
-          python-version: ${{ matrix.python-version }}
-          conda-channels: "conda-forge"
+        python-version: ["3.9", "3.10", "3.11"]
 
-      - name: Install GAUCHE
-        run: pip install -e .
-      - name: Install rnxfp
-        run: pip install --no-deps rxnfp
-      - name: Install drfp
-        run: pip install --no-deps drfp
-      - name: Install transformers
-        run: pip install transformers
-      - name: Run unit tests and generate coverage report
-        run: pytest .
-      - name: Test notebook execution
-        run: pytest --nbval-lax notebooks/ --current-env
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python.
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Set up GAUCHE and install all dependencies.
+      run: |
+        python -m pip install --upgrade pip
+        pip install pytest
+        pip install -e .[all]
+    - name: Run unit tests with pytest.
+      run: |
+        pytest tests/

.github/workflows/code-style.yaml

@@ -5,53 +5,34 @@ on: [push]
 jobs:
   black:
     name: "Ensure black compliance"
-    runs-on: "ubuntu-18.04"
+    runs-on: ubuntu-latest
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: Install Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: "3.10"
 
       - name: Install code style checking tools
         run: python -m pip install black
 
       - name: Run black
         run: black --check .
 
-  interrogate:
-    name: "Ensure docstring coverage"
-    runs-on: "ubuntu-18.04"
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v2
-
-      - name: Install Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.9
-
-      - name: Install code style checking tools
-        run: python -m pip install interrogate
-
-      - name: Run interrogate
-        run: interrogate .
-
-
   isort:
     name: "Ensure imports are correctly sorted"
-    runs-on: "ubuntu-18.04"
+    runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: Install Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: "3.10"
 
       - name: Install code style checking tools
         run: python -m pip install isort

benchmarks/benchmark_models.py

@@ -2,14 +2,13 @@
 GP Model definitions to be used in the benchmarks
 """
 
-from gauche.kernels.fingerprint_kernels.tanimoto_kernel import (
-    TanimotoKernel,
-)
 from gpytorch.distributions import MultivariateNormal
 from gpytorch.kernels import LinearKernel, ScaleKernel
 from gpytorch.means import ConstantMean
 from gpytorch.models import ExactGP
 
+from gauche.kernels.fingerprint_kernels.tanimoto_kernel import TanimotoKernel
+
 
 class TanimotoGP(ExactGP):
     def __init__(self, train_x, train_y, likelihood):

benchmarks/run_benchmark.py

@@ -11,8 +11,6 @@
 import torch
 from benchmark_models import ScalarProductGP, TanimotoGP
 from botorch import fit_gpytorch_model
-from gauche.dataloader import MolPropLoader
-from gauche.dataloader.data_utils import transform_data
 from gpytorch.likelihoods import GaussianLikelihood
 from gpytorch.mlls import ExactMarginalLogLikelihood
 from gpytorch_metrics import (
@@ -23,6 +21,9 @@
 from sklearn.metrics import mean_absolute_error, mean_squared_error, r2_score
 from sklearn.model_selection import train_test_split
 
+from gauche.dataloader import MolPropLoader
+from gauche.dataloader.data_utils import transform_data
+
 # Remove Graphein warnings
 logging.getLogger("graphein").setLevel("ERROR")