fixing tests once more

Author: blaiszik

.github/workflows/tests.yml

@@ -8,7 +8,7 @@ jobs:
     strategy:
       matrix:
         python-version: ['3.9', '3.10', '3.11']
-        install-type: [core]
+        install-type: [core, all]
     env:
       CLIENT_ID: ${{ secrets.CLIENT_ID }}
       CLIENT_SECRET: ${{ secrets.CLIENT_SECRET }}
@@ -23,18 +23,26 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
+        # Install base package
         if [ "${{ matrix.install-type }}" = "core" ]; then
           pip install -e .
         else
           pip install -e .[all]
         fi
+        # Install test dependencies
         pip install -r requirements-dev.txt
         pip install -r test-requirements.txt
+        # Install optional dependencies for testing
+        pip install rdkit pandas numpy h5py
         
     - name: Run tests with coverage
       run: |
         if [ "${{ matrix.install-type }}" = "core" ]; then
-          pytest --cov=foundry --cov-report=xml --cov-report=term-missing --ignore=tests/test_molecular.py --ignore=tests/test_ml_frameworks.py
+          # Skip tests that require optional dependencies
+          pytest --cov=foundry --cov-report=xml --cov-report=term-missing \
+            --ignore=tests/test_molecular.py \
+            --ignore=tests/test_ml_frameworks.py \
+            --ignore=tests/test_loaders_specialized.py
         else
           pytest --cov=foundry --cov-report=xml --cov-report=term-missing
         fi

test-requirements.txt

@@ -4,3 +4,7 @@ pytest-mock
 flake8
 jsonschema
 mdf_toolbox
+rdkit
+pandas
+numpy
+h5py