Fix tests (#6)

* Update CI.yaml

---------

Co-authored-by: wiederm <[email protected]>

.github/workflows/CI.yaml

@@ -36,12 +36,12 @@ jobs:
 
       # More info on options: https://github.com/marketplace/actions/provision-with-micromamba
       - uses: mamba-org/provision-with-micromamba@main
+        env:
+          CONDA_OVERRIDE_CUDA: "11.4"
         with:
+          python-version: ${{ matrix.python-version }}
           environment-file: devtools/conda-envs/test_env.yaml
-          environment-name: test
           channels: conda-forge,defaults
-          extra-specs: |
-            python=${{ matrix.python-version }}
 
       - name: Install package
         # conda setup requires this special shell

devtools/conda-envs/test_env.yaml

@@ -8,7 +8,6 @@ dependencies:
   - python
   - pip
   - openmm>=8.0
-  - openmm-ml
   - openmm-torch
   - openff-toolkit
   - openmmtools
@@ -21,9 +20,12 @@ dependencies:
   - seaborn
   - pytorch #=1.11.0
   - loguru
-  # Testing
   - nglview
-  - fire
+  # Testing
+  - pytest
+  - pytest-cov
+  - codecov
+  - black
 
     # Testing
   - pytest
@@ -32,5 +34,6 @@ dependencies:
 
     # Pip-only installs
   - pip:
-      - nvidia-ml-py3
-      - nptyping
+     - nvidia-ml-py3
+     - nptyping
+     - git+https://github.com/openmm/openmm-ml.git

guardowl/tests/stability_test_alanine_dipeptide.yaml

@@ -4,7 +4,7 @@ tests:
     env: "solvent"
     ensemble: "npt"
     nnp: "ani2x"
-    implementation: "nnpops"
+    implementation: "torchani"
     annealing: false
     nr_of_simulation_steps: 100
     temperature: 300

guardowl/tests/stability_test_hipen.yaml

@@ -3,6 +3,6 @@ tests:
   - protocol: "hipen_protocol"
     hipen_idx: 0
     nnp: "ani2x"
-    implementation: "nnpops"
+    implementation: "torchani"
     temperature: 300
     nr_of_simulation_steps: 100

guardowl/tests/stability_test_waterbox.yaml

@@ -4,7 +4,7 @@ tests:
     edge_length: 10
     ensemble: "npt"
     nnp: "ani2x"
-    implementation: "nnpops"
+    implementation: "torchani"
     annealing: false
     nr_of_simulation_steps: 100
     temperature: 300

guardowl/tests/test_simulation.py

@@ -9,6 +9,7 @@
 from guardowl.setup import create_system_from_mol, generate_molecule
 from guardowl.simulation import SimulationFactory, SystemFactory
 from guardowl.testsystems import hipen_systems
+from guardowl.utils import get_available_nnps_and_implementation
 
 
 @pytest.mark.parametrize(
@@ -69,9 +70,8 @@ def test_generate_simulation_instance(
     with open("initial_frame_lamb_1.0.pdb", "w") as f:
         PDBFile.writeFile(topology, pos, f)
 
-@pytest.mark.parametrize(
-    "nnp, implementation", [("ani2x", "nnpops"), ("ani2x", "torchani"), ("ani2x", "")]
-)
+
+@pytest.mark.parametrize("nnp, implementation", get_available_nnps_and_implementation())
 def test_simulating(nnp: str, implementation: str) -> None:
     """Test if we can run a simulation for a number of steps"""
 

guardowl/tests/test_stability_protocol.py

@@ -6,7 +6,6 @@
 from openmmml import MLPotential
 from openmmtools.utils import get_fastest_platform
 
-from guardowl.utils import available_nnps_and_implementation
 from guardowl.protocols import (
     BondProfileProtocol,
     DOFTestParameters,
@@ -20,9 +19,10 @@
     SmallMoleculeTestsystemFactory,
     WaterboxTestsystemFactory,
 )
+from guardowl.utils import get_available_nnps_and_implementation
 
 
-@pytest.mark.parametrize("nnp, implementation", available_nnps_and_implementation)
+@pytest.mark.parametrize("nnp, implementation", get_available_nnps_and_implementation())
 def test_setup_vacuum_protocol(nnp: str, implementation: str) -> None:
     """Test if we can run a simulation for a number of steps"""
 
@@ -71,7 +71,7 @@ def test_setup_vacuum_protocol(nnp: str, implementation: str) -> None:
 
 
 @pytest.mark.parametrize("ensemble", ["NVE", "NVT", "NpT"])
-@pytest.mark.parametrize("nnp, implementation", available_nnps_and_implementation)
+@pytest.mark.parametrize("nnp, implementation", get_available_nnps_and_implementation())
 def test_setup_waterbox_protocol(ensemble: str, nnp: str, implementation: str) -> None:
     """Test if we can run a simulation for a number of steps"""
 
@@ -126,7 +126,7 @@ def test_setup_waterbox_protocol(ensemble: str, nnp: str, implementation: str) -
     )
 
 
-@pytest.mark.parametrize("nnp, implementation", available_nnps_and_implementation)
+@pytest.mark.parametrize("nnp, implementation", get_available_nnps_and_implementation())
 def test_DOF_protocol(nnp: str, implementation: str) -> None:
     """Test if we can run a simulation for a number of steps"""
 

guardowl/utils.py

@@ -1,6 +1,19 @@
+import os
+
 available_nnps_and_implementation = [
     ("ani2x", "nnpops"),
     ("ani2x", "torchani"),
-    ("ani1ccx", "nnpops"),
-    ("ani1ccx", "torchani"),
 ]
+
+gh_available_nnps_and_implementation = [
+    ("ani2x", "torchani"),
+]
+
+
+def get_available_nnps_and_implementation() -> list:
+    """Return a list of available neural network potentials and implementations"""
+    IN_GITHUB_ACTIONS = os.getenv("GITHUB_ACTIONS") == "true"
+    if IN_GITHUB_ACTIONS:
+        return gh_available_nnps_and_implementation
+    else:
+        return available_nnps_and_implementation