Merge pull request #1104 from openforcefield/consolidate-config

mattwthompson · web-flow · commit 94c1ad1802e2 · 2025-01-21T16:41:30.000-06:00
Consolidate Python config files
diff --git a/.codecov.yml b/.codecov.yml
diff --git a/.github/workflows/beta.yaml b/.github/workflows/beta.yaml
@@ -28,7 +28,6 @@ jobs:
 
     env:
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
-      COV: --cov=openff/interchange --cov-report=xml --cov-config=setup.cfg --cov-append
 
     steps:
     - uses: actions/checkout@v4
@@ -52,9 +51,7 @@ jobs:
           python=${{ matrix.python-version }}
 
     - name: Install package
-      run: |
-        micromamba remove --force openff-interchange openff-interchange-base
-        python -m pip install . plugins/
+      run: python -m pip install . plugins/
 
     - name: Install and license OpenEye Toolkits
       if: ${{ matrix.openeye == true }}
@@ -71,7 +68,7 @@ jobs:
 
     - name: Run all tests
       if: always()
-      run: python -m pytest -v $COV openff/interchange/
+      run: python -m pytest -v openff/interchange/
 
     - name: Codecov
       uses: codecov/codecov-action@v5
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -20,7 +20,6 @@ jobs:
     name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}, OpenMM ${{ matrix.openmm }}, OpenEye ${{ matrix.openeye }}
     runs-on: ${{ matrix.os }}
     strategy:
-      fail-fast: false
       matrix:
         os:
           - macos-latest
@@ -33,11 +32,10 @@ jobs:
           - false
         openmm:
           - true
-          - false
 
     env:
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
-      COV: --cov=openff/interchange --cov-report=xml --cov-config=setup.cfg --cov-append
+      COV: --cov=openff/interchange --cov-report=xml --cov-config=pyproject.toml --cov-append
 
     steps:
     - uses: actions/checkout@v4
@@ -52,11 +50,7 @@ jobs:
           python=${{ matrix.python-version }}
 
     - name: Install package
-      run: |
-        # These packages are brought in by conda (via the toolkit) and must be removed manually
-        # since pip doesn't know about the -base split and does not uninstall the -base package
-        micromamba remove --force openff-interchange openff-interchange-base
-        python -m pip install . plugins/
+      run: python -m pip install . plugins/
 
     - name: Install and license OpenEye Toolkits
       if: ${{ matrix.openeye == true }}
@@ -85,9 +79,6 @@ jobs:
       # and also uninstalls RDKit
       run: micromamba install rdkit "ambertools =23" "lammps >=2023.08.02" "jax >=0.3" "jaxlib >=0.3" -c conda-forge
 
-    - name: Install Foyer
-      run: micromamba install "foyer >=0.12.1" -c conda-forge -yq
-
     - name: Run tests
       run: python -m pytest $COV openff/interchange/ -r fExs -n logical --durations=10
 
diff --git a/.github/workflows/examples.yaml b/.github/workflows/examples.yaml
@@ -17,9 +17,9 @@ defaults:
 
 jobs:
   test:
+    name: Examples on ${{ matrix.os }}, Python ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     strategy:
-      fail-fast: false
       matrix:
         os:
           - ubuntu-latest
@@ -45,8 +45,7 @@ jobs:
           python=${{ matrix.python-version }}
 
     - name: Install package
-      run: |
-        python -m pip install .
+      run: python -m pip install .
 
     - name: License OpenEye
       run: |
@@ -56,12 +55,10 @@ jobs:
         SECRET_OE_LICENSE: ${{ secrets.OE_LICENSE }}
 
     - name: Run docexamples
-      run: |
-        python -m pytest --doctest-modules openff/interchange/ --ignore=openff/interchange/_tests
+      run: python -m pytest -c /dev/null/ --doctest-modules openff/interchange/ --ignore=openff/interchange/_tests
 
     - name: Run example notebooks
-      if: always()
       run: |
-        python -m pytest --nbval-lax --dist loadscope -n logical --durations=20 examples/ \
+        python -m pytest -c /dev/null/ --nbval-lax --dist loadscope -n logical --durations=20 examples/ \
           --ignore=examples/deprecated/ \
           --ignore=examples/experimental
diff --git a/devtools/conda-envs/examples_env.yaml b/devtools/conda-envs/examples_env.yaml
@@ -15,9 +15,8 @@ dependencies:
   # Optional features
   - openff-nagl ~=0.5
   - openff-nagl-models ~=0.3
-  - mbuild ~=0.18
-  - foyer =1
-  - gmso ~=0.12
+  - mbuild
+  - foyer
   - nglview
   # Drivers
   - gromacs
diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
@@ -21,7 +21,6 @@ dependencies:
   - openff-nagl-models ~=0.3
   - mbuild =1
   - foyer =1
-  - gmso ~=0.12
   - nglview
   # Drivers
   - gromacs
diff --git a/docs/developing.md b/docs/developing.md
@@ -24,7 +24,7 @@ Style is enforced with automated linters that run in CI. See `.github/workflows/
 
 ### Type-checking
 
-Type hints are **optional** but encouraged. Many optional flags are passed to `mypy`; check the action for a recommended invocation. Check `setup.cfg` for some configuration, mostly ignoring libraries that do not have support for type-checking.
+Type hints are **optional** but encouraged. Many optional flags are passed to `mypy`; check the action for a recommended invocation. Check `pyproject.toml` for some configuration, mostly ignoring libraries that do not have support for type-checking.
 
 ### Pre-commit
 
diff --git a/openff/interchange/_tests/energy_tests/test_energies.py b/openff/interchange/_tests/energy_tests/test_energies.py
@@ -14,6 +14,7 @@
 )
 from openff.interchange.constants import kj_mol
 from openff.interchange.drivers import get_openmm_energies
+from openff.interchange.foyer._guard import has_foyer
 
 if has_package("openmm"):
     import openmm
@@ -31,7 +32,7 @@
     from openff.interchange.drivers.lammps import get_lammps_energies
 
 
-@skip_if_missing("foyer")
+@pytest.mark.skipif(not has_foyer, reason="Foyer is not installed")
 class TestEnergies:
     @pytest.fixture(scope="session")
     def oplsaa(self):
@@ -99,7 +100,7 @@ def test_energies_single_mol(self, constrained, sage, sage_unconstrained, mol_sm
             lmp_energies.compare(other_energies, tolerances)
 
     @needs_gmx
-    @skip_if_missing("foyer")
+    @pytest.mark.skipif(not has_foyer, reason="Foyer is not installed")
     @skip_if_missing("mbuild")
     def test_process_rb_torsions(self, oplsaa):
         """Test that the GROMACS driver reports Ryckaert-Bellemans torsions"""
diff --git a/openff/interchange/_tests/unit_tests/components/test_foyer.py b/openff/interchange/_tests/unit_tests/components/test_foyer.py
@@ -4,16 +4,17 @@
 import parmed as pmd
 import pytest
 from openff.toolkit import Molecule, Topology, unit
-from openff.utilities.testing import has_package, skip_if_missing
+from openff.utilities.testing import skip_if_missing
 
 from openff.interchange import Interchange
 from openff.interchange._tests import HAS_GROMACS, get_test_files_dir_path, needs_gmx
 from openff.interchange.components.potentials import Potential
 from openff.interchange.constants import kj_mol
 from openff.interchange.drivers import get_openmm_energies
+from openff.interchange.foyer._guard import has_foyer
 from openff.interchange.models import PotentialKey, TopologyKey
 
-if has_package("foyer"):
+if has_foyer:
     import foyer
 
     from openff.interchange.foyer._valence import _RBTorsionHandler
@@ -27,13 +28,13 @@
     )
 
 
-@skip_if_missing("foyer")
+@pytest.mark.skipif(not has_foyer, reason="Foyer is not installed")
 class TestFoyer:
-    @pytest.fixture(scope="session")
+    @pytest.fixture
     def oplsaa(self):
         return foyer.forcefields.load_OPLSAA()
 
-    @pytest.fixture(scope="session")
+    @pytest.fixture
     def oplsaa_interchange_ethanol(self, oplsaa):
         molecule = Molecule.from_file(
             get_test_files_dir_path("foyer_test_molecules") / "ethanol.sdf",
@@ -47,7 +48,7 @@ def oplsaa_interchange_ethanol(self, oplsaa):
         interchange.box = [4, 4, 4]
         return interchange
 
-    @pytest.fixture(scope="session")
+    @pytest.fixture
     def get_interchanges(self, oplsaa):
         def interchanges_from_path(molecule_path):
             molecule_or_molecules = Molecule.from_file(molecule_path)
@@ -150,7 +151,6 @@ def test_interchange_energies(self, molecule_path, get_interchanges, oplsaa):
         )
 
 
-@skip_if_missing("foyer")
 class TestRBTorsions(TestFoyer):
     @pytest.fixture
     def ethanol_with_rb_torsions(self, sage):
@@ -204,7 +204,6 @@ def test_rb_torsions(self, ethanol_with_rb_torsions):
         assert (gmx - omm).m_as(kj_mol) < 1e-6
 
     @pytest.mark.filterwarnings("ignore:Parameters have not been assigned to all impropers.")
-    @skip_if_missing("foyer")
     @skip_if_missing("mbuild")
     @needs_gmx
     def test_rb_torsions_vs_foyer(self, oplsaa, ethanol_with_rb_torsions):
diff --git a/openff/interchange/_tests/unit_tests/components/test_interchange.py b/openff/interchange/_tests/unit_tests/components/test_interchange.py
@@ -118,7 +118,6 @@ def test_input_topology_not_modified(self, sage):
     @needs_gmx
     @needs_lmp
     @pytest.mark.slow
-    @skip_if_missing("foyer")
     def test_atom_ordering(self):
         """Test that atom indices in bonds are ordered consistently between the slot map and topology"""
         import foyer
diff --git a/openff/interchange/_tests/unit_tests/interop/openmm/test_hmr.py b/openff/interchange/_tests/unit_tests/interop/openmm/test_hmr.py
@@ -1,7 +1,7 @@
 import random
 
 import pytest
-from openff.toolkit import Molecule, Topology, unit
+from openff.toolkit import Molecule, Quantity, Topology
 
 from openff.interchange._tests import MoleculeWithConformer
 from openff.interchange.exceptions import NegativeMassError
@@ -23,7 +23,7 @@ def test_hmr_basic(sage, reversed, ethanol, reversed_ethanol):
 
     system = interchange.to_openmm(hydrogen_mass=hydrogen_mass)
 
-    expected_mass = sum([atom.mass for atom in topology.atoms]).m_as(unit.dalton)
+    expected_mass = sum([atom.mass for atom in topology.atoms]).m_as("dalton")
 
     found_mass = sum(
         [
@@ -53,9 +53,7 @@ def test_hmr_not_applied_to_water(sage, water):
 
     system = interchange.to_openmm(hydrogen_mass=hydrogen_mass)
 
-    expected_mass = sum([atom.mass for atom in interchange.topology.atoms]).m_as(
-        unit.dalton,
-    )
+    expected_mass = sum([atom.mass for atom in interchange.topology.atoms]).m_as("dalton")
 
     found_mass = sum(
         [
@@ -109,10 +107,13 @@ def test_hmr_with_ligand_virtual_sites(sage_with_bond_charge, hydrogen_mass):
     import openmm
     import openmm.unit
 
-    molecule = MoleculeWithConformer.from_mapped_smiles("[H:5][C:2]([H:6])([C:3]([H:7])([H:8])[Cl:4])[Cl:1]")
+    topology = MoleculeWithConformer.from_mapped_smiles(
+        "[H:5][C:2]([H:6])([C:3]([H:7])([H:8])[Cl:4])[Cl:1]",
+    ).to_topology()
+    topology.box_vectors = Quantity([4, 4, 4], "nanometer")
 
     # should work fine with 4 fs, but be conservative and just use 3 fs
-    simulation = sage_with_bond_charge.create_interchange(molecule.to_topology()).to_openmm_simulation(
+    simulation = sage_with_bond_charge.create_interchange(topology).to_openmm_simulation(
         integrator=openmm.VerletIntegrator(3.0 * openmm.unit.femtosecond),
         hydrogen_mass=hydrogen_mass,
     )
diff --git a/openff/interchange/components/interchange.py b/openff/interchange/components/interchange.py
@@ -48,8 +48,14 @@
     import openmm.app
     from openff.toolkit import ForceField
 
-    if has_package("foyer"):
-        from foyer import Forcefield as FoyerForcefield
+    from openff.interchange.foyer._guard import has_foyer
+
+    if has_foyer:
+        try:
+            from foyer import Forcefield as FoyerForcefield
+        except ModuleNotFoundError:
+            # case of openff/interchange/foyer/ being detected as the real package
+            pass
     if has_package("nglview"):
         import nglview
 
@@ -836,13 +842,13 @@ def from_foyer(
 
             >>> from openff.interchange import Interchange
             >>> from openff.toolkit import Molecule, Topology
-            >>> from foyer import Forcefield
+            >>> from foyer import Forcefield  # doctest: +SKIP
             >>> mol = Molecule.from_smiles("CC")
             >>> mol.generate_conformers(n_conformers=1)
             >>> top = Topology.from_molecules([mol])
-            >>> oplsaa = Forcefield(name="oplsaa")
-            >>> interchange = Interchange.from_foyer(topology=top, force_field=oplsaa)
-            >>> interchange
+            >>> oplsaa = Forcefield(name="oplsaa")  # doctest: +SKIP
+            >>> interchange = Interchange.from_foyer(topology=top, force_field=oplsaa)  # doctest: +SKIP
+            >>> interchange  # doctest: +SKIP
             Interchange with 8 collections, non-periodic topology with 8 atoms.
 
         """
diff --git a/openff/interchange/foyer/_base.py b/openff/interchange/foyer/_base.py
@@ -5,10 +5,15 @@
 from openff.toolkit import Topology
 
 from openff.interchange.components.potentials import Collection, Potential
+from openff.interchange.foyer._guard import has_foyer
 from openff.interchange.models import PotentialKey, TopologyKey
 
 if TYPE_CHECKING:
-    from foyer import Forcefield
+    if has_foyer:
+        try:
+            from foyer import Forcefield
+        except ModuleNotFoundError:
+            pass
 
 
 # Is this the safest way to achieve PotentialKey id separation?
diff --git a/openff/interchange/foyer/_create.py b/openff/interchange/foyer/_create.py
@@ -2,11 +2,11 @@
 from numpy.typing import NDArray
 from openff.toolkit import Topology
 from openff.units import Quantity, unit
-from openff.utilities.utilities import has_package
 
 from openff.interchange import Interchange
 from openff.interchange.common._positions import _infer_positions
 from openff.interchange.components.potentials import Collection
+from openff.interchange.foyer._guard import has_foyer
 from openff.interchange.foyer._nonbonded import (
     FoyerElectrostaticsHandler,
     FoyerVDWHandler,
@@ -21,8 +21,11 @@
 )
 from openff.interchange.models import TopologyKey
 
-if has_package("foyer"):
-    from foyer.forcefield import Forcefield
+if has_foyer:
+    try:
+        from foyer import Forcefield
+    except ModuleNotFoundError:
+        pass
 
 _CollectionAlias = type[Collection]
 
diff --git a/openff/interchange/foyer/_guard.py b/openff/interchange/foyer/_guard.py
@@ -0,0 +1,10 @@
+"""Import guard."""
+
+# openff/interchange/foyer.py causes "import foyer" to not crash, which breaks has_packge("foyer")
+# and breaks @skip_if_missing("foyer"), so need a more specific way of checking Foyer installation
+try:
+    from foyer import Forcefield
+
+    has_foyer = True
+except (ImportError, AttributeError):
+    has_foyer = False
diff --git a/openff/interchange/foyer/_nonbonded.py b/openff/interchange/foyer/_nonbonded.py
diff --git a/pyproject.toml b/pyproject.toml
diff --git a/pytest.ini b/pytest.ini
diff --git a/setup.cfg b/setup.cfg
diff --git a/setup.py b/setup.py
