MAINT: Update handling of test/optional dependencies (#1357)

Author: mattwthompson

.gitattributes

@@ -17,7 +17,7 @@ defaults:
 
 jobs:
   test:
-    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}, OpenMM ${{ matrix.openmm }}, OpenEye ${{ matrix.openeye }}, RDKit ${{ matrix.rdkit }}, NAGL ${{ matrix.nagl }}
+    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}, OpenMM ${{ matrix.openmm }}, OpenEye ${{ matrix.openeye }}, RDKit ${{ matrix.rdkit }}, AmberTools ${{ matrix.ambertools }}, NAGL ${{ matrix.nagl }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
@@ -33,6 +33,9 @@ jobs:
           - false
         rdkit:
           - true
+        ambertools:
+          - true
+          - false
         nagl:
           - true
           - false
@@ -41,6 +44,8 @@ jobs:
         exclude:
           - python-version: "3.13"
             openeye: true
+          - ambertools: false
+            openeye: false
 
     env:
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
@@ -75,15 +80,21 @@ jobs:
     - name: Install RDKit
       if: ${{ matrix.rdkit == true }}
       run: |
-        micromamba install rdkit -c conda-forge
+        micromamba install rdkit "ambertools =24" intermol -c conda-forge
+
+    - name: Remove AmberTools
+      if: ${{ matrix.ambertools == false }}
+      run: |
+        micromamba remove ambertools parmed
+        micromamba install "packmol >=20.15.0" "lammps>=2024" "numpy>=2.3"
 
     - name: Install OpenFF NAGL
       if: ${{ matrix.nagl == true }}
       run: |
         micromamba install openff-nagl -c conda-forge
 
     - name: Install Python <3.13 dependencies
-      if: ${{ matrix.python-version != '3.13' }}
+      if: ${{ matrix.python-version != '3.13' && matrix.ambertools == true }}
       run: micromamba install --file devtools/conda-envs/test_not_py313.yaml python=${{ matrix.python-version }}
 
     - name: Install package

.github/workflows/ci.yaml

@@ -12,7 +12,7 @@ repos:
   hooks:
   - id: add-trailing-comma
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.14.2
+  rev: v0.14.3
   hooks:
     - id: ruff
       args: ["--fix"]
@@ -39,12 +39,6 @@ repos:
   hooks:
     - id: nbstripout
       files: ^examples
-- repo: https://github.com/asottile/pyupgrade
-  rev: v3.21.0
-  hooks:
-  - id: pyupgrade
-    args:
-      - --py310-plus
 - repo: https://github.com/tox-dev/pyproject-fmt
   rev: v2.11.0
   hooks:

.pre-commit-config.yaml

@@ -14,11 +14,11 @@ dependencies:
   - ambertools =24
   # Optional features
   - openmm
-  # smirnoff-plugins =2024
-  # de-forcefields  # add back after smirnoff-plugins update
+  - smirnoff-plugins =2025
+  - de-forcefields
   - openff-nagl
   - openff-nagl-models
-  - mbuild =1
+  - mbuild-base =1
   - foyer =1
   - gmso ~=0.12
   - nglview

devtools/conda-envs/dev_env.yaml

@@ -8,11 +8,11 @@ dependencies:
   - setuptools !=76.0.0
   - versioningit
   - pip
-  - numpy =1
+  - numpy =2
   - pydantic >=2,<2.12
   - openff-toolkit-base =0.17
   - openmm
-  - mbuild
+  - mbuild-base =1
   - foyer =1
   - nglview
   - pyedr

devtools/conda-envs/docs_env.yaml

@@ -7,7 +7,7 @@ dependencies:
   # Core
   - python
   - versioningit
-  - numpy
+  - numpy =2.2
   - pydantic >=2,<2.12
   # OpenFF stack
   - openff-toolkit-base =0.17
@@ -16,7 +16,7 @@ dependencies:
   # Optional features
   - openff-nagl
   - openff-nagl-models
-  - mbuild
+  - mbuild-base
   - foyer
   - nglview
   # Drivers

devtools/conda-envs/examples_env.yaml

@@ -10,7 +10,6 @@ dependencies:
   # OpenFF stack
   - openff-toolkit-base =0.17
   - openff-units
-  - ambertools =24
   # Optional features
   - openmm
   - nglview
@@ -19,7 +18,6 @@ dependencies:
   - pyedr
   # Testing
   - mdtraj
-  - intermol
   - jax
   - pytest
   - pytest-cov

devtools/conda-envs/test_env.yaml

@@ -10,20 +10,17 @@ dependencies:
   # OpenFF stack
   - openff-toolkit-base =0.17
   - openff-units
-  - ambertools =24
   # Optional features
   - openmm
-  - smirnoff-plugins =2024
-  # de-forcefields  # add back after smirnoff-plugins update
+  - smirnoff-plugins =2025
+  - de-forcefields
   # https://github.com/mosdef-hub/foyer/pull/574
-  # https://github.com/conda-forge/mbuild-feedstock/issues/46
-  # https://github.com/conda-forge/mbuild-feedstock/pull/49
-  # mbuild =1
+  - mbuild-base =1
   - foyer =1
   - nglview
   # Drivers
   - gromacs
-  - lammps
+  # lammps
   - pyedr
   # Testing
   - mdtraj

devtools/conda-envs/test_not_py313.yaml

@@ -1,5 +1,4 @@
 import numpy as np
-import parmed
 import pytest
 from openff.toolkit import ForceField, Molecule, unit
 from openff.utilities import (
@@ -22,6 +21,8 @@
 class TestAmber:
     @pytest.mark.skip(reason="Need replacement route to reference positions")
     def test_inpcrd(self, sage):
+        parmed = pytest.importorskip("parmed")
+
         mol = Molecule.from_smiles(10 * "C")
         mol.name = "HPER"
         mol.generate_conformers(n_conformers=1)
@@ -129,6 +130,7 @@ def test_single_residue_system_residue_name(
         ethanol,
         patch_residue_name,
     ):
+        parmed = pytest.importorskip("parmed")
         if patch_residue_name:
             for atom in ethanol.atoms:
                 atom.metadata["residue_name"] = "YUP"

openff/interchange/_tests/interoperability_tests/internal/test_amber.py

@@ -1,7 +1,6 @@
 from importlib import resources
 
 import numpy
-import parmed
 import pytest
 from openff.toolkit import ForceField, Molecule, Quantity, Topology, unit
 from openff.toolkit.typing.engines.smirnoff import VirtualSiteHandler
@@ -25,13 +24,17 @@
     import openmm.unit
 
 
+@skip_if_missing("intermol")
 @skip_if_missing("mdtraj")
 @skip_if_missing("openmm")
 @needs_gmx
 class TestGROMACSGROFile:
-    _INTERMOL_PATH = resources.files(
-        "intermol.tests.gromacs.unit_tests",
-    )
+    try:
+        _INTERMOL_PATH = resources.files(
+            "intermol.tests.gromacs.unit_tests",
+        )
+    except ImportError:
+        _INTERMOL_PATH = None
 
     @skip_if_missing("intermol")
     def test_load_gro(self):
@@ -54,6 +57,7 @@ def test_load_gro(self):
         assert numpy.allclose(box, openmm_box)
 
     @skip_if_missing("intermol")
+    @pytest.mark.skip("don't run parmed tests")
     def test_load_gro_nonstandard_precision(self):
         file = self._INTERMOL_PATH / "lj3_bulk/lj3_bulk.gro"
 
@@ -126,8 +130,9 @@ def test_simple_roundtrip(self, sage, smiles, reader):
             },
         )
 
-    @skip_if_missing("parmed")
+    @pytest.mark.skip("don't run parmed tests")
     def test_num_impropers(self, sage):
+        parmed = pytest.importorskip("parmed")
         out = Interchange.from_smirnoff(
             sage,
             MoleculeWithConformer.from_smiles("CC1=CC=CC=C1").to_topology(),
@@ -174,12 +179,14 @@ def test_unsupported_mixing_rule(self, ethanol_top, sage):
             interchange.to_top("out.top")
 
     @pytest.mark.slow
+    @pytest.mark.skip("don't run parmed tests")
     @skip_if_missing("openmm")
     def test_residue_info(self, sage):
         """Test that residue information is passed through to .top files."""
-        import parmed
         from openff.units.openmm import from_openmm
 
+        parmed = pytest.importorskip("parmed")
+
         protein = get_protein("MainChain_HIE")
 
         box_vectors = from_openmm(
@@ -272,6 +279,8 @@ def sage_with_monovalent_lone_pair(self, sage):
     @skip_if_missing("parmed")
     def test_sigma_hole_example(self, sage_with_sigma_hole):
         """Test that a single-molecule sigma hole example runs"""
+        parmed = pytest.importorskip("parmed")
+
         molecule = MoleculeWithConformer.from_smiles("CCl", name="Chloromethane")
 
         out = Interchange.from_smirnoff(