MAINT: Consolidate Python config in pyproject.toml

.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

.github/workflows/ci.yaml

@@ -37,7 +37,6 @@ 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
@@ -52,11 +51,7 @@ 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 +80,6 @@ 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
 

devtools/conda-envs/examples_env.yaml

@@ -30,6 +30,7 @@ dependencies:
   - mdtraj
   - pytest
   - pytest-xdist
+  - pytest-cov
   - nbval
   # Examples
   - openmmforcefields

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

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
 

pyproject.toml

@@ -13,8 +13,54 @@ authors = [{name = "Open Force Field Initiative", email = "[email protected]
 license = {text = "MIT"}
 dynamic = ["version"]
 
+[tool.setuptools.packages.find]
+where = ["openff/interchange"]
+
 [tool.versioningit]
 
+[tool.mypy]
+mypy_path = "stubs/"
+python_version = "3.11"
+plugins = "numpy.typing.mypy_plugin,pydantic.mypy"
+warn_unused_configs = true
+warn_unused_ignores = true
+warn_incomplete_stub = true
+show_error_codes = true
+
+[[tool.mypy.overrides]]
+module = [
+    "pandas",
+    "networkx",
+    "openmm",
+    "openmm.app",
+    "openmm.app.element",
+    "openmm.unit",
+    "intermol.*",
+    "rdkit",
+    "openff.toolkit.*",
+    "openff.units.*",
+    "openff.utilities.*",
+    "openff.recharge.*",
+    "parmed",
+    "parmed.amber",
+    "pmdtest.utils",
+    "pytest",
+    "pint",
+    "unyt",
+    "openeye",
+    "jax",
+    "scipy.spatial",
+    "nonbonded_plugins.*",
+    "lammps",
+]
+ignore_missing_imports = true
+
+[tool.pytest.ini_options]
+markers = [
+    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
+]
+addopts = "--cov=openff/interchange --cov-report=xml"
+
 [tool.interrogate]
 ignore-init-method = true
 ignore-init-module = true
@@ -60,3 +106,16 @@ known-first-party = ["openff.interchange"]
 
 [tool.ruff.lint.pydocstyle]
 property-decorators=["validator"]
+
+[tool.coverage.run]
+omit = [
+    "*/*/_tests/*",
+]
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "if TYPE_CHECKING:",
+    "raise NotImplementedError",
+    "@overload",
+]