Swap to ruff and setuptools-scm (#112)

.pre-commit-config.yaml

@@ -1,38 +1,15 @@
 repos:
-  - repo: local
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
     hooks:
-      - id: isort
-        name: "[Package] Import formatting"
-        language: system
-        entry: isort
-        files: \.py$
-
-      - id: black
-        name: "[Package] Code formatting"
-        language: system
-        entry: black
-        files: \.py$
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
 
-      - id: flake8
-        name: "[Package] Linting"
+-   repo: local
+    hooks:
+    -   id: ruff
+        name: Autoformat python code
         language: system
-        entry: flake8
+        entry: ruff
+        args: [check]
         files: \.py$
-
-      - id: isort-examples
-        name: "[Examples] Import formatting"
-        language: system
-        entry: nbqa isort
-        files: examples/.+\.ipynb$
-
-      - id: black-examples
-        name: "[Examples] Code formatting"
-        language: system
-        entry: nbqa black
-        files: examples/.+\.ipynb$
-
-      - id: flake8-examples
-        name: "[Examples] Linting"
-        language: system
-        entry: nbqa flake8 --ignore=E402
-        files: examples/.+\.ipynb$

Makefile

@@ -4,32 +4,23 @@ CONDA_ENV_RUN := conda run --no-capture-output --name $(PACKAGE_NAME)
 EXAMPLES_SKIP := examples/md-simulations.ipynb
 EXAMPLES := $(filter-out $(EXAMPLES_SKIP), $(wildcard examples/*.ipynb))
 
-.PHONY: pip-install env lint format test test-examples docs-build docs-deploy docs-insiders
-
-pip-install:
-	$(CONDA_ENV_RUN) pip install --no-build-isolation --no-deps -e .
+.PHONY: env lint format test test-examples docs-build docs-deploy docs-insiders
 
 env:
 	mamba create     --name $(PACKAGE_NAME)
 	mamba env update --name $(PACKAGE_NAME) --file devtools/envs/base.yaml
-	$(CONDA_ENV_RUN) pip install --no-build-isolation --no-deps -e .
+	$(CONDA_ENV_RUN) pip install --no-deps -e .
 	$(CONDA_ENV_RUN) pre-commit install || true
 
 lint:
-	$(CONDA_ENV_RUN) isort --check-only $(PACKAGE_NAME)
-	$(CONDA_ENV_RUN) black --check      $(PACKAGE_NAME)
-	$(CONDA_ENV_RUN) flake8             $(PACKAGE_NAME)
-	$(CONDA_ENV_RUN) nbqa isort   --check-only  examples
-	$(CONDA_ENV_RUN) nbqa black   --check       examples
-	$(CONDA_ENV_RUN) nbqa flake8  --ignore=E402 examples
+	$(CONDA_ENV_RUN) ruff check $(PACKAGE_NAME)
+	$(CONDA_ENV_RUN) ruff check examples
 
 format:
-	$(CONDA_ENV_RUN) isort  $(PACKAGE_NAME)
-	$(CONDA_ENV_RUN) black  $(PACKAGE_NAME)
-	$(CONDA_ENV_RUN) flake8 $(PACKAGE_NAME)
-	$(CONDA_ENV_RUN) nbqa isort                examples
-	$(CONDA_ENV_RUN) nbqa black                examples
-	$(CONDA_ENV_RUN) nbqa flake8 --ignore=E402 examples
+	$(CONDA_ENV_RUN) ruff format $(PACKAGE_NAME)
+	$(CONDA_ENV_RUN) ruff check --fix --select I $(PACKAGE_NAME)
+	$(CONDA_ENV_RUN) ruff format examples
+	$(CONDA_ENV_RUN) ruff check --fix --select I examples
 
 test:
 	$(CONDA_ENV_RUN) pytest -v --cov=$(PACKAGE_NAME) --cov-report=xml --color=yes $(PACKAGE_NAME)/tests/

devtools/envs/base.yaml

@@ -40,13 +40,10 @@ dependencies:
   - scipy  # test logsumexp implementation
   - smirnoff-plugins
 
-  - versioneer
+  - setuptools_scm >=8
 
   - pre-commit
-  - isort
-  - black
-  - flake8
-  - flake8-pyproject
+  - ruff
   - nbqa
 
   - pytest

examples/parameter-gradients.ipynb

@@ -123,13 +123,13 @@
     "energy.backward()\n",
     "\n",
     "for parameter_key, gradient in zip(\n",
-    "    vdw_potential.parameter_keys, vdw_potential.parameters.grad.numpy()\n",
+    "    vdw_potential.parameter_keys, vdw_potential.parameters.grad.numpy(), strict=True\n",
     "):\n",
     "    parameter_cols = vdw_potential.parameter_cols\n",
     "\n",
     "    parameter_grads = \", \".join(\n",
     "        f\"dU/d{parameter_col} = {parameter_grad: 8.3f}\"\n",
-    "        for parameter_col, parameter_grad in zip(parameter_cols, gradient)\n",
+    "        for parameter_col, parameter_grad in zip(parameter_cols, gradient, strict=True)\n",
     "    )\n",
     "    print(f\"{parameter_key.id.ljust(15)} - {parameter_grads}\")"
    ],

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools>=61.0", "wheel", "versioneer"]
+requires = ["setuptools>=61.0", "setuptools_scm>=8", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -12,35 +12,20 @@ readme = "README.md"
 requires-python = ">=3.10"
 classifiers = ["Programming Language :: Python :: 3"]
 
-[tool.setuptools]
-zip-safe = false
-include-package-data = true
+[tool.setuptools.packages.find]
+include = ["smee*"]
 
-[tool.setuptools.dynamic]
-version = {attr = "smee.__version__"}
+[tool.setuptools_scm]
 
-[tool.setuptools.packages.find]
-namespaces = true
-where = ["."]
-
-[tool.versioneer]
-VCS = "git"
-style = "pep440"
-versionfile_source = "smee/_version.py"
-versionfile_build = "smee/_version.py"
-tag_prefix = ""
-parentdir_prefix = "smee-"
-
-[tool.black]
-line-length = 88
-
-[tool.isort]
-profile = "black"
-
-[tool.flake8]
-max-line-length = 88
-ignore = ["E203", "E266", "E501", "W503"]
-select = ["B","C","E","F","W","T4","B9"]
+[tool.ruff]
+extend-include = ["*.ipynb"]
+
+[tool.ruff.lint]
+ignore = ["C901","E402","E501"]
+select = ["B","C","E","F","W","B9"]
+
+[tool.ruff.lint.pydocstyle]
+convention = "google"
 
 [tool.coverage.run]
 omit = ["**/tests/*", "**/_version.py"]

smee/__init__.py

@@ -4,7 +4,8 @@
 Differentiably evaluate energies of molecules using SMIRNOFF force fields
 """
 
-from . import _version
+import importlib.metadata
+
 from ._constants import CUTOFF_ATTRIBUTE, SWITCH_ATTRIBUTE, EnergyFn, PotentialType
 from ._models import (
     NonbondedParameterMap,
@@ -21,7 +22,10 @@
 from .geometry import add_v_site_coords, compute_v_site_coords
 from .potentials import compute_energy, compute_energy_potential
 
-__version__ = _version.get_versions()["version"]
+try:
+    __version__ = importlib.metadata.version("smee")
+except importlib.metadata.PackageNotFoundError:
+    __version__ = "0+unknown"
 
 __all__ = [
     "CUTOFF_ATTRIBUTE",

smee/_models.py

@@ -246,15 +246,15 @@ def n_atoms(self) -> int:
         """The number of atoms in the system."""
         return sum(
             topology.n_atoms * n_copies
-            for topology, n_copies in zip(self.topologies, self.n_copies)
+            for topology, n_copies in zip(self.topologies, self.n_copies, strict=True)
         )
 
     @property
     def n_v_sites(self) -> int:
         """The number of v-sites in the system."""
         return sum(
             topology.n_v_sites * n_copies
-            for topology, n_copies in zip(self.topologies, self.n_copies)
+            for topology, n_copies in zip(self.topologies, self.n_copies, strict=True)
         )
 
     @property