Reformat with ruff

.pre-commit-config.yaml

@@ -1,38 +1,9 @@
 repos:
   - repo: local
     hooks:
-      - id: isort
-        name: "[Package] Import formatting"
+      - id: ruff
+        name: "[Package] Formatting"
         language: system
-        entry: isort
+        entry: make
+        args: [ lint ]
         files: \.py$
-
-      - id: black
-        name: "[Package] Code formatting"
-        language: system
-        entry: black
-        files: \.py$
-
-      - id: flake8
-        name: "[Package] Linting"
-        language: system
-        entry: flake8
-        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

@@ -1,4 +1,6 @@
-PACKAGE_NAME  := descent
+PACKAGE_NAME := descent
+PACKAGE_DIR  := $(PACKAGE_NAME)
+
 CONDA_ENV_RUN := conda run --no-capture-output --name $(PACKAGE_NAME)
 
 .PHONY: pip-install env lint format test test-examples
@@ -13,23 +15,16 @@ env:
 	$(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_DIR)
 
 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_DIR)
+	$(CONDA_ENV_RUN) ruff check --fix --select I $(PACKAGE_DIR)
+	$(CONDA_ENV_RUN) nbqa 'ruff format'                 examples
+	$(CONDA_ENV_RUN) nbqa 'ruff check' --fix --select=I examples
 
 test:
-	$(CONDA_ENV_RUN) pytest -v --cov=$(PACKAGE_NAME) --cov-report=xml --color=yes $(PACKAGE_NAME)/tests/
+	$(CONDA_ENV_RUN) pytest -v --cov=$(PACKAGE_NAME) --cov-report=xml --color=yes $(PACKAGE_DIR)/tests/
 
 docs-build:
 	$(CONDA_ENV_RUN) mkdocs build

descent/targets/dimers.py

@@ -275,7 +275,8 @@ def predict(
         *[
             _predict(dimer, force_field, topologies)
             for dimer in descent.utils.dataset.iter_dataset(dataset)
-        ]
+        ],
+        strict=True,
     )
     return torch.cat(reference), torch.cat(predicted)
 

descent/targets/thermo.py

@@ -610,7 +610,7 @@ def predict(
 
     per_type_scales = per_type_scales if per_type_scales is not None else {}
 
-    for entry, keys in zip(entries, entry_to_simulation):
+    for entry, keys in zip(entries, entry_to_simulation, strict=True):
         value, std = _predict(entry, keys, observables, required_simulations)
 
         type_scale = per_type_scales.get(entry["type"], 1.0)

descent/tests/optim/test_lm.py

@@ -143,7 +143,8 @@ def test_damping_factor_loss_fn(mocker):
 
 
 @pytest.mark.parametrize(
-    "n_convergence_criteria, n_convergence_steps, step_quality, expected_converged, expected_logs",
+    "n_convergence_criteria, n_convergence_steps, step_quality, expected_converged, "
+    "expected_logs",
     [
         (0, 2, 1.0, False, []),
         (1, 2, 0.0, False, []),
@@ -283,7 +284,7 @@ def mock_loss_fn(_x, *_):
     ]
     assert len(trust_radius_messages) == len(expected_messages)
 
-    for message, expected in zip(trust_radius_messages, expected_messages):
+    for message, expected in zip(trust_radius_messages, expected_messages, strict=True):
         assert message.startswith(expected)
 
     # mock_step_fn.assert_has_calls(expected_loss_traj, any_order=False)

descent/tests/utils/test_loss.py

@@ -39,7 +39,6 @@ def mock_loss_fn(x: torch.Tensor, a: float, b: float) -> torch.Tensor:
 
 
 def test_combine_closures():
-
     def mock_closure_a(x_, compute_gradient, compute_hessian):
         loss = x_[0] ** 2
         grad = 2 * x_[0] if compute_gradient else None

descent/utils/dataset.py

@@ -19,5 +19,5 @@ def iter_dataset(dataset: datasets.Dataset) -> typing.Iterator[dict[str, typing.
 
     columns = [*dataset.features]
 
-    for row in zip(*[dataset[column] for column in columns]):
-        yield {column: v for column, v in zip(columns, row)}
+    for row in zip(*[dataset[column] for column in columns], strict=True):
+        yield dict(zip(columns, row, strict=True))

descent/utils/loss.py

@@ -84,15 +84,13 @@ def combine_closures(
     def combined_closure_fn(
         x: torch.Tensor, compute_gradient: bool, compute_hessian: bool
     ) -> tuple[torch.Tensor, torch.Tensor | None, torch.Tensor | None]:
-
         loss = []
         grad = None if not compute_gradient else []
         hess = None if not compute_hessian else []
 
         verbose_rows = []
 
         for name, closure_fn in closures.items():
-
             local_loss, local_grad, local_hess = closure_fn(
                 x, compute_gradient, compute_hessian
             )

descent/utils/reporting.py

@@ -14,7 +14,8 @@
 
 
 DEFAULT_COLORS, DEFAULT_MARKERS = zip(
-    *itertools.product(["red", "green", "blue", "black"], ["x", "o", "+", "^"])
+    *itertools.product(["red", "green", "blue", "black"], ["x", "o", "+", "^"]),
+    strict=True,
 )
 
 
@@ -103,11 +104,15 @@ def print_potential_summary(potential: smee.TensorPotential):
 
     parameter_rows = []
 
-    for key, value in zip(potential.parameter_keys, potential.parameters.detach()):
+    for key, value in zip(
+        potential.parameter_keys, potential.parameters.detach(), strict=True
+    ):
         row = {"ID": _format_parameter_id(key.id)}
         row.update(
             {
-                f"{col}{_format_unit(potential.parameter_units[idx])}": f"{value[idx].item():.4f}"
+                f"{col}{_format_unit(potential.parameter_units[idx])}": (
+                    f"{value[idx].item():.4f}"
+                )
                 for idx, col in enumerate(potential.parameter_cols)
             }
         )
@@ -119,7 +124,9 @@ def print_potential_summary(potential: smee.TensorPotential):
     if potential.attributes is not None:
         attribute_rows = [
             {
-                f"{col}{_format_unit(potential.attribute_units[idx])}": f"{potential.attributes[idx].item():.4f} "
+                f"{col}{_format_unit(potential.attribute_units[idx])}": (
+                    f"{potential.attributes[idx].item():.4f} "
+                )
                 for idx, col in enumerate(potential.attribute_cols)
             }
         ]
@@ -139,7 +146,7 @@ def print_v_site_summary(v_sites: smee.TensorVSites):
 
     parameter_rows = []
 
-    for key, value in zip(v_sites.keys, v_sites.parameters.detach()):
+    for key, value in zip(v_sites.keys, v_sites.parameters.detach(), strict=True):
         row = {"ID": _format_parameter_id(key.id)}
         row.update(
             {

devtools/envs/base.yaml

@@ -41,10 +41,7 @@ dependencies:
   - versioneer
 
   - pre-commit
-  - isort
-  - black
-  - flake8
-  - flake8-pyproject
+  - ruff
   - nbqa
 
   - pytest

pyproject.toml

@@ -31,16 +31,10 @@ versionfile_build = "descent/_version.py"
 tag_prefix = ""
 parentdir_prefix = "descent-"
 
-[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.lint]
+ignore = ["C901"]
+select = ["B","C","E","F","W","B9"]
+ignore-init-module-imports = true
 
 [tool.coverage.run]
 omit = ["**/tests/*", "**/_version.py"]