Merge pull request #44 from chrisjonesBSU/add-ruff

Update pre-commit config, bump to numpy 2.0 and hoomd 5.0 in environment files.

Author: chrisjonesBSU

.pre-commit-config.yaml

@@ -1,32 +1,34 @@
 ci:
-  autofix_commit_msg: |
-    [pre-commit.ci] auto fixes from pre-commit.com hooks
-    for more information, see https://pre-commit.ci
-  autofix_prs: true
-  autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
-  autoupdate_schedule: weekly
-  skip: [ ]
-  submodules: false
+    autofix_commit_msg: |
+        [pre-commit.ci] auto fixes from pre-commit.com hooks
+        for more information, see https://pre-commit.ci
+    autofix_prs: true
+    autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
+    autoupdate_schedule: weekly
+    skip: []
+    submodules: false
 repos:
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.1 # Ruff version
-    hooks:
-      - id: ruff
-        args: [--fix, --extend-ignore=E203]
-      - id: ruff-format
-        args: [--line-length=80]
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
-    hooks:
-      - id: check-yaml
-      - id: end-of-file-fixer
-      - id: trailing-whitespace
-        exclude: 'msibi/tests/assets/.*'
-  - repo: https://github.com/pycqa/isort
-    rev: 5.13.2
-    hooks:
-      - id: isort
-        name: isort (python)
-        args:
-          [ --profile=black, --line-length=80 ]
-        exclude: 'msibi/tests/assets/.* '
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.12.3
+  hooks:
+    # Run the linter.
+    - id: ruff
+      args: [--line-length=80, --fix]
+    # Run the formatter.
+    - id: ruff-format
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0
+  hooks:
+    - id: check-yaml
+    - id: end-of-file-fixer
+    - id: trailing-whitespace
+      exclude: 'setup.cfg|msibi/tests/assets/.*'
+
+- repo: https://github.com/pycqa/isort
+  rev: 6.0.1
+  hooks:
+    - id: isort
+      name: isort (python)
+      args: [--profile=black, --line-length=80]
+      exclude: "msibi/tests/assets/.*"

docs/source/conf.py

@@ -34,4 +34,4 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
 html_theme = "sphinx_rtd_theme"
-#html_static_path = ["_static"]
+# html_static_path = ["_static"]

environment-dev.yml

@@ -4,11 +4,11 @@ channels:
 dependencies:
 - freud >=3.0,<3.2
 - gsd >=3.0
-- hoomd >=4.0,<5.0
+- hoomd >=5.0
 - python >=3.10
 - pandas
 - cmeutils >=1.3
-- numpy <2.0
+- numpy >=2.0,<2.3
 - more-itertools
 - pytest
 - pytest-cov

environment.yml

@@ -4,9 +4,9 @@ channels:
 dependencies:
 - freud >=3.0,<3.2
 - gsd >=3.0
-- hoomd >=4.0,<5.0
+- hoomd >=5.0
 - python >=3.10
 - pandas
 - cmeutils >=1.3
-- numpy <2.0
+- numpy >=2.0,<2.3
 - more-itertools

msibi/forces.py

@@ -264,9 +264,7 @@ def save_state_data(self, state: msibi.state.State, file_path: str) -> None:
         state_data = {
             "target_distribution": state_dict["target_distribution"],
             "current_distribution": state_dict["current_distribution"],
-            "distribution_history": np.asarray(
-                state_dict["distribution_history"]
-            ),
+            "distribution_history": np.asarray(state_dict["distribution_history"]),
             "f_fit": np.asarray(state_dict["f_fit"]),
         }
         np.savez(file_path, **state_data)
@@ -321,9 +319,7 @@ def plot_target_distribution(
         if file_path:
             plt.savefig(file_path)
 
-    def plot_fit_scores(
-        self, state: msibi.state.State, file_path: str = None
-    ) -> None:
+    def plot_fit_scores(self, state: msibi.state.State, file_path: str = None) -> None:
         """Plot the evolution of the distribution matching fit scores.
 
         Parameters
@@ -563,9 +559,7 @@ def _add_state(self, state: msibi.state.State) -> None:
             Instance of a State object previously created.
         """
         if self.optimize:
-            target_distribution = self._get_state_distribution(
-                state=state, query=False
-            )
+            target_distribution = self._get_state_distribution(state=state, query=False)
             if self.smoothing_window and self.smoothing_order:
                 target_distribution[:, 1] = savitzky_golay(
                     y=target_distribution[:, 1],
@@ -669,9 +663,7 @@ def _update_potential(self) -> None:
             self.x_range, self.potential, self.correction_form
         )
         self.potential_history.append(np.copy(self.potential))
-        self._head_correction_history.append(
-            np.copy(self.potential[0:head_cut])
-        )
+        self._head_correction_history.append(np.copy(self.potential[0:head_cut]))
         self._tail_correction_history.append(np.copy(self.potential[tail_cut:]))
         self._learned_potential_history.append(np.copy(self.potential[real]))
 
@@ -767,9 +759,7 @@ def _table_entry(self) -> dict:
         }
         return table_entry
 
-    def _get_distribution(
-        self, state: msibi.state.State, gsd_file: str
-    ) -> np.ndarray:
+    def _get_distribution(self, state: msibi.state.State, gsd_file: str) -> np.ndarray:
         """Calculate a bond length distribution.
 
         Parameters
@@ -881,9 +871,7 @@ def _table_entry(self) -> dict:
         table_entry = {"U": self.potential, "tau": self.force}
         return table_entry
 
-    def _get_distribution(
-        self, state: msibi.state.State, gsd_file: str
-    ) -> np.ndarray:
+    def _get_distribution(self, state: msibi.state.State, gsd_file: str) -> np.ndarray:
         """Calculate a bond angle distribution.
 
         Parameters
@@ -996,9 +984,7 @@ def set_lj(
         self.x_range = np.arange(r_min, r_cut + self.dx, self.dx)
         self.x_min = self.x_range[0]
         self.r_cut = self.x_range[-1]
-        self.potential = lennard_jones(
-            r=self.x_range, epsilon=epsilon, sigma=sigma
-        )
+        self.potential = lennard_jones(r=self.x_range, epsilon=epsilon, sigma=sigma)
         self.force_init = "Table"
 
     def _table_entry(self) -> dict:
@@ -1010,9 +996,7 @@ def _table_entry(self) -> dict:
         }
         return table_entry
 
-    def _get_distribution(
-        self, state: msibi.state.State, gsd_file: str
-    ) -> np.ndarray:
+    def _get_distribution(self, state: msibi.state.State, gsd_file: str) -> np.ndarray:
         """Calculate a pair distribution (RDF).
 
         Parameters
@@ -1142,9 +1126,7 @@ def _table_entry(self) -> dict:
         table_entry = {"U": self.potential, "tau": self.force}
         return table_entry
 
-    def _get_distribution(
-        self, state: msibi.state.State, gsd_file: str
-    ) -> np.ndarray:
+    def _get_distribution(self, state: msibi.state.State, gsd_file: str) -> np.ndarray:
         """Calculate a dihedral angle distribution.
 
         Parameters

msibi/optimize.py

@@ -146,9 +146,7 @@ def dihedrals(self) -> list:
 
     def _add_optimize_force(self, force: msibi.forces.Force) -> None:
         """Check that all forces to be optimized are the same type."""
-        if not all(
-            [isinstance(force, f.__class__) for f in self._optimize_forces]
-        ):
+        if not all([isinstance(force, f.__class__) for f in self._optimize_forces]):
             raise RuntimeError(
                 "Only one type of force (i.e., Bonds, Angles, Pairs, etc) "
                 "can be set to optimize at a time."
@@ -182,7 +180,7 @@ def run_optimization(
             are saved in their respective :class:`msibi.state.State` directory.
         """
         for n in range(n_iterations):
-            print(f"---Optimization: {n+1} of {n_iterations}---")
+            print(f"---Optimization: {n + 1} of {n_iterations}---")
             forces = self._build_force_objects()
             for state in self.states:
                 state._run_simulation(
@@ -216,9 +214,7 @@ def pickle_forces(self, file_path: str) -> None:
         """
         forces = self._build_force_objects()
         if len(forces) == 0:
-            raise RuntimeError(
-                "No forces have been created yet. See MSIBI.add_force()"
-            )
+            raise RuntimeError("No forces have been created yet. See MSIBI.add_force()")
         f = open(file_path, "wb")
         pickle.dump(forces, f)
 
@@ -269,9 +265,7 @@ def _build_force_objects(self) -> list:
         dihedral_force = None
         for dih in self.dihedrals:
             if not dihedral_force:
-                hoomd_dihedral_force = getattr(
-                    hoomd.md.dihedral, dih.force_init
-                )
+                hoomd_dihedral_force = getattr(hoomd.md.dihedral, dih.force_init)
                 if dih.force_init == "Table":
                     dihedral_force = hoomd_dihedral_force(width=dih.nbins + 1)
                 else:

msibi/potentials.py

@@ -59,9 +59,7 @@ def pair_correction(r, V, form, r_switch=2.5):
                     pass
         # Trim off edge cases
         _real_idx = np.where(np.isfinite(V))[0]
-        real_idx = max(
-            [list(g) for g in mit.consecutive_groups(_real_idx)], key=len
-        )
+        real_idx = max([list(g) for g in mit.consecutive_groups(_real_idx)], key=len)
 
     head_cutoff = real_idx[0] - 1
     tail_cutoff = real_idx[-1] + 1
@@ -104,9 +102,7 @@ def bond_correction(r, V, form):
                     pass
         # Trim off edge cases
         _real_idx = np.where(np.isfinite(V))[0]
-        real_idx = max(
-            [list(g) for g in mit.consecutive_groups(_real_idx)], key=len
-        )
+        real_idx = max([list(g) for g in mit.consecutive_groups(_real_idx)], key=len)
 
     head_cutoff = real_idx[0] - 1
     tail_cutoff = real_idx[-1] + 1

msibi/tests/base_test.py

@@ -105,9 +105,7 @@ def bond(self):
 
     @pytest.fixture
     def angle(self):
-        angle = Angle(
-            type1="A", type2="B", type3="A", optimize=False, nbins=100
-        )
+        angle = Angle(type1="A", type2="B", type3="A", optimize=False, nbins=100)
         return angle
 
     @pytest.fixture

msibi/tests/test_forces.py

@@ -43,9 +43,7 @@ def test_smooth_potential(self, bond):
             x_min=1,
             x_max=3,
         )
-        bond.potential = bond.potential + np.random.normal(
-            0, 0.5, bond.potential.shape
-        )
+        bond.potential = bond.potential + np.random.normal(0, 0.5, bond.potential.shape)
         noisy_pot = np.copy(bond.potential)
         bond.smoothing_window = 5
         bond.smooth_potential()
@@ -241,18 +239,14 @@ def test_set_dihedral_harmonic(self, dihedral):
         assert dihedral.force_entry["n"] == 1
 
     def test_set_dihedral_polynomail(self, dihedral):
-        dihedral.set_polynomial(
-            x0=0, k4=0, k3=0, k2=100, x_min=-np.pi, x_max=np.pi
-        )
+        dihedral.set_polynomial(x0=0, k4=0, k3=0, k2=100, x_min=-np.pi, x_max=np.pi)
         assert dihedral.format == "table"
         assert len(dihedral.x_range) == dihedral.nbins + 1
         assert np.allclose(dihedral.x_range[0], -np.pi, atol=1e-3)
         assert np.allclose(dihedral.x_range[-1], np.pi, atol=1e-3)
 
     def test_save_angle_potential(self, tmp_path, dihedral):
-        dihedral.set_polynomial(
-            x0=0, k4=0, k3=0, k2=100, x_min=-np.pi, x_max=np.pi
-        )
+        dihedral.set_polynomial(x0=0, k4=0, k3=0, k2=100, x_min=-np.pi, x_max=np.pi)
         path = os.path.join(tmp_path, "ABAA_dihedral.csv")
         dihedral.save_potential(path)
         assert os.path.isfile(path)

msibi/tests/test_optimize.py

@@ -81,9 +81,7 @@ def test_run_with_static_force(self, msibi, stateX, stateY):
         ff = msibi._build_force_objects()
         assert len(ff) == 2
 
-    def test_optimize_pairs_linear_alpha(
-        self, msibi, stateX_linear_alpha, stateY
-    ):
+    def test_optimize_pairs_linear_alpha(self, msibi, stateX_linear_alpha, stateY):
         msibi.gsd_period = 10
         msibi.add_state(stateX_linear_alpha)
         msibi.add_state(stateY)
@@ -185,9 +183,7 @@ def test_run_with_all_forces(self, msibi, stateX, stateY):
         pair3.set_lj(sigma=1.5, epsilon=1, r_cut=2.0, r_min=0.1)
         msibi.add_force(pair3)
 
-        dihedral = Dihedral(
-            type1="B", type2="A", type3="B", type4="A", optimize=False
-        )
+        dihedral = Dihedral(type1="B", type2="A", type3="B", type4="A", optimize=False)
         dihedral.set_periodic(k=100, phi0=0, d=-1, n=1)
         msibi.add_force(dihedral)