Fixes for ruff 0.16

.github/workflows/pytest.yml

@@ -36,10 +36,11 @@ jobs:
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@v6
 
     - name: Build environment
-      uses: mamba-org/setup-micromamba@v2
+      uses: mamba-org/setup-micromamba@v3
+
       with:
         environment-file: environment-dev.yml
         create-args: >-
@@ -54,7 +55,7 @@ jobs:
       run: python -m pytest -rs -v --cov=./ --cov-report=xml
 
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v5
+      uses: codecov/codecov-action@v7
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ ci:
   submodules: false
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.22 # Ruff version
+    rev: v0.16.6 # Ruff version
     hooks:
       - id: ruff
         args: [--fix, --extend-ignore=E203]

cmeutils/__init__.py

@@ -3,8 +3,8 @@
 
 __all__ = [
     "__version__",
+    "dynamics",
     "gsd_utils",
     "structure",
-    "dynamics",
     "visualize",
 ]

cmeutils/dynamics.py

@@ -33,7 +33,7 @@ def msd_from_gsd(
     with gsd.hoomd.open(gsdfile, "r") as trajectory:
         init_box = trajectory[start].configuration.box
         final_box = trajectory[stop].configuration.box
-        assert all([i == j for i, j in zip(init_box, final_box)]), (
+        assert all(i == j for i, j in zip(init_box, final_box)), (
             f"The box is not consistent over the range {start}:{stop}"
         )
 

cmeutils/geometry.py

@@ -126,7 +126,7 @@ def get_plane_normal(points):
     assert points.shape[0] >= 3, "Need at least 3 points to calculate a plane."
     ctr = points.mean(axis=0)
     shiftpoints = points - ctr
-    U, S, Vt = svd(shiftpoints.T @ shiftpoints)
+    U, _S, _Vt = svd(shiftpoints.T @ shiftpoints)
     normal = U[:, -1]
     return ctr, normal
 
@@ -197,7 +197,7 @@ def dihedral_angle(pos1, pos2, pos3, pos4, degrees=False):
     return phi
 
 
-def moit(points, masses, center=np.zeros(3)):
+def moit(points, masses, center=(0, 0, 0)):
     """Calculates moment of inertia tensor (moit) for rigid bodies.
 
     Assumes rigid body center is at origin unless center is provided.
@@ -218,6 +218,7 @@ def moit(points, masses, center=np.zeros(3)):
         moment of inertia tensor for the rigid body center
 
     """
+    center = np.asarray(center)
     points -= center
     x = points[:, 0]
     y = points[:, 1]
@@ -231,7 +232,7 @@ def moit(points, masses, center=np.zeros(3)):
 def radial_grid_positions(
     init_radius,
     final_radius,
-    init_position=np.zeros(2),
+    init_position=(0, 0),
     n_circles=10,
     circle_slice=1,
     circle_coverage=2 * np.pi,
@@ -260,6 +261,7 @@ def radial_grid_positions(
         xy coordinates of the grid positions
     """
 
+    init_position = np.asarray(init_position)
     grid_positions = []
     for radius in np.linspace(init_radius, final_radius, n_circles):
         for d_theta in np.linspace(0, circle_coverage, circle_slice):
@@ -278,7 +280,7 @@ def radial_grid_positions(
 def spherical_grid_positions(
     init_radius,
     final_radius,
-    init_position=np.zeros(3),
+    init_position=None,
     n_circles=10,
     circle_slice=1,
     circle_coverage=2 * np.pi,
@@ -292,8 +294,9 @@ def spherical_grid_positions(
         initial radius of the grid (first circle)
     final_radius: float
         final radius of the grid (last circle)
-    init_position: numpy.ndarray (3,), default np.array([0,0,0])
+    init_position: numpy.ndarray (3,), default None
         initial position of the grid (center of the first circle)
+        If left as `None`, defaults to (0,0,0).
     n_circles: int, default 10
         number of circles in the grid
     circle_slice: int, default 1
@@ -308,7 +311,8 @@ def spherical_grid_positions(
     grid_positions: numpy.ndarray
         xyz coordinates of the grid positions
     """
-
+    if init_position is None:
+        init_position = np.zeros(3)
     z_slice = circle_slice * 2
     grid_positions = []
     for radius in np.linspace(init_radius, final_radius, n_circles):

cmeutils/gsd_utils.py

@@ -174,9 +174,9 @@ def _validate_inputs(gsd_file, snap, gsd_frame):
         try:
             with gsd.hoomd.open(name=gsd_file, mode="r") as f:
                 snap = f[gsd_frame]
-        except Exception as e:
+        except Exception:
             print("Unable to open the gsd_file")
-            raise e
+            raise
     elif snap:
         assert isinstance(snap, gsd.hoomd.Frame)
     return snap
@@ -254,24 +254,26 @@ def ellipsoid_gsd(gsd_file, new_file, ellipsoid_types, lpar, lperp):
         Value of lperp of the ellipsoids
 
     """
-    with gsd.hoomd.open(new_file, "w") as new_t:
-        with gsd.hoomd.open(gsd_file) as old_t:
-            for snap in old_t:
-                shape_dicts_list = []
-                for ptype in snap.particles.types:
-                    if ptype == ellipsoid_types or ptype in ellipsoid_types:
-                        shapes_dict = {
-                            "type": "Ellipsoid",
-                            "a": lperp,
-                            "b": lperp,
-                            "c": lpar,
-                        }
-                    else:
-                        shapes_dict = {"type": "Sphere", "diameter": 0.001}
-                    shape_dicts_list.append(shapes_dict)
-                snap.particles.type_shapes = shape_dicts_list
-                snap.validate()
-                new_t.append(snap)
+    with (
+        gsd.hoomd.open(new_file, "w") as new_t,
+        gsd.hoomd.open(gsd_file) as old_t,
+    ):
+        for snap in old_t:
+            shape_dicts_list = []
+            for ptype in snap.particles.types:
+                if ptype == ellipsoid_types or ptype in ellipsoid_types:
+                    shapes_dict = {
+                        "type": "Ellipsoid",
+                        "a": lperp,
+                        "b": lperp,
+                        "c": lpar,
+                    }
+                else:
+                    shapes_dict = {"type": "Sphere", "diameter": 0.001}
+                shape_dicts_list.append(shapes_dict)
+            snap.particles.type_shapes = shape_dicts_list
+            snap.validate()
+            new_t.append(snap)
 
 
 def xml_to_gsd(xmlfile, gsdfile):
@@ -491,7 +493,7 @@ def _detect_connections(compound_line_graph, type_="angle"):
         conn_matches = _trim_duplicates(conn_matches)
 
     # Do more sorting of individual connection
-    sorted_conn_matches = list()
+    sorted_conn_matches = []
     for match in conn_matches:
         if match[0] < match[-1]:
             sorted_conn = match
@@ -524,7 +526,7 @@ def _detect_connections(compound_line_graph, type_="angle"):
 def _get_sorted_by_n_connections(m):
     """Return sorted by n connections for the matching graph."""
     small = nx.Graph()
-    for k, v in m.items():
+    for k in m:
         small.add_edge(k[0], k[1])
     return sorted(small.adj, key=lambda x: len(small[x])), small
 

cmeutils/plotting.py

@@ -100,9 +100,9 @@ def threedplot(
     """
     fig = plt.figure(figsize=(10, 10), facecolor="white")
     ax = plt.axes(projection="3d")
-    ax.set_xlabel(xlabel, fontdict=dict(weight="bold"), fontsize=12)
-    ax.set_ylabel(ylabel, fontdict=dict(weight="bold"), fontsize=12)
-    ax.set_zlabel(zlabel, fontdict=dict(weight="bold"), fontsize=12)
+    ax.set_xlabel(xlabel, fontdict={"weight": "bold"}, fontsize=12)
+    ax.set_ylabel(ylabel, fontdict={"weight": "bold"}, fontsize=12)
+    ax.set_zlabel(zlabel, fontdict={"weight": "bold"}, fontsize=12)
     p = ax.scatter(x, y, z, c=z, cmap="rainbow", linewidth=7)
     plt.colorbar(p, pad=0.1, aspect=2.3)
 

cmeutils/sampling.py

@@ -122,4 +122,4 @@ def autocorr1D(array):
     """
     ft = np.fft.rfft(array - np.average(array))
     acorr = np.fft.irfft(ft * np.conjugate(ft)) / (len(array) * np.var(array))
-    return acorr[0 : len(acorr) // 2]  # noqa: E203
+    return acorr[0 : len(acorr) // 2]

cmeutils/structure.py

@@ -107,8 +107,8 @@ def angle_distribution(
         theta_max = 180
 
     trajectory = gsd.hoomd.open(gsd_file, mode="r")
-    name = "-".join([A_name, B_name, C_name])
-    name_rev = "-".join([C_name, B_name, A_name])
+    name = f"{A_name}-{B_name}-{C_name}"
+    name_rev = f"{C_name}-{B_name}-{A_name}"
 
     angles = []
     for snap in trajectory[start:stop:stride]:
@@ -237,8 +237,8 @@ def bond_distribution(
         )
 
     trajectory = gsd.hoomd.open(gsd_file, mode="r")
-    name = "-".join([A_name, B_name])
-    name_rev = "-".join([B_name, A_name])
+    name = f"{A_name}-{B_name}"
+    name_rev = f"{B_name}-{A_name}"
 
     bonds = []
     for snap in trajectory[start:stop:stride]:
@@ -358,8 +358,8 @@ def dihedral_distribution(
         )
 
     trajectory = gsd.hoomd.open(gsd_file, mode="r")
-    name = "-".join([A_name, B_name, C_name, D_name])
-    name_rev = "-".join([D_name, C_name, B_name, A_name])
+    name = f"{A_name}-{B_name}-{C_name}-{D_name}"
+    name_rev = f"{D_name}-{C_name}-{B_name}-{A_name}"
 
     dihedrals = []
     for snap in trajectory[start:stop:stride]:

cmeutils/tests/test_gsd.py

@@ -51,7 +51,7 @@ def test_snapshot_to_graph(self, pekk_cg_gsd, p3ht_gsd):
     def test_get_centers(self, gsdfile):
         new_gsdfile = "centers.gsd"
         centers = get_centers(gsdfile, new_gsdfile)
-        assert isinstance(centers, type(None))
+        assert centers is None
 
     def test_frame_to_freud_system(self, butane_gsd):
         with gsd.hoomd.open(butane_gsd) as traj:
@@ -248,9 +248,9 @@ def test_identify_connection_no_connections(self):
         snapshot.particles.typeid = [0, 1]
         with pytest.warns(UserWarning):
             updated_snapshot = identify_snapshot_connections(snapshot)
-            assert updated_snapshot.bonds.N == 0
-            assert updated_snapshot.angles.N == 0
-            assert updated_snapshot.dihedrals.N == 0
+        assert updated_snapshot.bonds.N == 0
+        assert updated_snapshot.angles.N == 0
+        assert updated_snapshot.dihedrals.N == 0
 
     def test_identify_connections_pekk_cg(self, pekk_cg_gsd):
         with gsd.hoomd.open(pekk_cg_gsd) as traj:

cmeutils/tests/test_sampling.py

@@ -63,7 +63,7 @@ def test_incorrect_threshold_neff(self, correlated_data_tau100_n10000):
 
     def test_return_trimmed_data(self, correlated_data_tau100_n10000):
         data = correlated_data_tau100_n10000
-        [equil_data, uncorr_indices, prod_start, Neff] = equil_sample(
+        [equil_data, _uncorr_indices, _prod_start, _Neff] = equil_sample(
             data, threshold_fraction=0.2, threshold_neff=10
         )
         assert np.shape(equil_data)[0] < np.shape(data)[0]
@@ -73,14 +73,14 @@ def test_trim_high_threshold(self, correlated_data_tau100_n10000):
         with pytest.raises(
             ValueError, match=r"Property does not have requisite threshold"
         ):
-            [equil_data, uncorr_indices, prod_start, Neff] = equil_sample(
+            [_equil_data, _uncorr_indices, _prod_start, _Neff] = equil_sample(
                 data, threshold_fraction=0.98
             )
         with pytest.raises(
             ValueError,
             match=r"More production data is needed",
         ):
-            [equil_data, uncorr_indices, prod_start, Neff] = equil_sample(
+            [_equil_data, _uncorr_indices, _prod_start, _Neff] = equil_sample(
                 data, threshold_fraction=0.75, threshold_neff=10000
             )
 

cmeutils/tests/test_structure.py

@@ -322,7 +322,7 @@ def test_gsd_rdf(self, AB_chain_gsd):
             exclude_all_bonded=False,
         )
         assert isinstance(rdf, freud.density.RDF)
-        rdf.rdf
+        _ = rdf.rdf
         assert scale_factor == 1
 
     def test_gsd_rdf_exclude_all_bonded(self, AB_chain_gsd):
@@ -370,7 +370,7 @@ def test_gsd_rdf_normalization(self, AB_chain_gsd):
         # All pairs are being used, N total = (10 * 9) / 2 = 45
         # Exclude bond depth of 1 should exclude all bonded pairs = 9
         # 45 / (45 - 9) = 1.25
-        rdf, scale_factor = gsd_rdf(
+        _, scale_factor = gsd_rdf(
             gsdfile=AB_chain_gsd,
             start=0,
             stop=10,
@@ -382,7 +382,7 @@ def test_gsd_rdf_normalization(self, AB_chain_gsd):
         # Excl bond depth of 2 should result in 9 (bonds) + 8 (angles) exclusions
         # 45 / (45 - 17) = 1.607
 
-        rdf, scale_factor = gsd_rdf(
+        _, scale_factor = gsd_rdf(
             gsdfile=AB_chain_gsd,
             start=0,
             stop=10,
@@ -393,15 +393,15 @@ def test_gsd_rdf_normalization(self, AB_chain_gsd):
 
     def test_gsd_rdf_r_max(self, LJ_gsd):
         """Test 2 RDFs with different r_cuts. The values of the shared r_cut region should be very close"""
-        rdf, scale_factor = gsd_rdf(
+        rdf, _ = gsd_rdf(
             gsdfile=LJ_gsd,
             start=0,
             stop=10,
             r_max=3,
             exclude_bond_depth=0,
             exclude_all_bonded=False,
         )
-        rdf2, scale_factor2 = gsd_rdf(
+        rdf2, _ = gsd_rdf(
             gsdfile=LJ_gsd,
             start=0,
             stop=10,

cmeutils/tests/test_visualize.py

@@ -69,11 +69,11 @@ def test_set_bad_view(self, p3ht_fresnel):
             p3ht_fresnel.view_axis = 10
 
     def test_bad_color_dict(self, p3ht_fresnel):
-        with pytest.raises(ValueError):
+        with pytest.raises(TypeError):
             p3ht_fresnel.color_dict = np.array([0.1, 0.1, 0.1])
 
     def test_set_bad_unwrap_pos(self, p3ht_fresnel):
-        with pytest.raises(ValueError):
+        with pytest.raises(TypeError):
             p3ht_fresnel.unwrap_positions = "true"
 
     def set_set_colors(self, p3ht_fresnel):