[pre-commit.ci] pre-commit autoupdate (#307)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.8.6 → v0.9.1](astral-sh/ruff-pre-commit@v0.8.6...v0.9.1)

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Format black

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Update snap.py

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: pyiron-runner <pyiron@mpie.de>
Co-authored-by: Jan Janssen <jan-janssen@users.noreply.github.com>

Author: 3 people

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.6
+    rev: v0.9.1
     hooks:
       - id: ruff
         name: ruff lint

structuretoolkit/analyse/snap.py

@@ -545,9 +545,8 @@ def _extract_computes_snap(
         np.ndarray: Output of the LAMMPS compute command
     """
     lmp_atom_ids = lmp.numpy.extract_atom_iarray("id", num_atoms).flatten()
-    assert np.all(
-        lmp_atom_ids == 1 + np.arange(num_atoms)
-    ), "LAMMPS seems to have lost atoms"
+    cond = np.all(lmp_atom_ids == 1 + np.arange(num_atoms))
+    assert cond, "LAMMPS seems to have lost atoms"
 
     # Extract types
     lmp_types = lmp.numpy.extract_atom_iarray(name="type", nelem=num_atoms).flatten()
@@ -569,16 +568,14 @@ def _extract_computes_snap(
 
     lmp_dbarr = _extract_compute_np(lmp, "db", 1, 2, (num_atoms, num_types, 3, n_coeff))
     lmp_dbsum = _extract_compute_np(lmp, "db_sum", 0, 1, (num_types, 3, n_coeff))
-    assert np.allclose(
-        lmp_dbsum, lmp_dbarr.sum(axis=0), rtol=1e-12, atol=1e-12
-    ), "db_sum doesn't match sum of db"
+    cond = np.allclose(lmp_dbsum, lmp_dbarr.sum(axis=0), rtol=1e-12, atol=1e-12)
+    assert cond, "db_sum doesn't match sum of db"
     db_atom = np.transpose(lmp_dbarr, (0, 2, 1, 3))
 
     lmp_vbarr = _extract_compute_np(lmp, "vb", 1, 2, (num_atoms, num_types, 6, n_coeff))
     lmp_vbsum = _extract_compute_np(lmp, "vb_sum", 0, 1, (num_types, 6, n_coeff))
-    assert np.allclose(
-        lmp_vbsum, lmp_vbarr.sum(axis=0), rtol=1e-12, atol=1e-12
-    ), "vb_sum doesn't match sum of vb"
+    cond = np.allclose(lmp_vbsum, lmp_vbarr.sum(axis=0), rtol=1e-12, atol=1e-12)
+    assert cond, "vb_sum doesn't match sum of vb"
     vb_sum = np.transpose(lmp_vbsum, (1, 0, 2)) / lmp_volume * eV_div_A3_to_bar
 
     dbatom_shape = db_atom.shape

structuretoolkit/build/mesh.py

@@ -41,8 +41,7 @@ def create_mesh(
         n_mesh = np.rint(np.linalg.norm(cell, axis=-1) / density).astype(int)
     elif density is not None:
         raise MeshInputError(
-            "You cannot set n_mesh at density at the same time. Set one of"
-            " them to None"
+            "You cannot set n_mesh at density at the same time. Set one of them to None"
         )
     n_mesh = np.atleast_1d(n_mesh).astype(int)
     if len(n_mesh) == 1:

structuretoolkit/build/random.py

@@ -99,6 +99,6 @@ def generate(group):
                 structures.append({"atoms": s, "symmetry": g, "repeat": i})
         if len(failed_groups) > 0:
             warnings.warn(
-                f'Groups [{", ".join(map(str,failed_groups))}] could not be generated with stoichiometry {stoich}!'
+                f"Groups [{', '.join(map(str, failed_groups))}] could not be generated with stoichiometry {stoich}!"
             )
         return structures