Merge pull request #239 from phonopy/ruff

Migrate to ruff

.pre-commit-config.yaml

@@ -10,31 +10,12 @@ repos:
     exclude: ^conda/
   - id: check-added-large-files
 
-- repo: https://github.com/pycqa/flake8
-  rev: 7.1.0
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.1.13
   hooks:
-  - id: flake8
-    args:
-    - "--max-line-length=88"
-    - "--ignore=E203,W503"
-
-- repo: https://github.com/psf/black
-  rev: 24.4.2
-  hooks:
-  - id: black
-    args:
-    - --line-length=88
-
-- repo: https://github.com/pycqa/pydocstyle
-  rev: 6.3.0
-  hooks:
-  - id: pydocstyle
-
-- repo: https://github.com/pycqa/isort
-  rev: 5.13.2
-  hooks:
-    - id: isort
-      name: isort (python)
+  - id: ruff
+    args: [ "--fix", "--show-fixes" ]
+  - id: ruff-format
 
 - repo: https://github.com/Takishima/cmake-pre-commit-hooks
   rev: v1.9.6

phono3py/api_jointdos.py

@@ -40,12 +40,12 @@
 from phonopy.units import VaspToTHz
 
 from phono3py.file_IO import write_joint_dos
+from phono3py.phonon.grid import BZGrid
 from phono3py.phonon3.imag_self_energy import (
     get_freq_points_batches,
     get_frequency_points,
 )
 from phono3py.phonon3.joint_dos import JointDos
-from phono3py.phonon.grid import BZGrid
 
 
 class Phono3pyJointDos:

phono3py/api_phono3py.py

@@ -72,19 +72,20 @@
 from phono3py.conductivity.rta import get_thermal_conductivity_RTA
 from phono3py.interface.fc_calculator import get_fc3
 from phono3py.interface.phono3py_yaml import Phono3pyYaml
+from phono3py.phonon.grid import BZGrid
 from phono3py.phonon3.dataset import get_displacements_and_forces_fc3
 from phono3py.phonon3.displacement_fc3 import (
     direction_to_displacement,
     get_third_order_displacements,
 )
-from phono3py.phonon3.fc3 import cutoff_fc3_by_zero
-from phono3py.phonon3.fc3 import get_fc3 as get_phono3py_fc3
 from phono3py.phonon3.fc3 import (
+    cutoff_fc3_by_zero,
     set_permutation_symmetry_compact_fc3,
     set_permutation_symmetry_fc3,
     set_translational_invariance_compact_fc3,
     set_translational_invariance_fc3,
 )
+from phono3py.phonon3.fc3 import get_fc3 as get_phono3py_fc3
 from phono3py.phonon3.imag_self_energy import (
     get_imag_self_energy,
     write_imag_self_energy,
@@ -95,7 +96,6 @@
     write_real_self_energy,
 )
 from phono3py.phonon3.spectral_function import run_spectral_function
-from phono3py.phonon.grid import BZGrid
 from phono3py.version import __version__
 
 

phono3py/conductivity/base.py

@@ -45,10 +45,10 @@
 from phonopy.units import EV, Angstrom, Kb, THz, THzToEv
 
 from phono3py.other.isotope import Isotope
+from phono3py.phonon.grid import get_grid_points_by_rotations, get_ir_grid_points
 from phono3py.phonon3.collision_matrix import CollisionMatrix
 from phono3py.phonon3.imag_self_energy import ImagSelfEnergy
 from phono3py.phonon3.interaction import Interaction
-from phono3py.phonon.grid import get_grid_points_by_rotations, get_ir_grid_points
 
 unit_to_WmK = (
     (THz * Angstrom) ** 2 / (Angstrom**3) * EV / THz / (2 * np.pi)
@@ -81,6 +81,7 @@ def get_mode_heat_capacities(self):
             "Use attribute, Conductivity.mode_heat_capacities "
             "instead of Conductivity.get_mode_heat_capacities().",
             DeprecationWarning,
+            stacklevel=2,
         )
         return self.mode_heat_capacities
 
@@ -129,6 +130,7 @@ def get_kappa(self):
         warnings.warn(
             "Use attribute, Conductivity.kappa " "instead of Conductivity.get_kappa().",
             DeprecationWarning,
+            stacklevel=2,
         )
         return self.kappa
 
@@ -143,6 +145,7 @@ def get_mode_kappa(self):
             "Use attribute, Conductivity.mode_kappa "
             "instead of Conductivity.get_mode_kappa().",
             DeprecationWarning,
+            stacklevel=2,
         )
         return self.mode_kappa
 
@@ -165,6 +168,7 @@ def get_group_velocities(self):
             "Use attribute, Conductivity.group_velocities "
             "instead of Conductivity.get_group_velocities().",
             DeprecationWarning,
+            stacklevel=2,
         )
         return self.group_velocities
 
@@ -179,6 +183,7 @@ def get_gv_by_gv(self):
             "Use attribute, Conductivity.gv_by_gv "
             "instead of Conductivity.get_gv_by_gv().",
             DeprecationWarning,
+            stacklevel=2,
         )
         return self.gv_by_gv
 
@@ -413,6 +418,7 @@ def get_mesh_numbers(self):
             "Use attribute, Conductivity.mesh_numbers "
             "instead of Conductivity.get_mesh_numbers().",
             DeprecationWarning,
+            stacklevel=2,
         )
         return self.mesh_numbers
 
@@ -440,6 +446,7 @@ def get_frequencies(self):
             "Use attribute, Conductivity.frequencies "
             "instead of Conductivity.get_frequencies().",
             DeprecationWarning,
+            stacklevel=2,
         )
         return self.frequencies
 
@@ -458,6 +465,7 @@ def get_qpoints(self):
             "Use attribute, Conductivity.qpoints "
             "instead of Conductivity.get_qpoints().",
             DeprecationWarning,
+            stacklevel=2,
         )
         return self.qpoints
 
@@ -480,6 +488,7 @@ def get_grid_points(self):
             "Use attribute, Conductivity.grid_points "
             "instead of Conductivity.get_grid_points().",
             DeprecationWarning,
+            stacklevel=2,
         )
         return self.grid_points
 
@@ -494,6 +503,7 @@ def get_grid_weights(self):
             "Use attribute, Conductivity.grid_weights "
             "instead of Conductivity.get_grid_weights().",
             DeprecationWarning,
+            stacklevel=2,
         )
         return self.grid_weights
 
@@ -513,6 +523,7 @@ def get_temperatures(self):
             "Use attribute, Conductivity.temperatures "
             "instead of Conductivity.get_temperatures().",
             DeprecationWarning,
+            stacklevel=2,
         )
         return self.temperatures
 
@@ -522,6 +533,7 @@ def set_temperatures(self, temperatures):
             "Use attribute, Conductivity.temperatures "
             "instead of Conductivity.set_temperatures().",
             DeprecationWarning,
+            stacklevel=2,
         )
         self.temperatures = temperatures
 
@@ -540,6 +552,7 @@ def get_gamma(self):
         warnings.warn(
             "Use attribute, Conductivity.gamma " "instead of Conductivity.get_gamma().",
             DeprecationWarning,
+            stacklevel=2,
         )
         return self.gamma
 
@@ -548,6 +561,7 @@ def set_gamma(self, gamma):
         warnings.warn(
             "Use attribute, Conductivity.gamma " "instead of Conductivity.set_gamma().",
             DeprecationWarning,
+            stacklevel=2,
         )
         self.gamma = gamma
 
@@ -567,6 +581,7 @@ def get_gamma_isotope(self):
             "Use attribute, Conductivity.gamma_isotope "
             "instead of Conductivity.get_gamma_isotope().",
             DeprecationWarning,
+            stacklevel=2,
         )
         return self.gamma_isotope
 
@@ -576,6 +591,7 @@ def set_gamma_isotope(self, gamma_iso):
             "Use attribute, Conductivity.gamma_isotope "
             "instead of Conductivity.set_gamma_isotope().",
             DeprecationWarning,
+            stacklevel=2,
         )
         self.gamma_isotope = gamma_iso
 
@@ -590,6 +606,7 @@ def get_sigmas(self):
             "Use attribute, Conductivity.sigmas "
             "instead of Conductivity.get_sigmas().",
             DeprecationWarning,
+            stacklevel=2,
         )
         return self.sigmas
 
@@ -604,6 +621,7 @@ def get_sigma_cutoff_width(self):
             "Use attribute, Conductivity.sigma_cutoff_width "
             "instead of Conductivity.get_sigma_cutoff_width().",
             DeprecationWarning,
+            stacklevel=2,
         )
         return self.sigma_cutoff_width
 
@@ -618,6 +636,7 @@ def get_grid_point_count(self):
             "Use attribute, Conductivity.grid_point_count "
             "instead of Conductivity.get_grid_point_count().",
             DeprecationWarning,
+            stacklevel=2,
         )
         return self.grid_point_count
 
@@ -632,6 +651,7 @@ def get_averaged_pp_interaction(self):
             "Use attribute, Conductivity.averaged_pp_interaction "
             "instead of Conductivity.get_averaged_pp_interaction().",
             DeprecationWarning,
+            stacklevel=2,
         )
         return self.averaged_pp_interaction
 

phono3py/conductivity/direct_solution.py

@@ -56,9 +56,9 @@
     get_conversion_factor_WTE,
 )
 from phono3py.file_IO import read_pp_from_hdf5
+from phono3py.phonon.grid import get_grid_points_by_rotations
 from phono3py.phonon3.collision_matrix import CollisionMatrix
 from phono3py.phonon3.interaction import Interaction, all_bands_exist
-from phono3py.phonon.grid import get_grid_points_by_rotations
 
 
 class ConductivityLBTEBase(ConductivityBase):
@@ -163,6 +163,7 @@ def get_collision_matrix(self):
             "Use attribute, Conductivity_LBTE.collision_matrix "
             "instead of Conductivity_LBTE.get_collision_matrix().",
             DeprecationWarning,
+            stacklevel=2,
         )
         return self.collision_matrix
 
@@ -172,6 +173,7 @@ def set_collision_matrix(self, collision_matrix):
             "Use attribute, Conductivity_LBTE.collision_matrix "
             "instead of Conductivity_LBTE.set_collision_matrix().",
             DeprecationWarning,
+            stacklevel=2,
         )
         self.collision_matrix = collision_matrix
 
@@ -517,9 +519,9 @@ def _set_collision_matrix_at_sigmas(self, i_gp):
                 else:
                     i_data = 0
                 self._gamma[j, k, i_data] = self._collision.imag_self_energy
-                self._collision_matrix[j, k, i_data] = (
-                    self._collision.get_collision_matrix()
-                )
+                self._collision_matrix[
+                    j, k, i_data
+                ] = self._collision.get_collision_matrix()
 
     def _prepare_collision_matrix(self):
         """Collect pieces and construct collision matrix."""
@@ -1271,6 +1273,7 @@ def get_kappa_RTA(self):
             "Use attribute, Conductivity_LBTE.kappa_RTA "
             "instead of Conductivity_LBTE.get_kappa_RTA().",
             DeprecationWarning,
+            stacklevel=2,
         )
         return self.kappa_RTA
 
@@ -1285,6 +1288,7 @@ def get_mode_kappa_RTA(self):
             "Use attribute, Conductivity_LBTE.mode_kappa_RTA "
             "instead of Conductivity_LBTE.get_mode_kappa_RTA().",
             DeprecationWarning,
+            stacklevel=2,
         )
         return self.mode_kappa_RTA
 

phono3py/conductivity/rta.py

@@ -54,9 +54,9 @@
 )
 from phono3py.file_IO import read_pp_from_hdf5
 from phono3py.other.tetrahedron_method import get_tetrahedra_relative_grid_address
+from phono3py.phonon.grid import get_grid_points_by_rotations
 from phono3py.phonon3.imag_self_energy import ImagSelfEnergy, average_by_degeneracy
 from phono3py.phonon3.interaction import Interaction, all_bands_exist
-from phono3py.phonon.grid import get_grid_points_by_rotations
 
 
 class ConductivityRTABase(ConductivityBase):
@@ -298,9 +298,9 @@ def _set_gamma_at_sigmas(self, i):
                     self._gamma_N[j, k, i] = g_N
                     self._gamma_U[j, k, i] = g_U
                 if self._is_gamma_detail:
-                    self._gamma_detail_at_q[k] = (
-                        self._collision.get_detailed_imag_self_energy()
-                    )
+                    self._gamma_detail_at_q[
+                        k
+                    ] = self._collision.get_detailed_imag_self_energy()
 
     def _set_gamma_at_sigmas_lowmem(self, i):
         """Calculate gamma without storing ph-ph interaction strength.
@@ -921,7 +921,7 @@ def _set_kappa_at_sigmas(self, j, k, i_gp, i_band, g_sum, frequencies):
                 return
 
             g = g_sum[i_band] + g_sum[j_band]
-            for i_pair, (a, b) in enumerate(
+            for i_pair, _ in enumerate(
                 ([0, 0], [1, 1], [2, 2], [1, 2], [0, 2], [0, 1])
             ):
                 old_settings = np.seterr(all="raise")

phono3py/conductivity/utils.py

@@ -34,7 +34,6 @@
 # ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 # POSSIBILITY OF SUCH DAMAGE.
 
-
 import sys
 from typing import TYPE_CHECKING, Optional, Union
 
@@ -367,7 +366,7 @@ def write_gamma_detail(
         all_triplets = get_all_triplets(gp, interaction.bz_grid)
 
         if all_bands_exist(interaction):
-            for j, sigma in enumerate(sigmas):
+            for sigma in sigmas:
                 write_gamma_detail_to_hdf5(
                     temperatures,
                     mesh,
@@ -384,7 +383,7 @@ def write_gamma_detail(
                     verbose=verbose,
                 )
         else:
-            for j, sigma in enumerate(sigmas):
+            for sigma in sigmas:
                 for k, bi in enumerate(interaction.get_band_indices()):
                     write_gamma_detail_to_hdf5(
                         temperatures,
@@ -871,7 +870,7 @@ def kappa_RTA(br: "ConductivityRTA", log_level):
                     ("#%6s       " + " %-10s" * 6)
                     % ("T(K)", "xx", "yy", "zz", "yz", "xz", "xy")
                 )
-                for j, (t, k) in enumerate(zip(temperatures, kappa[i])):
+                for t, k in zip(temperatures, kappa[i]):
                     print(("%7.1f " + " %10.3f" * 6) % ((t,) + tuple(k)))
             print("")
 
@@ -936,13 +935,13 @@ def kappa_Wigner_RTA(br: "ConductivityWignerRTA", log_level):
                     % ("      \t   T(K)", "xx", "yy", "zz", "yz", "xz", "xy")
                 )
                 if kappa_P_RTA is not None:
-                    for j, (t, k) in enumerate(zip(temperatures, kappa_P_RTA[i])):
+                    for t, k in zip(temperatures, kappa_P_RTA[i]):
                         print("K_P\t" + ("%7.1f " + " %10.3f" * 6) % ((t,) + tuple(k)))
                     print(" ")
-                    for j, (t, k) in enumerate(zip(temperatures, kappa_C[i])):
+                    for t, k in zip(temperatures, kappa_C[i]):
                         print("K_C\t" + ("%7.1f " + " %10.3f" * 6) % ((t,) + tuple(k)))
                 print(" ")
-                for j, (t, k) in enumerate(zip(temperatures, kappa_TOT_RTA[i])):
+                for t, k in zip(temperatures, kappa_TOT_RTA[i]):
                     print("K_T\t" + ("%7.1f " + " %10.3f" * 6) % ((t,) + tuple(k)))
             print("")