add ruff formatter

.ci_support/release.py

@@ -1,12 +1,19 @@
 def get_setup_version_and_pattern(setup_content):
     depend_lst, version_lst = [], []
     for l in setup_content:
-        if '==' in l:
-            lst = l.split('[')[-1].split(']')[0].replace(' ', '').replace('"', '').replace("'", '').split(',')
+        if "==" in l:
+            lst = (
+                l.split("[")[-1]
+                .split("]")[0]
+                .replace(" ", "")
+                .replace('"', "")
+                .replace("'", "")
+                .split(",")
+            )
             for dep in lst:
-                if dep != '\n':
-                    version_lst.append(dep.split('==')[1])
-                    depend_lst.append(dep.split('==')[0])
+                if dep != "\n":
+                    version_lst.append(dep.split("==")[1])
+                    depend_lst.append(dep.split("==")[0])
 
     version_high_dict = {d: v for d, v in zip(depend_lst, version_lst)}
     return version_high_dict
@@ -16,14 +23,14 @@ def get_env_version(env_content):
     read_flag = False
     depend_lst, version_lst = [], []
     for l in env_content:
-        if 'dependencies:' in l:
+        if "dependencies:" in l:
             read_flag = True
         elif read_flag:
-            lst = l.replace('-', '').replace(' ', '').replace('\n', '').split("=")
+            lst = l.replace("-", "").replace(" ", "").replace("\n", "").split("=")
             if len(lst) == 2:
                 depend_lst.append(lst[0])
                 version_lst.append(lst[1])
-    return {d:v for d, v in zip(depend_lst, version_lst)}
+    return {d: v for d, v in zip(depend_lst, version_lst)}
 
 
 def update_dependencies(setup_content, version_low_dict, version_high_dict):
@@ -35,27 +42,29 @@ def update_dependencies(setup_content, version_low_dict, version_high_dict):
             version_combo_dict[dep] = dep + "==" + ver
 
     setup_content_new = ""
-    pattern_dict = {d:d + "==" + v for d, v in version_high_dict.items()}
+    pattern_dict = {d: d + "==" + v for d, v in version_high_dict.items()}
     for l in setup_content:
         for k, v in pattern_dict.items():
             if v in l:
                 l = l.replace(v, version_combo_dict[k])
-        setup_content_new +=l
+        setup_content_new += l
     return setup_content_new
 
 
 if __name__ == "__main__":
-    with open('pyproject.toml', "r") as f:
+    with open("pyproject.toml", "r") as f:
         setup_content = f.readlines()
 
-    with open('environment.yml', "r") as f:
+    with open("environment.yml", "r") as f:
         env_content = f.readlines()
 
     setup_content_new = update_dependencies(
         setup_content=setup_content[2:],
         version_low_dict=get_env_version(env_content=env_content),
-        version_high_dict=get_setup_version_and_pattern(setup_content=setup_content[2:]),
+        version_high_dict=get_setup_version_and_pattern(
+            setup_content=setup_content[2:]
+        ),
     )
 
-    with open('pyproject.toml', "w") as f:
+    with open("pyproject.toml", "w") as f:
         f.writelines("".join(setup_content[:2]) + setup_content_new)

.pre-commit-config.yaml

@@ -0,0 +1,10 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.4
+    hooks:
+      - id: ruff
+        name: ruff lint
+        args: ["--fix"]
+        files: ^atomistics/
+      - id: ruff-format
+        name: ruff format

atomistics/calculators/__init__.py

@@ -42,3 +42,31 @@
     )
 except ImportError:
     pass
+
+
+__all__ = [
+    calc_molecular_dynamics_langevin_with_ase,
+    calc_molecular_dynamics_npt_with_ase,
+    calc_molecular_dynamics_thermal_expansion_with_ase,
+    calc_static_with_ase,
+    evaluate_with_ase,
+    optimize_positions_with_ase,
+    optimize_positions_and_volume_with_ase,
+    evaluate_with_hessian,
+    calc_static_with_qe,
+    evaluate_with_qe,
+    optimize_positions_and_volume_with_qe,
+    calc_molecular_dynamics_thermal_expansion_with_lammps,
+    calc_molecular_dynamics_nph_with_lammps,
+    calc_molecular_dynamics_npt_with_lammps,
+    calc_molecular_dynamics_nvt_with_lammps,
+    calc_molecular_dynamics_langevin_with_lammps,
+    calc_static_with_lammps,
+    evaluate_with_lammps,
+    evaluate_with_lammps_library,
+    get_potential_dataframe,
+    get_potential_by_name,
+    optimize_positions_and_volume_with_lammps,
+    optimize_positions_with_lammps,
+    calc_molecular_dynamics_phonons_with_lammps,
+]

atomistics/calculators/interface.py

@@ -1,5 +1,5 @@
 from enum import Enum
-from typing import NewType, Union, Any, TYPE_CHECKING
+from typing import Union, Any, TYPE_CHECKING
 
 # best would be StrEnum from py3.11
 import sys

atomistics/calculators/lammps/__init__.py

@@ -21,3 +21,20 @@
     )
 except ImportError:
     pass
+
+
+__all__ = [
+    calc_molecular_dynamics_thermal_expansion_with_lammps,
+    calc_molecular_dynamics_nph_with_lammps,
+    calc_molecular_dynamics_npt_with_lammps,
+    calc_molecular_dynamics_nvt_with_lammps,
+    calc_molecular_dynamics_langevin_with_lammps,
+    calc_static_with_lammps,
+    evaluate_with_lammps,
+    evaluate_with_lammps_library,
+    optimize_positions_and_volume_with_lammps,
+    optimize_positions_with_lammps,
+    get_potential_dataframe,
+    get_potential_by_name,
+    calc_molecular_dynamics_phonons_with_lammps,
+]

atomistics/calculators/lammps/helpers.py

@@ -41,8 +41,8 @@ def lammps_run(
         lmp.interactive_lib_command(c)
 
     if input_template is not None:
-        for l in input_template.split("\n"):
-            lmp.interactive_lib_command(l)
+        for line in input_template.split("\n"):
+            lmp.interactive_lib_command(line)
 
     return lmp
 
@@ -131,8 +131,8 @@ def lammps_thermal_expansion_loop(
             Pstop=Pstop,
             Pdamp=Pdamp,
         )
-        for l in run_str_rendered.split("\n"):
-            lmp_instance.interactive_lib_command(l)
+        for line in run_str_rendered.split("\n"):
+            lmp_instance.interactive_lib_command(line)
         volume_md_lst.append(lmp_instance.interactive_volume_getter())
         temperature_md_lst.append(lmp_instance.interactive_temperatures_getter())
     lammps_shutdown(lmp_instance=lmp_instance, close_instance=lmp is None)

atomistics/calculators/lammps/potential.py

@@ -290,18 +290,18 @@ def update_potential_paths(
         ]
         potential_dict = {os.path.basename(f): f for f in potential_file_path_lst}
         potential_commands = []
-        for l in row.Config:
-            l = l.replace("\n", "")
+        for line in row.Config:
+            line = line.replace("\n", "")
             for key, value in potential_dict.items():
-                l = l.replace(key, value)
-            potential_commands.append(l)
+                line = line.replace(key, value)
+            potential_commands.append(line)
         config_lst.append(potential_commands)
     df_pot["Config"] = config_lst
     return df_pot
 
 
 def get_resource_path_from_conda(
-    env_variables: tuple[str] = ("CONDA_PREFIX", "CONDA_DIR")
+    env_variables: tuple[str] = ("CONDA_PREFIX", "CONDA_DIR"),
 ) -> str:
     env = os.environ
     for conda_var in env_variables:

atomistics/calculators/wrapper.py

@@ -5,17 +5,15 @@
 
 from __future__ import annotations
 
-from typing import NewType, Union, Any, TYPE_CHECKING
+from typing import TYPE_CHECKING
 
 from atomistics.calculators.interface import TaskEnum, TaskOutputEnum
 
 if TYPE_CHECKING:
     from ase import Atoms
     from atomistics.calculators.interface import (
         TaskName,
-        TaskSpec,
         TaskDict,
-        TaskResults,
         ResultsDict,
         SimpleEvaluator,
     )

atomistics/workflows/__init__.py

@@ -14,3 +14,15 @@
     from atomistics.workflows.quasiharmonic import QuasiHarmonicWorkflow
 except ImportError:
     pass
+
+
+__all__ = [
+    ElasticMatrixWorkflow,
+    EnergyVolumeCurveWorkflow,
+    LangevinWorkflow,
+    calc_molecular_dynamics_thermal_expansion,
+    optimize_positions,
+    optimize_positions_and_volume,
+    PhonopyWorkflow,
+    QuasiHarmonicWorkflow,
+]

atomistics/workflows/evcurve/fit.py

@@ -135,7 +135,8 @@ def fit_leastsq(
     """
     # http://stackoverflow.com/questions/14581358/getting-standard-errors-on-fitted-parameters-using-the-optimize-leastsq-method-i
 
-    errfunc = lambda p, x, y, fittype: fitfunction(p, x, fittype) - y
+    def errfunc(p, x, y, fittype):
+        return fitfunction(p, x, fittype) - y
 
     pfit, pcov, infodict, errmsg, success = scipy.optimize.leastsq(
         errfunc, p0, args=(datax, datay, fittype), full_output=1, epsfcn=0.0001
@@ -153,7 +154,7 @@ def fit_leastsq(
     for i in range(len(pfit)):
         try:
             error.append(np.absolute(pcov[i][i]) ** 0.5)
-        except:
+        except TypeError:
             error.append(0.00)
     pfit_leastsq = pfit
     perr_leastsq = np.array(error)

atomistics/workflows/evcurve/thermo.py

@@ -269,7 +269,7 @@ def get_minimum_energy_path(self, pressure: np.ndarray = None) -> np.ndarray:
 
         """
         if pressure is not None:
-            raise NotImplemented()
+            raise NotImplementedError()
         v_min_lst = []
         for c in self._coeff.T:
             v_min = np.roots(np.polyder(c, 1))

atomistics/workflows/evcurve/workflow.py

@@ -9,7 +9,6 @@
     OutputThermodynamic,
 )
 from atomistics.workflows.evcurve.helper import (
-    get_volume_lst,
     generate_structures_helper,
     analyse_structures_helper,
 )

atomistics/workflows/phonons/units.py

@@ -1,5 +1,4 @@
 import scipy.constants
-from phonopy.units import VaspToTHz, THzToEv, EvTokJmol
 
 kJ_mol_to_eV = 1000 / scipy.constants.Avogadro / scipy.constants.electron_volt
 kb = scipy.constants.physical_constants["Boltzmann constant in eV/K"][0]

setup.py

@@ -5,4 +5,4 @@
 setup(
     version=versioneer.get_version(),
     cmdclass=versioneer.get_cmdclass(),
-)
+)

tests/test_ase_interface/test_ase_md_mace.py

@@ -19,10 +19,7 @@ class TestASEMD(unittest.TestCase):
     def test_ase_langevin(self):
         structure = bulk("Al", cubic=True).repeat([2, 2, 2])
         ase_calculator = mace_mp(
-            model="medium",
-            dispersion=False,
-            default_dtype="float32",
-            device='cpu'
+            model="medium", dispersion=False, default_dtype="float32", device="cpu"
         )
         result_dict = calc_molecular_dynamics_langevin_with_ase(
             structure=structure,
@@ -37,9 +34,9 @@ def test_ase_langevin(self):
         self.assertEqual(result_dict["velocities"].shape, (10, 32, 3))
         self.assertEqual(result_dict["cell"].shape, (10, 3, 3))
         self.assertEqual(result_dict["forces"].shape, (10, 32, 3))
-        self.assertEqual(result_dict["temperature"].shape, (10, ))
-        self.assertEqual(result_dict["energy_pot"].shape, (10, ))
-        self.assertEqual(result_dict["energy_tot"].shape, (10, ))
+        self.assertEqual(result_dict["temperature"].shape, (10,))
+        self.assertEqual(result_dict["energy_pot"].shape, (10,))
+        self.assertEqual(result_dict["energy_tot"].shape, (10,))
         self.assertEqual(result_dict["pressure"].shape, (10, 3, 3))
         self.assertTrue(result_dict["temperature"][-1] > 25)
-        self.assertTrue(result_dict["temperature"][-1] < 75)
+        self.assertTrue(result_dict["temperature"][-1] < 75)

tests/test_ase_interface/test_ase_md_matgl.py

@@ -33,9 +33,9 @@ def test_ase_langevin(self):
         self.assertEqual(result_dict["velocities"].shape, (10, 32, 3))
         self.assertEqual(result_dict["cell"].shape, (10, 3, 3))
         self.assertEqual(result_dict["forces"].shape, (10, 32, 3))
-        self.assertEqual(result_dict["temperature"].shape, (10, ))
-        self.assertEqual(result_dict["energy_pot"].shape, (10, ))
-        self.assertEqual(result_dict["energy_tot"].shape, (10, ))
+        self.assertEqual(result_dict["temperature"].shape, (10,))
+        self.assertEqual(result_dict["energy_pot"].shape, (10,))
+        self.assertEqual(result_dict["energy_tot"].shape, (10,))
         self.assertEqual(result_dict["pressure"].shape, (10, 3, 3))
         self.assertTrue(result_dict["temperature"][-1] > 25)
-        self.assertTrue(result_dict["temperature"][-1] < 75)
+        self.assertTrue(result_dict["temperature"][-1] < 75)

tests/test_ase_interface/test_elastic_ase_gpaw.py

@@ -23,18 +23,20 @@ def test_calc_elastic(self):
             num_of_point=5,
             eps_range=0.05,
             sqrt_eta=True,
-            fit_order=2
+            fit_order=2,
         )
         task_dict = workflow.generate_structures()
         result_dict = evaluate_with_ase(
             task_dict=task_dict,
-            ase_calculator=GPAW(
-                xc="PBE",
-                mode=PW(300),
-                kpts=(3, 3, 3)
-            )
+            ase_calculator=GPAW(xc="PBE", mode=PW(300), kpts=(3, 3, 3)),
         )
         elastic_dict = workflow.analyse_structures(output_dict=result_dict)
-        self.assertTrue(np.isclose(elastic_dict["elastic_matrix"][0, 0], 125.66807354, atol=1e-04))
-        self.assertTrue(np.isclose(elastic_dict["elastic_matrix"][0, 1], 68.41418321, atol=1e-04))
-        self.assertTrue(np.isclose(elastic_dict["elastic_matrix"][3, 3], 99.29916329, atol=1e-04))
+        self.assertTrue(
+            np.isclose(elastic_dict["elastic_matrix"][0, 0], 125.66807354, atol=1e-04)
+        )
+        self.assertTrue(
+            np.isclose(elastic_dict["elastic_matrix"][0, 1], 68.41418321, atol=1e-04)
+        )
+        self.assertTrue(
+            np.isclose(elastic_dict["elastic_matrix"][3, 3], 99.29916329, atol=1e-04)
+        )