Remove abinit __all__ module star exports (#804)

* refactor CommonEosMaker

* ruff auto-fixes including removing __all__ module star exports

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ default_language_version:
 exclude: ^(.github/|tests/test_data/abinit/)
 repos:
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.3.4
+  rev: v0.3.5
   hooks:
   - id: ruff
     args: [--fix]

src/atomate2/abinit/files.py

@@ -21,13 +21,6 @@
 
     from atomate2.abinit.sets.base import AbinitInputGenerator
 
-__all__ = [
-    "out_to_in",
-    "fname2ext",
-    "load_abinit_input",
-    "write_abinit_input_set",
-]
-
 
 logger = logging.getLogger(__name__)
 

src/atomate2/abinit/jobs/core.py

@@ -34,8 +34,6 @@
 
 logger = logging.getLogger(__name__)
 
-__all__ = ["StaticMaker", "NonSCFMaker", "RelaxMaker"]
-
 
 @dataclass
 class StaticMaker(BaseAbinitMaker):

src/atomate2/abinit/sets/base.py

@@ -43,7 +43,6 @@
 
     from pymatgen.core.structure import Structure
 
-__all__ = ["AbinitInputSet", "AbinitInputGenerator"]
 
 logger = logging.getLogger(__name__)
 
@@ -99,7 +98,7 @@ def write_input(
             zip_inputs=zip_inputs,
         )
         del self.inputs["abinit_input.json"]
-        indir, outdir, tmpdir = self.set_workdir(workdir=directory)
+        indir, _outdir, _tmpdir = self.set_workdir(workdir=directory)
 
         if self.input_files:
             out_to_in(
@@ -718,7 +717,7 @@ def _get_kpoints(
         if kconfig.get("line_density"):
             # handle line density generation
             kpath = HighSymmKpath(structure, **kconfig.get("kpath_kwargs", {}))
-            frac_k_points, k_points_labels = kpath.get_kpoints(
+            frac_k_points, _k_points_labels = kpath.get_kpoints(
                 line_density=kconfig["line_density"], coords_are_cartesian=False
             )
             base_kpoints = KSampling(

src/atomate2/abinit/sets/core.py

@@ -23,14 +23,8 @@
     from pymatgen.io.abinit import PseudoTable
     from pymatgen.io.abinit.abiobjects import KSampling
 
-__all__ = [
-    "StaticSetGenerator",
-    "NonSCFSetGenerator",
-    "RelaxSetGenerator",
-]
 
-
-GS_RESTART_FROM_DEPS: tuple = (f"{SCF}|{RELAX}|{MOLECULAR_DYNAMICS}:WFK|DEN",)
+GS_RESTART_FROM_DEPS = (f"{SCF}|{RELAX}|{MOLECULAR_DYNAMICS}:WFK|DEN",)
 
 
 @dataclass
@@ -123,13 +117,13 @@ def _get_nband(self, prev_outputs: list[str] | None) -> int:
                 f"Should have exactly one previous output. Found {len(abinit_inputs)}"
             )
         previous_abinit_input = next(iter(abinit_inputs.values()))
-        nband = previous_abinit_input.get(
+        n_band = previous_abinit_input.get(
             "nband",
             previous_abinit_input.structure.num_valence_electrons(
                 previous_abinit_input.pseudos
             ),
         )
-        return int(np.ceil(nband * self.nbands_factor))
+        return int(np.ceil(n_band * self.nbands_factor))
 
 
 @dataclass
@@ -154,7 +148,7 @@ class NonScfWfqInputGenerator(AbinitInputGenerator):
 
     calc_type: str = "nscf_wfq"
 
-    wfq_tol: dict = field(default_factory=lambda: {"tolwfr": 1.0e-18})
+    wfq_tol: dict = field(default_factory=lambda: {"tolwfr": 1e-18})
 
     restart_from_deps: tuple = (f"{NSCF}:WFQ",)
     prev_outputs_deps: tuple = (f"{SCF}:DEN",)
@@ -201,7 +195,7 @@ class RelaxSetGenerator(AbinitInputGenerator):
     factory: Callable = ion_ioncell_relax_input
     restart_from_deps: tuple = GS_RESTART_FROM_DEPS
     relax_cell: bool = True
-    tolmxf: float = 5.0e-5
+    tolmxf: float = 5e-5
 
     def get_abinit_input(
         self,

src/atomate2/common/flows/eos.py

@@ -36,7 +36,7 @@ class CommonEosMaker(Maker):
     initial_relax_maker : .Maker | None
         Maker to relax the input structure, defaults to None (no initial relaxation).
     eos_relax_maker : .Maker
-        Maker to relax deformationed structures for the EOS fit.
+        Maker to relax deformed structures for the EOS fit.
     static_maker : .Maker | None
         Maker to generate statics after each relaxation, defaults to None.
     strain : tuple[float]
@@ -122,19 +122,19 @@ def make(self, structure: Structure, prev_dir: str | Path = None) -> Flow:
         if self.initial_relax_maker:
             # Cell without applied strain already included from relax/equilibrium steps.
             # Perturb this point (or these points) if included
-            zero_strain_mask = np.abs(strain_l) < 1.0e-15
+            zero_strain_mask = np.abs(strain_l) < 1e-15
             if np.any(zero_strain_mask):
                 nzs = len(strain_l[zero_strain_mask])
                 shift = strain_delta / (nzs + 1.0) * np.linspace(-1.0, 1.0, nzs)
-                strain_l[np.abs(strain_l) < 1.0e-15] += shift
+                strain_l[np.abs(strain_l) < 1e-15] += shift
 
         deformation_l = [(np.identity(3) * (1.0 + eps)).tolist() for eps in strain_l]
 
         # apply strain to structures, return list of transformations
         transformations = apply_strain_to_structure(structure, deformation_l)
         jobs["utility"] += [transformations]
 
-        for idef in range(self.number_of_frames):
+        for frame_idx in range(self.number_of_frames):
             if self._store_transformation_information:
                 with contextlib.suppress(Exception):
                     # write details of the transformation to the
@@ -144,44 +144,46 @@ def make(self, structure: Structure, prev_dir: str | Path = None) -> Flow:
                     # is automatically converted to a "." in the filename.
                     self.eos_relax_maker.write_additional_data[
                         "transformations:json"
-                    ] = transformations.output[idef]
+                    ] = transformations.output[frame_idx]
 
             relax_job = self.eos_relax_maker.make(
-                structure=transformations.output[idef].final_structure,
+                structure=transformations.output[frame_idx].final_structure,
                 prev_dir=prev_dir,
             )
-            relax_job.name += f" deformation {idef}"
+            relax_job.name += f" deformation {frame_idx}"
             jobs["relax"].append(relax_job)
 
             if self.static_maker:
                 static_job = self.static_maker.make(
                     structure=relax_job.output.structure,
                     prev_dir=relax_job.output.dir_name,
                 )
-                static_job.name += f" {idef}"
+                static_job.name += f" {frame_idx}"
                 jobs["static"].append(static_job)
 
         for key in job_types:
-            for i in range(len(jobs[key])):
-                flow_output[key]["energy"].append(jobs[key][i].output.output.energy)
-                flow_output[key]["volume"].append(jobs[key][i].output.structure.volume)
-                flow_output[key]["stress"].append(jobs[key][i].output.output.stress)
+            for idx in range(len(jobs[key])):
+                output = jobs[key][idx].output.output
+                flow_output[key]["energy"] += [output.energy]
+                flow_output[key]["volume"] += [output.structure.volume]
+                flow_output[key]["stress"] += [output.stress]
 
         if self.postprocessor is not None:
-            if len(jobs["relax"]) < self.postprocessor.min_data_points:
+            min_points = self.postprocessor.min_data_points
+            if len(jobs["relax"]) < min_points:
                 raise ValueError(
                     "To perform least squares EOS fit with "
-                    f"{self.postprocessor.__class__}, you must specify "
-                    f"self.number_of_frames >= {self.postprocessor.min_data_points}."
+                    f"{type(self.postprocessor).__name__}, you must specify "
+                    f"self.number_of_frames >= {min_points}."
                 )
 
-            postprocess = self.postprocessor.make(flow_output)
-            postprocess.name = self.name + " postprocessing"
-            flow_output = postprocess.output
-            jobs["utility"] += [postprocess]
+            post_process = self.postprocessor.make(flow_output)
+            post_process.name = self.name + " postprocessing"
+            flow_output = post_process.output
+            jobs["utility"] += [post_process]
 
-        joblist = []
+        job_list = []
         for key in jobs:
-            joblist += jobs[key]
+            job_list += jobs[key]
 
-        return Flow(jobs=joblist, output=flow_output, name=self.name)
+        return Flow(jobs=job_list, output=flow_output, name=self.name)

src/atomate2/qchem/sets/base.py

@@ -71,7 +71,7 @@ def write_input(
         for k, v in inputs.items():
             if v is not None and (overwrite or not (directory / k).exists()):
                 with zopen(directory / k, "wt") as f:
-                    f.write(v.__str__())
+                    f.write(str(v))
             elif not overwrite and (directory / k).exists():
                 raise FileExistsError(f"{directory / k} already exists.")
 

src/atomate2/vasp/jobs/eos.py

@@ -51,9 +51,11 @@
 if TYPE_CHECKING:
     from atomate2.vasp.sets.base import VaspInputGenerator
 
-# No prefix, base atomate 2 parameters
+
+copy_wavecar = lambda: {"additional_vasp_files": ("WAVECAR",)}  # noqa: E731
 
 
+# No prefix, base atomate 2 parameters
 @dataclass
 class EosRelaxMaker(BaseVaspMaker):
     """
@@ -85,14 +87,10 @@ class EosRelaxMaker(BaseVaspMaker):
 
     name: str = "EOS GGA relax"
     input_set_generator: VaspInputGenerator = field(default_factory=EosSetGenerator)
-    copy_vasp_kwargs: dict = field(
-        default_factory=lambda: {"additional_vasp_files": ("WAVECAR",)}
-    )
+    copy_vasp_kwargs: dict = field(default_factory=copy_wavecar)
 
 
 # MPLegacy prefix, legacy MP PBE-GGA
-
-
 @dataclass
 class MPLegacyEosRelaxMaker(BaseVaspMaker):
     """
@@ -126,9 +124,7 @@ class MPLegacyEosRelaxMaker(BaseVaspMaker):
     input_set_generator: VaspInputGenerator = field(
         default_factory=MPLegacyEosRelaxSetGenerator
     )
-    copy_vasp_kwargs: dict = field(
-        default_factory=lambda: {"additional_vasp_files": ("WAVECAR",)}
-    )
+    copy_vasp_kwargs: dict = field(default_factory=copy_wavecar)
 
 
 @dataclass
@@ -164,14 +160,10 @@ class MPLegacyEosStaticMaker(BaseVaspMaker):
     input_set_generator: VaspInputGenerator = field(
         default_factory=MPLegacyEosStaticSetGenerator
     )
-    copy_vasp_kwargs: dict = field(
-        default_factory=lambda: {"additional_vasp_files": ("WAVECAR",)}
-    )
+    copy_vasp_kwargs: dict = field(default_factory=copy_wavecar)
 
 
 # MPGGA prefix, MP PBE-GGA compatible parameters
-
-
 @dataclass
 class MPGGAEosRelaxMaker(BaseVaspMaker):
     """
@@ -205,9 +197,7 @@ class MPGGAEosRelaxMaker(BaseVaspMaker):
     input_set_generator: VaspInputGenerator = field(
         default_factory=MPGGAEosRelaxSetGenerator
     )
-    copy_vasp_kwargs: dict = field(
-        default_factory=lambda: {"additional_vasp_files": ("WAVECAR",)}
-    )
+    copy_vasp_kwargs: dict = field(default_factory=copy_wavecar)
 
 
 @dataclass
@@ -243,14 +233,10 @@ class MPGGAEosStaticMaker(BaseVaspMaker):
     input_set_generator: VaspInputGenerator = field(
         default_factory=MPGGAEosStaticSetGenerator
     )
-    copy_vasp_kwargs: dict = field(
-        default_factory=lambda: {"additional_vasp_files": ("WAVECAR",)}
-    )
+    copy_vasp_kwargs: dict = field(default_factory=copy_wavecar)
 
 
 # MPMetaGGA prefix, MP r2SCAN-meta-GGA compatible
-
-
 @dataclass
 class MPMetaGGAEosPreRelaxMaker(BaseVaspMaker):
     """
@@ -319,9 +305,7 @@ class MPMetaGGAEosRelaxMaker(BaseVaspMaker):
     input_set_generator: VaspInputGenerator = field(
         default_factory=MPMetaGGAEosRelaxSetGenerator
     )
-    copy_vasp_kwargs: dict = field(
-        default_factory=lambda: {"additional_vasp_files": ("WAVECAR",)}
-    )
+    copy_vasp_kwargs: dict = field(default_factory=copy_wavecar)
 
 
 @dataclass
@@ -357,6 +341,4 @@ class MPMetaGGAEosStaticMaker(BaseVaspMaker):
     input_set_generator: VaspInputGenerator = field(
         default_factory=MPMetaGGAEosStaticSetGenerator
     )
-    copy_vasp_kwargs: dict = field(
-        default_factory=lambda: {"additional_vasp_files": ("WAVECAR",)}
-    )
+    copy_vasp_kwargs: dict = field(default_factory=copy_wavecar)