lammpsparser 0.0.8__tar.gz → 0.0.10__tar.gz

{lammpsparser-0.0.8 → lammpsparser-0.0.10}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.4
+Metadata-Version: 2.5
 Name: lammpsparser
-Version: 0.0.8
+Version: 0.0.10
 Summary: Vector-oriented LAMMPS interface to rapidly iterate over series of atomistic structures or interatomic potentials.
 Project-URL: Homepage, https://github.com/pyiron/lammpsparser
 Project-URL: Documentation, https://github.com/pyiron/lammpsparser
@@ -50,11 +50,11 @@ Classifier: Programming Language :: Python :: 3.14
 Classifier: Topic :: Scientific/Engineering :: Physics
 Requires-Python: <3.15,>=3.9
 Requires-Dist: ase<=3.29.0,>=3.22.1
-Requires-Dist: numpy<=2.4.6,>=1.26.0
-Requires-Dist: pandas<=3.0.5,>=2.0.3
-Requires-Dist: scipy<=1.17.1,>=1.11.1
+Requires-Dist: numpy<=2.5.3,>=1.26.0
+Requires-Dist: pandas<=3.0.6,>=2.0.3
+Requires-Dist: scipy<=1.18.1,>=1.11.1
 Provides-Extra: compatibility
-Requires-Dist: structuretoolkit<=0.0.45,>=0.0.30; extra == 'compatibility'
+Requires-Dist: structuretoolkit<=0.0.47,>=0.0.30; extra == 'compatibility'
 Provides-Extra: h5md
 Requires-Dist: h5py<=3.16.0,>=3.9.0; extra == 'h5md'
 Description-Content-Type: text/markdown

{lammpsparser-0.0.8 → lammpsparser-0.0.10}/pyproject.toml

@@ -5,7 +5,7 @@ requires = [
     "h5py", 
     "pandas", 
     "scipy", 
-    "hatchling==1.31.0",
+    "hatchling==1.32.4",
     "hatch-vcs==0.5.0",
 ]
 build-backend = "hatchling.build"
@@ -35,9 +35,9 @@ classifiers = [
 ]
 dependencies = [
     "ase>=3.22.1,<=3.29.0",
-    "numpy>=1.26.0,<=2.4.6",
-    "pandas>=2.0.3,<=3.0.5",
-    "scipy>=1.11.1,<=1.17.1",
+    "numpy>=1.26.0,<=2.5.3",
+    "pandas>=2.0.3,<=3.0.6",
+    "scipy>=1.11.1,<=1.18.1",
 ]
 dynamic = ["version"]
 
@@ -48,7 +48,7 @@ Repository = "https://github.com/pyiron/lammpsparser"
 
 [project.optional-dependencies]
 h5md = ["h5py>=3.9.0,<=3.16.0"]
-compatibility = ["structuretoolkit>=0.0.30,<=0.0.45"]
+compatibility = ["structuretoolkit>=0.0.30,<=0.0.47"]
 
 [tool.hatch.build]
 include = [

{lammpsparser-0.0.8 → lammpsparser-0.0.10}/src/lammpsparser/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '0.0.8'
-__version_tuple__ = version_tuple = (0, 0, 8)
+__version__ = version = '0.0.10'
+__version_tuple__ = version_tuple = (0, 0, 10)
 
 __commit_id__ = commit_id = None

{lammpsparser-0.0.8 → lammpsparser-0.0.10}/src/lammpsparser/compatibility/calculate.py

@@ -245,10 +245,9 @@ def calc_minimize(
                     "No rotation matrix given while trying to convert pressure. "
                     "This is most likely due to no structure being defined."
                 )
-            else:
-                rotation_matrix, structure = _get_rotation_matrix(
-                    structure=structure, pressure=pressure
-                )
+            rotation_matrix, structure = _get_rotation_matrix(
+                structure=structure, pressure=pressure
+            )
         # force_skewed = False
         pressure = _pressure_to_lammps(
             pressure=pressure, rotation_matrix=rotation_matrix, units=units

{lammpsparser-0.0.8 → lammpsparser-0.0.10}/src/lammpsparser/compatibility/file.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import os
+import pathlib
 import shutil
 import subprocess
 from dataclasses import asdict
@@ -120,7 +121,7 @@ def lammps_file_interface_function(
             + " -in lmp.in"
         )
 
-    os.makedirs(working_directory, exist_ok=True)
+    pathlib.Path(working_directory).mkdir(exist_ok=True, parents=True)
     potential_lst, potential_replace, species = _get_potential(
         potential=potential, resource_path=resource_path
     )
@@ -233,7 +234,7 @@ def lammps_file_interface_function(
     if write_restart_file:
         lmp_str_lst.append(f"write_restart {os.path.basename(restart_file)}")
 
-    with open(os.path.join(working_directory, "lmp.in"), "w") as f:
+    with pathlib.Path(os.path.join(working_directory, "lmp.in")).open("w") as f:
         f.writelines([line + "\n" for line in lmp_str_lst])
 
     write_lammps_datafile(
@@ -344,8 +345,7 @@ def _modify_input_dict(
                 lmp_tmp_lst.append(k + " " + v)
 
         return lmp_tmp_lst
-    else:
-        return lmp_str_lst
+    return lmp_str_lst
 
 
 def _get_potential(potential, resource_path: str | None = None):

{lammpsparser-0.0.8 → lammpsparser-0.0.10}/src/lammpsparser/compatibility/structure.py

@@ -81,7 +81,7 @@ class LammpsStructureCompatibility(LammpsStructure):
 
         elements = self._structure.get_chemical_symbols()
 
-        ## Standard atoms stuff
+        # Standard atoms stuff
         atoms = "Atoms \n\n"
         # atom_style bond
         # format: atom-ID, molecule-ID, atom_type, x, y, z
@@ -117,7 +117,7 @@ class LammpsStructureCompatibility(LammpsStructure):
         else:
             raise ValueError("dimension 1 not yet implemented")
 
-        ## Bond related.
+        # Bond related.
         # This seems independent from the lammps atom type ids, because bonds only use atom ids
         el_list = set(self._structure.get_chemical_symbols())
         el_dict = OrderedDict()
@@ -199,10 +199,7 @@ class LammpsStructureCompatibility(LammpsStructure):
                 for species_name in set(self.structure.get_chemical_symbols())
             }
         else:
-            q_dict = {
-                species_name: 0.0
-                for species_name in set(self.structure.get_chemical_symbols())
-            }
+            q_dict = dict.fromkeys(set(self.structure.get_chemical_symbols()), 0.0)
 
         bonds_lst, angles_lst = [], []
         bond_type_lst, angle_type_lst = [], []

{lammpsparser-0.0.8 → lammpsparser-0.0.10}/src/lammpsparser/output.py

@@ -1,8 +1,10 @@
 from __future__ import annotations
 
 import os
+import pathlib
 import warnings
-from typing import Any, Callable
+from collections.abc import Callable
+from typing import Any
 
 import numpy as np
 import pandas as pd
@@ -200,7 +202,7 @@ def _parse_dump(
         RuntimeError: If an H5MD file is present but the prism is not orthorhombic.
         FileNotFoundError: If neither dump file exists.
     """
-    if os.path.isfile(dump_h5_full_file_name):
+    if pathlib.Path(dump_h5_full_file_name).is_file():
         if not _check_ortho_prism(prism=prism):
             raise RuntimeError(
                 "The Lammps output will not be mapped back onto the structure correctly."
@@ -208,7 +210,7 @@ def _parse_dump(
         return parse_raw_dump_from_h5md(
             file_name=dump_h5_full_file_name,
         )
-    elif os.path.exists(dump_out_full_file_name):
+    if pathlib.Path(dump_out_full_file_name).exists():
         return _collect_dump_from_text(
             file_name=dump_out_full_file_name,
             prism=prism,
@@ -216,10 +218,9 @@ def _parse_dump(
             potential_elements=potential_elements,
             remap_indices_funct=remap_indices_funct,
         )
-    else:
-        raise FileNotFoundError(
-            f"Neither {dump_h5_full_file_name} nor {dump_out_full_file_name} exist."
-        )
+    raise FileNotFoundError(
+        f"Neither {dump_h5_full_file_name} nor {dump_out_full_file_name} exist."
+    )
 
 
 def _collect_dump_from_text(
@@ -306,13 +307,12 @@ def _parse_log(
     Raises:
         (RuntimeError): If there are "ERROR" tags in the log.
     """
-    if os.path.exists(log_lammps_full_file_name):
+    if pathlib.Path(log_lammps_full_file_name).exists():
         return _collect_output_log(
             file_name=log_lammps_full_file_name,
             prism=prism,
         )
-    else:
-        return None, None, None
+    return None, None, None
 
 
 def _collect_output_log(

{lammpsparser-0.0.8 → lammpsparser-0.0.10}/src/lammpsparser/output_raw.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import pathlib
 import warnings
 from dataclasses import asdict, dataclass, field
 from io import StringIO
@@ -162,7 +163,7 @@ def parse_raw_dump_from_text(file_name: str) -> dict:
         - ``"positions"`` (list of numpy.ndarray): Wrapped fractional coordinates, shape ``(N, 3)``.
         - ``"computes"`` (dict): Per-atom compute results keyed by compute ID (``c_`` prefix stripped).
     """
-    with open(file_name, "r") as f:
+    with pathlib.Path(file_name).open("r") as f:
         dump = DumpData()
 
         for line in f:
@@ -302,7 +303,7 @@ def parse_raw_lammps_log(file_name: str) -> pd.DataFrame:
         are present a ``LogStep`` column (integer run index, 0-based) is
         appended.
     """
-    with open(file_name, "r") as f:
+    with pathlib.Path(file_name).open("r") as f:
         dfs = []
         read_thermo = False
         for line in f:

{lammpsparser-0.0.8 → lammpsparser-0.0.10}/src/lammpsparser/potential.py

@@ -277,8 +277,7 @@ class PotentialAvailable:
     def __getattr__(self, name):
         if name in self._list_of_potentials:
             return self._list_of_potentials[name]
-        else:
-            raise AttributeError
+        raise AttributeError
 
     def __dir__(self):
         return list(self._list_of_potentials.keys())
@@ -312,9 +311,9 @@ def find_potential_file_base(path, resource_path_lst, rel_path):
         for resource_path in resource_path_lst:
             path_direct = os.path.join(resource_path, path)
             path_indirect = os.path.join(resource_path, rel_path, path)
-            if os.path.exists(path_direct):
+            if Path(path_direct).exists():
                 return path_direct
-            elif os.path.exists(path_indirect):
+            if Path(path_indirect).exists():
                 return path_indirect
     raise ValueError(
         "Either the filename or the functional has to be defined.",
@@ -424,7 +423,7 @@ def get_resource_path_from_conda(
     for conda_var in env_variables:
         if conda_var in env:
             resource_path = os.path.join(env[conda_var], "share", "iprpy")
-            if os.path.exists(resource_path):
+            if Path(resource_path).exists():
                 return resource_path
     raise ValueError("No resource_path found" + potential_installation)
 
@@ -507,21 +506,19 @@ def validate_potential_dataframe(
     """
     if isinstance(potential_dataframe, pandas.Series):
         return potential_dataframe
-    elif isinstance(potential_dataframe, pandas.DataFrame):
+    if isinstance(potential_dataframe, pandas.DataFrame):
         if len(potential_dataframe) == 1:
             return potential_dataframe.iloc[0]
-        elif len(potential_dataframe) == 0:
+        if len(potential_dataframe) == 0:
             raise ValueError(
                 "The potential_dataframe is an empty pandas.DataFrame:",
                 potential_dataframe,
             )
-        else:
-            raise ValueError(
-                "The potential_dataframe contains more than one interatomic potential, please select one:",
-                potential_dataframe,
-            )
-    else:
-        raise TypeError(
-            "The potential_dataframe should be a pandas.DataFrame or pandas.Series, but instead it is of type:",
-            type(potential_dataframe),
+        raise ValueError(
+            "The potential_dataframe contains more than one interatomic potential, please select one:",
+            potential_dataframe,
         )
+    raise TypeError(
+        "The potential_dataframe should be a pandas.DataFrame or pandas.Series, but instead it is of type:",
+        type(potential_dataframe),
+    )

{lammpsparser-0.0.8 → lammpsparser-0.0.10}/src/lammpsparser/structure.py

@@ -4,6 +4,7 @@
 from __future__ import annotations
 
 import decimal as dec
+import pathlib
 import posixpath
 import warnings
 from typing import Any, cast
@@ -524,7 +525,7 @@ class LammpsStructure:
         if cwd is not None:
             file_name = posixpath.join(cwd, file_name)
 
-        with open(file_name, "w") as f:
+        with pathlib.Path(file_name).open("w") as f:
             f.writelines(self._string_input)
 
 

{lammpsparser-0.0.8 → lammpsparser-0.0.10}/src/lammpsparser/units.py

@@ -237,9 +237,8 @@ class UnitConverter:
                 np.array(array) * self.lammps_to_pyiron(quantity_dict[label]),
                 dtype=dtype_dict[label],
             )
-        else:
-            warnings.warn(
-                message="Warning: Couldn't determine the LAMMPS to pyiron unit conversion type of quantity "
-                f"{label}. Returning un-normalized quantity"
-            )
-            return np.array(array)
+        warnings.warn(
+            message="Warning: Couldn't determine the LAMMPS to pyiron unit conversion type of quantity "
+            f"{label}. Returning un-normalized quantity"
+        )
+        return np.array(array)