Linting error fixes

pytaser/__init__.py

@@ -1,2 +1,3 @@
-"""PyTASER is a package for the generation, analysis and plotting of Transient Absorption Spectra of bulk materials."""
-
+"""PyTASER is a package for the generation, analysis and plotting of Transient Absorption Spectra of bulk
+materials.
+"""

pytaser/das_generator.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python3
 """Created on Thu Aug  3 16:42:36 2023.
 
 @author: lucasverga
@@ -32,6 +31,12 @@ def __init__(
         new_system,
         reference_system,
     ):
+        """
+
+        Args:
+            new_system: Internal_Abs object from internal_abs_generator for the new system
+            reference_system: Internal_Abs object from internal_abs_generator for the reference system.
+        """
         self.new_system = new_system
         self.reference_system = reference_system
 
@@ -55,7 +60,8 @@ def from_vasp_outputs(
             waveder_file_ref: The WAVEDER file for the reference system.
 
         Returns:
-            A DASGenerator object containing the Internal_Abs object for the new system and reference system.
+            A DASGenerator object containing the Internal_Abs object for the new system and reference
+            system.
         """
         warnings.filterwarnings("ignore", category=UnknownPotcarWarning)
         warnings.filterwarnings("ignore", message="No POTCAR file with matching TITEL fields")
@@ -91,7 +97,8 @@ def from_mpid(
             mpr_ref: An MPRester object for the reference system if already generated by user.
 
         Returns:
-            A DASGenerator object containing the Internal_Abs object for the new system and reference system.
+            A DASGenerator object containing the Internal_Abs object for the new system and reference
+            system.
         """
         new_system = Internal_Abs.internal_from_mpid(mpid, bg=None, api_key=None, mpr=None)
         reference_system = Internal_Abs.internal_from_mpid(mpid_ref, bg_ref, api_key=None, mpr_ref=None)

pytaser/generator.py

@@ -3,6 +3,7 @@
 """
 
 import warnings
+from itertools import zip_longest
 from multiprocessing import Array, Pool, cpu_count
 
 import numpy as np
@@ -211,7 +212,7 @@ def get_nonzero_band_transitions(
     )
 
     return list(
-        zip(
+        zip_longest(
             ib_vals[condition].ravel(),
             jb_vals[condition].ravel(),
             ik_vals[condition].ravel(),
@@ -221,13 +222,14 @@ def get_nonzero_band_transitions(
             [nedos] * np.sum(condition),
             [deltae] * np.sum(condition),
             [ismear] * np.sum(condition),
+            fillvalue=None,
         )
     )
 
 
 def _init_shared_memory(cder, occs, eigs_shifted, norm_kweights):
-    global _cder, _occs, _eigs_shifted, _norm_kweights
-    global _cder_shape, _occs_shape, _eigs_shifted_shape, _norm_kweights_shape
+    global _cder, _occs, _eigs_shifted, _norm_kweights  # noqa: PLW0603
+    global _cder_shape, _occs_shape, _eigs_shifted_shape, _norm_kweights_shape  # noqa: PLW0603
 
     _cder_shape = cder.shape
     _cder = Array("d", cder.ravel())

pytaser/kpoints.py

@@ -1,3 +1,8 @@
+"""
+This module generates kpoint-weights for uniform-mesh non-magnetic materials. This is vital when using
+the Materials Project database to generate spectra in PyTASER.
+"""
+
 import numpy as np
 from pymatgen.core import Structure
 from pymatgen.electronic_structure.bandstructure import BandStructureSymmLine
@@ -8,7 +13,7 @@ def get_kpoint_weights(bandstructure, time_reversal=True, symprec=0.1):
 
     Args:
         bandstructure: PMG bandstructure object
-        time_reversal:
+        time_reversal: Time reversal operator, bool (True for +1, False for -1)
         symprec: Symmetry precision in Angstrom.(Lower value is more precise, but
             computationally more expensive)
 
@@ -35,6 +40,15 @@ def get_kpoint_weights(bandstructure, time_reversal=True, symprec=0.1):
 
 
 def get_kpoints_from_bandstructure(bandstructure, cartesian=False):
+    """Function to pull the kpoint from the bandstructure.
+
+    Args:
+        bandstructure: PMG bandstructure object
+        cartesian: bool, indicate if cartesian or fractional coordinates used.
+
+    Returns:
+        k-points
+    """
     if cartesian:
         kpoints = np.array([k.cart_coords for k in bandstructure.kpoints])
     else:
@@ -50,6 +64,19 @@ def expand_kpoints(
     return_mapping=False,
     time_reversal=True,
 ):
+    """Function to expand the kpoints.
+
+    Args:
+        structure: PMG structure object
+        kpoints: uniform mesh kpoints array.
+        symprec: Symmetry precision in Angstrom.(Lower value is more precise, but
+            computationally more expensive)
+        return_mapping: bool
+        time_reversal: Time reversal operator, bool (True for +1, False for -1)
+
+    Returns:
+        full_kpoints, rotations, translations, is_tr, op_mapping, kp_mapping
+    """
     kpoints = np.array(kpoints).round(8)
 
     # due to limited input precision of the k-points, the mesh is returned as a float
@@ -90,7 +117,7 @@ def expand_kpoints(
     in_uniform_mesh = (np.abs(unique_addresses) < 1e-5).all(axis=1)
 
     n_mapped = int(np.sum(in_uniform_mesh))
-    n_expected = int(np.product(mesh))
+    n_expected = int(np.prod(mesh))
     if n_mapped != n_expected:
         raise ValueError(f"Expected {n_expected} points but found {n_mapped}")
 
@@ -107,6 +134,15 @@ def expand_kpoints(
 
 
 def get_mesh_from_kpoint_diff(kpoints, ktol=1e-5):
+    """Function to get the uniform mesh from kpoint differences.
+
+    Args:
+        kpoints: uniform mesh kpoints array.
+        ktol: threshold for filtering changes in kpoint-mesh points.
+
+    Returns:
+        np.array([na, nb, nc]), is_shifted
+    """
     kpoints = np.array(kpoints)
 
     # whether the k-point mesh is shifted or Gamma centered mesh
@@ -147,6 +183,17 @@ def get_reciprocal_point_group_operations(
     symprec: float = 0.01,
     time_reversal: bool = True,
 ):
+    """Function to get the reciprocal point group operations.
+
+    Args:
+        structure: PMG structure object
+        symprec: Symmetry precision in Angstrom.(Lower value is more precise, but
+            computationally more expensive)
+        time_reversal: Time reversal operator, bool (True for +1, False for -1)
+
+    Returns:
+        rotations[sort_idx], translations[sort_idx], is_tr[sort_idx]
+    """
     from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 
     sga = SpacegroupAnalyzer(structure, symprec=symprec)

pytaser/tas.py

@@ -1,25 +1,41 @@
-"""This module generates container classes from the generator modules. These will be used to communicate with the
-plotter module. """
+"""This module generates container classes from the generator modules. These will be used to communicate
+with the plotter module.
+"""
 
 import ast
 
 from monty.json import MontyDecoder
 
 
 def convert_to_tuple(subdict):
+    """Converts subdict representation to tuple.
+
+    Args:
+        subdict: dict,
+
+    Returns:
+        subdict: tuple
+    """
     if isinstance(subdict, dict) and "@module" not in subdict:
         return {ast.literal_eval(k) if "(" in k and ")" in k else k: v for k, v in subdict.items()}
     return subdict
 
 
 def decode_dict(subdict):
+    """Decode subdict from a dict representation using MontyDecoder.
+
+    Args:
+        subdict: dict
+
+    Returns:
+        subdict: decoded dict
+    """
     if isinstance(subdict, dict):
         if "@module" in subdict:
             return MontyDecoder().process_decoded(subdict)
-        else:
-            for k, v in subdict.items():
-                if isinstance(v, dict) and "@module" in v:
-                    subdict[k] = MontyDecoder().process_decoded(v)
+        for k, v in subdict.items():
+            if isinstance(v, dict) and "@module" in v:
+                subdict[k] = MontyDecoder().process_decoded(v)
     return subdict
 
 
@@ -73,6 +89,35 @@ def __init__(
         weighted_jdos_dark_if=None,
         weighted_jdos_diff_if=None,
     ):
+        """
+        Args:
+            tas_total: overall TAS spectrum for a material under the specified conditions
+            jdos_diff_if: JDOS difference (from dark to light) across the energy mesh for a
+                specific band transition i (initial) -> f (final) [dict]
+            jdos_light_total: overall JDOS (pump-on) for a material under the specified
+                conditions
+            jdos_light_if: JDOS (pump-on) across the energy mesh for a specific band
+                transition i (initial) -> f (final) [dict]
+            jdos_dark_total: overall JDOS (pump-off) for a material under the specified
+                conditions
+            jdos_dark_if: JDOS (pump-off) across the energy mesh for a specific band
+                transition i (initial) -> f (final) [dict]
+            energy_mesh_ev: Energy mesh of spectra in eV, with an interval of 'step'.
+            bandgap: Bandgap of the system in electronvolts (eV).
+            temp: Temperature (K) of material we wish to investigate (affects the FD distribution)
+            conc: Carrier concentration (cm^-3) of holes and electrons (both are equivalent).
+                Inversely proportional to pump-probe time delay.
+            alpha_dark: Absorption coefficient of the material in the dark, in cm^-1.
+            alpha_light_dict: Dictionary of band-to-band absorption, stimulated emission and summed
+                contributions to the total overall absorption coefficient under illumination, in cm^-1.
+            weighted_jdos_light_if: JDOS weighted by the transition dipole matrix (TDM) (pump-on)
+                across the energy mesh for a specific band transition i (initial) -> f (final) [dict]
+            weighted_jdos_dark_if: JDOS weighted by the transition dipole matrix (TDM) (pump-off)
+                across the energy mesh for a specific band transition i (initial) -> f (final) [dict]
+            weighted_jdos_diff_if: Difference in JDOS weighted by the transition dipole matrix
+                (TDM) from dark to illumination across the energy mesh for a specific band transition
+                i (initial) -> f (final) [dict].
+        """
         self.tas_total = tas_total
         self.jdos_diff_if = jdos_diff_if
         self.jdos_light_total = jdos_light_total
@@ -184,6 +229,35 @@ def __init__(
         weighted_jdos_new_sys_if=None,
         weighted_jdos_ref_if=None,
     ):
+        """
+        Args:
+            das_total: overall DAS spectrum between new_system and reference system.
+            jdos_diff_if: JDOS difference (from reference to newsystem) across the energy mesh for a
+                specific band transition i (initial) -> f (final) [dict]
+            jdos_new_sys_total: overall JDOS for the new system under the specified
+                conditions
+            jdos_new_sys_if: JDOS for the new system across the energy mesh for a specific band
+                transition i (initial) -> f (final) [dict]
+            jdos_ref_total: overall JDOS for the reference system under the specified
+                conditions
+            jdos_ref_if: JDOS for the reference system across the energy mesh for a specific band
+                transition i (initial) -> f (final) [dict]
+            energy_mesh_ev: Energy mesh of spectra in eV, with an interval of 'step'.
+            bandgap_new_sys: Bandgap of the new system in electronvolts (eV).
+            bandgap_ref: Bandgap of the reference system in electronvolts (eV).
+            temp: Temperature (K) of material we wish to investigate (affects the FD distribution)
+            alpha_new_sys: Absorption coefficient of the new system in the dark, in cm^-1.
+            alpha_ref: Absorption coefficient of the reference system in the dark, in cm^-1.
+            weighted_jdos_new_sys_if: JDOS weighted by the transition dipole matrix (TDM) for the new
+                system across the energy mesh for a specific band transition i (initial) -> f (final)
+                [dict]
+            weighted_jdos_ref_if: JDOS weighted by the transition dipole matrix (TDM) for the reference
+                system across the energy mesh for a specific band transition i (initial) -> f (final)
+                [dict]
+            weighted_jdos_diff_if: Difference in JDOS weighted by the transition dipole matrix
+                (TDM) from reference to new system across the energy mesh for a specific band transition
+                i (initial) -> f (final) [dict].
+        """
         self.das_total = das_total
         self.jdos_new_sys_total = jdos_new_sys_total
         self.jdos_new_sys_if = jdos_new_sys_if

setup.py

@@ -1,6 +1,4 @@
-""""
-PyTASER: transient absorption prediction tool.
-"""
+"""PyTASER: transient absorption prediction tool."""
 
 
 import pathlib

tests/conftest.py

@@ -1,6 +1,4 @@
-"""
-Setup for pytest.
-"""
+"""Setup for pytest."""
 
 from pathlib import Path