removing small issues with linting and formatting

.github/workflows/run_tests.yml

@@ -59,4 +59,4 @@ jobs:
  pip install -e ichor_cli
  - name: Run example notebooks
  run: |
- git ls-files -- '*.ipynb' | xargs pytest --nbval-lax --current-env
+ git ls-files -- '*.ipynb' | xargs pytest --nbval-lax --nbval-current-env

ichor_core/ichor/core/atoms/list_of_atoms.py

@@ -140,12 +140,12 @@ def features_to_csv(
 
  :param feature_calculator: Calculator function to be used to calculate features
  :param fname: A string to be appended to the default csv file names.
- A .csv file is written out for every atom with default name \``atom_name\``_features.csv
- If an fname is given, the name becomes \``fname\``_\``atom_name\``_features.csv
+ A .csv file is written out for every atom with default name ``atom_name_features.csv``
+ If an fname is given, the name becomes ``fname_atom_name_features.csv``
  :param atom_names: A list of atom names for which to write csv files.
  If None, then write out the features for every atom in the system.
- :param \*args: positional arguments to pass to calculator function
- :param \**kwargs: key word arguments to be passed to the feature calculator function
+ :param args: positional arguments to pass to calculator function
+ :param kwargs: key word arguments to be passed to the feature calculator function
  """
  import pandas as pd
 

ichor_core/ichor/core/atoms/list_of_atoms_atom_view.py

@@ -75,7 +75,7 @@ def features(self, feature_calculator: Callable, *args, **kwargs) -> np.ndarray:
 
  :param alf: A list of integers or a numpy array corresponding to the alf of one atom
  The atom which the atom view is for.
- :return: The array has shape \`n_timesteps\` x \`n_features\`.
+ :return: The array has shape ``n_timesteps`` x ``n_features``.
  """
 
  return np.array(

ichor_core/ichor/core/calculators/spherical_to_cartesian_calculator.py

@@ -5,7 +5,14 @@
 
 def spherical_to_cartesian(r, theta, phi) -> List[float]:
  """
- Spherical to cartesian transformation, where r in [0, \inf), \theta in [0, \pi], \phi in [-\pi, \pi).
+ Spherical to cartesian transformation
+
+ .. math::
+
+ r \in [0, \inf)
+ \theta in [0, \pi]
+ \phi in [-\pi, \pi)
+
  x = r sin \theta cos\phi
  y = r sin \phi sin\theta
  z = r cos\theta

ichor_core/ichor/core/database/sql/database.py

@@ -2,8 +2,7 @@
 from typing import Union
 
 from sqlalchemy import Column, create_engine, Float, ForeignKey, Integer, String
-from sqlalchemy.ext.declarative import declarative_base
-from sqlalchemy.orm import relationship
+from sqlalchemy.orm import declarative_base, relationship
 
 Base = declarative_base()
 

ichor_core/ichor/core/files/file_data.py

@@ -108,7 +108,6 @@ def center_geometry_on_atom_and_write_xyz(
  central_atom_alf: ALF,
  central_atom_name: str,
  fname: Optional[Union[str, Path]] = None,
- **kwargs,
  ):
  """Centers all geometries (from a Trajectory of PointsDirectory instance)
  onto a central atom and then writes out a new xyz file with all geometries centered on that atom.
@@ -119,8 +118,7 @@ def center_geometry_on_atom_and_write_xyz(
  :param feature_calculator: Function which calculates features
  :param central_atom_name: the name of the central atom to center all geometries on. Eg. `O1`
  :param fname: Optional file name in which to save the rotated geometries.
- :param \*args: Positional arguments to pass to calculator function
- :param \**kwargs: Key word arguments to pass to calculator function
+ :param kwargs: Key word arguments to pass to calculator function
  """
 
  from ichor.core.atoms import Atoms

ichor_core/ichor/core/files/points_directory.py

@@ -182,8 +182,8 @@ def alf(self, alf_calculator: Callable[..., ALF], *args, **kwargs) -> List[ALF]:
  Returns the Atomic Local Frame (ALF) for all Atom instances that are held in Atoms
  e.g. ``[[0,1,2],[1,0,2], [2,0,1]]``.
 
- :param \*args: positional arguments to pass to alf calculator
- :param \**kwargs: key word arguments to pass to alf calculator
+ :param args: positional arguments to pass to alf calculator
+ :param kwargs: key word arguments to pass to alf calculator
  """
  return [
  alf_calculator(atom_instance, *args, **kwargs)
@@ -527,8 +527,8 @@ def features_with_properties_to_csv(
  If None, then writes out files for all atoms in the system, defaults to None
  :param property_types: A list of property names (iqa, multipole names) for which to write columns.
  If None, then writes out columns for all properties, defaults to None
- :param \*args: positional arguments to pass to calculator function
- :param \**kwargs: key word arguments to be passed to the feature calculator function
+ :param args: positional arguments to pass to calculator function
+ :param kwargs: key word arguments to be passed to the feature calculator function
  :raises TypeError: This method only works for PointsDirectory instances because it
  needs access to AIMALL information. Does not work for Trajectory instances.
  """

ichor_core/ichor/core/files/xyz/trajectory.py

@@ -118,8 +118,8 @@ def alf(self, alf_calculator: Callable[..., ALF], *args, **kwargs) -> List[ALF]:
  Returns the Atomic Local Frame (ALF) for all Atom instances that are held in Atoms.
  e.g. ``[[0,1,2],[1,0,2], [2,0,1]]``
 
- :param \*args: positional arguments to pass to alf calculator
- :param \**kwargs: key word arguments to pass to alf calculator
+ :param args: positional arguments to pass to alf calculator
+ :param kwargs: key word arguments to pass to alf calculator
  """
  return [
  alf_calculator(atom_instance, *args, **kwargs) for atom_instance in self[0]

ichor_core/ichor/core/models/kernels/periodic_kernel.py

@@ -5,7 +5,23 @@
 
 
 class PeriodicKernel(Kernel):
- """Implemtation of the Periodic Kernel."""
+ """Implemtation of the Periodic Kernel.
+
+ :param lengthscale: np.ndarray of n_features array of lengthscales
+ :param period: np.ndarray of n_features array of period lengths
+
+ .. note::
+ Lengthscales is typically n_features long because we want a separate lengthscale for each dimension.
+ The periodic kernel is going to be used for phi features
+ because these are the features we know can be cyclic.
+ The period of the phi angle is always :math:`2\pi`,
+ however this period can change if there is normalization
+ or standardization applied to features. The new period then becomes
+ the distance between where :math:`\pi` and :math:`-\pi`
+ land after the features are scaled. Because the period can vary
+ for individual phi angles for standardization, it is
+ still passed in as an array that is n_features long.
+ """
 
  def __init__(
  self,
@@ -14,26 +30,6 @@ def __init__(
  period_length: np.ndarray,
  active_dims: Optional[np.ndarray] = None,
  ):
- """
-
- Args:
- :param: `lengthscale` np.ndarray of n_features:
- array of lengthscales
- :param: `period` np.ndarray of n_features:
- array of period lengths
-
- .. note::
- Lengthscales is typically n_features long because we want a separate lengthscale for each dimension.
- The periodic kernel is going to be used for phi features
- because these are the features we know can be cyclic.
- The period of the phi angle is always :math:`2\pi`,
- however this period can change if there is normalization
- or standardization applied to features. The new period then becomes
- the distance between where :math:`\pi` and :math:`-\pi`
- land after the features are scaled. Because the period can vary
- for individual phi angles for standardization, it is
- still passed in as an array that is n_features long.
- """
  super().__init__(name, active_dims)
  self._thetas = thetas
  self._period_length = period_length