Merge pull request #39 from SpinW/more-lints

Adds more lint rules (and lints accordingly)

Author: lucas-wilkins

pyproject.toml

@@ -11,5 +11,16 @@ version = {attr = "pyspinw.__version__"}
 line-length = 120
 
 [tool.ruff.lint]
-select = ["PL"]
-ignore = ["PLR"]
+select = ["D1",  # undocumented objects 
+          "D2",  # docstring formating w.r.t. whitespace
+          "E",  # pycodestyle errors
+          "PL",  # pylint
+          "W",  # pycodestyle warnings
+          ]
+
+ignore = ["D107",  # undocumented __init__
+          "D203",  # 1 blank line before class docstring
+          "D210",  # whitespace surrounding docstring text
+          "D213",  # multi-line summary starts at second line
+          "PLR",  # pylint refactor suggestions
+          ]

pyspinw/__init__.py

@@ -0,0 +1,6 @@
+"""pySpinW: spin Hamiltonian calculation in Python
+
+SpinW is a Python library that can plot and numerically simulate
+magnetic structures and excitations of given spin Hamiltonian using
+classical Monte Carlo simulation and linear spin wave theory.
+"""

pyspinw/_base.py

@@ -1,4 +1,4 @@
-""" Base classes for PySpinW
+"""Base classes for PySpinW
 
 This is an abstract outline, the actual implementations are in different files
 
@@ -13,13 +13,15 @@
 
 
 class MagneticStructure(ABC):
-    """ Base class for representations of the Magnetic Structures """
+    """Base class for representations of the Magnetic Structures"""
+
     def __init__(self):
         pass
 
 
 class Hamiltonian(ABC):
-    """ Hamiltonian base class"""
+    """Hamiltonian base class"""
+
     def __init__(self,
                  crystal_structure: BravaisLattice,
                  magnetic_structure: MagneticStructure):
@@ -29,26 +31,28 @@ def __init__(self,
 
     @abstractmethod
     def energies(self, q_vectors: np.ndarray):
-        """ Get the energy levels of the system at the given q vectors """
+        """Get the energy levels of the system at the given q vectors"""
 
 class Sample(ABC):
-    """ Representation of the macrostructure of a sample used in an experiment (Twin, Powder etc)"""
+    """Representation of the macrostructure of a sample used in an experiment (Twin, Powder etc)"""
+
     def __init__(self, hamiltonian: Hamiltonian):
         self.hamiltonian = hamiltonian
 
 Identifier = str # temporary choice for now
 
 
 class Coupling:
-    """ Coupling between different sites """
+    """Coupling between different sites"""
+
     def __init__(self, site_1: Identifier, site_2: Identifier):
         self._site_1 = site_1
         self._site_2 = site_2
         self._coupling_matrix = None
 
     @property
     def coupling_matrix(self) -> np.ndarray:
-        """ The coupling matrix for this coupling
+        """The coupling matrix for this coupling
 
         i.e. if H is the energy contribution for this coupling, S is the spin state, and
         M is the coupling matrix, we have
@@ -62,24 +66,26 @@ def coupling_matrix(self) -> np.ndarray:
 
 
 class Anisotropy:
-    """ Defines the anisotropy at a given site"""
+    """Defines the anisotropy at a given site"""
+
     def __init__(self, site: Identifier):
         self._site = site
         self._anisotropy_matrix = None
 
     @property
     def anisotropy_matrix(self) -> np.ndarray:
-        """ Matrix spefifying the anisotropy - `A` term in the Hamiltonian """
+        """Matrix spefifying the anisotropy - `A` term in the Hamiltonian"""
         if self._anisotropy_matrix is None:
             raise ValueError("Anisotropy matrix not initialised - this shouldn't happen")
         else:
             return self._anisotropy_matrix
 
 
 class Data:
-    """ Placeholder """
+    """Placeholder"""
 
 class Experiment:
-    """ The setup of a neutron experiment (base class)"""
+    """The setup of a neutron experiment (base class)"""
+
     def __init__(self, sample: Sample, data: Data | None = None):
         pass

pyspinw/anisotropy.py

@@ -1,12 +1,12 @@
-""" Different kinds of anisotropy """
+"""Different kinds of anisotropy"""
 import numpy as np
 
 from pyspinw._base import Anisotropy, Identifier
 from pyspinw.checks import check_sizes
 
 
 class GeneralAnisotropy(Anisotropy):
-    """ General anisotropy specification """
+    """General anisotropy specification"""
 
     @check_sizes(a=(3,3), force_numpy=True)
     def __init__(self, site: Identifier, a: np.ndarray):
@@ -16,11 +16,12 @@ def __init__(self, site: Identifier, a: np.ndarray):
 
     @property
     def anisotropy_matrix(self) -> np.ndarray:
+        """The matrix defining the anisotropy."""
         return self._a
 
 
 class DiagonalAnisotropy(GeneralAnisotropy):
-    """ Anisotropy oriented with axes, but variable amount in x, y and z"""
+    """Anisotropy oriented with axes, but variable amount in x, y and z"""
 
     @check_sizes(a=(3,), force_numpy=True)
     def __init__(self, site: Identifier, a: np.ndarray):
@@ -29,21 +30,24 @@ def __init__(self, site: Identifier, a: np.ndarray):
 
 
 class XAxisAnisotropy(DiagonalAnisotropy):
-    """ Pure X anisotropy"""
+    """Pure X anisotropy"""
+
     def __init__(self, site: Identifier, a: float):
         super().__init__(site, np.array([1,0,0], dtype=float))
         self.a_x = a
 
 
 class YAxisAnisotropy(DiagonalAnisotropy):
-    """ Pure Y anisotropy"""
+    """Pure Y anisotropy"""
+
     def __init__(self, site: Identifier, a: float):
         super().__init__(site, np.array([0,1,0], dtype=float))
         self.a_y = a
 
 
 class ZAxisAnisotropy(DiagonalAnisotropy):
-    """ Pure Z anisotropy"""
+    """Pure Z anisotropy"""
+
     def __init__(self, site: Identifier, a: float):
         super().__init__(site, np.array([0,0,1], dtype=float))
         self.a_z = a

pyspinw/basis.py

@@ -1,16 +1,15 @@
-""" Functions for working with different basis vectors"""
+"""Functions for working with different basis vectors"""
 
 import numpy as np
 from pyspinw.checks import check_sizes
 
 @check_sizes(vectors=(-1, 3))
 def find_aligned_basis(vectors: np.ndarray, rcond: float | None = None) -> tuple[np.ndarray, np.ndarray, np.ndarray]:
-    """ Find a set of orthonormal basis vectors aligned with the first being aligned to the input vectors
+    """Find a set of orthonormal basis vectors aligned with the first being aligned to the input vectors
 
     :param vectors: an n-by-3 numpy array containing the vectors to use to calculate the basis
     :param rcond: tolerance on the calculation, default is 3 * machine precision
     """
-
     if rcond is None:
         rcond = 3*np.finfo(vectors.dtype).eps # N * floating point epsilon
 
@@ -51,8 +50,7 @@ def find_aligned_basis(vectors: np.ndarray, rcond: float | None = None) -> tuple
 
 
 def demo_find_aligned_basis():
-    """ Example / test for find_aligned_basis"""
-
+    """Example / test for find_aligned_basis"""
     test_vectors = np.array([
         [2, 0, 0],
         [0, 3, 0],

pyspinw/calculations/__init__.py

@@ -0,0 +1 @@
+"""Functions for performing spin wave calculations."""

pyspinw/calculations/spinwave.py

@@ -1,4 +1,4 @@
-""" Spinwave Calculations"""
+"""Spinwave Calculations"""
 
 from dataclasses import dataclass
 from enum import Enum
@@ -8,22 +8,29 @@
 
 from pyspinw.checks import check_sizes
 
+
+# Disable linting for bad variable names, because they should match the docs
+# ruff: noqa: E741
+
 @dataclass
 class Coupling:
-    """ Temporary description of the coupling between atoms"""
+    """Temporary description of the coupling between atoms"""
+
     index1: int
     index2: int
     matrix: np.ndarray
     inter_site_vector: np.ndarray
 
 class CalculationMethod(Enum):
-    """ Type of method used (for debugging purposes) """
+    """Type of method used (for debugging purposes)"""
+
     CHOLESKY = 0
     LDL = 1
 
 @dataclass
 class SpinwaveResult:
-    """ Results from a spinwave calculation"""
+    """Results from a spinwave calculation"""
+
     q_vectors: np.ndarray
     raw_energies: list[np.ndarray]
     method: list[CalculationMethod]
@@ -36,15 +43,11 @@ def spinwave_calculation(rotations: np.ndarray,
                          magnitudes: np.ndarray,
                          q_vectors: np.ndarray,
                          couplings: list[Coupling]):
-    """ Main calculation step
+    """Main calculation step
 
     Unlike the main interface it takes indexed arrays, the meaning of the arrays is set elsewhere
 
     """
-
-    # Disable linting for bad variable names, because they should match the docs
-    # pylint: disable=C0103
-
     n_sites = rotations.shape[0]
 
     z = rotations[:,:,0] + 1j*rotations[:,:,1] # n-by-3, complex

pyspinw/checks.py

@@ -1,4 +1,4 @@
-""" Tools for checking input shapes """
+"""Tools for checking input shapes"""
 
 import functools
 
@@ -9,11 +9,11 @@
 
 
 class DimensionalityError(ValueError):
-    """ The dimensions of a numpy array don't match the specification """
+    """The dimensions of a numpy array don't match the specification"""
 
 
 def check_sizes(force_numpy: bool = False, **kwargs):
-    """ Decorator to check the dimensionality of a given vector
+    """Decorator to check the dimensionality of a given vector
 
     Example usage:
         check that a function has an n-by-3 vector input called `a`, and
@@ -29,7 +29,6 @@ def my_function(a, b):
     :param force_numpy: default=True, Convert the named arrays into numpy form if they are not already
 
     """
-
     # If assertions are not enabled, give a decorator that just return the function as is
     if not __debug__:
         def identity(fun):

pyspinw/coupling.py

@@ -1,4 +1,4 @@
-""" Coupling Terms """
+"""Coupling Terms"""
 
 import numpy as np
 
@@ -8,7 +8,7 @@
 
 
 class HeisenbergCoupling(Coupling):
-    """ Heisenberg Coupling, which takes the form
+    """Heisenberg Coupling, which takes the form
 
     H_ij = J_ij (S_i . S_j)
 
@@ -26,7 +26,7 @@ def __init__(self, site_1: Identifier, site_2: Identifier, j):
 
 
 class DiagonalCoupling(Coupling):
-    """ Diagonal coupling, which takes the form
+    """Diagonal coupling, which takes the form
 
     H_ij = J^x_ij S^x_i S^x_j + J^y_ij S^y_i S^y_j + J^z_ij S^z_i S^z_j
 
@@ -46,8 +46,7 @@ def __init__(self, site_1: Identifier, site_2: Identifier, j: np.ndarray):
 
 
 class XYCoupling(Coupling):
-
-    """ "XY" coupling, which takes the form
+    """ "XY"  coupling, which takes the form
 
     H_ij = J_ij (S^x_i S^x_j + S^y_i S^y_j)
 
@@ -65,7 +64,6 @@ def __init__(self, site_1: Identifier, site_2: Identifier, j):
 
 
 class XXZCoupling(Coupling):
-
     """ "XXZ" coupling, which takes the form
 
     H_ij = J_xy (S^x_i S^x_j + S^y_i S^y_j) + J_z (S^z_i S^z_j)
@@ -76,6 +74,7 @@ class XXZCoupling(Coupling):
     :param j_z: The coupling coefficient for the z component
 
     """
+
     def __init__(self, site_1: Identifier, site_2: Identifier, j_xy, j_z):
         super().__init__(site_1, site_2)
         self._j_xy = j_xy
@@ -84,7 +83,7 @@ def __init__(self, site_1: Identifier, site_2: Identifier, j_xy, j_z):
 
 
 class IsingCoupling(Coupling):
-    """ Ising coupling (z component only), which takes the form
+    """Ising coupling (z component only), which takes the form
 
     H_ij = J_ij S^z_i S^z_j
 
@@ -101,7 +100,7 @@ def __init__(self, site_1: Identifier, site_2: Identifier, j):
 
 
 class DMCoupling(Coupling):
-    """ Dzyaloshinskii–Moriya coupling, which takes the form
+    """Dzyaloshinskii–Moriya coupling, which takes the form
 
     H_ij = D_ij (S_i x S_j)
 
@@ -110,6 +109,7 @@ class DMCoupling(Coupling):
     :param dm_vector: The vector D above
 
     """
+
     @check_sizes(d_vector=(3,), force_numpy=True)
     def __init__(self, site_1: Identifier, site_2: Identifier, dm_vector: np.ndarray):
         super().__init__(site_1, site_2)

pyspinw/data/__init__.py

@@ -0,0 +1 @@
+"""Data used by pySpinW."""

pyspinw/experiment.py

@@ -1,4 +1,4 @@
-""" Different kinds of experimental setups """
+"""Different kinds of experimental setups"""
 
 #pylint: disable=W0611
 from pyspinw._base import Experiment

pyspinw/gui/__init__.py

@@ -0,0 +1 @@
+"""Visualisation and crystal structure editing GUI utilities."""