Clean up a bit using new dependencies

CHANGELOG.rst

@@ -1,5 +1,5 @@
 `Unreleased <https://github.com/pace-neutrons/Euphonic/compare/v1.2.1...HEAD>`_
-----------
+-------------------------------------------------------------------------------
 
 - Requirements
 
@@ -49,7 +49,7 @@
 
 
 `v1.2.1 <https://github.com/pace-neutrons/Euphonic/compare/v1.2.0...v1.2.1>`_
-------
+-----------------------------------------------------------------------------
 
 - Improvements
 
@@ -82,7 +82,7 @@
   - A deprecation in Numpy 1.25, which indirectly caused a test failure, has been addressed.
 
 `v1.2.0 <https://github.com/pace-neutrons/Euphonic/compare/v1.1.0...v1.2.0>`_
-------
+-----------------------------------------------------------------------------
 
 - Improvements:
 
@@ -105,7 +105,7 @@
     and ``--brille-npts-density`` arguments.
 
 `v1.1.0 <https://github.com/pace-neutrons/Euphonic/compare/v1.0.0...v1.1.0>`_
-----------
+-----------------------------------------------------------------------------
 
 - New features:
 
@@ -121,7 +121,7 @@
     interactions, see `#239 <https://github.com/pace-neutrons/Euphonic/issues/239>`_.
 
 `v1.0.0 <https://github.com/pace-neutrons/Euphonic/compare/v0.6.5...v1.0.0>`_
-----------
+-----------------------------------------------------------------------------
 
 - Changes:
 
@@ -163,7 +163,7 @@
     by default. To recover previous behaviour set this to ``False``.
 
 `v0.6.5 <https://github.com/pace-neutrons/Euphonic/compare/v0.6.4...v0.6.5>`_
-------
+-----------------------------------------------------------------------------
 
 - New Features:
 
@@ -212,7 +212,7 @@
     Previously this was interpreted as an astronomical unit by Pint.
 
 `v0.6.4 <https://github.com/pace-neutrons/Euphonic/compare/v0.6.3...v0.6.4>`_
-------
+-----------------------------------------------------------------------------
 
 - Improvements:
 
@@ -243,7 +243,7 @@
     which will just emit a warning.
 
 `v0.6.3 <https://github.com/pace-neutrons/Euphonic/compare/v0.6.2...v0.6.3>`_
-------
+-----------------------------------------------------------------------------
 
 - New Features:
 
@@ -273,7 +273,7 @@
     they refer to, and to match other arguments like ``vmin``, ``vmax``.
 
 `v0.6.2 <https://github.com/pace-neutrons/Euphonic/compare/v0.6.1...v0.6.2>`_
-------
+-----------------------------------------------------------------------------
 
 - Improvements:
 
@@ -289,7 +289,7 @@
     factor is not present
 
 `v0.6.1 <https://github.com/pace-neutrons/Euphonic/compare/v0.6.0...v0.6.1>`_
-------
+-----------------------------------------------------------------------------
 
 - Bug fixes:
 
@@ -302,7 +302,7 @@
     can now be correctly recovered by multiplying S(Q,w) by the energy bin width.
 
 `v0.6.0 <https://github.com/pace-neutrons/Euphonic/compare/v0.5.2...0.6.0>`_
-------
+----------------------------------------------------------------------------
 
 - Euphonic can now calculate neutron-weighted partial density of states, and
   has new ``Spectra`` features to handle PDOS data:
@@ -361,7 +361,7 @@
     ``euphonic-optimise-dipole-parameter``.
 
 `v0.5.2 <https://github.com/pace-neutrons/Euphonic/compare/v0.5.1...v0.5.2>`_
-------
+-----------------------------------------------------------------------------
 
 - Improvements:
 
@@ -386,7 +386,7 @@
     ``ebins - 1`` bins were generated
 
 `v0.5.1 <https://github.com/pace-neutrons/Euphonic/compare/v0.5.0...v0.5.1>`_
-----------
+-----------------------------------------------------------------------------
 
 - New Features:
 
@@ -417,7 +417,7 @@
     implementation: moved ``1/2`` factor and added explicit q-point weights
 
 `v0.5.0 <https://github.com/pace-neutrons/Euphonic/compare/v0.4.0...v0.5.0>`_
-----------
+-----------------------------------------------------------------------------
 
 - New Features:
 
@@ -436,7 +436,7 @@
     ``Spectrum1DCollection.from_castep_phonon_dos``
   - **Adaptive broadening** is now available for DOS, which can obtain a
     more representative DOS than standard fixed-width broadening. See
-    `the docs <https://euphonic.readthedocs.io/en/latest/dos.html#adaptive-broadening>`_
+    `the docs <https://euphonic.readthedocs.io/en/latest/dos.html#adaptive-broadening>`__
     for details
   - Adaptive broadening can be used in the ``euphonic-dos`` tool with the
     ``--adaptive`` argument
@@ -494,7 +494,7 @@
     in implementation
 
 `v0.4.0 <https://github.com/pace-neutrons/Euphonic/compare/v0.3.2...v0.4.0>`_
-----------
+-----------------------------------------------------------------------------
 
 - There have been some major changes and improvements to spectra, plotting
   and command line tools, including:
@@ -549,7 +549,7 @@
     `#108 <https://github.com/pace-neutrons/Euphonic/issues/108>`_
 
 `v0.3.2 <https://github.com/pace-neutrons/Euphonic/compare/v0.3.1...v0.3.2>`_
-----------
+-----------------------------------------------------------------------------
 
 - New Features:
 
@@ -594,7 +594,7 @@
     there is only one q-point (which is gamma) and ``splitting=True``
 
 `v0.3.1 <https://github.com/pace-neutrons/Euphonic/compare/v0.3.0...v0.3.1>`_
-----------
+-----------------------------------------------------------------------------
 
 - New Features:
 
@@ -625,7 +625,7 @@
     `#77 <https://github.com/pace-neutrons/Euphonic/issues/77>`_
 
 `v0.3.0 <https://github.com/pace-neutrons/Euphonic/compare/v0.2.2...v0.3.0>`_
-----------
+-----------------------------------------------------------------------------
 
 - Breaking Changes:
 
@@ -665,22 +665,22 @@
     in C, `#45 <https://github.com/pace-neutrons/Euphonic/issues/45>`_
 
 `v0.2.2 <https://github.com/pace-neutrons/Euphonic/compare/v0.2.1...v0.2.2>`_
-------
+-----------------------------------------------------------------------------
 
 - Bug fixes:
 
   - Add MANIFEST.in for PyPI distribution
 
 `v0.2.1 <https://github.com/pace-neutrons/Euphonic/compare/v0.2.0...v0.2.1>`_
-------
+-----------------------------------------------------------------------------
 
 - Bug fixes:
 
   - Cannot easily upload C header files to PyPI without an accompanying source
     file, so refactor C files to avoid this
 
 `v0.2.0 <https://github.com/pace-neutrons/Euphonic/compare/v0.1-dev3...v0.2.0>`_
-------
+--------------------------------------------------------------------------------
 
 - There are several breaking changes:
 

doc/source/python-api.rst

@@ -9,6 +9,7 @@ Python API
   Force Constants <force-constants>
   Phonon Frequencies and Eigenvectors <qpoint-phonon-modes>
   Phonon Frequencies Only <qpoint-frequencies>
+  Crystal Structure <crystal>
   Density of States <dos>
   Structure Factors <structure-factor>
   Scattering Intensities <scattering-intensities>

doc/source/spectra.rst

@@ -86,7 +86,7 @@ apply this resolution function to a Spectrum1D we package the polynomial into a
   def tosca_resolution(energy):
       poly_in_wavenumber = Polynomial([2.5, 0.005, 1e-7])
       return poly_in_wavenumber(energy.to('1/cm').magnitude) * ureg('1/cm')
-  dos_tosca = dos.broaden(tosca_resolution, shape='gauss', width_convention='STD')
+  dos_tosca = dos.broaden(tosca_resolution, shape='gauss', width_convention='std')
 
 Plotting
 --------

euphonic/broadening.py

@@ -1,27 +1,34 @@
 """
 Functions for broadening spectra
 """
-from typing import Callable, Union
+from typing import Callable, Literal, Union
 import warnings
 
 import numpy as np
 from numpy.polynomial import Chebyshev
+from pint import Quantity
 from scipy.optimize import nnls
 from scipy.stats import norm
 from scipy.signal import convolve
 
-from euphonic import ureg, Quantity
+from euphonic import ureg
 
 
-def variable_width_broadening(bins: Quantity,
-                              x: Quantity,
-                              width_function: Callable[[Quantity], Quantity],
-                              weights: Union[np.ndarray, Quantity],
-                              width_lower_limit: Quantity = None,
-                              width_convention: str = 'fwhm',
-                              adaptive_error: float = 1e-2,
-                              shape: str = 'gauss',
-                              fit: str = 'cheby-log') -> Quantity:
+ErrorFit = Literal['cheby-log', 'cubic']
+KernelShape = Literal['gauss', 'lorentz']
+
+
+def variable_width_broadening(
+    bins: Quantity,
+    x: Quantity,
+    width_function: Callable[[Quantity], Quantity],
+    weights: Union[np.ndarray, Quantity],
+    width_lower_limit: Quantity = None,
+    width_convention: Literal['fwhm', 'std'] = 'fwhm',
+    adaptive_error: float = 1e-2,
+    shape: KernelShape = 'gauss',
+    fit: ErrorFit = 'cheby-log'
+    ) -> Quantity:
     r"""Apply x-dependent Gaussian broadening to 1-D data series
 
     Typically this is an energy-dependent instrumental resolution function.
@@ -49,14 +56,14 @@
         (default) the bin width will be used. To disable any lower limit, set
         to 0 or lower.
     width_convention
-        Either 'std' or 'fwhm', to indicate if polynomial function yields
-        standard deviation (sigma) or full-width half-maximum.
+        Indicate if polynomial function yields standard deviation (sigma) or
+        full-width half-maximum.
     adaptive_error
         Acceptable error for gaussian approximations, defined
         as the absolute difference between the areas of the true and
         approximate gaussians.
     shape
-        Select 'gauss' or 'lorentz' kernel.
+        Select broadening kernel function.
     fit
         Select parametrisation of kernel width spacing to adaptive_error.
         'cheby-log' is recommended: for shape 'gauss', 'cubic' is also
@@ -76,15 +83,10 @@
 
     widths = sigma_function(x)
 
-    # With newer versions of Numpy/Pint we could dispense with most of the unit
-    # and magnitude shuffling as the numpy functions are handled more cleanly.
-
     if width_lower_limit is None:
-        width_lower_limit = np.diff(bins.magnitude).max() * bins.units
+        width_lower_limit = np.diff(bins).max()
 
-    widths = np.maximum(widths.magnitude,
-                        width_lower_limit.to(widths.units).magnitude
-                        ) * widths.units
+    widths = np.maximum(widths, width_lower_limit)
 
     if isinstance(weights, np.ndarray):
         weights = weights * ureg('dimensionless')
@@ -99,13 +101,15 @@
                                          fit=fit) * weights_unit
 
 
-def width_interpolated_broadening(bins: Quantity,
-                                  x: Quantity,
-                                  widths: Quantity,
-                                  weights: np.ndarray,
-                                  adaptive_error: float,
-                                  shape: str = 'gauss',
-                                  fit: str = 'cheby-log') -> Quantity:
+def width_interpolated_broadening(
+    bins: Quantity,
+    x: Quantity,
+    widths: Quantity,
+    weights: np.ndarray,
+    adaptive_error: float,
+    shape: KernelShape = 'gauss',
+    fit: ErrorFit = 'cheby-log'
+    ) -> Quantity:
     """
     Uses a fast, approximate method to broaden a spectrum
     with a variable-width kernel. Exact Gaussians are calculated
@@ -131,8 +135,8 @@
         as the absolute difference between the areas of the true and
         approximate gaussians.
     shape
-        Select 'gauss' or 'lorentz' kernel. Widths will correspond to sigma or
-        gamma parameters respectively.
+        Select kernel shape. Widths will correspond to sigma or gamma
+        parameters respectively.
     fit
         Select parametrisation of kernel width spacing to adaptive_error.
         'cheby-log' is recommended: for shape 'gauss', 'cubic' is also
@@ -159,7 +163,9 @@
     return gamma / (2 * np.pi * (x**2 + (gamma / 2)**2))
 
 
-def _get_spacing(error, shape='gauss', fit='cheby-log'):
+def _get_spacing(error,
+                 shape: KernelShape = 'gauss',
+                 fit: ErrorFit = 'cheby-log'):
     """
     Determine suitable spacing value for mode_width given accepted error level
 
@@ -198,13 +204,14 @@
                          f'"Lorentz" shapes.')
 
 
-def _width_interpolated_broadening(bins: np.ndarray,
-                                   x: np.ndarray,
-                                   widths: np.ndarray,
-                                   weights: np.ndarray,
-                                   adaptive_error: float,
-                                   shape='gauss',
-                                   fit='cheby-log') -> np.ndarray:
+def _width_interpolated_broadening(
+    bins: np.ndarray,
+    x: np.ndarray,
+    widths: np.ndarray,
+    weights: np.ndarray,
+    adaptive_error: float,
+    shape: KernelShape = 'gauss',
+    fit: ErrorFit = 'cheby-log') -> np.ndarray:
     """
     Broadens a spectrum using a variable-width kernel, taking the
     same arguments as `variable_width` but expects arrays with
@@ -277,7 +284,8 @@
     return spectrum
 
 
-def find_coeffs(spacing: float, shape='gauss') -> np.ndarray:
+def find_coeffs(spacing: float,
+                shape: KernelShape = 'gauss') -> np.ndarray:
     """"
     Function that, for a given spacing value, gives the coefficients of the
     polynomial which describes the relationship between kernel width and the