General cleanup (#238)

* Avoid UnitStrippedWarning

* Ensure double escaped commands in docstrings

* Avoid deprecated importlib_resources.open_text

* Avoid use of deprecated pyest.warns(None)

See https://github.com/pytest-dev/pytest issue 9404

* Avoid deprecated axes.image (matplotlib 3.5+)

* Remove performance benchmarking tests

* Small review updates:

* Use pytest.warns to check warning type instead of just length
* Use '/' syntax instead of joinpath with importlib_resources.files

* Add whitespace around / path operator

doc/source/cite.rst

@@ -12,9 +12,9 @@ or it can be read programatically as follows:
 
   import yaml
   import euphonic
-  from importlib_resources import open_text
+  from importlib_resources import files
 
-  with open_text(euphonic, 'CITATION.cff') as fp:
+  with open(files(euphonic) / 'CITATION.cff') as fp:
       citation_data = yaml.safe_load(fp)
 
 The latest version of the citation file can also be found in Euphonic's code

euphonic/force_constants.py

@@ -281,7 +281,7 @@ def calculate_qpoint_phonon_modes(
         direction :math:`\\alpha` from its equilibrium position. This can be
         used to calculate the dynamical matrix
         :math:`D_{\\alpha {\\alpha}^\\prime}^{\\kappa {\\kappa}^\\prime}` at
-        :math:`\mathbf{q}`:
+        :math:`\\mathbf{q}`:
 
         .. math::
 
@@ -296,7 +296,7 @@ def calculate_qpoint_phonon_modes(
 
         .. math::
 
-          \sum_{\\kappa^\\prime \\alpha^\\prime}D_{\\alpha {\\alpha}^\\prime}^{\\kappa {\\kappa}^\\prime}(\\mathbf{q}) {e}_{\\mathbf{q}\\nu{\\kappa^\\prime}{\\alpha^\\prime}} =
+          \\sum_{\\kappa^\\prime \\alpha^\\prime}D_{\\alpha {\\alpha}^\\prime}^{\\kappa {\\kappa}^\\prime}(\\mathbf{q}) {e}_{\\mathbf{q}\\nu{\\kappa^\\prime}{\\alpha^\\prime}} =
           {\\omega}_{\\mathbf{q}\\nu}^2 {e}_{\\mathbf{q}\\nu\\kappa\\alpha}
 
         where the eigenvalues :math:`{\\omega}_{\\mathbf{q}\\nu}^2` are the
@@ -327,7 +327,7 @@ def calculate_qpoint_phonon_modes(
         width. The mode widths are proportional to the mode gradients and
         can be estimated using ``euphonic.util.mode_gradients_to_widths``
 
-        The mode gradients :math:`\\frac{d\\omega_{\\mathbf{q}\\nu}}{d\\mathbf{q}}` at each :math:`\mathbf{q}`
+        The mode gradients :math:`\\frac{d\\omega_{\\mathbf{q}\\nu}}{d\\mathbf{q}}` at each :math:`\\mathbf{q}`
         are calculated at the same time as the phonon frequencies and
         eigenvectors as follows.
 
@@ -345,9 +345,9 @@ def calculate_qpoint_phonon_modes(
         Where :math:`\\Omega(\\mathbf{q})` is the diagonal matrix of phonon
         frequencies squared :math:`\\omega_{\\mathbf{q}\\nu}^{2}` and :math:`E(\\mathbf{q})`
         is the matrix containing eigenvectors for all modes.
-        :math:`\\frac{d\\omega_{\\mathbf{q}\\nu}}{d\mathbf{q}}`, can then
+        :math:`\\frac{d\\omega_{\\mathbf{q}\\nu}}{d\\mathbf{q}}`, can then
         be obtained by differentiating the above equation with respect
-        to :math:`\mathbf{q}` using the product rule:
+        to :math:`\\mathbf{q}` using the product rule:
 
         .. math::
 
@@ -376,8 +376,8 @@ def calculate_qpoint_phonon_modes(
         .. math::
 
           \\frac{dD_{\\alpha {\\alpha}^\\prime}^{\\kappa {\\kappa}^\\prime}}{d\\mathbf{q}} =
-          \\frac{-i \mathbf{R}_l}{\\sqrt{M_\\kappa M_{\\kappa ^\\prime}}}
-          \\sum_{l}\\Phi_{\\alpha\\alpha^\\prime}^{\\kappa\\kappa^\\prime}\\exp\\left(-i\\mathbf{q}\\cdot \mathbf{R}_l\\right)
+          \\frac{-i \\mathbf{R}_l}{\\sqrt{M_\\kappa M_{\\kappa ^\\prime}}}
+          \\sum_{l}\\Phi_{\\alpha\\alpha^\\prime}^{\\kappa\\kappa^\\prime}\\exp\\left(-i\\mathbf{q}\\cdot \\mathbf{R}_l\\right)
 
         .. [3] J. R. Yates, X. Wang, D. Vanderbilt and I. Souza, Phys. Rev. B, 2007, 75, 195121
         """

euphonic/plot.py

@@ -236,7 +236,7 @@ def plot_2d_to_axis(spectrum: Spectrum2D, ax: Axes,
     image.set_data(spectrum.get_bin_centres('x').to(x_unit).magnitude,
                    spectrum.get_bin_centres('y').to(y_unit).magnitude,
                    spectrum.z_data.to(z_unit).magnitude.T)
-    ax.images.append(image)
+    ax.add_image(image)
     ax.set_xlim(min(x_bins), max(x_bins))
     ax.set_ylim(min(y_bins), max(y_bins))
 

euphonic/qpoint_phonon_modes.py

@@ -347,10 +347,10 @@ def calculate_debye_waller(
         .. math::
 
           W^{\\alpha\\beta}_{\\kappa} =
-          \\frac{\\hbar}{4M_{\\kappa}\\sum\\limits_{\mathbf{q}}{\\mathrm{weight}_\mathbf{q}}}
-          \\sum\\limits_{\mathbf{q}\\nu \in{BZ}}\\mathrm{weight}_\mathbf{q}\\frac{e_{\mathbf{q}\\nu\\kappa\\alpha}e^{*}_{\mathbf{q}\\nu\\kappa\\beta}}
-          {\\omega_{\mathbf{q}\\nu}}
-          \\mathrm{coth}\\left(\\frac{\\hbar\\omega_{\mathbf{q}\\nu}}{2k_BT}\\right)
+          \\frac{\\hbar}{4M_{\\kappa}\\sum\\limits_{\\mathbf{q}}{\\mathrm{weight}_\\mathbf{q}}}
+          \\sum\\limits_{\\mathbf{q}\\nu \\in{BZ}}\\mathrm{weight}_\\mathbf{q}\\frac{e_{\\mathbf{q}\\nu\\kappa\\alpha}e^{*}_{\\mathbf{q}\\nu\\kappa\\beta}}
+          {\\omega_{\\mathbf{q}\\nu}}
+          \\mathrm{coth}\\left(\\frac{\\hbar\\omega_{\\mathbf{q}\\nu}}{2k_BT}\\right)
 
         Where the sum is over q-points and modes :math:`\\nu` in the
         first Brillouin Zone (BZ), :math:`\\kappa` runs over atoms,

euphonic/structure_factor.py

@@ -211,7 +211,7 @@ def calculate_sqw_map(self,
 
         .. math::
 
-          n_\\nu = \\frac{1}{\exp{\\frac{\\hbar\\omega_{\\mathbf{q}\\nu}}{k_{B}T}} - 1}
+          n_\\nu = \\frac{1}{\\exp{\\frac{\\hbar\\omega_{\\mathbf{q}\\nu}}{k_{B}T}} - 1}
 
         .. [1] M.T. Dove, Structure and Dynamics, Oxford University Press,
                Oxford, 2003, 225-226

euphonic/util.py

@@ -11,7 +11,7 @@
 import numpy as np
 import seekpath
 from seekpath.hpkot import SymmetryDetectionError
-from importlib_resources import open_text
+from importlib_resources import files
 from pint import UndefinedUnitError
 
 from euphonic import ureg, Quantity
@@ -222,7 +222,7 @@ def custom_decode(dct):
 
     if collection in _reference_data_files:
         filename = _reference_data_files[collection]
-        with open_text(euphonic.data, filename) as fd:
+        with open(files(euphonic.data) / filename) as fd:
             file_data = json.load(fd, object_hook=custom_decode)
 
     elif os.path.isfile(collection):

release.py

@@ -4,7 +4,6 @@
 import re
 import requests
 import subprocess
-from importlib_resources import open_text
 import yaml
 from euphonic import __version__