Merge branch 'main' into develop

pyfar · Mar 15, 2024 · 2eea379 · 2eea379
2 parents 65465b0 + bfd3719
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -159,6 +159,7 @@ workflows:
                 - "3.9"
                 - "3.10"
                 - "3.11"
+                - "3.12"
       - flake:
           matrix:
             parameters:
@@ -196,6 +197,7 @@ workflows:
                 - "3.9"
                 - "3.10"
                 - "3.11"
+                - "3.12"
           filters:
             branches:
               ignore: /.*/

diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
@@ -59,7 +59,7 @@ Ready to contribute? Here's how to set up `pyfar` for local development using th
     $ flake8 pyfar tests
     $ pytest
 
-   flake8 test must pass without any warnings for `./pyfar` and `./tests` using the default or a stricter configuration. Flake8 ignores `E123/E133, E226` and `E241/E242` by default. If necessary adjust the your flake8 and linting configuration in your IDE accordingly.
+   flake8 test must pass without any warnings for `./pyfar` and `./tests` using the default or a stricter configuration. Flake8 ignores `E123/E133, E226` and `E241/E242` by default. If necessary adjust your flake8 and linting configuration in your IDE accordingly.
 
 6. Commit your changes and push your branch to GitHub::
 
@@ -207,7 +207,7 @@ Here are a few tips to make things run smoothly
 - Use ``[#]_`` and ``.. [#]`` to get automatically numbered footnotes.
 - Do not use footnotes in the short summary. Only use footnotes in the extended summary if there is a short summary. Otherwise, it messes with the auto-footnotes.
 - If a method or class takes or returns pyfar objects for example write ``parameter_name : Signal``. This will create a link to the ``pyfar.Signal`` class.
-- Plots can be included in by using the prefix ``.. plot::`` followed by an empty line and an indented block containing the code for the plot. See `pyfar.plot.line.time.py` for examples.
+- Plots can be included in the documentation by using the prefix ``.. plot::`` followed by an empty line and an indented block containing the code for the plot. See `pyfar.plot.line.time.py` for examples.
 
 See the `Sphinx homepage <https://www.sphinx-doc.org>`_ for more information.
 

diff --git a/HISTORY.rst b/HISTORY.rst
@@ -2,6 +2,13 @@
 History
 =======
 
+0.6.5 (2024-03-15)
+------------------
+* `Coordinates.show` now plots on equally scaled axis (PR #554)
+* Update documentation to pydata theme (PR #560)
+* Improve documentation (PR #544, #548, #549, #556)
+* Add testing for Python 3.12 (PR #561)
+
 0.6.4 (2024-02-16)
 ------------------
 * Bugfix in `pyfar.io.read_comsol_header`: Fix for reading expressions containing the characters '-', '[', and ']' (PR #535)

diff --git a/docs/_static/css/custom.css b/docs/_static/css/custom.css
@@ -0,0 +1,8 @@
+
+html[data-theme="light"] {
+    --pst-color-primary: #18609d; /* pyfar blue as primary color */
+}
+
+html[data-theme="dark"] {
+    --pst-color-primary: #18609d; /* pyfar blue as primary color */
+}
diff --git a/docs/_static/favicon.ico b/docs/_static/favicon.ico
diff --git a/docs/_templates/navbar-nav.html b/docs/_templates/navbar-nav.html
@@ -0,0 +1,41 @@
+<div class="navbar-item">
+    <nav class="navbar-nav">
+      <ul class="bd-navbar-elements navbar-nav">
+
+                        <li class="nav-item">
+                            <a class="nav-link" href="https://pyfar-gallery.readthedocs.io/en/latest/">
+                            Home
+                            </a>
+                        </li>
+
+                        <li class="nav-item">
+                            <a class="nav-link" href="https://pyfar-gallery.readthedocs.io/en/latest/examples_gallery.html">
+                                Examples
+                            </a>
+                        </li>
+
+                        <li class="nav-item">
+                            <a class="nav-link" href="https://pyfar.readthedocs.io/en/stable/">
+                              pyfar
+                            </a>
+                          </li>
+
+                        <li class="nav-item">
+                          <a class="nav-link" href="https://sofar.readthedocs.io/en/stable/">
+                            sofar
+                          </a>
+                        </li>
+
+                        <li class="nav-item">
+                          <a class="nav-link" href="https://spharpy.readthedocs.io/en/latest/">
+                            spharpy
+                          </a>
+                        </li>
+
+                        <li class="nav-item">
+                          <a class="nav-link" href="https://pyrato.readthedocs.io/en/latest/">
+                            pyrato
+                          </a>
+                        </li>
+      </ul>
+    </nav></div>
diff --git a/docs/concepts/resources/coordinate_systems.ai b/docs/concepts/resources/coordinate_systems.ai
diff --git a/docs/concepts/resources/coordinate_systems.png b/docs/concepts/resources/coordinate_systems.png
diff --git a/docs/conf.py b/docs/conf.py
@@ -1,37 +1,20 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
+# Configuration file for the Sphinx documentation builder.
 #
-# pyfar documentation build configuration file, created by
-# sphinx-quickstart on Fri Jun  9 13:47:02 2017.
-#
-# This file is execfile()d with the current directory set to its
-# containing dir.
-#
-# Note that not all possible configuration values are present in this
-# autogenerated file.
-#
-# All configuration values have a default; values that are commented out
-# serve to show the default.
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-# If extensions (or modules to document with autodoc) are in another
-# directory, add these directories to sys.path here. If the directory is
-# relative to the documentation root, use os.path.abspath to make it
-# absolute, like shown here.
-#
 import os
 import sys
 sys.path.insert(0, os.path.abspath('..'))
 
 import pyfar  # noqa
 
-# -- General configuration ---------------------------------------------
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
-# If your documentation needs a minimal Sphinx version, state it here.
-#
-# needs_sphinx = '1.0'
-
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = [
     'sphinx.ext.autodoc',
     'sphinx.ext.viewcode',
@@ -40,7 +23,10 @@
     'matplotlib.sphinxext.plot_directive',
     'sphinx.ext.mathjax',
     'sphinx.ext.intersphinx',
-    'autodocsumm']
+    'autodocsumm',
+    'sphinx_design',
+    'sphinx_favicon',
+]
 
 # show tocs for classes and functions of modules using the autodocsumm
 # package
@@ -51,21 +37,19 @@
 plot_include_source = True
 
 # Add any paths that contain templates here, relative to this directory.
-# templates_path = ['_templates']
+templates_path = ['_templates']
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
-#
-# source_suffix = ['.rst', '.md']
 source_suffix = '.rst'
 
 # The master toctree document.
 master_doc = 'index'
 
 # General information about the project.
-project = u'pyfar'
-copyright = u"2020-2022, The pyfar developers"
-author = u"The pyfar developers"
+project = 'pyfar'
+copyright = '2020, The pyfar developers'
+author = 'The pyfar developers'
 
 # The version info for the project you're documenting, acts as replacement
 # for |version| and |release|, also used in various other places throughout
@@ -76,9 +60,6 @@
 # The full version, including alpha/beta/rc tags.
 release = pyfar.__version__
 
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-#
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
 language = 'en'
@@ -109,86 +90,40 @@
     'spharpy': ('https://spharpy.readthedocs.io/en/stable/', None)
     }
 
-# -- Options for HTML output -------------------------------------------
-
-# The theme to use for HTML and HTML Help pages.  See the documentation for
-# a list of builtin themes.
-#
-html_theme = 'insipid'
-
-# Theme options are theme-specific and customize the look and feel of a
-# theme further.  For a list of options available for each theme, see the
-# documentation.
-#
-# html_theme_options = {}
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-# html_static_path = ['_static']
-
-
-# -- Options for HTMLHelp output ---------------------------------------
-
-# Output file base name for HTML help builder.
-htmlhelp_basename = 'pyfardoc'
-
-
-# -- Options for LaTeX output ------------------------------------------
-
-latex_elements = {
-    # The paper size ('letterpaper' or 'a4paper').
-    #
-    # 'papersize': 'letterpaper',
-
-    # The font size ('10pt', '11pt' or '12pt').
-    #
-    # 'pointsize': '10pt',
-
-    # Additional stuff for the LaTeX preamble.
-    #
-    # 'preamble': '',
-
-    # Latex figure (float) alignment
-    #
-    # 'figure_align': 'htbp',
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'pydata_sphinx_theme'
+html_static_path = ['_static']
+html_css_files = ['css/custom.css']
+html_logo = 'resources/logos/pyfar_logos_fixed_size_pyfar.png'
+html_title = "pyfar"
+html_favicon = '_static/favicon.ico'
+
+# -- HTML theme options
+# https://pydata-sphinx-theme.readthedocs.io/en/stable/user_guide/layout.html
+
+html_theme_options = {
+    "navbar_start": ["navbar-logo"],
+    "navbar_end": ["navbar-icon-links", "theme-switcher"],
+    "navbar_align": "content",
+    "icon_links": [
+        {
+          "name": "GitHub",
+          "url": "https://github.com/pyfar",
+          "icon": "fa-brands fa-square-github",
+          "type": "fontawesome",
+        },
+    ],
+    # Configure secondary (right) side bar
+    "show_toc_level": 3,  # Show all subsections of notebooks
+    "secondary_sidebar_items": ["page-toc"],  # Omit 'show source' link that that shows notebook in json format
+    "navigation_with_keys": True,
 }
 
-# Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title, author, documentclass
-# [howto, manual, or own class]).
-latex_documents = [
-    (master_doc, 'pyfar.tex',
-     u'pyfar Documentation',
-     u'Marco Berzborn', 'manual'),
-]
-
-
-# -- Options for manual page output ------------------------------------
-
-# One entry per manual page. List of tuples
-# (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'pyfar',
-     u'pyfar Documentation',
-     [author], 1)
-]
-
-
-# -- Options for Texinfo output ----------------------------------------
-
-# Grouping the document tree into Texinfo files. List of tuples
-# (source start file, target name, title, author,
-#  dir menu entry, description, category)
-texinfo_documents = [
-    (master_doc, 'pyfar',
-     u'pyfar Documentation',
-     author,
-     'pyfar',
-     'One line description of project.',
-     'Miscellaneous'),
-]
-
+html_context = {
+   "default_mode": "light"
+}
 
 # -- pyfar specifics -----------------------------------------------------
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -2,9 +2,6 @@
    :width: 150
    :alt: Alternative text
 
-|pyfar_logo|
-
-
 Getting Started
 ===============
 
@@ -35,7 +32,7 @@ Contributing
 ===============
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 1
 
    contributing
 

diff --git a/docs/resources/logos/pyfar_logos_fixed_size_pyfar.png b/docs/resources/logos/pyfar_logos_fixed_size_pyfar.png
diff --git a/pyfar/__init__.py b/pyfar/__init__.py
@@ -4,7 +4,7 @@
 
 __author__ = """The pyfar developers"""
 __email__ = ''
-__version__ = '0.6.4'
+__version__ = '0.6.5'
 
 
 from .classes.audio import Signal, TimeData, FrequencyData

diff --git a/pyfar/_concepts/coordinates.py b/pyfar/_concepts/coordinates.py
@@ -19,9 +19,10 @@
 Coordinate Systems
 ------------------
 
-Coordinate systems are defined by their `domain` (e.g. ``'spherical'``),
-`convention` (e.g. ``'top_elev'``), and `unit` (e.g. ``'deg'``). The available
-coordinate systems are shown in the image below
+Coordinate systems are defined by their domain (cartesian, spherical,
+cylindrical), and, if multiple definitions of the domain exist, also by
+their convention. The available coordinate systems are shown
+in the image below
 
 |coordinate_systems|
 

diff --git a/pyfar/classes/coordinates.py b/pyfar/classes/coordinates.py
@@ -1399,12 +1399,20 @@ def show(self, mask=None, **kwargs):
 
         """
         if mask is None:
-            pf.plot.scatter(self, **kwargs)
+            ax = pf.plot.scatter(self, **kwargs)
         else:
             mask = np.asarray(mask)
             colors = np.full(self.cshape, pf.plot.color('b'))
             colors[mask] = pf.plot.color('r')
-            pf.plot.scatter(self, c=colors.flatten(), **kwargs)
+            ax = pf.plot.scatter(self, c=colors.flatten(), **kwargs)
+
+        ax.set_box_aspect([
+            np.ptp(self.x),
+            np.ptp(self.y),
+            np.ptp(self.z)])
+        ax.set_aspect('equal')
+
+        return ax
 
     def find_nearest(self, find, k=1, distance_measure='euclidean'):
         """
@@ -2651,17 +2659,8 @@ def __repr__(self):
         else:
             obj = "Empty Coordinates object"
 
-        # coordinate convention
-        conv = "domain: {}, convention: {}, unit: {}".format(
-            self._system['domain'], self._system['convention'],
-            self._system['unit'])
-
-        # coordinates and units
-        coords = ["{} in {}".format(c, u) for c, u in
-                  zip(self._system['coordinates'], self._system['units'])]
-
         # join information
-        _repr = obj + "\n" + conv + "\n" + "coordinates: " + ", ".join(coords)
+        _repr = obj + "\n"
 
         # check for sampling weights
         if self._weights is None: