waltsims · waltsims · Dec 10, 2022 · Nov 26, 2022 · Nov 26, 2022 · Nov 27, 2022
diff --git a/README.md → docs/README.md b/README.md → docs/README.md
@@ -6,9 +6,6 @@ This project is a Python implementation of most of the [MATLAB toolbox k-Wave](h
 
 With this project, we hope to increase accessibility and reproducablitiy of [k-Wave](http://www.k-wave.org/) simulations for medical imaging, algorithmic prototyping and testing. Many tools and methods of [k-Wave](http://www.k-wave.org/) can be found here, but this project has and will continue to diverge from the original [k-Wave](http://www.k-wave.org/) APIs in order to leverage pythonic practices.
 
-## Documentation
-
-The documentation for k-wave-python can be found [here](http://waltersimson.com/k-wave-python/)
 
 ## Installation
 To install the most recent build of k-Wave-python from PyPI, run:
@@ -20,7 +17,7 @@ Currently, we are looking for beta testers on Windows.
 
 
 ## Getting started
-![](docs/images/example_bmode.png)
+![](_static/example_bmode.png)
 
 After installation, run the B-mode reconstruction example in the `examples` directory of the repository:
 
@@ -42,18 +39,25 @@ This example expects an NVIDIA GPU by default to simulate with k-Wave.
 
 To test the reconstruction on a machine with a GPU,
 set `RUN_SIMULATION` [on line 14 of `bmode_reconstruction_example.py`](https://github.com/waltsims/k-wave-python/blob/master/examples/bmode_reconstruction_example.py#L18)
-to `True` and the exmaple will run without the pre-computed data.
+to `True` and the example will run without the pre-computed data.
 
 ## Development
 
-If you're enjoying k-Wave-python and want to contribute, development instructions can be found [here](https://waltersimson.com/k-wave-python/development/development_environment.html).
+If you're enjoying k-Wave-python and want to contribute, development instructions can be
+found [here](https://waltersimson.com/k-wave-python/development/development_environment.html).
 
 ## Related Projects
 
-1. [`k-Wave`](https://github.com/ucl-bug/k-wave): A MATLAB toolbox for the time-domain simulation of acoustic wave fields. 
-2. [`j-wave`](https://github.com/ucl-bug/jwave): Differentiable acoustic simulations in JAX.
-3. [`ADSeismic.jl`](https://github.com/kailaix/ADSeismic.jl): a finite difference acoustic simulator with support for AD and JIT compilation in Julia.
-4. [`stride`](https://github.com/trustimaging/stride): a general optimisation framework for medical ultrasound tomography. 
+1. [k-Wave](https://github.com/ucl-bug/k-wave): A MATLAB toolbox for the time-domain simulation of acoustic wave fields.
+2. [j-wave](https://github.com/ucl-bug/jwave): Differentiable acoustic simulations in JAX.
+3. [ADSeismic.jl](https://github.com/kailaix/ADSeismic.jl): a finite difference acoustic simulator with support for AD
+   and JIT compilation in Julia.
+4. [stride](https://github.com/trustimaging/stride): a general optimisation framework for medical ultrasound tomography.
+
+## Documentation
+
+The documentation for k-wave-python can be found [here](http://waltersimson.com/k-wave-python/)
 
 ## Contact
+
 e-mail [walter.simson@tum.de](mailto:walter.simson@tum.de).
diff --git a/docs/images/example_bmode.png → docs/_static/example_bmode.png b/docs/images/example_bmode.png → docs/_static/example_bmode.png
diff --git a/docs/array.rst b/docs/array.rst
diff --git a/docs/conf.py b/docs/conf.py
@@ -1,69 +1,57 @@
 # Configuration file for the Sphinx documentation builder.
 #
-# This file only contains a selection of the most common options. For a full
-# list see the documentation:
+# For the full list of built-in configuration values, see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
-# -- Path setup --------------------------------------------------------------
-
-# 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('..'))
-
 # -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = 'k-Wave-python'
-copyright = '2021, Walter Simson, Farid Yagubbayli'
+project = 'k-wave-python'
+copyright = '2022, Walter Simson, Farid Yagubbayli'
 author = 'Walter Simson, Farid Yagubbayli'
+version = '0.1.0'
 
 # -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
-# 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.githubpages',
     'sphinx_toolbox.code',
+    'sphinx_copybutton',
     'sphinx.ext.coverage',
     'sphinx.ext.napoleon',
-    'sphinx.ext.viewcode'
+    'sphinx.ext.viewcode',
+    "m2r2"
 ]
 
-# Add any paths that contain templates here, relative to this directory.
+source_suffix = [".rst", ".md"]
 templates_path = ['_templates']
+exclude_patterns = ['README.md', '_build', 'Thumbs.db', '.DS_Store']
 
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-# This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+language = 'en'
 
 # -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+html_theme = 'furo'
+html_theme_options = {
+    "source_repository": "https://github.com/waltsims/k-wave-python",
+    "source_branch": "master",
+    "source_directory": "docs/",
+}
+html_static_path = ['_static']
 
-# The theme to use for HTML and HTML Help pages.  See the documentation for
-# a list of builtin themes.
-#
-html_theme = 'sphinx_rtd_theme'
+# -- Options for todo extension ----------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/extensions/todo.html#configuration
 
-# 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 = ['']
+todo_include_todos = True
 
-autodoc_default_options = {
-    'member-order': 'groupwise',
-    'undoc-members': True
-}
+# -- Options for autodoc ----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html#configuration
 
-html_context = {
-    "display_github": True,  # Integrate GitHub
-    "github_user": "waltsims",  # Username
-    "github_repo": "k-wave-python",  # Repo name
-    "github_version": "master",  # Version
-    "conf_py_path": "/docs/",  # Path in the checkout to the docs root
-}
+# Automatically extract typehints when specified and place them in
+# descriptions of the relevant function/method.
+autodoc_typehints = "description"
+
+# Don't show class signature with the class' name.
+autodoc_class_signature = "separated"
diff --git a/docs/examples/bmode.rst b/docs/examples/bmode.rst
diff --git a/docs/get_started/installation.rst b/docs/get_started/installation.rst
diff --git a/docs/index.rst b/docs/index.rst
@@ -3,50 +3,47 @@ Welcome to k-Wave-python's documentation!
 
 k-Wave is an open source acoustics toolbox for MATLAB and C++ developed by Bradley Treeby and Ben Cox (University College London) and Jiri Jaros (Brno University of Technology). The software is designed for time domain acoustic and ultrasound simulations in complex and tissue-realistic media. The simulation functions are based on the k-space pseudospectral method and are both fast and easy to use.
 
+.. mdinclude:: README.md
+   :start-line: 5
+   :end-line: -7
 
 .. toctree::
    :maxdepth: 2
    :caption: Getting Started
+   :hidden:
 
-   get_started/installation
    get_started/contrib
    get_started/license
 
-.. toctree::
-   :maxdepth: 2
-   :caption: Examples
-
-   examples/bmode
-
-
-.. toctree::
-   :maxdepth: 3
-   :caption: Base Modules
-
-   kgrid
-   kmedium
-   ksensor
-   ksource
-   kspace_fo
-   ksimulation
-
-.. toctree::
-   :maxdepth: 2
-   :caption: Helper Modules
-
-   simopt
-   array
-   recorder
-
 .. toctree::
    :maxdepth: 2
    :caption: Development
+   :hidden:
 
    development/development_environment
 
-Indices and tables
-==================
+.. toctree::
+   :caption: kwave
+   :titlesonly:
+   :maxdepth: 4
+   :hidden:
+
+   kwave.data
+   kwave.enums
+   kwave.executor
+   kwave.kWaveSimulation
+   kwave.kgrid
+   kwave.kmedium
+   kwave.ksensor
+   kwave.ksource
+   kwave.kspaceFirstOrder
+   kwave.kspaceFirstOrder2D
+   kwave.kspaceFirstOrder3D
+   kwave.kspaceFirstOrderAS
+   kwave.ktransducer
+   kwave.options
+   kwave.recorder
+   kwave.utils
+   kwave.kWaveSimulation_helper
+   kwave.reconstruction
 
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
diff --git a/docs/kgrid.rst b/docs/kgrid.rst
diff --git a/docs/kmedium.rst b/docs/kmedium.rst
diff --git a/docs/ksensor.rst b/docs/ksensor.rst
diff --git a/docs/ksimulation.rst b/docs/ksimulation.rst
diff --git a/docs/ksource.rst b/docs/ksource.rst
diff --git a/docs/kspace_fo.rst b/docs/kspace_fo.rst
diff --git a/docs/kwave.data.rst b/docs/kwave.data.rst
@@ -0,0 +1,7 @@
+kwave.data module
+=================
+
+.. automodule:: kwave.data
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/kwave.enums.rst b/docs/kwave.enums.rst
@@ -0,0 +1,7 @@
+kwave.enums module
+==================
+
+.. automodule:: kwave.enums
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/kwave.executor.rst b/docs/kwave.executor.rst
@@ -0,0 +1,7 @@
+kwave.executor module
+=====================
+
+.. automodule:: kwave.executor
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/kwave.kWaveSimulation.rst b/docs/kwave.kWaveSimulation.rst
@@ -0,0 +1,7 @@
+kwave.kWaveSimulation module
+============================
+
+.. automodule:: kwave.kWaveSimulation
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/kwave.kWaveSimulation_helper.create_absorption_variables.rst b/docs/kwave.kWaveSimulation_helper.create_absorption_variables.rst
@@ -0,0 +1,7 @@
+kwave.kWaveSimulation\_helper.create\_absorption\_variables module
+==================================================================
+
+.. automodule:: kwave.kWaveSimulation_helper.create_absorption_variables
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/kwave.kWaveSimulation_helper.create_storage_variables.rst b/docs/kwave.kWaveSimulation_helper.create_storage_variables.rst
@@ -0,0 +1,7 @@
+kwave.kWaveSimulation\_helper.create\_storage\_variables module
+===============================================================
+
+.. automodule:: kwave.kWaveSimulation_helper.create_storage_variables
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/kwave.kWaveSimulation_helper.data_cast.rst b/docs/kwave.kWaveSimulation_helper.data_cast.rst
@@ -0,0 +1,7 @@
+kwave.kWaveSimulation\_helper.data\_cast module
+===============================================
+
+.. automodule:: kwave.kWaveSimulation_helper.data_cast
+   :members:
+   :undoc-members:
+   :show-inheritance: