LungNoodle · behdadebsh · Dec 2, 2024 · Dec 2, 2024 · Dec 2, 2024
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -0,0 +1,14 @@
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
+sphinx:
+  configuration: documentation/conf.py
+
+python:
+  install:
+    - requirements: documentation/requirements.txt
+
diff --git a/documentation/Modules/geometry.rst b/documentation/Modules/geometry.rst
@@ -1,11 +1,9 @@
-
 ==============================
 Geometry module (geometry.f90)
 ==============================
 
 **Module** :f:mod:`geometry`
 ============================
 
-.. f:module:: geometry
-
 .. f:automodule:: geometry
+
diff --git a/documentation/_build/html/.buildinfo b/documentation/_build/html/.buildinfo
@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 2158315c2475c53ae41f5d33cf603b62
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/documentation/_build/html/.doctrees/Modules/arrays.doctree b/documentation/_build/html/.doctrees/Modules/arrays.doctree
diff --git a/documentation/_build/html/.doctrees/Modules/geometry.doctree b/documentation/_build/html/.doctrees/Modules/geometry.doctree
diff --git a/documentation/_build/html/.doctrees/acquiring.doctree b/documentation/_build/html/.doctrees/acquiring.doctree
diff --git a/documentation/_build/html/.doctrees/adding_modules.doctree b/documentation/_build/html/.doctrees/adding_modules.doctree
diff --git a/documentation/_build/html/.doctrees/building.doctree b/documentation/_build/html/.doctrees/building.doctree
diff --git a/documentation/_build/html/.doctrees/environment.pickle b/documentation/_build/html/.doctrees/environment.pickle
diff --git a/documentation/_build/html/.doctrees/fortranstyles.doctree b/documentation/_build/html/.doctrees/fortranstyles.doctree
diff --git a/documentation/_build/html/.doctrees/index.doctree b/documentation/_build/html/.doctrees/index.doctree
diff --git a/documentation/_build/html/.doctrees/modules.doctree b/documentation/_build/html/.doctrees/modules.doctree
diff --git a/documentation/_build/html/.doctrees/running.doctree b/documentation/_build/html/.doctrees/running.doctree
diff --git a/documentation/_build/html/.doctrees/testing.doctree b/documentation/_build/html/.doctrees/testing.doctree
diff --git a/documentation/_build/html/.doctrees/wrapping.doctree b/documentation/_build/html/.doctrees/wrapping.doctree
diff --git a/documentation/_build/html/Modules/arrays.html b/documentation/_build/html/Modules/arrays.html
@@ -0,0 +1,96 @@
+<!DOCTYPE html>
+
+<html lang="en">
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
+
+    <title>Arrays module (arrays.f90) &#8212; Ventilation 1.0.0 documentation</title>
+    <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
+    <link rel="stylesheet" type="text/css" href="../_static/alabaster.css" />
+    <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
+    <script src="../_static/doctools.js"></script>
+    <script src="../_static/sphinx_highlight.js"></script>
+    <link rel="icon" href="../_static/airways_transparent.ico"/>
+    <link rel="index" title="Index" href="../genindex.html" />
+    <link rel="search" title="Search" href="../search.html" />
+    <link rel="next" title="Geometry module (geometry.f90)" href="geometry.html" />
+    <link rel="prev" title="Wrapping a module" href="../wrapping.html" />
+
+  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
+
+
+  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
+
+  </head><body>
+
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+
+
+          <div class="body" role="main">
+
+  <section id="arrays-module-arrays-f90">
+<h1>Arrays module (arrays.f90)<a class="headerlink" href="#arrays-module-arrays-f90" title="Permalink to this heading">¶</a></h1>
+<section id="f/arrays">
+<span id="module-arrays"></span><h2><strong>Module</strong> <a class="reference internal" href="#f/arrays" title="f/arrays"><code class="xref f f-mod docutils literal notranslate"><span class="pre">arrays</span></code></a><a class="headerlink" href="#f/arrays" title="Permalink to this heading">¶</a></h2>
+</section>
+</section>
+
+
+          </div>
+
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+        <div class="sphinxsidebarwrapper">
+            <p class="logo"><a href="../index.html">
+              <img class="logo" src="../_static/airways_transparent.jpg" alt="Logo"/>
+            </a></p>
+  <div>
+    <h3><a href="../index.html">Table of Contents</a></h3>
+    <ul>
+<li><a class="reference internal" href="#">Arrays module (arrays.f90)</a><ul>
+<li><a class="reference internal" href="#f/arrays"><strong>Module</strong> <code class="xref f f-mod docutils literal notranslate"><span class="pre">arrays</span></code></a></li>
+</ul>
+</li>
+</ul>
+
+  </div><div>
+<h3>Get the source code</h3>
+<iframe src="https://ghbtns.com/github-btn.html?user=LungNoodle&repo=lungsim&type=fork&count=true&size=large" frameborder="0" scrolling="0" width="170px" height="30px"></iframe>
+</div>
+<div id="searchbox" style="display: none" role="search">
+  <h3 id="searchlabel">Quick search</h3>
+    <div class="searchformwrapper">
+    <form class="search" action="../search.html" method="get">
+      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
+      <input type="submit" value="Go" />
+    </form>
+    </div>
+</div>
+<script>document.getElementById('searchbox').style.display = "block"</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="footer">
+      &copy;2022, Lung Group ABI.
+
+      |
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 7.0.1</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.13</a>
+
+    </div>
+
+
+    <a href="https://github.com/LungNoodle/lungsim" class="github">
+        <img style="position: absolute; top: 0; right: 0; border: 0;" src="https://s3.amazonaws.com/github/ribbons/forkme_right_darkblue_121621.png" alt="Fork me on GitHub"  class="github"/>
+    </a>
+
+
+
+  </body>
+</html>
diff --git a/documentation/_build/html/Modules/geometry.html b/documentation/_build/html/Modules/geometry.html
@@ -0,0 +1,95 @@
+<!DOCTYPE html>
+
+<html lang="en">
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
+
+    <title>Geometry module (geometry.f90) &#8212; Ventilation 1.0.0 documentation</title>
+    <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
+    <link rel="stylesheet" type="text/css" href="../_static/alabaster.css" />
+    <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
+    <script src="../_static/doctools.js"></script>
+    <script src="../_static/sphinx_highlight.js"></script>
+    <link rel="icon" href="../_static/airways_transparent.ico"/>
+    <link rel="index" title="Index" href="../genindex.html" />
+    <link rel="search" title="Search" href="../search.html" />
+    <link rel="prev" title="Arrays module (arrays.f90)" href="arrays.html" />
+
+  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
+
+
+  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
+
+  </head><body>
+
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+
+
+          <div class="body" role="main">
+
+  <section id="geometry-module-geometry-f90">
+<h1>Geometry module (geometry.f90)<a class="headerlink" href="#geometry-module-geometry-f90" title="Permalink to this heading">¶</a></h1>
+<section id="module-geometry">
+<h2><strong>Module</strong> <code class="xref f f-mod docutils literal notranslate"><span class="pre">geometry</span></code><a class="headerlink" href="#module-geometry" title="Permalink to this heading">¶</a></h2>
+</section>
+</section>
+
+
+          </div>
+
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+        <div class="sphinxsidebarwrapper">
+            <p class="logo"><a href="../index.html">
+              <img class="logo" src="../_static/airways_transparent.jpg" alt="Logo"/>
+            </a></p>
+  <div>
+    <h3><a href="../index.html">Table of Contents</a></h3>
+    <ul>
+<li><a class="reference internal" href="#">Geometry module (geometry.f90)</a><ul>
+<li><a class="reference internal" href="#module-geometry"><strong>Module</strong> <code class="xref f f-mod docutils literal notranslate"><span class="pre">geometry</span></code></a></li>
+</ul>
+</li>
+</ul>
+
+  </div><div>
+<h3>Get the source code</h3>
+<iframe src="https://ghbtns.com/github-btn.html?user=LungNoodle&repo=lungsim&type=fork&count=true&size=large" frameborder="0" scrolling="0" width="170px" height="30px"></iframe>
+</div>
+<div id="searchbox" style="display: none" role="search">
+  <h3 id="searchlabel">Quick search</h3>
+    <div class="searchformwrapper">
+    <form class="search" action="../search.html" method="get">
+      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
+      <input type="submit" value="Go" />
+    </form>
+    </div>
+</div>
+<script>document.getElementById('searchbox').style.display = "block"</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="footer">
+      &copy;2022, Lung Group ABI.
+
+      |
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 7.0.1</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.13</a>
+
+    </div>
+
+
+    <a href="https://github.com/LungNoodle/lungsim" class="github">
+        <img style="position: absolute; top: 0; right: 0; border: 0;" src="https://s3.amazonaws.com/github/ribbons/forkme_right_darkblue_121621.png" alt="Fork me on GitHub"  class="github"/>
+    </a>
+
+
+
+  </body>
+</html>
diff --git a/documentation/_build/html/_sources/Modules/arrays.rst.txt b/documentation/_build/html/_sources/Modules/arrays.rst.txt
@@ -0,0 +1,11 @@
+
+==========================
+Arrays module (arrays.f90)
+==========================
+
+**Module** :f:mod:`arrays`
+==========================
+
+.. f:module:: arrays
+
+.. f:automodule:: arrays
diff --git a/documentation/_build/html/_sources/Modules/geometry.rst.txt b/documentation/_build/html/_sources/Modules/geometry.rst.txt
@@ -0,0 +1,9 @@
+==============================
+Geometry module (geometry.f90)
+==============================
+
+**Module** :f:mod:`geometry`
+============================
+
+.. f:automodule:: geometry
+
diff --git a/documentation/_build/html/_sources/acquiring.rst.txt b/documentation/_build/html/_sources/acquiring.rst.txt
@@ -0,0 +1,55 @@
+
+=========
+Acquiring
+=========
+
+The first step to working with the pulmonary simulation library is to acquire it.
+The easiest way to obtain the codebase is to use git and clone the source code.
+It is also possible to acquire the codebase as a zip archive if git is not available.
+
+---
+Git
+---
+
+Git is the distributed source control management tool in wide use by millions of software developers and engineers.
+If git is not available on your platform the following sub-sections provide guidance an how to acquire it.
+
+Windows
+=======
+
+On Windows download `Git for windows <https://git-scm.com/download/win>`_ and install in the usual manner.
+
+OS X
+====
+
+OS X comes preloaded with git and is available directly from the command prompt.
+
+GNU/Linux
+=========
+
+The package manager for the distro will (most likely) have the required package to install.
+Before installing check to see if git is already available::
+
+  git --version
+
+If git is not available you can install the package on an Ubuntu distribution with the following command::
+
+  sudo apt-get install git
+
+Other distributions will have a similar command.
+
+Get the Source Code with Git
+============================
+
+With git installed we can acquire the codebase with the command::
+
+  git clone https://github.com/LungNoodle/lungsim.git
+
+---
+Zip
+---
+
+To download a zip archive of the current *develop* branch use a web browser to visit this page https://github.com/LungNoodle/lungsim/archive/develop.zip.
+Then simply unzip the archive::
+
+  unzip lungsim-develop.zip
diff --git a/documentation/_build/html/_sources/adding_modules.rst.txt b/documentation/_build/html/_sources/adding_modules.rst.txt
@@ -0,0 +1,32 @@
+===================
+How to add a module
+===================
+
+First using the correct fortran style, begin to write your module:
+
+.. toctree::
+   :maxdepth: 1
+
+   fortranstyles 
+
+Next we need to include it as a module for CMake. From your lungsim root directory, open CMakeLists.txt in the ./src/lib directory and insert the module into the list of source files by adding the following line in the appropriate place (source files are listed in alphabetical order under the *LIB_SRCS* variable, CMake will sort out the compilation order)::
+
+    module_name.f90
+
+Now we need to set up bindings. Create the following files, and fill in their contents appropriately (the details of which can be found in :doc:`wrapping`)::
+
+    ./src/bindings/c/module_name.c
+
+    ./src/bindings/c/module_name.f90
+
+    ./src/bindings/c/module_name.h
+
+    ./src/bindings/interface/module_name.i
+
+and add the c bindings sources named after your module into the appropriate CMake variable (one of *C_FORTRAN_LIB_SRCS*, *C_C_LIB_SRCS*, *C_LIB_HDRS*) in::
+
+    ./src/bindings/c/CMakeLists.txt
+
+and lastly add the interface source named after your module into the CMake variable *INTERFACE_SRCS* in::
+
+    ./src/bindings/python/CMakeLists.txt