update build instructions, especially how to install requirements in windows

.gitignore

@@ -52,3 +52,5 @@ __pycache__/
 # PyCharm
 .idea/
 
+# Sphinx documentation
+documentation/_build/

documentation/building.rst

@@ -57,14 +57,14 @@ For installing the packages required for building the documentation with Sphinx:
 
 Windows
 =======
+Install the following requirements:
 
-On Windows, Visual Studio is the recommended toolchain with the Intel fortran compiler.
-CMake is readily available and a binary is supplied on the CMake `download page <CMakeDownload_>`_.
-SWIG 4.0 is available from the SWIG `download page <SWIGDownload_>`_.
-The latest release at this time is version 4.0.2.
-For Sphinx you will first need to have Python installed, which is required when creating the Python bindings anyway.
-Python 3.9 works well with Visual Studio 2017 when building Python extension libraries (which is what the bindings are when used from Python).
-Python 3.9 is availble from the Python `download page <PythonDownload>`_.
+* **Git**: `download page <GitDownload_>`_
+* **Python**: `download page <PythonDownload_>`_. Select the add to path option
+* **CMake**: `download page <CMakeDownload_>`_. Select the add to path option
+* **SWIG**: `download page <SWIGDownload_>`_. Extract and put in your Program Files (x86) directory, e.g.: C:\\Program Files (x86)\\SWIG\\swigwin-4.1.1
+* **Visual Studio**: `download page <VisualStudioDownload_>`_. (The community version is free). Install with C++ desktop development. Add the IDE folder to your Path environment variable, e.g.: C:\\Program Files\\Microsoft Visual Studio\\2022\\Community\\Common7\\IDE
+* **Intel Fortran Compiler**: `download page <IntelFortranCompilerDownload_>`_. Select the integrate with Visual Studio option.
 
 macOS
 =====
@@ -85,6 +85,7 @@ GNU/Linux
 The package manager for the distro will (most likely) have the required packages to install.
 Before installing check to see if any of the requirements are already available::
 
+  git --version
   gfortran --version
   cmake --version
   python --version
@@ -93,10 +94,12 @@ Before installing check to see if any of the requirements are already available:
 In the case of the python package we require the *development* package for python this must be installed for the python bindings to become available.
 For the Ubuntu distribution you can get the missing packages with the following commands::
 
-  sudo apt-get install gfortran
-  sudo apt-get install cmake
-  sudo apt-get install pythonX.Y-dev # Where X and Y are the major and minor version numbers of the Python you want to install, any version above 3.7 will work
-  sudo apt-get install swig
+    sudo apt install git
+    sudo apt install python3-dev
+    sudo apt install python-is-python3
+    sudo apt install cmake
+    sudo apt install gfortran
+    sudo apt install swig
 
 -----
 CMake
@@ -171,6 +174,13 @@ From the terminal change into the 'lungsim' directory, then run the **make** com
 .. note:: Not recently checked to see if this is still working.
 
 
+
+.. _IntelFortranCompilerDownload: https://www.intel.com/content/www/us/en/developer/tools/oneapi/hpc-toolkit-download.html
+
+.. _VisualStudioDownload: https://visualstudio.microsoft.com/downloads/
+
+.. _GitDownload: https://git-scm.com/downloads
+
 .. _CMakeDownload: https://cmake.org/download
 
 .. _SWIGDownload: http://www.swig.org/download.html

documentation/conf.py

@@ -36,7 +36,9 @@
     'sphinx.ext.ifconfig',
     'sphinxfortran.fortran_domain',
     'sphinxfortran.fortran_autodoc',
+    'sphinx.ext.autosectionlabel'
 ]
+autosectionlabel_prefix_document = True
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -53,7 +55,7 @@
 master_doc = 'index'
 
 # General information about the project.
-project = 'Ventilation'
+project = 'Aether'
 copyright = '2022, Lung Group ABI'
 author = 'Lung Group ABI'
 
@@ -81,7 +83,7 @@
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = []
+exclude_patterns = ["_build"]
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents.
@@ -167,9 +169,9 @@
 
 # Custom sidebar templates, maps document names to template names.
 #html_sidebars = {}
-html_sidebars = {
-   '**': ['localtoc.html', 'forksidebar.html', 'sourcelink.html', 'searchbox.html'],
-}
+# html_sidebars = {
+#    '**': ['localtoc.html', 'forksidebar.html', 'sourcelink.html', 'searchbox.html'],
+# }
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.

documentation/welcome.rst

@@ -0,0 +1,58 @@
+.. Auckland Bioengineering Lung Simulator master file, created by
+   Alys Clark on Fri 18 March 2016.
+
+========================================
+Welcome to the documentation for Aether!
+========================================
+
+Hello everyone! Welcome to the documentation for our lung code!
+
+The first thing we need to do to get going using this code is to :doc:`acquire </acquiring>` it then we can :doc:`build </building>` the aether library.
+Once we have built the library we can :doc:`run </running>` it.
+Before you start to develop the code make sure you read the section on :doc:`testing </testing>`.
+Lastly, before you ask to get your code merged make sure you have looked at the :doc:`modules </modules>` and :doc:`fortran styles </fortranstyles>` sections to ensure that you have followed the conventions for this codebase.
+
+Thanks and enjoy!
+
+Quick Start
+===========
+Install the requirements for :ref:`building:GNU/Linux` or :ref:`building:Windows`
+
+If you have all the requirements for building the aether libraries and bindings then the following commands are a quick description on how to get setup and using the library, for further information or clarification read the full documentation.
+
+Quick start instructions for GNU/Linux and macOS
+
+(bash)::
+
+  git clone https://github.com/LungNoodle/lungsim.git
+  python -m venv venv-aether
+  source venv-aether/bin/activate
+  pip install --upgrade pip
+  pip install numpy
+  here=$(pwd)
+  cmake -S lungsim -B build-lungsim -D Python_EXECUTABLE=$here/venv-aether/bin/python
+  cd build-lungsim
+  make
+  pip install -e src/bindings/python
+  python ../lungsim/.github/scripts/diagnostics_test.py
+
+Quick start instructions for Windows
+
+(Note: replace paths for -D SWIG_EXECUTABLE and -D SWIG_DIR with the relevant paths for your SWIG install)
+
+(cmd)::
+
+  git clone https://github.com/LungNoodle/lungsim.git
+  python -m venv venv-aether
+  python -m pip install --upgrade pip
+  venv-aether\Scripts\activate
+  pip install numpy
+  cmake -S lungsim -B build-lungsim -D Python_EXECUTABLE=%cd%/venv-aether/Scripts/python -D SWIG_EXECUTABLE="C:/Program Files (x86)/SWIG/swigwin-4.1.1/swig.exe" -D SWIG_DIR="C:/Program Files (x86)/SWIG/swigwin-4.1.1/lib"
+  cd build-lungsim
+  cmake --build . --config Release
+  pip install -e src\bindings\python\Release
+  python ..\lungsim\.github\scripts\diagnostics_test.py
+
+
+
+If all is successful, the final command should run a test python script with the output "test succeeded".