Development Notes

Notes on how to build the Documentation using Sphinx

We have chosen to use Google's style for writing the Python Docstrings because is easy to read in the code and also allows to generate documentation in different formats. The guidelines for writing Docstrings are stated in the PEP257 But no style is defined in there.

By default, Sphinx uses its own format for Python's Docstrings. But it is a bit hard to read, for instance:

def some_function(name, state):  
    """This function does something.

    :param name: The name to use.
    :type name: str.
    :param state: Current state to be in.
    :type state: bool.
    :returns: int -- the return code.
    :raises: AttributeError, KeyError
    
    """
    return True

The same function with Google Style Docstrings would be:

def some_function(name, state):
    """This Function does something
    
    Args:
        name (str): The name to use.
        state (bol): Current State to be in.
    
    Returns:
        int: The return code.
        
    Raises:
        AttributeError: Some description
        KeyError: Some other description

Everyone in our team agrees that Google style is easier to read. Sphinx's style produces better formatted output and gives you more control on formatting.

The good news is that it is possible to produce documentation using Google Style and Sphinx. There are a few necessary steps to achieve this:

Install Sphinx

Install sphinx.
```
$ pip install sphinx
```
Install Napoleon Plugin. Allows to use Google style with Sphinx.
```
$ pip install sphinxcontrib.napoleon
```

Go to your source folder and run sphinx-quickstart and adapt the following answers to your needs. (some parts were omitted)

$ sphinx-quickstart 
Welcome to the Sphinx 1.4.5 quickstart utility.

Please enter values for the following settings (just press Enter to
accept a default value, if one is given in brackets).

Enter the root path for documentation.
> Root path for the documentation [.]: docs

You have two options for placing the build directory for Sphinx output.
Either, you use a directory "_build" within the root path, or you separate
"source" and "build" directories within the root path.
> Separate source and build directories (y/n) [n]: y

Inside the root directory, two more directories will be created; "_templates"
for custom HTML templates and "_static" for custom stylesheets and other static
files. You can enter another prefix (such as ".") to replace the underscore.
> Name prefix for templates and static dir [_]: 

The project name will occur in several places in the built documentation.
> Project name: MyProject
> Author name(s): The Author
...
> Project version: 1.0
> Project release [1.0]: 
...
> Create Makefile? (y/n) [y]:

A file conf.py has been created in the folder docs. In there you need to change some settings:

Add sphinxcontrib.napoleon
Insert $PATH variable into the system
Add napoleon settings

# conf.py

# Add autodoc and napoleon to the extensions list
extensions = ['sphinx.ext.autodoc', 'sphinxcontrib.napoleon']

# Add source directory to PATH (where the modules are)
import sys
sys.path.append('/path/to/source')

# Napoleon settings
napoleon_google_docstring = True
napoleon_numpy_docstring = True
napoleon_include_init_with_doc = False
napoleon_include_private_with_doc = False
napoleon_include_special_with_doc = False
napoleon_use_admonition_for_examples = False
napoleon_use_admonition_for_notes = False
napoleon_use_admonition_for_references = False
napoleon_use_ivar = False
napoleon_use_param = True
napoleon_use_rtype = True
napoleon_use_keyword = True

Use sphinx-apidoc to build your documentation.

$ sphinx-apidoc -f -o docs/source projectdir

Or as I did from the home directory:

$ sphinx-apidoc -f -o ~/development/soar/goodman/docs/source ~/development/soar/goodman

Make your documentation. Go to ~/development/soar/goodman/docs and run the command below. There are more options for the output.
```
$ make html
```

Configure PyCharm to do it.

In PyCharm go to Run > Edit Configurations... and then click the green + symbol in the upper left corner (Pycharm Community Edition 2016.2) and choose Python Docs > Sphinx Task
A new dialog will open and it should look like this:

Apply or click OK. In the upper right corner of pycharm you should find the option for build-documentation if you used the same name for this particular configuration.

Local Management - How to use github pages

This section is incomplete if you need assistance in this regard please contact me

In oder to minimize the chance of making a mistake I set up the following configuration.

The code development directory is in ~/development/soar/goodman and the documentation is in ~/documentation/soar/goodman. The git repository is basically the same with the only difference being that in the documentation folder I checkout gh-pages and in development I work with the master branch or any of the project's branch.

Procedure

Create directories and clone from github

$ mkdir ~/development/soar
$ cd !*
$ git clone [email protected]:simontorres/goodman.git
$ 
$ cd
$ mkdir ~/documentation/soar/
$ cd !*
$ git clone [email protected]:simontorres/goodman.git
$ cd goodman
$ git checkout gh-pages

Inside your code development directory is a folder called docs. Here is where you run sphinx-quickstart. After this it will contain a file named Makefile and two folders source and build

Modify Makefile to build the documentation in a different location. Open the file using your favourite editor and change the BUILDDIR variable to:

BUILDDIR      = /HOME/USER/documentation/soar/goodman

It should look like this: (Note that I change the home directory for security reasons, change /HOME/USER by whatever matches your system)

# Minimal makefile for Sphinx documentation
#

# You can set these variables from the command line.
SPHINXOPTS    =
SPHINXBUILD   = sphinx-build
SPHINXPROJ    = GoodmanPipelines
SOURCEDIR     = source
BUILDDIR      = /HOME/USER/documentation/soar/goodman

# Put it first so that "make" without argument is like "make help".
help:
        @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

.PHONY: help Makefile

# Catch-all target: route all unknown targets to Sphinx using the new
# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
%: Makefile
        @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

How to include Markdown README to index

Although I will recomend to write an .rst file instead, I will include the necessary steps to achieve that. I didn't get the results I wanted with Markdown.

Install recommonmark
```
$ sudo pip2.7 install recommonmark
```

Edit Sphinx's conf.py and add the following lines.

from recommonmark.parser import CommonMarkParser

source_suffix = ['.rst', '.md']

source_parsers = {
    '.md' : CommonMarkParser,
}

go to docs/sources and add the following line to index.rst:

.. include:: README.md

So it will look like this:

Welcome to Goodman Spectroscopic Tools's documentation!
===========================================================

.. include:: README.md

Contents:

.. toctree::
   :maxdepth: 2

Indices and tables
======================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`

Use make html in your documentation's root folder (where the Makefile is located)
```
~/development/soar/goodman/docs$ make html
```
The new html documentation will be located at ~/documentation/soar/goodman/html. You need to move all its content to the parent directory i.e. ~/documentation/soar/goodman
```
$ cp -vr ~/documentation/soar/goodman/html/* ~/documentation/soar/goodman
```
Finally in add commit and push
```
$ git add *
$ git commit -m "updating html documentation"
$ git push
```
Then you can see the page in https://simontorres.github.io/goodman/

But you can also convert your Markdown README to .rst using pandoc.

```shell
$ sudo yum install pandoc
```

And you can use it with:

```shell
$ pandoc --from=markdown --to=rst --output=README.rst README.md 
```

Converting Markdown to .rst worked better for me. Also I would recommend some editing since you don't want all the README information to go to the web page, such as the link to the page itself for instance.

Final Thoughts

These tools are highly customizable so expect some troubles setting this up. Keep your eyes open and read very well the debug or feedback on the problem.

Goodman Data Reduction Pipeline WIKI

Goodman Pipeline

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Development Notes

Development Notes

Notes on how to build the Documentation using Sphinx

Install Sphinx

Configure PyCharm to do it.

Local Management - How to use github pages

Procedure

How to include Markdown README to index

Final Thoughts

Clone this wiki locally