.. Vector3D documentation master file, created by
   sphinx-quickstart on Sun Sep  1 19:45:24 2019.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Welcome to Vector3D's documentation!
====================================

This is a simple example of how to test and document your code using `travis-ci` and `sphinx`.


Testing CI and github-pages
===========================

Testing with Continous Itegration (CI)
--------------------------------------

.. |Build Status| image:: https://travis-ci.com/finsberg/vector3D.svg?branch=master
   :target: https://travis-ci.com/finsberg/vector3D


We would like to run our tests every time we push in order to make sure
that any update to the code does not break any core functionality.

Follow the `instructions <https://docs.travis-ci.com/user/tutorial/>`__
on how to set up travis-ci.

For more information about how to test your python project check out the
`documentation <https://docs.travis-ci.com/user/languages/python/>`__

Add a badge with the information about whether test passed or not. In my
case this was

|Build Status|

Creating documentation for your code.
-------------------------------------

We will use ``sphinx`` to generate documentation and we will publish the
documentation using github pages. Create a the directory ``docs`` where we will
put the documentation

:: 

   mkdir docs
   cd docs 

Now we run the ``sphinx-quickstart`` which is the
first step in generating documentation. This will ask you some
questions, and I will reply as follows

::

   $ sphinx-quickstart
   Welcome to the Sphinx 1.8.3 quickstart utility.

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

   Selected root path: .

   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: Vector3D
   > Author name(s): Henrik Finsberg
   > Project release []: 2.0

   If the documents are to be written in a language other than English,
   you can select a language here by its language code. Sphinx will then
   translate text that it generates into that language.

   For a list of supported codes, see
   http://sphinx-doc.org/config.html#confval-language.
   > Project language [en]:

   The file name suffix for source files. Commonly, this is either ".txt"
   or ".rst".  Only files with this suffix are considered documents.
   > Source file suffix [.rst]:

   One document is special in that it is considered the top node of the
   "contents tree", that is, it is the root of the hierarchical structure
   of the documents. Normally, this is "index", but if your "index"
   document is a custom template, you can also set this to another filename.
   > Name of your master document (without suffix) [index]:
   Indicate which of the following Sphinx extensions should be enabled:
   > autodoc: automatically insert docstrings from modules (y/n) [n]: y
   > doctest: automatically test code snippets in doctest blocks (y/n) [n]:
   > intersphinx: link between Sphinx documentation of different projects (y/n) [n]: y
   > todo: write "todo" entries that can be shown or hidden on build (y/n) [n]:
   > coverage: checks for documentation coverage (y/n) [n]:
   > imgmath: include math, rendered as PNG or SVG images (y/n) [n]:
   > mathjax: include math, rendered in the browser by MathJax (y/n) [n]: y
   > ifconfig: conditional inclusion of content based on config values (y/n) [n]:
   > viewcode: include links to the source code of documented Python objects (y/n) [n]: y
   > githubpages: create .nojekyll file to publish the document on GitHub pages (y/n) [n]: y

   A Makefile and a Windows command file can be generated for you so that you
   only have to run e.g. `make html' instead of invoking sphinx-build
   directly.
   > Create Makefile? (y/n) [y]:
   > Create Windows command file? (y/n) [y]: n

   Creating file ./source/conf.py.
   Creating file ./source/index.rst.
   Creating file ./Makefile.

   Finished: An initial directory structure has been created.

   You should now populate your master file ./source/index.rst and create other documentation
   source files. Use the Makefile to build the docs, like so:
      make builder
   where "builder" is one of the supported builders, e.g. html, latex or linkcheck.

You can look at your documentation by running

::

   make html
   python -m http.server

Then open a web-browser and go to http://localhost:8000, and navigate to
build/html.

Creating API documentation
~~~~~~~~~~~~~~~~~~~~~~~~~~

Now we will make the documentation for our python package

::

   sphinx-apidoc -o source/ ..

If you now try to run ``make html`` then you will get the following
error:

::

   WARNING: autodoc: failed to import module 'test_vector'; the following exception was raised:
   No module named 'test_vector'
   WARNING: autodoc: failed to import module 'vector'; the following exception was raised:
   No module named 'vector'.

To fix this open ``source/conf.py`` and add the following lines at the
top

.. code:: python

   import os
   import sys

   sys.path.insert(0, os.path.abspath("../.."))

Now if you try to run ``make html``, you will get a new warining saying:
``Unexpected section title``, and this is because I have documented the
code using the numpy style, which is not default. Open source/conf.py
and add ``sphinx.ext.napoleon`` to the list called extensions. Let us
also change the html theme. Scroll down and set
``html_theme = "sphinx_rtd_theme"``, and run pip install
sphinx-rtd-theme.

You can look at your documentation by running

::

   make html
   python -m http.server

Then open a web-browser and go to http://localhost:8000, and navigate to
build/html.

Now you can also add some more information to ``source/index.rst`` in
order to display some more information on the index page. I have in this
example converted the README file to restructured text (.rst) and pasted
this in.

Building documenation that will be hosted on github pages
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Create a new branch called ``gh-pages``

::

   git checkout -b gh-pages

Now delete everything in the repo and commit it

::

   rm -r *
   git add -u
   git commit -m "Remove all files"

Now go back to the ``master`` brach and build the documentation.

::

   git checkout master
   cd docs
   make html

This will build the html documentation. Now checkout the ``gh-pages``
branch again, move the html files to the root folder and add them.

::

   git checkout gh-pages
   mv docs/build/html/* .
   rm -r docs
   git add .
   commit -m "Adding documentation"

All steps can be summarized in the following bash script

.. code:: shell

   git checkout master
   cd docs
   make html
   cd ..
   git checkout gh-pages
   cp -r docs/build/html/* .
   rm -r docs *py README.md LICENSE
   git add .
   git commit -m "Update documentation"
   git push -u origin gh-pages
   git checkout master

Finally go to GitHub, click on settings. Scroll down to the section
called GitHub pages, and select ``gh-pages branch``. It will now tell
you that your site will be published at
https://username.github.io/vector3D, in my case this is
https://finsberg.github.io/vector3D


Problems with style-sheets
~~~~~~~~~~~~~~~~~~~~~~~~~~

If your site is displaying but the styling is wrong then you can try to
add an empty file called ``.nojekyll`` to the ``gh-pages`` branch, i.e

::

   git checkout gh-pages
   touch .nojekyll
   git add .nojekyll
   git commit -m "Add .nojekyll"
   git push -u origin gh-pages
   git checkout master


Installing a pre-commit hooks
=============================

A pre-commit hook is a hook (or a small program) that runs every time
you try to commit to you repository. In this tutorial we will show how
you can set up a pre-commit hook that runs black and flake8 every time
you try to commit. If black and flake8 gives you thumbs up, then your
changes will be commited, otherwise you will be asked to revise your
code and change it so that black and flake8 passes.

First you need to install the ``pre-commit`` package
(https://pre-commit.com). Therearefter you need to add a
pre-commit-config file to your repository. Add a file called
``.pre-commit-config.yaml`` with the following content (taken from
https://ljvmiranda921.github.io/notebook/2018/06/21/precommits-using-black-and-flake8/)

::

   -   repo: https://github.com/ambv/black
       rev: stable
       hooks:
       - id: black
         language_version: python3.7
   -   repo: https://github.com/pre-commit/pre-commit-hooks
       rev: v1.2.3
       hooks:
       - id: flake8

Now commit this file to your repository and run the command
``pre-commit install``

.. toctree::
   :maxdepth: 2
   :caption: Contents:

   modules

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

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