Fix #2: Create a documentation

I added the structure for a documentation using Sphinx. I started as
well to add the documentation API.

This is not perfect though as no autodoc processor exists for such type
of files.

Signed-off-by: Matthieu Berjon <matthieu@berjon.net>

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = PsychHead
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# 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)

docs/make.bat

@@ -0,0 +1,36 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+set SPHINXPROJ=PsychHead
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

docs/source/api.rst

@@ -0,0 +1,40 @@
+Psych Head API
+==============
+
+The package include several functions that are distributed along a certain
+architecture.
+
+Analysis
+--------
+
+This part is related to data analysis and plotting such as psychometric
+functions, p50's and Probit analysis.
+
+**ComputePsychFunc**
+  Compute the psychometric function for one parameter based on a 2AFC. The
+  parameters has to be the first column. The answer on the second column.
+
+.. code-block:: matlab
+
+  [param good_ans_perc] = ComputePsychFunc(data, answer_comp)
+
+**LauraPlot**
+  Plot the psychometric function for the intensity experiment.
+
+.. code-block:: matlab
+
+  [figure_handle p50] = LauraPlot(filename)
+
+**ProbitFit**
+  Curve fitting using a probit analysis.
+
+.. code-block:: matlab
+  
+  [fitlogsignal, prob_perc, p50, logsignal, n, p75, p84, chi_sq, rsq, D] = ProbitFit(signal, pcCorrent, numstim)
+
+**ProbitStripped**
+  Curve fitting using a probit analysis with a less verbose output.
+
+.. code-block:: matlab
+  
+  [figure, p50, p75, p84, ch_sq, Rsq, D] = ProbitStripped(signal, pcCorrect, numstim, isPlot, asymptotes)

docs/source/conf.py

@@ -0,0 +1,157 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# Psych Head documentation build configuration file, created by
+# sphinx-quickstart on Sun Jan  1 18:28:14 2017.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+# 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('.'))
+
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = []
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = 'Psych Head'
+copyright = '2017, Matthieu Berjon'
+author = 'Matthieu Berjon'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = '1.0.1'
+# The full version, including alpha/beta/rc tags.
+release = '1.0.1'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# 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 = ['_static']
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'PsychHeaddoc'
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'PsychHead.tex', 'Psych Head Documentation',
+     'Matthieu Berjon', 'manual'),
+]
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'psychhead', 'Psych Head Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'PsychHead', 'Psych Head Documentation',
+     author, 'PsychHead', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+

docs/source/index.rst

@@ -0,0 +1,27 @@
+.. Psych Head documentation master file, created by
+   sphinx-quickstart on Sun Jan  1 18:28:14 2017.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to Psych Head
+=====================
+
+This project has been developed within the Action and Perception group of the
+school of Psychology at Cardiff University. A new audiovisual lab has been
+created and needed a bit of code in order to be analyse the data provided by
+the measurements and simulations. [Octave][1] has been chosen for several
+reasons:
+
+* Open source software
+* Good compatibility with Matlab (used inside the Lab)
+* Good toolboxes for signal processing
+
+Please, download it, study it, improve it and share it!
+
+.. toctree::
+   :maxdepth: 2
+
+   install
+   api
+
+

docs/source/install.rst

@@ -0,0 +1,13 @@
+Installation
+============
+
+At the moment, even if the library isn't a proper package, the installation
+process is straight forward. Clone the repository or extract the archive in
+your home directory `~/` (or wherever it suits you best) and edit the
+`~/Octaverc` file by adding the following line:
+
+.. code-block:: bash
+
+  addpath('<directory/where/are/stored/the/files>')
+
+This will load the library at startup.