changed theme and added chapters

docs/1. Philosophical Foundations.rst

@@ -0,0 +1,14 @@
+Philosophical Foundations
+=========================
+
+Origins of Epistemology: from Socrates to Descartes 
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Insert subchapter here
+
+Fallibilism and Falsificationism: Hume and Popper 
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Insert subchapter here
+
+What is probability? Bayes contra Hume
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Insert subchapter here

docs/2. Computer stuff.rst

@@ -0,0 +1,24 @@
+Computer stuff
+==============
+
+Computers
+^^^^^^^^^
+Insert subchapter here
+
+Setting up a scientific research environment
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Insert subchapter here
+
+Version Control, Git and Github
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Insert subchapter here
+Docker (?)
+^^^^^^^^^^
+Insert subchapter here
+...
+^^^
+Insert subchapter here
+
+Introduction to Programming with Python
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Insert subchapter here

docs/3. Conducting Experiments.rst

@@ -0,0 +1,16 @@
+Conducting Experiments
+======================
+
+Variables in Psychology 
+^^^^^^^^^^^^^^^^^^^^^^^
+Contrafactual Causality
+^^^^^^^^^^^^^^^^^^^^^^^ 
+Experimental Designs 
+^^^^^^^^^^^^^^^^^^^^
+e.g. 2*2 Design gambling task
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Programming Experiments in Psychopy 
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+reaction time experiment
+
+jpsych online survey

docs/4. Analysing Experimental Data.rst

@@ -0,0 +1,17 @@
+Analysing Experimental Data
+===========================
+
+Introduction to Programming with R 
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Basic Visualisation 
+^^^^^^^^^^^^^^^^^^^
+Descriptive Statistics
+^^^^^^^^^^^^^^^^^^^^^^
+The Generalized Linear Model
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+ $t$-Tests
+ Correlation tests
+ ...
+
+Multivariate data
+^^^^^^^^^^^^^^^^^

docs/5. Reporting the Results of Scientific Experiments.rst

@@ -0,0 +1,7 @@
+Reporting the Results of Scientific Experiments
+===============================================
+
+Pandoc intro / simple markup forms
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Loop of submission, review, and revision
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

docs/6. Abbendum.rst

@@ -0,0 +1,29 @@
+Abbendum
+========
+
+Data wrangling
+^^^^^^^^^^^^^^
+- Introduction to the tidyverse
+
+Multivariate Analysis and Machine Learning
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+- Introduction to scikit-learn
+
+Special methods
+^^^^^^^^^^^^^^^
+- Advanced Modeling of Behavior
+- IRT etc.
+- Modeling decisions
+
+Neuroscience
+^^^^^^^^^^^^
+Eye tracking 
+^^^^^^^^^^^^
+Online Experiments
+^^^^^^^^^^^^^^^^^^
+ - Mechanical Turk
+
+Formatting / saving data (ext.)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
+Data protection / security (ext.)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

docs/conf.py

@@ -75,7 +75,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+html_theme = 'sphinx_rtd_theme'
 
 # 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
@@ -156,4 +156,4 @@
 ]
 
 
-# -- Extension configuration -------------------------------------------------
+# -- Extension configuration -------------------------------------------------

docs/conf_old.py

@@ -0,0 +1,159 @@
+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- Path setup --------------------------------------------------------------
+
+# 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('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'smobsc'
+copyright = '2018, everyone'
+author = 'everyone'
+
+# The short X.Y version
+version = ''
+# The full version, including alpha/beta/rc tags
+release = '0.0.1'
+
+
+# -- 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 = [
+    'sphinx.ext.autodoc',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['ntemplates']
+
+# 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'
+
+# 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 pattern also affects html_static_path and html_extra_path .
+exclude_patterns = ['nbuild', 'Thumbs.db', '.DS_Store']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+
+# -- 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 = ['nstatic']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'smobscdoc'
+
+
+# -- 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, 'smobsc.tex', 'smobsc Documentation',
+     'everyone', '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, 'smobsc', 'smobsc 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, 'smobsc', 'smobsc Documentation',
+     author, 'smobsc', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+# -- Extension configuration -------------------------------------------------

docs/index.rst

@@ -1,19 +1,26 @@
-First Try at sphinx and read the docs
-=====================================
-Let's see if this worked...
-Some text explaining very important complicated stuff.
-Some code:
+Scientific methods ebook for social and cognitive scientists: an open and collaborative repository
+==================================================================================================
+Open Science requires more than conviction and good intentions: it is not only a philosophy, but also a technical skillset and knowledge base. Open Science practices -- e.g., data management and sharing, transparent and open-source software, and preregistering projects -- present a steep learning curve. Undeveloped incentive structures shift scientists’ priorities away from these initially time-consuming processes, despite saving a significant amount of time in the long run. Establishing Open Science practices can only succeed if acquired as an essential part of general methodological skill building, i.e., in the first undergraduate classes -- combined with the acquisition of canonised methodological knowledge (e.g., on experimental design or statistical analysis). To facilitate teaching -- as well as practicing -- Open Science, for both junior and senior scientists, we will develop a comprehensive online textbook, combining a state-of-the-art presentation of core methodological skills already embedded in Open Science practices.
 
-   print 'hello'
-   >> hello
+The text will unify scientific theory, open science, and the practical skills necessary to conduct research into a single framework. Theoretical and practical lessons will go hand in hand, e.g. the proper ways of pre-registering a study, counterbalancing experimental stimuli with Python and the underlying theory of experimental design, determining sampling size using R, and publishing the created code. Students will learn about version control and sustainable data management, while building up their skillset and codebase.
 
-Second try to see if it worked 
+In the spirit of Open Science, the book will be hosted on a GitHub repository, open for contributions. This eliminates the need for multiple editions, and a simple text, markup-based structure allows straight-forward conversion into multiple formats, from HTML to ePub or PDF. After establishing the core components and sections on fundamental topics, we will invite experts from different domains to contribute. Contributors will be able to create associated repositories with teaching materials for specialized cases.
 
-Some header
-^^^^^^^^^^^
+The dynamic nature of a GitHub-based website allows searchable content, a modular structure, combined with an overarching narrative. Students can complete all necessary steps for preparing, conducting, and presenting scientific work. Our aim is to provide a standalone
+
+fully-comprehensible online book that can be integrated into different teaching formats: assisting lectures, theoretical seminars, practical workshops, student-organized tutorials, or self-paced online learning. We hope this resource will change the skillsets and thinking of developing researchers early on. We believe such a project is essential to achieving transparent, open, and reproducible scientific disciplines.  
+
+Chapters
+^^^^^^^^
 .. toctree::
    :maxdepth: 2
 
+   1. Philosophical Foundations
+   2. Computer stuff
+   3. Conducting Experiments
+   4. Analysing Experimental Data
+   5. Reporting the Results of Scientific Experiments
+   6. Abbendum
    license
    help
    How to contribute

docs/nbuild/html/.buildinfo

@@ -1,4 +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: 7d7fab95516cc9c8be9e0c5a8625f126
+config: c64227f6202a243355f9778090f940b0
 tags: 645f666f9bcd5a90fca523b33c5a78b7