init rtd

.gitignore

@@ -5,3 +5,4 @@ tests/.env
 .buildpath
 .project
 .settings/
+docs/_build/

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    = Tripal
+SOURCEDIR     = .
+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/conf.py

@@ -0,0 +1,155 @@
+# -*- 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 = u'Tripal'
+copyright = u'2018, Stephen Ficklin, Lacey Sanderson, Bradford Condon et al'
+author = u'Stephen Ficklin, Lacey Sanderson, Bradford Condon et al'
+
+# The short X.Y version
+version = u''
+# The full version, including alpha/beta/rc tags
+release = u'7.x-3.x'
+
+
+# -- 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'
+
+# 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 = [u'_build', '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 = "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
+# 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']
+
+# 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 = 'Tripaldoc'
+
+
+# -- 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, 'Tripal.tex', u'Tripal Documentation',
+     u'Stephen Ficklin, Lacey Sanderson, Bradford Condon et al', '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, 'tripal', u'Tripal 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, 'Tripal', u'Tripal Documentation',
+     author, 'Tripal', 'One line description of project.',
+     'Miscellaneous'),
+]

docs/dev_guide.rst

@@ -0,0 +1,10 @@
+Developer's Guide
+==============
+
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Table of Contents
+   :glob:
+
+   dev_guide/*

docs/dev_guide/lorem_ipsum.rst

@@ -0,0 +1,4 @@
+Example file
+===============
+
+Lorem ipsum

docs/index.rst

@@ -0,0 +1,14 @@
+.. Tripal documentation master file, created by
+   sphinx-quickstart on Tue Aug 21 17:25:20 2018.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to Tripal's documentation!
+==================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   user_guide
+   dev_guide

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=.
+set BUILDDIR=_build
+set SPHINXPROJ=Tripal
+
+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/user_guide.rst

@@ -0,0 +1,10 @@
+User's Guide
+==============
+
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Table of Contents
+   :glob:
+
+   user_guide/*

docs/user_guide/bulk_loader.rst

@@ -0,0 +1,5 @@
+
+Bulk Loader
+===============
+
+Lorem ipsum

docs/user_guide/configuring_page_display.rst

@@ -0,0 +1,5 @@
+
+Configuring Page Display
+===============
+
+Lorem ipsum

docs/user_guide/creating_content.rst

@@ -0,0 +1,4 @@
+Lorem Ipsum
+===============
+
+Lorem ipsum

docs/user_guide/customize_site.rst

@@ -0,0 +1,4 @@
+Customizing Your Site
+===============
+
+Lorem ipsum

docs/user_guide/drupal_overview.rst

@@ -0,0 +1,4 @@
+Brief Drupal Overview
+===============
+
+Lorem ipsum

docs/user_guide/example_setup.rst

@@ -0,0 +1,4 @@
+Example Setup
+===============
+
+Lorem ipsum

docs/user_guide/galaxy_integration.rst

@@ -0,0 +1,4 @@
+Galaxy Integration
+===============
+
+Lorem ipsum

docs/user_guide/install_tripal.rst

@@ -0,0 +1,4 @@
+Install Tripal
+===============
+
+Lorem ipsum

docs/user_guide/job_management.rst

@@ -0,0 +1,4 @@
+Lorem Ipsum
+===============
+
+Lorem ipsum

docs/user_guide/learn_chado.rst

@@ -0,0 +1,4 @@
+Lorem Ipsum
+===============
+
+Lorem ipsum

docs/user_guide/mviews.rst

@@ -0,0 +1,4 @@
+Lorem Ipsum
+===============
+
+Lorem ipsum

docs/user_guide/searching.rst

@@ -0,0 +1,4 @@
+Lorem Ipsum
+===============
+
+Lorem ipsum

docs/user_guide/setting_page_urls.rst

@@ -0,0 +1,4 @@
+Lorem Ipsum
+===============
+
+Lorem ipsum

docs/user_guide/web_services.rst

@@ -0,0 +1,4 @@
+Lorem Ipsum
+===============
+
+Lorem ipsum

docs/user_guide/what_is_tripal.rst

@@ -0,0 +1,4 @@
+Lorem Ipsum
+===============
+
+Lorem ipsum