Read The Docs (#91)

* setting up sphinx

* added readme

* added documentation outline

generated by sphinx-apidoc

* fixed warnings for doc string formatting

* update header name

* generate proper header

* sphinx autodoc mock imports

* formatting red-warnings

* modules in index

* don't doc the setup script

* flake8 set to 79 cols

* flake8

* Updates to some meta information.

* Changes to document titles.

docs/README.md

@@ -0,0 +1,23 @@
+# Maestro Workflow Conductor Documentation
+
+[maestrowf.rtfd.io](http://maestrowf.readthedocs.io/en/latest/)
+
+This documentation is built with Sphinx for ReadTheDocs.
+The contents are automatically generated from the doc strings found in the code.
+
+## Building the Documentation
+
+To build the documentation locally simply use:
+
+``` shell
+make html
+```
+
+## Updating the Documentation
+
+If the structure of the modules changes, then the documentation will have to be re-generated.
+This can be done easily with:
+
+``` shell
+sphinx-apidoc -f -M -H 'Maestro Workflow Conductor' -o ./source/ ../../maestrowf
+```

docs/source/conf.py

@@ -15,17 +15,15 @@
 # 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('.'))
-
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../../'))
 
 # -- General configuration ------------------------------------------------
 
-# If your documentation needs a minimal Sphinx version, state it here.
+# 1.3 needed for autodoc_mock_imports
 #
-# needs_sphinx = '1.0'
+needs_sphinx = '1.3'
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
@@ -34,6 +32,8 @@
               'sphinx.ext.todo',
               'sphinx.ext.coverage']
 
+autodoc_mock_imports = ['filelock', 'tabulate', 'setup']
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
@@ -47,7 +47,7 @@
 master_doc = 'index'
 
 # General information about the project.
-project = u'SimMananger'
+project = u'Maestro Workflow Conductor'
 copyright = u'2017, Francesco Di Natale'
 author = u'Francesco Di Natale'
 
@@ -101,7 +101,7 @@
 # -- Options for HTMLHelp output ------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'SimManangerdoc'
+htmlhelp_basename = 'MaestroWFdoc'
 
 
 # -- Options for LaTeX output ---------------------------------------------
@@ -128,7 +128,7 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'SimMananger.tex', u'SimMananger Documentation',
+    (master_doc, 'MaestroWF.tex', u'MaestroWF Documentation',
      u'Francesco Di Natale', 'manual'),
 ]
 
@@ -138,7 +138,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'simmananger', u'SimMananger Documentation',
+    (master_doc, 'MaestroWF', u'MaestroWF Documentation',
      [author], 1)
 ]
 
@@ -149,7 +149,7 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'SimMananger', u'SimMananger Documentation',
-     author, 'SimMananger', 'One line description of project.',
+    (master_doc, 'MaestroWF', u'MaestroWF Documentation',
+     author, 'MaestroWF', 'One line description of project.',
      'Miscellaneous'),
 ]

docs/source/index.rst

@@ -3,14 +3,14 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to SimMananger's documentation!
-=======================================
+Welcome to Maestro Workflow Conductor Documentation
+===================================================
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 4
    :caption: Contents:
 
-
+   modules
 
 Indices and tables
 ==================

docs/source/maestrowf.abstracts.enums.rst

@@ -0,0 +1,8 @@
+maestrowf.abstracts.enums package
+=================================
+
+.. automodule:: maestrowf.abstracts.enums
+    :members:
+    :undoc-members:
+    :show-inheritance:
+

docs/source/maestrowf.abstracts.interfaces.rst

@@ -0,0 +1,28 @@
+maestrowf.abstracts.interfaces package
+======================================
+
+.. automodule:: maestrowf.abstracts.interfaces
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Submodules
+----------
+
+maestrowf.abstracts.interfaces.schedulerscriptadapter module
+------------------------------------------------------------
+
+.. automodule:: maestrowf.abstracts.interfaces.schedulerscriptadapter
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+maestrowf.abstracts.interfaces.scriptadapter module
+---------------------------------------------------
+
+.. automodule:: maestrowf.abstracts.interfaces.scriptadapter
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+

docs/source/maestrowf.abstracts.rst

@@ -0,0 +1,60 @@
+maestrowf.abstracts package
+===========================
+
+.. automodule:: maestrowf.abstracts
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+    maestrowf.abstracts.enums
+    maestrowf.abstracts.interfaces
+
+Submodules
+----------
+
+maestrowf.abstracts.abstractclassmethod module
+----------------------------------------------
+
+.. automodule:: maestrowf.abstracts.abstractclassmethod
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+maestrowf.abstracts.envobject module
+------------------------------------
+
+.. automodule:: maestrowf.abstracts.envobject
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+maestrowf.abstracts.graph module
+--------------------------------
+
+.. automodule:: maestrowf.abstracts.graph
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+maestrowf.abstracts.simobject module
+------------------------------------
+
+.. automodule:: maestrowf.abstracts.simobject
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+maestrowf.abstracts.specification module
+----------------------------------------
+
+.. automodule:: maestrowf.abstracts.specification
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+

docs/source/maestrowf.datastructures.core.rst

@@ -0,0 +1,44 @@
+maestrowf.datastructures.core package
+=====================================
+
+.. automodule:: maestrowf.datastructures.core
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Submodules
+----------
+
+maestrowf.datastructures.core.executiongraph module
+---------------------------------------------------
+
+.. automodule:: maestrowf.datastructures.core.executiongraph
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+maestrowf.datastructures.core.parameters module
+-----------------------------------------------
+
+.. automodule:: maestrowf.datastructures.core.parameters
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+maestrowf.datastructures.core.study module
+------------------------------------------
+
+.. automodule:: maestrowf.datastructures.core.study
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+maestrowf.datastructures.core.studyenvironment module
+-----------------------------------------------------
+
+.. automodule:: maestrowf.datastructures.core.studyenvironment
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+

docs/source/maestrowf.datastructures.environment.rst

@@ -0,0 +1,44 @@
+maestrowf.datastructures.environment package
+============================================
+
+.. automodule:: maestrowf.datastructures.environment
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Submodules
+----------
+
+maestrowf.datastructures.environment.gitdependency module
+---------------------------------------------------------
+
+.. automodule:: maestrowf.datastructures.environment.gitdependency
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+maestrowf.datastructures.environment.pathdependency module
+----------------------------------------------------------
+
+.. automodule:: maestrowf.datastructures.environment.pathdependency
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+maestrowf.datastructures.environment.script module
+--------------------------------------------------
+
+.. automodule:: maestrowf.datastructures.environment.script
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+maestrowf.datastructures.environment.variable module
+----------------------------------------------------
+
+.. automodule:: maestrowf.datastructures.environment.variable
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+

docs/source/maestrowf.datastructures.rst

@@ -0,0 +1,36 @@
+maestrowf.datastructures package
+================================
+
+.. automodule:: maestrowf.datastructures
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+    maestrowf.datastructures.core
+    maestrowf.datastructures.environment
+
+Submodules
+----------
+
+maestrowf.datastructures.dag module
+-----------------------------------
+
+.. automodule:: maestrowf.datastructures.dag
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+maestrowf.datastructures.yamlspecification module
+-------------------------------------------------
+
+.. automodule:: maestrowf.datastructures.yamlspecification
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+

docs/source/maestrowf.interfaces.rst

@@ -0,0 +1,15 @@
+maestrowf.interfaces package
+============================
+
+.. automodule:: maestrowf.interfaces
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+    maestrowf.interfaces.script
+

docs/source/maestrowf.interfaces.script.rst

@@ -0,0 +1,28 @@
+maestrowf.interfaces.script package
+===================================
+
+.. automodule:: maestrowf.interfaces.script
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Submodules
+----------
+
+maestrowf.interfaces.script.localscriptadapter module
+-----------------------------------------------------
+
+.. automodule:: maestrowf.interfaces.script.localscriptadapter
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+maestrowf.interfaces.script.slurmscriptadapter module
+-----------------------------------------------------
+
+.. automodule:: maestrowf.interfaces.script.slurmscriptadapter
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+