Merge branch '27-sphinx-building' into 'master'

Sphinx Building

Initial sphinx doc stuff created!
Closes #27

See merge request !24

.gitignore

@@ -9,3 +9,5 @@ examples/all_files.list
 chipathlon/test/auth.yaml
 meta/*.json
 meta/data/*.json
+doc/source/_static
+doc/source/_templates

chipathlon/generators/idr_generator.py

@@ -48,7 +48,7 @@ class IdrGenerator(ModuleGenerator):
     def create_final_results(self, run):
         """
         :param run: The target run to generate jobs for.
-        :type run: :py:class:chipathlon.run.Run
+        :type run: :py:class:`~chipathlon.run.Run`
         """
         module_jobs = [self.workflow_jobs[job_name] for job_name in self.module.get_job_names({})]
         peak_results = self._find_prev_results(run)

chipathlon/generators/module_generator.py

@@ -198,10 +198,13 @@ class ModuleGenerator(object):
         were necessary to get to the current results.  Based on the existance
         of previous results / current results in the database, we add jobs to
         the workflow.
+
         If result exists -> Do nothing.  No need to add jobs since the result
-            already exists.  Result will be downloaded at a future step.
+        already exists.  Result will be downloaded at a future step.
+
         If result doesn't exist and prev_result does -> Queue download jobs
-            for previous results, then add jobs normally.
+        for previous results, then add jobs normally.
+
         If result doesn't exists and prev_result doesn't -> Add jobs normally.
         """
         final_results = self.create_final_results(run)

chipathlon/workflow_job.py

@@ -355,14 +355,53 @@ class WorkflowJob(object):
         :type outputs: list
 
         Creates an actual Pegasus.Dax3.Job instance from the provided
-        information:
-        - inputs should be a list of dictionaries:
-            [{"name": FILE_NAME, "type": "file", "file": FILE_OBJECT},
-             {"name": ARUGMENT_NAME, "type": "argument", "value": ARGUMENT_VALUE},...]
-        - additional_files should be a list of dictionaries:
-            [{"name": FILE_NAME, "type": "file", "file": FILE_OBJECT},...]
-        - outputs should be a list of dictionaries:
-            [{"name": FILE_NAME, "transfer": True/False, "type": "file", "file": FILE_OBJECT},...]
+        information.  Inputs, additional_inputs, and outputs should
+        all be a list of dictionaries:
+
+        **inputs**
+
+        .. code-block:: python
+
+            [
+                {
+                    "name": "FULL-FILE-NAME",
+                    "type": "file",
+                    "file": PEGASUS-FILE-OBJECT
+                },
+                {
+                    "name": "ARGUMENT-NAME",
+                    "type": "argument",
+                    "value": ARGUMENT-VALUE
+                },
+                ...
+            ]
+
+        **additional_inputs**
+
+        .. code-block:: python
+
+            [
+                {
+                    "name": "FULL-FILE-NAME",
+                    "type": "file",
+                    "file": PEGASUS-FILE-OBJECT
+                },
+                ...
+            ]
+
+        **outputs**
+
+        .. code-block:: python
+
+            [
+                {
+                    "name": "FULL-FILE-NAME",
+                    "type": "file",
+                    "transfer": True/False,
+                    "file": PEGASUS-FILE-OBJECT
+                },
+                ...
+            ]
         """
         if self._params_are_valid(inputs, additional_inputs, outputs):
             job = Job(self.executable)

doc/Makefile

+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = chipathlon
+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)
\ No newline at end of file

doc/source/conf.py

+import sphinx_rtd_theme
+
+# -*- coding: utf-8 -*-
+#
+# chipathlon documentation build configuration file, created by
+# sphinx-quickstart on Tue Apr 11 15:50:17 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 = ['sphinx.ext.autodoc']
+
+# 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 = u'chipathlon'
+copyright = u'2017, Avi Knecht'
+author = u'Avi Knecht'
+
+# 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 = u'1.0'
+# The full version, including alpha/beta/rc tags.
+release = u'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 = 'sphinx_rtd_theme'
+html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+
+# 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 = 'chipathlondoc'
+
+
+# -- 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, 'chipathlon.tex', u'chipathlon Documentation',
+     u'Avi Knecht', '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, 'chipathlon', u'chipathlon 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, 'chipathlon', u'chipathlon Documentation',
+     author, 'chipathlon', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+

doc/source/db.rst

+MongoDB
+==============
+
+.. autoclass:: chipathlon.db.MongoDB
+    :members:

doc/source/examples.rst

+Examples
+==========
+
+**Config**
+
+.. code-block:: yaml
+
+    notify:
+    pegasus_home: "/usr/share/pegasus/"
+    email: "avi@kurtknecht.com"
+    profile:
+    pegasus:
+      style: "glite"
+    condor:
+      grid_resource: "pbs"
+      universe: "vanilla"
+      batch_queue: "batch"
+    env:
+      PYTHONPATH: "/home/swanson/aknecht/.conda/envs/ih_env/lib/python2.7/site-packages/"
+      PATH: "/home/swanson/aknecht/.conda/envs/ih_env/bin:/bin/:/usr/bin/:/usr/local/bin/"
+      PEGASUS_HOME: "/usr/"
+
+**Run**
+
+.. code-block:: yaml
+
+    genomes:
+      mm9:
+        bowtie2: /work/ladunga/SHARED/mouse/mm9/mm9.genome.fa
+        bwa: /work/ladunga/SHARED/mouse/mm9/mm9.genome.fa
+        chrom.sizes: /work/ladunga/SHARED/mouse/mm9/mm9.chrom.sizes
+    runs:
+    - align: bwa
+      assembly: mm9
+      controls: &id001
+      - ENCFF001NIM
+      file_type: fastq
+      idr: &id002
+      - ENCFF001NIP
+      - ENCFF001NIS
+      peak: spp
+      peak_type: narrow
+      signals: &id003
+      - ENCFF001NIP
+      - ENCFF001NIS
+    - align: bowtie2
+      assembly: mm9
+      controls: *id001
+      file_type: fastq
+      idr: *id002
+      peak: spp
+      peak_type: narrow
+      signals: *id003

doc/source/generators.rst

+Generators
+===========
+
+Module Generator
+-----------------
+
+.. autoclass:: chipathlon.generators.module_generator.ModuleGenerator
+    :members:
+
+Align Generator
+------------------
+
+.. autoclass:: chipathlon.generators.align_generator.AlignGenerator
+    :members:
+
+Remove Duplicate Generator
+---------------------------
+
+.. autoclass:: chipathlon.generators.remove_duplicates_generator.RemoveDuplicatesGenerator
+    :members:
+
+Peak Call Generator
+--------------------
+
+.. autoclass:: chipathlon.generators.peak_call_generator.PeakCallGenerator
+    :members:
+
+Idr Generator
+---------------
+
+.. autoclass:: chipathlon.generators.idr_generator.IdrGenerator
+    :members:

doc/source/genome.rst

+Genome
+==============
+
+.. autoclass:: chipathlon.genome.Genome
+    :members:

doc/source/index.rst

+.. chipathlon documentation master file, created by
+   sphinx-quickstart on Tue Apr 11 15:50:17 2017.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to chipathlon's documentation!
+======================================
+
+`GitHub <https://git.unl.edu/aknecht2/chipathlon/>`_
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   introduction
+   installation
+   examples
+   workflow
+   workflow_module
+   workflow_job
+   generators
+   run
+   genome
+   result
+   db
+
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

doc/source/installation.rst

+Installation
+==============
+
+Dependencies for chipathlon
+----------------------------
+*
+
+Dependencies for running workflows
+-----------------------------------
+* gem
+* zerone
+* macs2
+* spp
+* ccat
+* peakranger
+* music
+* samtools
+* bamtools
+* picard
+* bwa
+* bowtie2

doc/source/introduction.rst

+Introduction
+=============
+
+Chipathlon is an open-source library for running multiple peak calling tools in
+parallel. `Pegasus <pegasus.isi.edu>`_ is used to create and submit workflows
+to super computers.
+
+Chipathlon is currently being worked on.  For help and questions, please
+contact: avi@kurtknecht.com.

doc/source/result.rst

+Result
+==============
+
+.. autoclass:: chipathlon.result.Result
+    :members:

doc/source/run.rst

+Run
+==============
+
+.. autoclass:: chipathlon.run.Run
+    :members:

doc/source/workflow.rst

+Workflow
+=========
+
+.. autoclass:: chipathlon.workflow.Workflow
+    :members:

doc/source/workflow_job.rst

+Workflow Job
+==============
+
+.. autoclass:: chipathlon.workflow_job.WorkflowJob
+    :members:

doc/source/workflow_module.rst

+Workflow Module
+=================
+
+.. autoclass:: chipathlon.workflow_module.WorkflowModule
+    :members: