added autosummary to docs

docs/Makefile

@@ -1,20 +1,196 @@
-# Minimal makefile for Sphinx documentation
+# Makefile for Sphinx documentation
 #
 
 # You can set these variables from the command line.
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
-SPHINXPROJ    = epitome
-SOURCEDIR     = .
+PAPER         =
 BUILDDIR      = _build
+USAGEDIR			= usage
+
+
+# User-friendly check for sphinx-build
+ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
+$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
+endif
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest coverage gettext
 
-# Put it first so that "make" without argument is like "make help".
 help:
-	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  applehelp  to make an Apple Help Book"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  xml        to make Docutils-native XML files"
+	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+	@echo "  coverage   to run coverage check of the documentation (if enabled)"
+
+clean:
+	rm -rf $(BUILDDIR)/*
+	rm -rf $(USAGEDIR)/_generate
+
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/Toil.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/Toil.qhc"
+
+applehelp:
+	$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
+	@echo
+	@echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
+	@echo "N.B. You won't be able to view it unless you put it in" \
+	      "~/Library/Documentation/Help or install it in your application" \
+	      "bundle."
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/Toil"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/Toil"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+latexpdfja:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through platex and dvipdfmx..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+
+coverage:
+	$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
+	@echo "Testing of coverage in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/coverage/python.txt."
 
-.PHONY: help Makefile
+xml:
+	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+	@echo
+	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
 
-# 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)
+pseudoxml:
+	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+	@echo
+	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."

docs/conf.py

@@ -17,10 +17,43 @@
 # 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 sphinx_rtd_theme
+import os
+import sys
+import mock
+
+# These lines added to enable Sphinx autodocumentation in Epitome.
+MOCK_MODULES = [
+    "tensorflow",
+    "tensorflow_probability",
+    "numpy",
+    "h5py",
+    "scipy",
+    "scipy.io",
+    "scipy.sparse",
+    "pyranges",
+    "sklearn",
+    "sklearn.metrics",
+    "pandas",
+    "tqdm",
+    "seaborn",
+    "matplotlib",
+    "matplotlib.pyplot",
+    "matplotlib.backends",
+    "matplotlib.lines",
+    "matplotlib.transforms"
+
+
+]
+
+for mod_name in MOCK_MODULES:
+    sys.modules[mod_name] = mock.Mock()
+
+# 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.
+this_dir = os.path.dirname(os.path.abspath(__file__))
+epitome_dir = os.path.abspath(os.path.join(this_dir, '..'))
+sys.path.insert(0, epitome_dir)
 
 # -- General configuration ------------------------------------------------
 
@@ -31,7 +64,24 @@
 # 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']
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+]
+
+def skip(app, what, name, obj, skip, options):
+    return name != '__init__' and (skip
+                                   or inspect.isclass(obj)
+                                   or name.startswith('_') and not inspect.ismodule(obj))
+
+def setup(app):
+    app.connect('autodoc-skip-member', skip)
+
+# Include doc string for __init__ method in the documentation
+autosummary_generate = True
+
+autoclass_content = 'class'
+autodoc_member_order = 'bysource'
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -89,7 +139,15 @@
 # further.  For a list of options available for each theme, see the
 # documentation.
 #
-# html_theme_options = {}
+html_theme_options = {
+    'collapse_navigation': True,
+}
+
+extlinks = {
+    'issue': ('https://github.com/akmorrow13/epitome/issues/%s', '#'),
+    'pr': ('https://github.com/akmorrow13/epitome/pull/%s', 'PR #'),
+}
+
 
 # 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,
@@ -152,6 +210,3 @@
      author, 'epitome', 'One line description of project.',
      'Miscellaneous'),
 ]
-
-
-

docs/index.rst

@@ -3,23 +3,26 @@
 Introduction
 ============
 
-Epitome is a computation model that leverages chromatin accessibility data to predict transcription factor binding sites on a novel cell type of interest. Epitome computes the chromatin similarity between 11 cell types in ENCODE and the novel cell types, and uses chromatin similarity to transfer binding information in known cell types to a novel cell type of interest.
+Epitome is a computational model that leverages chromatin accessibility data to predict ChIP-seq peaks on unseen cell types. Epitome computes the chromatin similarity between 11 cell types in ENCODE and the novel cell types, and uses chromatin similarity to transfer ChIP-seq peaks in known cell types to a novel cell type of interest.
 
 .. image:: figures/epitome_diagram.png
 
 
 .. toctree::
-   :caption: Installation
+   :caption: Installation and Configuration
    :maxdepth: 2
 
    installation/source
+   usage/data
 
 .. toctree::
    :caption: Usage and Examples
    :maxdepth: 2
 
    usage/train
    usage/predict
+   usage/api
+
 
 
 

docs/installation/source.rst

@@ -1,23 +1,23 @@
 Building Epitome from Source
 ============================
 
-**Note**: Epitome is configured for tensorflow 1.12/Cuda 9. If you have a different
+**Note**: Epitome is configured for tensorflow 2/Cuda 9. If you have a different
 version of cuda, update tensorflow-gpu version accordingly.
 
 Requirements
 ------------
 
 * `conda <https://docs.conda.io/en/latest/miniconda.html>`__
-* python 3.6
+* python 3.7
 
 Installation
 ------------
 
-1. Create and activate a pytion 3.6 conda venv:
+1. Create and activate a pytion 3.7 conda venv:
 
 .. code:: bash
 
-	conda create --name EpitomeEnv python=3.6
+	conda create --name EpitomeEnv python=3.7
 	source activate EpitomeEnv
 
 
@@ -40,9 +40,5 @@ Installation
 Configuring Data
 ----------------
 
-To download and format training data, run ```bin/get_deepsea_data.py```:
-
-.. code:: bash
-
-	python bin/get_deepsea_data.py 
-	usage: get_deepsea_data.py [-h] --output_path OUTPUT_PATH
+Epitome requires data for training, validation and test. See `Configuring Epitome data <../usage/data.html>`__ for more information
+on how to download data for Epitome or generate your own dataset.

docs/requirements.txt

@@ -0,0 +1,4 @@
+sphinx==1.7.7
+nbsphinx==0.3.4
+sphinx_rtd_theme==0.4.2
+mock

docs/usage/api.rst

@@ -0,0 +1,4 @@
+API Documentation
+=================
+
+.. automodule:: epitome