added documentation

lewisacidic · Aug 14, 2016 · 19903ab · 19903ab
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diff --git a/ci/environment.yml b/ci/environment.yml
@@ -0,0 +1,81 @@
+channels:
+- https://conda.anaconda.org/richlewis
+
+dependencies:
+- bzip2=1.0.6=3
+- cycler=0.10.0=py35_0
+- decorator=4.0.10=py35_0
+- entrypoints=0.2.2=py35_0
+- freetype=2.5.5=1
+- h5py=2.6.0=np110py35_1
+- hdf5=1.8.16=0
+- ipykernel=4.4.1=py35_0
+- ipython=5.0.0=py35_0
+- ipython_genutils=0.1.0=py35_0
+- ipywidgets=4.1.1=py35_0
+- jbig=2.1=0
+- jinja2=2.8=py35_1
+- jpeg=8d=1
+- jsonschema=2.5.1=py35_0
+- jupyter_client=4.3.0=py35_0
+- jupyter_core=4.1.1=py35_0
+- libpng=1.6.22=0
+- libtiff=4.0.6=2
+- markupsafe=0.23=py35_2
+- matplotlib=1.5.1=np110py35_0
+- mkl=11.3.3=0
+- nbconvert=4.2.0=py35_0
+- nbformat=4.0.1=py35_0
+- notebook=4.2.2=py35_0
+- numexpr=2.5.2=np110py35_1
+- numpy=1.10.4=py35_2
+- openssl=1.0.2h=1
+- pandas=0.18.1=np110py35_0
+- path.py=8.2.1=py35_0
+- pexpect=4.0.1=py35_0
+- pickleshare=0.7.3=py35_0
+- pillow=3.3.0=py35_0
+- pip=8.1.2=py35_0
+- prompt_toolkit=1.0.3=py35_0
+- ptyprocess=0.5.1=py35_0
+- py=1.4.31=py35_0
+- pygments=2.1.3=py35_0
+- pyparsing=2.1.4=py35_0
+- pyqt=4.11.4=py35_4
+- pytables=3.2.2=np110py35_3
+- pytest=2.9.2=py35_0
+- python=3.5.2=0
+- python-dateutil=2.5.3=py35_0
+- pytz=2016.6.1=py35_0
+- pyyaml=3.11=py35_4
+- pyzmq=15.4.0=py35_0
+- qt=4.8.7=4
+- readline=6.2=2
+- requests=2.10.0=py35_0
+- boost=1.56.0=py35_3
+- fuel=0.2.0=py35_0
+- picklable-itertools=0.1.1=py35_0
+- progressbar2=3.10.0=py35_0
+- pytest-runner=2.9=py35_0
+- python-utils=2.0.0=py35_0
+- rdkit=2016.03.1=np110py35_0
+- scikit-learn=0.17.1=np110py35_2
+- scipy=0.17.1=np110py35_1
+- setuptools=25.1.6=py35_0
+- simplegeneric=0.8.1=py35_1
+- sip=4.18=py35_0
+- six=1.10.0=py35_0
+- sqlite=3.13.0=0
+- terminado=0.6=py35_0
+- tk=8.5.18=0
+- tornado=4.4.1=py35_0
+- traitlets=4.2.2=py35_0
+- wcwidth=0.1.7=py35_0
+- wheel=0.29.0=py35_0
+- xz=5.2.2=0
+- yaml=0.1.6=0
+- zlib=1.2.8=3
+
+- pip:
+  - sphinx-bootstrap-theme==0.4.12
+  - nbsphinx==0.2.9
diff --git a/docs/Makefile b/docs/Makefile
@@ -0,0 +1,231 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = _build
+
+# 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
+help:
+	@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 "  epub3      to make an epub3"
+	@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)"
+	@echo "  dummy      to check syntax errors of document sources"
+
+.PHONY: clean
+clean:
+	rm -rf $(BUILDDIR)/*
+
+.PHONY: html
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+
+.PHONY: livehtml
+livehtml:
+	sphinx-autobuild -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+
+.PHONY: dirhtml
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+.PHONY: singlehtml
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+.PHONY: pickle
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+.PHONY: json
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+.PHONY: htmlhelp
+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."
+
+.PHONY: qthelp
+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/scikit-chem.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/scikit-chem.qhc"
+
+.PHONY: applehelp
+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."
+
+.PHONY: devhelp
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/scikit-chem"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/scikit-chem"
+	@echo "# devhelp"
+
+.PHONY: epub
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+.PHONY: epub3
+epub3:
+	$(SPHINXBUILD) -b epub3 $(ALLSPHINXOPTS) $(BUILDDIR)/epub3
+	@echo
+	@echo "Build finished. The epub3 file is in $(BUILDDIR)/epub3."
+
+.PHONY: latex
+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)."
+
+.PHONY: latexpdf
+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."
+
+.PHONY: latexpdfja
+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."
+
+.PHONY: text
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+.PHONY: man
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+.PHONY: texinfo
+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)."
+
+.PHONY: info
+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."
+
+.PHONY: gettext
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+.PHONY: changes
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+.PHONY: linkcheck
+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."
+
+.PHONY: doctest
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+
+.PHONY: coverage
+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: xml
+xml:
+	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+	@echo
+	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+
+.PHONY: pseudoxml
+pseudoxml:
+	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+	@echo
+	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
+
+.PHONY: dummy
+dummy:
+	$(SPHINXBUILD) -b dummy $(ALLSPHINXOPTS) $(BUILDDIR)/dummy
+	@echo
+	@echo "Build finished. Dummy builder generates no files."
+
diff --git a/docs/_static/css/custom.css b/docs/_static/css/custom.css
@@ -0,0 +1,38 @@
+@media screen and (min-width: 992px) {
+	.alert, .highlight-bash {
+    	margin: 1.5em !important;
+	}
+}
+
+.alert.alert-warning a {
+    color: #C0392B !important;
+}
+
+.alert.alert-info a {
+    color: #446CB3 !important;
+}
+
+div.nbinput > :first-child[class^=highlight] {
+    display: none;
+}
+
+div.nboutput > :first-child[class^=highlight] {
+    display: none;
+}
+
+div.nboutput > :first-child {
+    display: none;
+}
+
+table.dataframe {
+    border: 2px solid #aaaaaa;
+    margin: 0.5em 0 0.5em 0;
+}
+
+table.dataframe td, table.dataframe th {
+    border: 1px solid #cccccc;
+    min-width: 3em;
+    padding: 0.5em;
+}
+
+
diff --git a/docs/_templates/layout.html b/docs/_templates/layout.html
@@ -0,0 +1,5 @@
+{# Import the theme's layout. #}
+{% extends "!layout.html" %}
+
+{# Custom CSS overrides #}
+{% set bootswatch_css_custom = ['_static/css/custom.css'] %}
diff --git a/docs/api/modules.rst b/docs/api/modules.rst
@@ -0,0 +1,11 @@
+.. _api:
+
+API
+===
+
+The API documentation, autogenerated from the docstrings.
+
+.. toctree::
+   :maxdepth: 4
+
+   skchem