Added more to the docs and included sphinx-apidoc in the build process

.gitignore

@@ -41,3 +41,5 @@ output/*/index.html
 
 # Sphinx
 docs/_build
+/maintain_repo.bat
+/maintain_repo.bsh

CONTRIBUTING.rst

@@ -83,7 +83,7 @@ To get tox, just pip install it.
 
 6. Submit a pull request through the GitHub website.
 
-.. _Fork: https://github.com/Nekroze/jopy/fork
+.. _Fork: https://github.com/jowr/jopy/fork
 
 Pull Request Guidelines
 -----------------------
@@ -94,7 +94,7 @@ Before you submit a pull request, check that it meets these guidelines:
 2. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a docstring, and add the
    feature to the list in README.rst.
-3. The pull request should work for Python 2.6, 2.7, and 3.3, and for PyPy.
+3. The pull request should work for Python 2.7, 3.3 and 3.4.
    Check https://travis-ci.org/jowr/jopy 
    under pull requests for active pull requests or run the ``tox`` command and
    make sure that the tests pass for all supported Python versions.

dev/builder.py

@@ -24,7 +24,7 @@
 
 bas_pkgs = ["conda-env", "conda-build", "binstar", "binstar-build", "jinja2"]
 
-cus_pkgs = ["numpy", "scipy", "matplotlib", "pandas"]
+cus_pkgs = ["numpy", "scipy", "matplotlib", "pandas", "blaze"]
 pip_cus_pkgs = ["coolprop", "texttable", "brewer2mpl","future"]
 
 dev_pkgs = cus_pkgs + ["pip", "pyyaml", "nose", "sphinx", "jinja2"]

docs/Makefile

@@ -49,38 +49,38 @@ help:
 clean:
 	rm -rf $(BUILDDIR)/*
 
-html:
+html: apidoc 
 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
 
-dirhtml:
+dirhtml: apidoc
 	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
 
-singlehtml:
+singlehtml: apidoc
 	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
 	@echo
 	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
 
-pickle:
+pickle: apidoc
 	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
 	@echo
 	@echo "Build finished; now you can process the pickle files."
 
-json:
+json: apidoc
 	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
 	@echo
 	@echo "Build finished; now you can process the JSON files."
 
-htmlhelp:
+htmlhelp: apidoc
 	$(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:
+qthelp: apidoc
 	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
 	@echo
 	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
@@ -89,7 +89,7 @@ qthelp:
 	@echo "To view the help file:"
 	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/complexity.qhc"
 
-devhelp:
+devhelp: apidoc
 	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
 	@echo
 	@echo "Build finished."
@@ -98,80 +98,88 @@ devhelp:
 	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/complexity"
 	@echo "# devhelp"
 
-epub:
+epub: apidoc
 	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
 	@echo
 	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
 
-latex:
+latex: apidoc
 	$(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:
+latexpdf: apidoc
 	$(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:
+latexpdfja: apidoc
 	$(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:
+text: apidoc
 	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
 	@echo
 	@echo "Build finished. The text files are in $(BUILDDIR)/text."
 
-man:
+man: apidoc
 	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
 	@echo
 	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
 
-texinfo:
+texinfo: apidoc
 	$(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:
+info: apidoc
 	$(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:
+gettext: apidoc
 	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
 	@echo
 	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
 
-changes:
+changes: apidoc
 	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
 	@echo
 	@echo "The overview file is in $(BUILDDIR)/changes."
 
-linkcheck:
+linkcheck: apidoc
 	$(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:
+doctest: apidoc
 	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
 	@echo "Testing of doctests in the sources finished, look at the " \
 	      "results in $(BUILDDIR)/doctest/output.txt."
 
-xml:
+xml: apidoc
 	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
 	@echo
 	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
 
-pseudoxml:
+pseudoxml: apidoc
 	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
 	@echo
 	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
+
+.PHONY: apidoc
+apidoc: 
+	pushd .. ; \
+	sphinx-apidoc -fM -o docs/code jopy ; \
+	popd
+	@echo
+	@echo "Build finished. Output of sphinx-apidoc is in docs/code."

docs/code/index.rst

@@ -0,0 +1,7 @@
+==========
+Source Code
+==========
+
+The package is documented by means of docstring with autodoc
+
+.. include:: jopy.rst 

docs/code/jopy.data.rst

@@ -0,0 +1,20 @@
+jopy.data package
+=================
+
+.. automodule:: jopy.data
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Submodules
+----------
+
+jopy.data.sources module
+------------------------
+
+.. automodule:: jopy.data.sources
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+

docs/code/jopy.recip.rst

@@ -0,0 +1,20 @@
+jopy.recip package
+==================
+
+.. automodule:: jopy.recip
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Submodules
+----------
+
+jopy.recip.mechanisms module
+----------------------------
+
+.. automodule:: jopy.recip.mechanisms
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+

docs/code/jopy.rst

@@ -0,0 +1,29 @@
+jopy package
+============
+
+.. automodule:: jopy
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+    jopy.data
+    jopy.recip
+    jopy.styles
+
+Submodules
+----------
+
+jopy.base module
+----------------
+
+.. automodule:: jopy.base
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+

docs/code/jopy.styles.rst

@@ -0,0 +1,20 @@
+jopy.styles package
+===================
+
+.. automodule:: jopy.styles
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Submodules
+----------
+
+jopy.styles.mplib module
+------------------------
+
+.. automodule:: jopy.styles.mplib
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+

docs/code/modules.rst

@@ -0,0 +1,7 @@
+jopy
+====
+
+.. toctree::
+   :maxdepth: 4
+
+   jopy

docs/conf.py

@@ -24,14 +24,27 @@
 
 import jopy
 
+# -- Special RTD configuration -------------------------------------------------
+
+on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
+if on_rtd:
+    from unittest.mock import MagicMock
+    class Mock(MagicMock):
+        @classmethod
+        def __getattr__(cls, name):
+                return Mock()
+    MOCK_MODULES = ['pygtk', 'gtk', 'gobject', 'argparse', 'numpy', 'pandas', 'scipy', 'scipy.interpolate', 'matplotlib', 'matplotlib.pyplot']
+    sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
+
+
 # -- 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', 'sphinx.ext.viewcode']
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.napoleon', 'sphinx.ext.viewcode']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -100,7 +113,10 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'default'
+if on_rtd:
+    html_theme = 'default'
+else:
+    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
@@ -180,10 +196,10 @@
 
 latex_elements = {
 # The paper size ('letterpaper' or 'a4paper').
-#'papersize': 'letterpaper',
+'papersize': 'a4paper',
 
 # The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
+'pointsize': '11pt',
 
 # Additional stuff for the LaTeX preamble.
 #'preamble': '',

docs/index.rst

@@ -16,6 +16,7 @@ Contents:
    contributing
    authors
    history
+   code/index
 
 Feedback
 ========
@@ -25,3 +26,11 @@ at [email protected].
 
 If you encounter any errors or problems with **Jorrit's Python Package**, please let me know!
 Open an Issue at the GitHub http://github.com/jowr/jopy main repository.
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`