Initial documentation

.gitignore

@@ -1,7 +1,7 @@
 # Sphinx & coverage
 build
-doc/_build
-doc/api
+docs/_build
+docs/api
 glue/tests/htmlcov
 *.coverage
 *htmlcov*

.travis.yml

@@ -26,9 +26,18 @@ install:
   - pip install -e .[test]
 
 script:
+
+  # Run test suite
   - pytest --cov glue_jupyter glue_jupyter -p no:warnings
+
+  # Check notebooks
   - pip install astroquery pyyaml
   - python .validate-notebooks.py
 
+  # Test documentation build
+  - pip install -e .[docs]
+  - cd docs
+  - make html
+
 after_success:
   - codecov

docs/Makefile

@@ -0,0 +1,133 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    = -W --keep-going
+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)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest
+
+#This is needed with git because git doesn't create a dir if it's empty
+$(shell [ -d "_static" ] || mkdir -p _static)
+
+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 "  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 "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  linkcheck  to check all external links for integrity"
+
+clean:
+	-rm -rf $(BUILDDIR)
+	-rm -rf api
+	-rm -rf generated
+
+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/Astropy.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/Astropy.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/Astropy"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/Astropy"
+	@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."
+
+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."
+
+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:
+	@echo "Run 'python setup.py test' in the root directory to run doctests " \
+	@echo "in the documentation."

docs/api.rst

@@ -0,0 +1,35 @@
+API Documentation
+=================
+General
+-------
+.. automodapi:: glue_jupyter
+
+.. automodapi:: glue_jupyter.app
+
+.. automodapi:: glue_jupyter.view
+
+.. automodapi:: glue_jupyter.common.state3d
+
+.. automodapi:: glue_jupyter.compat
+
+bqplot viewers
+--------------
+
+.. automodapi:: glue_jupyter.bqplot.common
+
+.. automodapi:: glue_jupyter.bqplot.histogram
+
+.. automodapi:: glue_jupyter.bqplot.image
+
+.. automodapi:: glue_jupyter.bqplot.profile
+
+.. automodapi:: glue_jupyter.bqplot.scatter
+
+ipyvolume viewers
+-----------------
+
+.. automodapi:: glue_jupyter.ipyvolume.common
+
+.. automodapi:: glue_jupyter.ipyvolume.scatter
+
+.. automodapi:: glue_jupyter.ipyvolume.volume

docs/source/conf.py → docs/conf.py

@@ -32,11 +32,15 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = ['sphinx.ext.autodoc',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.todo',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.viewcode',
-    'nbsphinx']
+              'sphinx.ext.intersphinx',
+              'sphinx.ext.todo',
+              'sphinx.ext.mathjax',
+              'sphinx.ext.viewcode',
+              'nbsphinx', 'numpydoc',
+              'sphinx_automodapi.automodapi',
+              'sphinx_automodapi.smart_resolver']
+
+numpydoc_show_class_members = False
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -170,8 +174,34 @@
      'Miscellaneous'),
 ]
 
-
-
-
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/': None}
+intersphinx_cache_limit = 10     # days to keep the cached inventories
+intersphinx_mapping = {
+    # 'sphinx': ('https://www.sphinx-doc.org/en/latest/', None),
+    'python': ('https://docs.python.org/3.7', None),
+    # 'matplotlib': ('https://matplotlib.org', None),
+    # 'numpy': ('https://docs.scipy.org/doc/numpy', None),
+    # 'astropy': ('http://docs.astropy.org/en/stable/', None),
+    'echo': ('https://echo.readthedocs.io/en/latest/', None),
+    'ipywidgets': ('https://ipywidgets.readthedocs.io/en/stable/', None),
+    'traitlets': ('https://traitlets.readthedocs.io/en/stable/', None),
+    'glue': ('http://docs.glueviz.org/en/latest/', None),
+}
+
+default_role = 'obj'
+nitpicky = True
+nitpick_ignore = [('py:class', 'ipywidgets.widgets.widget_box.Box'),
+                  ('py:class', 'ipywidgets.widgets.widget_box.VBox'),
+                  ('py:class', 'ipywidgets.widgets.widget.Widget'),
+                  ('py:class', 'ipywidgets.widgets.widget.LoggingHasTraits'),
+                  ('py:class', 'ipywidgets.widgets.domwidget.DOMWidget'),
+                  ('py:class', 'ipywidgets.widgets.widget_core.CoreWidget'),
+                  ('py:class', 'traitlets.traitlets.HasTraits'),
+                  ('py:class', 'traitlets.traitlets.HasDescriptors'),
+                  ('py:class', 'glue.external.echo.core.HasCallbackProperties'),
+                  ('py:class', 'glue.viewers.image.layer_artist.ImageLayerArtist'),
+                  ('py:class', 'glue.viewers.image.layer_artist.BaseImageLayerArtist'),
+                  ('py:class', 'glue_vispy_viewers.volume.layer_state.VolumeLayerState'),
+                  ('py:class', 'glue_vispy_viewers.common.layer_state.VispyLayerState')]
+
+automodapi_inheritance_diagram = False

docs/getting_started.rst

@@ -0,0 +1,40 @@
+Getting started
+===============
+
+To start using glue in the Jupyter notebook or Jupyter lab, you will need to
+call the :func:`~glue_jupyter.jglue` function::
+
+    >>> from glue_jupyter import jglue
+    >>> app = jglue()
+
+This will automatically set up a data container (called a *data collection* in
+glue) and the ``app`` object can then be used to load data, link data, and
+create visualizations. For instance, suppose that you have a CSV file that you
+want to visualize. Start off by loading it with::
+
+    >>> table = app.load_data('mytable.csv')
+
+The ``table`` variable points to a glue `~glue.core.data.Data` object. For more
+information about how to work with and extract values from this kind of object
+see `this tutorial <http://docs.glueviz.org/en/stable/python_guide/data_tutorial.html>`__
+in the main glue documentation.
+
+You can then create visualizations using methods on ``app`` - for example, to
+create a histogram visualization, use `~glue_jupyter.JupyterApplication.histogram1d`::
+
+    >>> histogram = app.histogram1d(data=table)
+
+for a 2-d scatter plot, use `~glue_jupyter.JupyterApplication.scatter2d`::
+
+    >>> scatter2d = app.scatter2d(data=table)
+
+and for a 3-d scatter plot, use `~glue_jupyter.JupyterApplication.scatter3d`::
+
+    >>> scatter3d = app.scatter3d(data=table)
+
+Other available visualizations include
+`~glue_jupyter.JupyterApplication.profile1d`,
+`~glue_jupyter.JupyterApplication.imshow`, and
+`~glue_jupyter.JupyterApplication.volshow`.
+
+.. TODO: continue writing this page!

docs/index.rst

@@ -0,0 +1,23 @@
+Glue in the Jupyter Notebook
+============================
+
+About
+-----
+
+The **glue-jupyter** package provides a way to use the `glue
+<http://glueviz.org/>`_ package for multi-dimensional linked-data exploration in
+the `Jupyter <https://jupyter.org/>`_ notebook and Jupyter Lab. This package is
+still in early development, but it is already possible to try out some of the
+functionality. If you run into any issues or would like to request features,
+please head over to our `issue tracker
+<https://github.com/glue-viz/glue-jupyter/issues>`_.
+
+User guide
+----------
+
+.. toctree::
+   :maxdepth: 1
+
+   installing.rst
+   getting_started.rst
+   api.rst

docs/installing.rst

@@ -0,0 +1,18 @@
+Installation
+============
+
+To install the latest developer version of the **glue-jupyter** package as
+well as its dependencies, you will need the latest developer version of some
+dependencies, including glue itself. If you are using conda, we therefore
+recommend that you create a new environment::
+
+    conda create -n glue-jupyter python=3.7
+
+To install glue-jupyter along with all its dependencies, you can do::
+
+    pip install git+https://github.com/glue-viz/glue-jupyter
+
+If you are interested in using glue-jupyter in Jupyter Lab, you will need to
+also install the following extensions manually::
+
+    jupyter labextension install @jupyter-widgets/jupyterlab-manager bqplot ipyvolume jupyter-threejs