Merge branch 'master' into window_fix

README.md

@@ -1,9 +1,12 @@
-# hera_pspec
+# ``hera_pspec``: HERA delay spectrum estimation
 
 [![Build Status](https://travis-ci.org/HERA-Team/hera_pspec.svg?branch=master)](https://travis-ci.org/HERA-Team/hera_pspec)
 [![Coverage Status](https://coveralls.io/repos/github/HERA-Team/hera_pspec/badge.svg?branch=master)](https://coveralls.io/github/HERA-Team/hera_pspec?branch=master)
+[![Documentation](https://readthedocs.org/projects/hera-pspec/badge/?version=latest)](https://readthedocs.org/projects/hera-pspec/badge/?version=latest)
 
-**hera_pspec description**
+The ``hera_pspec`` library provides all of the tools and data structures needed to perform a delay spectrum analysis on interferometric data. The input data can be in any format supported by ``pyuvdata``, and the output data are stored in HDF5 containers.
+
+For usage examples and documentation, see http://hera-pspec.readthedocs.io/en/latest/.
 
 ## Installation
 
@@ -15,6 +18,8 @@
 * scipy >= 0.19
 * astropy >= 2.0
 * hera_cal (https://github.com/HERA-Team/hera_cal.git)
+* pyyaml
+* hdf5
 
 For anaconda users, we suggest using conda to install astropy, numpy and scipy.
 
@@ -24,7 +29,6 @@ Clone the repo using
 
 Navigate into the directory and run `python setup.py install`.
 
-## Package Details and Usage
-
-
+## Running `hera_pspec`
 
+See the documentation for an [overview and examples](http://hera-pspec.readthedocs.io/en/latest/pspec.html) of how to run `hera_pspec`. There are also some example Jupyter notebooks, including [`examples/PS_estimation_examples.ipynb`](examples/PS_estimation_example.ipynb) (a brief tutorial on how to create delay spectra), and [`examples/PSpecBeam_tutorial.ipynb`](examples/PSpecBeam_tutorial.ipynb) (a brief tutorial on handling beam objects).

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = hera_pspec
+SOURCEDIR     = .
+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)

docs/conf.py

@@ -0,0 +1,186 @@
+# -*- coding: utf-8 -*-
+#
+# hera_pspec documentation build configuration file, created by
+# sphinx-quickstart on Tue Apr 24 13:55:12 2018.
+#
+# 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('.'))
+
+import os
+import sys
+
+# Mock-import modules to allow build to complete without throwing errors
+import mock
+MOCK_MODULES = ['numpy', 'scipy', 'scipy.interpolate', 'pyuvdata', 'h5py', 'aipy', 'omnical', 'linsolve', 'hera_qm', 'uvtools', 'hera_cal', 'healpy', 'scikit-learn']
+for mod_name in MOCK_MODULES:
+    sys.modules[mod_name] = mock.Mock()
+
+sys.path.insert(0, os.path.abspath('../'))
+#import hera_pspec
+
+
+# -- 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.napoleon',
+    'sphinx.ext.coverage',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.githubpages']
+
+# 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'hera_pspec'
+copyright = u'2018, HERA Collaboration'
+author = u'HERA Collaboration'
+
+# 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'0.1'
+# The full version, including alpha/beta/rc tags.
+release = u'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 = ['_build', 'Thumbs.db', '.DS_Store']
+
+# 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 = 'alabaster'
+html_theme = "default"
+html_theme_options = {
+    "rightsidebar": "false",
+    "relbarbgcolor": "black"
+}
+
+# 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 = 'hera_pspecdoc'
+
+
+# -- Options for numpydoc ------------------------------------------
+
+#numpydoc_show_class_members = False
+napoleon_google_docstring = False
+napoleon_use_param = False
+napoleon_use_ivar = True
+
+
+# -- 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, 'hera_pspec.tex', u'hera\\_pspec Documentation',
+     u'HERA Collaboration', '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, 'hera_pspec', u'hera_pspec 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, 'hera_pspec', u'hera_pspec Documentation',
+     author, 'hera_pspec', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+

docs/container.rst

@@ -0,0 +1,7 @@
+``PSpecContainer`` Class
+========================
+
+``PSpecContainer`` is a container for organizing collections of ``UVPSpec`` objects. It is based on HDF5.
+
+.. .. autoclass:: hera_pspec.PSpecContainer
+..   :members:

docs/index.rst

@@ -0,0 +1,29 @@
+
+HERA delay power spectrum estimation
+====================================
+
+The ``hera_pspec`` library provides all of the tools and data structures needed 
+to perform a delay spectrum analysis on interferometric data. The input data 
+can be in any format supported by ``pyuvdata``, and the output data are stored in 
+HDF5 containers.
+
+You can find the code in the ``hera_pspec`` `GitHub repository <https://github.com/HERA-Team/hera_pspec>`_. A set of `example Jupyter notebooks <https://github.com/HERA-Team/hera_pspec/tree/master/examples>`_ are also available on GitHub.
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   pspec
+   pspecbeam
+   pspecdata
+   uvpspec
+   container
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`