simpeg · sgkang · Jun 28, 2018 · Jun 2, 2018 · Jun 2, 2018 · Jun 4, 2018
diff --git a/.gitignore b/.gitignore
@@ -89,3 +89,9 @@ ENV/
 .ropeproject
 *.sublime-workspace
 *.sublime-project
+
+# sphinx-gallery
+/docs/auto_examples/*
+
+# Jupyter
+*.ipynb
diff --git a/.travis.yml b/.travis.yml
@@ -8,11 +8,24 @@ sudo: false
 env:
   - TEST_DIR='tests'
 
+before_install:
+  - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then
+      wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh;
+    else
+      wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+    fi
+  - chmod +x miniconda.sh
+  - ./miniconda.sh -b -p $HOME/miniconda
+  - export PATH=/home/travis/anaconda/bin:/home/travis/miniconda/bin:$PATH
+  - conda update --yes conda
+
 install:
+  - conda install --quiet --yes pip python=$TRAVIS_PYTHON_VERSION numpy scipy matplotlib pillow cython ipython;
   - pip install --upgrade pip;
   - pip install -r requirements.txt
   - pip install -r requirements_dev.txt
   - cd geoana; python setup.py install; cd ..
+  - export MPLBACKEND="agg"
 
 # Run test
 script:

diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2017 SimPEG Team
+Copyright (c) 2017-2018 SimPEG Team
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/README.rst b/README.rst
@@ -1,5 +1,8 @@
 .. _geoana:
 
+
+| :ref:`getting_started` | :ref:`connecting` | :ref:`installing` | :ref:`license` | `Documentation <http://geoana.readthedocs.io/en/latest/>`_ |
+
 geoana
 ======
 
@@ -20,5 +23,56 @@ geoana
     :alt: codacy status
 
 
-Interactive geoscience (mostly) analytic functions in geophysics.
+`geoana` is a collection of (mostly) analytic functions in geophysics. We take an object oriented
+approach with the aim of having users be able to readily interact with the functions using `Jupyter <https://jupyter.org>`_
+
+
+.. _getting_started:
+
+Getting started
+---------------
+
+- If you do not already have python installed, we recommend downloading and installing it through `anaconda <https://www.anaconda.com/download/>`_
+- :ref:`Install <installing>` geoana
+- Browse the :ref:`gallery <examples>` for ideas and example usage
+- Read the `documentation <http://geoana.readthedocs.io/en/latest/>`_ for more information on the library and what it can do
+
+.. - See the `contributor guide` and `code of conduct` if you are interested in helping develop or maintain geoana
+
+.. _connecting:
+
+Connecting with the community
+-----------------------------
+
+geoana is a part of the larger `SimPEG <https://www.simpeg.xyz>`_ ecosystem. There are several avenues for connecting:
+
+- a mailing list for questions and general news items: https://groups.google.com/forum/#!forum/simpeg
+- a newsletter where meeting notices and re-caps are posted: http://eepurl.com/bVUoOL
+- a slack group for real-time chat with users and developers of SimPEG: http://slack.simpeg.xyz/
+
+.. _installing:
+
+Installing
+----------
+
+geoana is available on `pypi <https://pypi.org/project/geoana/>`_ and can be installed by opening a command window and running:
+
+.. code::
+
+    pip install geoana
+
+
+To install from source, you can
+
+.. code::
+
+    git clone https://github.com/simpeg/geoana.git
+    python setup.py install
+
+.. _license:
+
+License
+-------
+
+geoana is licensed under the `MIT license <https://github.com/simpeg/geoana/blob/master/LICENSE>`_ .
 
diff --git a/docs/Makefile b/docs/Makefile
@@ -50,6 +50,8 @@ help:
 .PHONY: clean
 clean:
 	rm -rf $(BUILDDIR)/*
+	rm -rf auto_examples/
+	rm -rf modules/generated/*
 
 .PHONY: html
 html:

diff --git a/docs/conf.py b/docs/conf.py
@@ -12,13 +12,16 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
+import sys
 import os
 
 # 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.
 # sys.path.insert(0, os.path.abspath('.'))
 
+sys.path.append(os.path.abspath('../'))
+
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -33,6 +36,8 @@
     'sphinx.ext.coverage',
     'sphinx.ext.mathjax',
     'sphinx.ext.viewcode',
+    'matplotlib.sphinxext.plot_directive',
+    'sphinx_gallery.gen_gallery',
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -51,7 +56,7 @@
 
 # General information about the project.
 project = u'geoana'
-copyright = u'2017, SimPEG Team'
+copyright = u'2017-2018, SimPEG Team'
 author = u'SimPEG Team'
 
 # The version info for the project you're documenting, acts as replacement for
@@ -127,6 +132,14 @@
 linkcheck_retries = 3
 linkcheck_timeout = 500
 
+# Sphinx Gallery
+sphinx_gallery_conf = {
+    # path to your examples scripts
+    'examples_dirs' : '../examples',
+    'gallery_dirs'  : 'auto_examples',
+    'backreferences_dir' : False
+}
+
 # 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.
@@ -306,7 +319,14 @@
 
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/': None}
+intersphinx_mapping = {
+    'python': ('https://docs.python.org/3/', None),
+    'numpy': ('https://docs.scipy.org/doc/numpy/', None),
+    'scipy': ('https://docs.scipy.org/doc/scipy/reference/', None),
+    'matplotlib': ('http://matplotlib.org/', None),
+    'properties': ('http://propertiespy.readthedocs.io/en/latest/', None),
+
+}
 
 
 def supress_nonlocal_image_warn():
@@ -324,3 +344,6 @@ def _supress_nonlocal_image_warn(self, msg, node, **kwargs):
 
 supress_nonlocal_image_warn()
 
+nitpick_ignore = [
+    ('py:class', 'properties.base.base.HasProperties')
+]
diff --git a/docs/content/conventions.rst b/docs/content/conventions.rst
@@ -0,0 +1,52 @@
+Conventions
+===========
+
+Coordinate systems
+------------------
+
+Cartesian
+^^^^^^^^^
+
+We use a right-handed coordinate system :math:`(x, y, z)` with z-positive up as shown in the Figure below.
+
+.. image:: ../images/coordinates-02.png
+    :width: 40%
+    :align: center
+
+
+Cylindrical
+^^^^^^^^^^^
+
+We again work with z-positive up and use :math:`\theta` to denote the azimuthal angle, thus the coordinate
+system is defined as :math:`(r, \theta, z)`.
+
+.. image:: ../images/coordinates-03.png
+    :width: 40%
+    :align: center
+
+
+Spherical
+^^^^^^^^^
+
+We use :math:`r` for the radial direction, :math:`\theta` for the azimuthal direction, and :math:`\phi` for
+the polar direction as shown in the figure below.
+
+.. image:: ../images/coordinates-04.png
+    :width: 40%
+    :align: center
+
+
+Fourier Transform
+-----------------
+
+For analysis and solutions in the frequency domain we use the :math:`e^{i \omega t}`
+Fourier transform convention. Thus, we define our
+Fourier Transform pair as
+
+.. math ::
+    F(\omega) = \int_{-\infty}^{\infty} f(t) e^{- i \omega t} dt \\
+
+    f(t) = \frac{1}{2\pi}\int_{-\infty}^{\infty} F(\omega) e^{i \omega t} d \omega
+
+where :math:`\omega` is angular frequency, :math:`t` is time, :math:`F(\omega)` is the
+function defined in the frequency domain and :math:`f(t)` is the function defined in the time domain.
diff --git a/docs/content/earthquake.rst b/docs/content/earthquake.rst
@@ -3,6 +3,7 @@
 Earthquake
 ==========
 
-.. autoclass:: geoana.earthquake
+.. automodule:: geoana.earthquake.oksar
     :members:
     :undoc-members:
+    :show-inheritance:
diff --git a/docs/content/em.rst b/docs/content/em.rst
@@ -3,6 +3,37 @@
 Electromagnetics
 ================
 
-.. autoclass:: geoana.em
+Base
+----
+
+.. automodule:: geoana.em.base
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Static
+------
+
+.. automodule:: geoana.em.static
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Frequency Domain
+----------------
+
+.. automodule:: geoana.em.fdem
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Time Domain
+-----------
+
+.. automodule:: geoana.em.tdem
     :members:
     :undoc-members:
+    :show-inheritance:
diff --git a/docs/content/utils.rst b/docs/content/utils.rst
@@ -0,0 +1,23 @@
+.. _utils:
+
+Utilities
+=========
+
+Core Utils
+----------
+
+.. automodule:: geoana.utils
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Spatial
+-------
+
+.. automodule:: geoana.spatial
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
diff --git a/docs/images/coordinates-02.png b/docs/images/coordinates-02.png
diff --git a/docs/images/coordinates-03.png b/docs/images/coordinates-03.png
diff --git a/docs/images/coordinates-04.png b/docs/images/coordinates-04.png
diff --git a/docs/index.rst b/docs/index.rst
@@ -2,12 +2,17 @@
 
 .. include:: ../README.rst
 
+.. _contents:
 
-**Contents:**
+Contents
+--------
 
 .. toctree::
    :maxdepth: 2
 
-   content/earthquake
+   auto_examples/index
+   content/conventions
    content/em
+   content/earthquake
+   content/utils
 
diff --git a/examples/em/README.txt b/examples/em/README.txt
@@ -1,2 +1,2 @@
 Electromagnetics
-****************
+----------------