Merge 6a505c1 into 981d4b1

README.md

@@ -1,7 +1,7 @@
 # sami2py: sami2py is another model of the ionosphere python style
 [![Build Status](https://travis-ci.com/jklenzing/sami2py.svg?branch=develop)](https://travis-ci.com/jklenzing/sami2py)
 [![Coverage Status](https://coveralls.io/repos/github/jklenzing/sami2py/badge.svg?branch=develop)](https://coveralls.io/github/jklenzing/sami2py?branch=develop)
-
+[![Documentation Status](https://readthedocs.org/projects/sami2py/badge/?version=latest)](http://sami2py.readthedocs.io/en/latest/?badge=latest)
 
 # Overview
 
@@ -63,4 +63,4 @@ work uses the SAMI2 ionosphere model written and developed by the Naval Research
 # References
 - Huba, J.D., G. Joyce, and J.A. Fedder, Sami2 is Another Model of the Ionosphere (SAMI2): A new low‐latitude ionosphere model, *J. Geophys. Res.*, 105, Pages 23035-23053, https://doi.org/10.1029/2000JA000035, 2000.
 - Emmert, J.T., J.L. Lean, and J.M. Picone, Record‐low thermospheric density during the 2008 solar minimum, *Geophys. Res. Lett.*, 37, https://doi.org/10.1029/2010GL043671, 2010.
-- Klenzing, J., Burrell, A. G., Heelis, R. A., Huba, J. D., Pfaff, R., and Simões, F.: Exploring the role of ionospheric drivers during the extreme solar minimum of 2008, *Ann. Geophys.*, 31, 2147-2156, https://doi.org/10.5194/angeo-31-2147-2013, 2013.
+- Klenzing, J., A. G. Burrell, R. A. Heelis, J. D. Huba, R. Pfaff, and F. Simões, Exploring the role of ionospheric drivers during the extreme solar minimum of 2008, *Ann. Geophys.*, 31, 2147-2156, https://doi.org/10.5194/angeo-31-2147-2013, 2013.

docs/conf.py

@@ -0,0 +1,184 @@
+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- Path setup --------------------------------------------------------------
+
+# 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('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'sami2py'
+copyright = '2019, Jeff Klenzing'
+author = 'Jeff Klenzing \\and Jonathon Smith'
+
+# The short X.Y version
+version = '0.1a2'
+# The full version, including alpha/beta/rc tags
+release = ''
+
+
+# -- 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.doctest',
+    'sphinx.ext.todo',
+    'sphinx.ext.imgmath',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.napoleon',
+    'recommonmark',
+    'numpydoc',
+    'IPython.sphinxext.ipython_console_highlighting'
+]
+
+numpydoc_show_class_members = False
+
+# 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'
+
+# 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 pattern also affects 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 = None
+
+
+# -- 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'
+
+# 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']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'sami2pydoc'
+
+
+# -- 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, 'sami2py.tex', 'sami2py Documentation',
+     'Jeff Klenzing', '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, 'sami2py', 'sami2py 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, 'sami2py', 'sami2py Documentation',
+     author, 'sami2py', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+# -- Options for Epub output -------------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = project
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ['search.html']

docs/installation.rst

@@ -0,0 +1,24 @@
+Installation
+============
+
+First, checkout the repository:
+
+::
+
+  git clone git@gitlab.com:jklenzing/sami2py.git
+
+Change directories into the repository folder and run the setup.py file.  For
+a local install use the "--user" flag after "install".
+
+::
+
+  cd sami2py/
+  python setup.py install
+
+Additionally, you must make and install the fortran executables.
+
+::
+
+  make -C sami2py/fortran compile
+
+Now you can run the sami2 executable (sami2py.x) from anywhere.

docs/introduction.rst

@@ -0,0 +1,32 @@
+
+.. |br| raw:: html
+
+    <br>
+
+Introduction
+============
+
+Sami2py is a python module that runs the SAMI2 model, as well as archives, loads and plots the resulting modeled values. SAMI2 is a model developed by the Naval Research Laboratory to simulate the motions of plasma in a 2D ionospheric environment along a dipole magnetic field [Huba et al, 2000].  SAMI2 solves for the chemical and dynamical evolution of seven ion species in this environment (H\ :sup:`+`\, He\ :sup:`+`\, N\ :sup:`+`\, O\ :sup:`+`\, N\ :sub:`2` :sup:`+`\, NO\ :sup:`+`\, and O\ :sub:`2` :sup:`+`\).
+
+The implementation used here includes several added options to the original release of SAMI2.  A full list is included in ***add link to changes page***, but several of these include:
+ - The ability to scale the neutral atmosphere in which the ions form through direct modification of the exospheric neutral temperature for extreme solar minimum conditions, as discussed by Emmert et al [2010].
+ - The ability to switch between HWM93, HWM07, and HWM14 as a user option.
+ This implementation is based on the version used in Klenzing et al [2013].
+
+The open-source fortran version of SAMI2 is found at https://www.nrl.navy.mil/ppd/branches/6790/sami2
+
+
+How to Cite
+-----------
+
+When referring to this software package, please cite the original paper by Huba et al [2000] https://doi.org/10.1029/2000JA000035 as well as the package by Klenzing et al [2018]. ***add doi here***.
+
+Additionally, please include the following text in the acknowledgements: "This work uses the SAMI2 ionosphere model written and developed by the Naval Research Laboratory."
+
+
+References
+----------
+
+ - Huba, J.D., G. Joyce, and J.A. Fedder, Sami2 is Another Model of the Ionosphere (SAMI2): A new low‐latitude ionosphere model, *J. Geophys. Res.*, 105, Pages 23035-23053, https://doi.org/10.1029/2000JA000035, 2000.
+ - Emmert, J.T., J.L. Lean, and J.M. Picone, Record‐low thermospheric density during the 2008 solar minimum, *Geophys. Res. Lett.*, 37, https://doi.org/10.1029/2010GL043671, 2010.
+ - Klenzing, J., A. G. Burrell, R. A. Heelis, J. D. Huba, R. Pfaff, and F. Simões, Exploring the role of ionospheric drivers during the extreme solar minimum of 2008, *Ann. Geophys.*, 31, 2147-2156, https://doi.org/10.5194/angeo-31-2147-2013, 2013.

docs/requirements.txt

@@ -0,0 +1,2 @@
+numpydoc
+ipython

docs/sample_workflow.rst

@@ -0,0 +1,19 @@
+Sample Workflow
+===============
+
+In iPython, run:
+
+.. code:: python
+
+  import sami2py
+  sami2py.run_model(year=2012, day=210, lon=0, tag='test')
+
+Note that the sami2 model runs for 24 hours to clear transients, then begins to output data.
+
+Now load the resultant data:
+
+.. code:: python
+
+  ModelRun = sami2py.model(tag='test', lon=0, year=2012, day=210)
+
+Full description coming soon