Merge pull request #19 from jason-neal/develop

Update master after generation of docs.

.gitignore

@@ -1,3 +1,5 @@
+docs/.build/
+
 #sync
 .sync/
 

.readthedocs.yml

@@ -0,0 +1,17 @@
+# Read the Docs Configuration File
+
+# Build PDF aswell as HTML and JSON
+formats:
+    - pdf
+
+# Requirements file
+requirements_file:
+    requirements.txt
+
+python:
+    version: 3.5
+    setup_py_install: true
+    # From extras_require in setup.py
+    extra_requirements:
+        - tests
+        - docs

.travis.yml

@@ -3,11 +3,9 @@ python:
   - "2.7"
   - "3.4"
   - "3.5"
-  #- "3.5-dev" # 3.5 development branch
-  #- "nightly" # currently points to 3.6-dev
-# command to install dependencies
+  - "3.6"
 
-#install: "pip install -r requirements.txt"
+# command to install dependencies
 # Setup anaconda
 before_install:
   # http://conda.pydata.org/docs/travis.html
@@ -24,27 +22,20 @@ before_install:
   - conda update -q conda
   - conda info -a
 install:
-  #- conda install --yes python=$TRAVIS_PYTHON_VERSION  numpy scipy matplotlib #nose atlas dateutil pandas statsmodels
-  # Coverage packages are on my binstar channel
-  #- conda install --yes -c dan_blanchard python-coveralls nose-cov
   - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION numpy scipy astropy
   - source activate test-environment
+  - pip install pyastronomy
   - python setup.py install
 
-
-  - pip install pytest-cov python-coveralls
+  - pip install pytest-cov python-coveralls codeclimate-test-reporter
   - pip install -r requirements.txt
-# install:
-#  -  pip install numpy
-#  -  pip install tox
-#  -  pip install matplotlib
-#  -  pip install hypothesis
 
 # command to run tests
 script:
   # - py.test -cov coveralls --cov-report term-missing
   # - py.test --cov=spectrum_overload spectrum_overload/ --cov-report term-missing
-  - py.test --cov=spectrum_overload --cov-report term-missing
+  - pytest --cov=spectrum_overload --cov-report term-missing --durations 5
 
 after_success:
   - coveralls
+  - codeclimate-test-reporter

README.md

@@ -1,33 +1,84 @@
-# spectrum_overload [![Build Status](https://travis-ci.org/jason-neal/spectrum_overload.svg)](https://travis-ci.org/jason-neal/spectrum_overload) [![Coverage Status](https://coveralls.io/repos/github/jason-neal/spectrum_overload/badge.svg?branch=develop)](https://coveralls.io/github/jason-neal/spectrum_overload?branch=develop)
-Learn to use Classes by creating a Spectrum class to use in my Phd work.
+# spectrum_overload
+| Branch  | Docs | Build | Coverage | Code Climate | Code Issues |
+| :----: | :---: | :-----: | :----: | :----------: | :---------: |
+| master  | [![Documentation Status](https://readthedocs.org/projects/spectrum-overload/badge/?version=latest)](http://spectrum-overload.readthedocs.io/en/latest/?badge=latest) | [![Build Status](https://travis-ci.org/jason-neal/spectrum_overload.svg?branch=master)](https://travis-ci.org/jason-neal/spectrum_overload) | [![Coverage Status](https://coveralls.io/repos/github/jason-neal/spectrum_overload/badge.svg?branch=master)](https://coveralls.io/github/jason-neal/spectrum_overload?branch=master) [![Test Coverage](https://codeclimate.com/github/jason-neal/spectrum_overload/badges/coverage.svg)](https://codeclimate.com/github/jason-neal/spectrum_overload/coverage) | [![Code Climate](https://codeclimate.com/github/jason-neal/spectrum_overload/badges/gpa.svg)](https://codeclimate.com/github/jason-neal/spectrum_overload)[![Issue Count](https://codeclimate.com/github/jason-neal/spectrum_overload/badges/issue_count.svg)](https://codeclimate.com/github/jason-neal/spectrum_overload) | [![Code Issues](https://www.quantifiedcode.com/api/v1/project/6e918445f6f344c1af9c32f50718082e/snapshot/origin:master:HEAD/badge.svg)](https://www.quantifiedcode.com/app/project/6e918445f6f344c1af9c32f50718082e?branch=origin/master) |
+| develop | [![Documentation Status](https://readthedocs.org/projects/spectrum-overload/badge/?version=develop)](http://spectrum-overload.readthedocs.io/en/latest/?badge=develop) | [![Build Status](https://travis-ci.org/jason-neal/spectrum_overload.svg?branch=develop)](https://travis-ci.org/jason-neal/spectrum_overload) | [![Coverage Status](https://coveralls.io/repos/github/jason-neal/spectrum_overload/badge.svg?branch=develop)](https://coveralls.io/github/jason-neal/spectrum_overload?branch=develop) [![Test Coverage](https://codeclimate.com/github/jason-neal/spectrum_overload/badges/coverage.svg?branch=develop)](https://codeclimate.com/github/jason-neal/spectrum_overload/coverage?branch=develop) | [![Code Climate](https://codeclimate.com/github/jason-neal/spectrum_overload/badges/gpa.svg?branch=develop)](https://codeclimate.com/github/jason-neal/spectrum_overload?branch=develop)[![Issue Count](https://codeclimate.com/github/jason-neal/spectrum_overload/badges/issue_count.svg?branch=develop)](https://codeclimate.com/github/jason-neal/spectrum_overload?branch=develop) | [![Code Issues](https://www.quantifiedcode.com/api/v1/project/6e918445f6f344c1af9c32f50718082e/snapshot/origin:develop:HEAD/badge.svg)](https://www.quantifiedcode.com/app/project/6e918445f6f344c1af9c32f50718082e?branch=origin/develop) |
 
+## Overview
+The purpose of this was project was to learn how to use and create Classes, and to create a Spectrum object to use within my Phd work.
 
-Ideas to include:
+The main goals of this project are basically complete.
 
-Variables pixel, flux, wavelength
+- create a class to contain spectrum
+- automatic interpolation
+- overloaded operators
+especially
+- Spectral division (SpectrumA / SpectrumB )
+- Spectral subtraction (SpectrumA - SpectrumB)
+- Powers/exponents (Spectrum ** x)
 
-Spectral slicing method. (wav_selector)
+## Installation
+Currently to install and use Spectrum class for your own projects.
 
-Radial velocity shifts
+clone the git repository where you want it:
 
-Wavelength calibration method. pixel->wavelength
+    https://github.com/jason-neal/spectrum_overload.git
 
-Spectral subtraction:  SpectrumA - SpectrumB
+cd into the downloaded directory:
 
-Spectral division    SpectrumA/SpectrumB 
+    cd spectrum_overload
 
+and install using:
 
+    python setup.py install
 
-## Other Spectrum Classes:
 
-There are many other spectrum classes around but None (sofar) that overload the operators
+## Usage
+To use import the class using :
+
+    from spectrum_overload import Spectrum
+    ...
+    my_spectrum = Spectrum.Spectrum(flux, xaxis)
+
+or :
+
+    from spectrum_overload.Spectrum import Spectrum as spec
+    ...
+    my_spectrum = spec(flux, xaxis)
+
+or how ever else you would like to import it.
+
+A tutorial is provided [here](Notebooks/Tutorial.ipynb) to show an example of how to use this class.
+
+
+## Contributions
+Contributions are very welcome.
+
+I would really appreciate user feedback or suggested improvements if you have any.
+
+Feel free to submit issues or create pull requests.
+
+
+
+## Other Spectrum Classes
+
+There are many other spectrum classes around but I didn't see any that overload the operators. (I could be blind).
+
+One of these may better suit your needs
 
-I will list them here as I find them 
 - https://github.com/crawfordsm/specreduce
 - https://github.com/crawfordsm/pyspectrograph/tree/master/PySpectrograph/Spectra
 - http://pyspeckit.bitbucket.org/html/sphinx/spectrum.html#pyspeckit.spectrum.classes.Spectrum
 - https://github.com/cokelaer/spectrum
--https://github.com/astropy/specutils
+- https://github.com/astropy/specutils
 
 Wow A lot. I probably should not reinvent the wheel too much then...
 
+It turns out that astropy/specutils is very similar to what I have created but its direction is uncertain at the moment and they do not use overloaded operators and will not implement in the foreseeable future.
+
+## TO DO
+Some tasks still to do:
+
+- Improve Documentation
+- Generate Calibration solution (outside spectrum class)?
+- Push a version to pypi

docs/classes.rst

@@ -0,0 +1,49 @@
+.. _classes
+
+=================
+Available Classes
+=================
+Currently there are two classes available.
+    - :ref:`Spectrum <spectrumclass>`
+    - :ref:`DifferentialSpectrum <diffclass>`
+
+
+.. _spectrumclass:
+
+.. note::
+    Unfortunately the auto-documentation for these classes does not build properly yet due to the ``Pyastronomy`` install dependency `issue. <https://github.com/sczesla/PyAstronomy/issues/22>`_
+    I hope to see it here soon.
+
+    If you need you can try and build this documentation yourself from the root `spectrum_overload` directory::
+
+        pip install -e .[docs]   # editable installation, install docs dependencies.
+        cd docs
+        make html
+
+    This page will be docs/.build/classes.html
+
+Spectrum
+=========
+
+A class to contain a spectrum. The operators have been overloaded so that you can easily manipulate spectra.
+
+.. autoclass:: spectrum_overload.Spectrum.Spectrum
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+.. _diffclass:
+
+Differential Spectrum
+=====================
+Compute the difference between two :ref:`Spectrum <spectrumclass>` objects.
+
+This is in an introductory state and need more work.
+
+Would be useful add an s-profile function from `Ferluga et al. 1997 <http://aas.aanda.org/articles/aas/ps/1997/01/dst6676.ps.gz>`_. The subtraction of two gaussian lines with a RV offset.
+
+.. autoclass:: spectrum_overload.Differential.DifferentialSpectrum
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/conf.py

@@ -1,7 +1,8 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
-#
-# Spectrum documentation build configuration file, created by
+# Licensed under the MIT Licence
+
+# spectrum_overload documentation build configuration file, created by
 # sphinx-quickstart on Sun Sep 11 23:45:23 2016.
 #
 # This file is execfile()d with the current directory set to its
@@ -13,9 +14,24 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys
 import os
+import sys
+
+try:
+    import sphinx_rtd_theme
+except ImportError:
+    sphinx_rtd_theme = None
+
 
+base_dir = os.path.join(os.path.abspath(os.path.dirname(__file__)), "..")
+
+about = {}
+with open(os.path.join(base_dir, "spectrum_overload", "__about__.py")) as f:
+    exec(f.read(), about)
+
+
+sys.path.append(os.path.join(os.path.abspath(os.path.dirname(__file__)), ".."))
+sys.path.append(os.path.join(os.path.abspath(os.path.dirname(__file__)), "..", "spectrum_overload"))
 # 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.
@@ -37,6 +53,7 @@
     'sphinx.ext.mathjax',
     'sphinx.ext.viewcode',
     'sphinx.ext.githubpages',
+    'sphinx.ext.napoleon'
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -54,18 +71,18 @@
 master_doc = 'index'
 
 # General information about the project.
-project = 'Spectrum'
-copyright = '2016, Jason Neal'
-author = 'Jason Neal'
+project = 'spectrum_overload'
+copyright = about["__copyright__"]
+author = about["__author__"]
 
 # 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 = '0.1'
+version = about["__version__"]
 # The full version, including alpha/beta/rc tags.
-release = '0.1'
+release = about["__version__"]
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -117,7 +134,13 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'alabaster'
+#html_theme = 'alabaster'
+if sphinx_rtd_theme:
+    html_theme = "sphinx_rtd_theme"
+    html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+else:
+    # html_theme = "default"
+    html_theme = "sphinxdoc"
 
 # 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
@@ -129,7 +152,7 @@
 
 # The name for this set of Sphinx documents.
 # "<project> v<release> documentation" by default.
-#html_title = 'Spectrum v0.1'
+#html_title = 'spectrum_overload v0.1'
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
 #html_short_title = None
@@ -138,9 +161,9 @@
 # of the sidebar.
 #html_logo = None
 
-# The name of an image file (relative to this directory) to use as a favicon of
-# the docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
-# pixels large.
+# The name of an image file (relative to this directory) to use as a favicon
+# of the docs.  This file should be a Windows icon file (.ico) being 16x16 or
+# 32x32 pixels large.
 #html_favicon = None
 
 # Add any paths that contain custom static files (such as style sheets) here,
@@ -211,31 +234,31 @@
 #html_search_scorer = 'scorer.js'
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'Spectrumdoc'
+htmlhelp_basename = 'spectrum_overloaddoc'
 
 # -- Options for LaTeX output ---------------------------------------------
 
 latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-#'papersize': 'letterpaper',
+    # The paper size ('letterpaper' or 'a4paper').
+    #'papersize': 'letterpaper',
 
-# The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
+    # The font size ('10pt', '11pt' or '12pt').
+    #'pointsize': '10pt',
 
-# Additional stuff for the LaTeX preamble.
-#'preamble': '',
+    # Additional stuff for the LaTeX preamble.
+    #'preamble': '',
 
-# Latex figure (float) alignment
-#'figure_align': 'htbp',
-}
+    # 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, 'Spectrum.tex', 'Spectrum Documentation',
-     'Jason Neal', 'manual'),
-]
+    (master_doc, 'spectrum_overload.tex', 'spectrum_overload Documentation',
+     author, 'manual'),
+    ]
 
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
@@ -263,9 +286,9 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'spectrum', 'Spectrum Documentation',
+    (master_doc, 'spectrum_overload', 'spectrum_overload Documentation',
      [author], 1)
-]
+    ]
 
 # If true, show URL addresses after external links.
 #man_show_urls = False
@@ -277,10 +300,10 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'Spectrum', 'Spectrum Documentation',
-     author, 'Spectrum', 'One line description of project.',
+    (master_doc, 'spectrum_overload', 'spectrum_overload Documentation',
+     author, 'spectrum_overload', 'One line description of project.',
      'Miscellaneous'),
-]
+    ]
 
 # Documents to append as an appendix to all manuals.
 #texinfo_appendices = []