Created basic documentation with sphinx

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = python -msphinx
+SPHINXPROJ    = sunburn
+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 +1,185 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# sunburn documentation build configuration file, created by
+# sphinx-quickstart on Fri Jan 19 09:16:10 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('.'))
+
+
+# -- 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.intersphinx',
+    'sphinx.ext.todo',
+    'sphinx.ext.coverage',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.githubpages',
+    'sphinx.ext.napoleon'
+]
+
+# 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 = 'sunburn'
+copyright = '2018, Leonardo dos Santos'
+author = 'Leonardo dos Santos'
+
+# 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'
+# The full version, including alpha/beta/rc tags.
+release = '0.1a'
+
+# 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 = True
+
+
+# -- 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 = 'sphinx_rtd_theme'
+
+# 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.
+#
+# This is required for the alabaster theme
+# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
+html_sidebars = {
+    '**': [
+        'about.html',
+        'navigation.html',
+        'relations.html',  # needs 'show_related': True theme option to display
+        'searchbox.html',
+        'donate.html',
+    ]
+}
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'sunburndoc'
+
+
+# -- 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, 'sunburn.tex', 'sunburn Documentation',
+     'Leonardo dos Santos', '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, 'sunburn', 'sunburn 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, 'sunburn', 'sunburn Documentation',
+     author, 'sunburn', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'https://docs.python.org/': None}

docs/index.rst

@@ -0,0 +1,24 @@
+.. sunburn documentation master file, created by
+   sphinx-quickstart on Fri Jan 19 09:16:10 2018.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to sunburn's documentation!
+===================================
+
+``sunburn`` is a Python package aimed at facilitating the data analysis of ultraviolet spectra obtained with the Hubble Space Telescope, and more specifically designed towards the study of transiting exoplanets. The code is completely object-oriented and designed to be used with Python scripts and Jupyter Notebooks. If you find any bugs or have questions and feature requests, feel free to submit an `issue on GitHub <https://github.com/ladsantos/sunburn/issues>`_. ``sunburn`` is fully compatible with Python 3, and may have incompatibility issues with Python 2.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   install
+   source/sunburn.rst
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/install.rst

@@ -0,0 +1,33 @@
+Installation
+============
+
+``sunburn`` currently works with Python 3; compatibility with Python 2 was not tested.
+
+Dependencies
+------------
+
+* ``numpy`` >= 1.12
+* ``scipy`` >= 0.19
+* ``matplotlib`` >= 2.0
+* ``astropy`` >= 2.0.2
+* ``astroquery`` >= 0.3.7.dev4234
+* ``astroplan``
+
+**Note**: The development version of `astroquery` is necessary because of a specific implementation of queries to the NASA Exoplanet Archive. In order to install this development version, you will have to `build it from source <http://astroquery.readthedocs.io/en/latest/#building-from-source>`_. In the near future this may not be necessary anymore because `astroquery` will eventually consolidate the development version into the stable version.
+
+Build from source
+-----------------
+Clone the repository::
+
+    git clone https://github.com/ladsantos/sunburn.git
+
+Navigate to the source code and install it in your Python environment::
+
+    cd sunburn
+    python setup.py install
+
+.. Indices and tables
+   ==================
+   * :ref:`genindex`
+   * :ref:`modindex`
+   * :ref:`search`

docs/make.bat

@@ -0,0 +1,36 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=python -msphinx
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+set SPHINXPROJ=sunburn
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The Sphinx module was not found. Make sure you have Sphinx installed,
+	echo.then set the SPHINXBUILD environment variable to point to the full
+	echo.path of the 'sphinx-build' executable. Alternatively you may add the
+	echo.Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

docs/source/sunburn.rst

@@ -0,0 +1,34 @@
+API
+===
+
+sunburn\.hst_observation module
+-------------------------------
+
+.. automodule:: sunburn.hst_observation
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+sunburn\.analysis module
+------------------------
+
+.. automodule:: sunburn.analysis
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+sunburn\.spectroscopy module
+----------------------------
+
+.. automodule:: sunburn.spectroscopy
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+sunburn\.tools module
+---------------------
+
+.. automodule:: sunburn.tools
+    :members:
+    :undoc-members:
+    :show-inheritance:

sunburn/hst_observation.py

@@ -62,7 +62,7 @@ def plot_spectra(self, wavelength_range, uncertainties=False,
                      figure_sizes=(9.0, 6.5), axes_font_size=18,
                      legend_font_size=13):
         """
-        Method used to plot all the spectra in the visitexamples
+        Method used to plot all the spectra in the visit.
 
         Args: