Commit 21f74ec4 authored by Yannick Roehlly's avatar Yannick Roehlly

Start documentation

Use sphinx with astropy _templates (it would be great to make pcigale an
affilated package).
Make the skeleton of the documentation.
Start to write pcigale script usage.
parent d9351c66
# Makefile for Sphinx documentation
#
# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build
PAPER =
BUILDDIR = _build
# User-friendly check for sphinx-build
ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
endif
# Internal variables.
PAPEROPT_a4 = -D latex_paper_size=a4
PAPEROPT_letter = -D latex_paper_size=letter
ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
# the i18n builder cannot share the environment and doctrees with the others
I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
help:
@echo "Please use \`make <target>' where <target> is one of"
@echo " html to make standalone HTML files"
@echo " dirhtml to make HTML files named index.html in directories"
@echo " singlehtml to make a single large HTML file"
@echo " pickle to make pickle files"
@echo " json to make JSON files"
@echo " htmlhelp to make HTML files and a HTML help project"
@echo " qthelp to make HTML files and a qthelp project"
@echo " devhelp to make HTML files and a Devhelp project"
@echo " epub to make an epub"
@echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
@echo " latexpdf to make LaTeX files and run them through pdflatex"
@echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
@echo " text to make text files"
@echo " man to make manual pages"
@echo " texinfo to make Texinfo files"
@echo " info to make Texinfo files and run them through makeinfo"
@echo " gettext to make PO message catalogs"
@echo " changes to make an overview of all changed/added/deprecated items"
@echo " xml to make Docutils-native XML files"
@echo " pseudoxml to make pseudoxml-XML files for display purposes"
@echo " linkcheck to check all external links for integrity"
@echo " doctest to run all doctests embedded in the documentation (if enabled)"
clean:
rm -rf $(BUILDDIR)/*
html:
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
dirhtml:
$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
singlehtml:
$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
@echo
@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
pickle:
$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
@echo
@echo "Build finished; now you can process the pickle files."
json:
$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
@echo
@echo "Build finished; now you can process the JSON files."
htmlhelp:
$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
@echo
@echo "Build finished; now you can run HTML Help Workshop with the" \
".hhp project file in $(BUILDDIR)/htmlhelp."
qthelp:
$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
@echo
@echo "Build finished; now you can run "qcollectiongenerator" with the" \
".qhcp project file in $(BUILDDIR)/qthelp, like this:"
@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/pcigale.qhcp"
@echo "To view the help file:"
@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/pcigale.qhc"
devhelp:
$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
@echo
@echo "Build finished."
@echo "To view the help file:"
@echo "# mkdir -p $$HOME/.local/share/devhelp/pcigale"
@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/pcigale"
@echo "# devhelp"
epub:
$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
@echo
@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
latex:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@echo
@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
@echo "Run \`make' in that directory to run these through (pdf)latex" \
"(use \`make latexpdf' here to do that automatically)."
latexpdf:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@echo "Running LaTeX files through pdflatex..."
$(MAKE) -C $(BUILDDIR)/latex all-pdf
@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
latexpdfja:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@echo "Running LaTeX files through platex and dvipdfmx..."
$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
text:
$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
@echo
@echo "Build finished. The text files are in $(BUILDDIR)/text."
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$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
@echo
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@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
@echo "Run \`make' in that directory to run these through makeinfo" \
"(use \`make info' here to do that automatically)."
info:
$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
@echo "Running Texinfo files through makeinfo..."
make -C $(BUILDDIR)/texinfo info
@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
gettext:
$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
@echo
@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
changes:
$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
@echo
@echo "The overview file is in $(BUILDDIR)/changes."
linkcheck:
$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
@echo
@echo "Link check complete; look for any errors in the above output " \
"or in $(BUILDDIR)/linkcheck/output.txt."
doctest:
$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
@echo "Testing of doctests in the sources finished, look at the " \
"results in $(BUILDDIR)/doctest/output.txt."
xml:
$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
@echo
@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
pseudoxml:
$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
@echo
@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
{% extends "autosummary_core/base.rst" %}
{# The template this is inherited from is in astropy/sphinx/ext/templates/autosummary_core. If you want to modify this template, it is strongly recommended that you still inherit from the astropy template. #}
\ No newline at end of file
{% extends "autosummary_core/class.rst" %}
{# The template this is inherited from is in astropy/sphinx/ext/templates/autosummary_core. If you want to modify this template, it is strongly recommended that you still inherit from the astropy template. #}
\ No newline at end of file
{% extends "autosummary_core/module.rst" %}
{# The template this is inherited from is in astropy/sphinx/ext/templates/autosummary_core. If you want to modify this template, it is strongly recommended that you still inherit from the astropy template. #}
\ No newline at end of file
# -*- coding: utf-8 -*-
#
# pcigale documentation build configuration file, created by
# sphinx-quickstart on Wed Sep 11 16:32:56 2013.
#
# 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.
import sys, 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('..'))
# -- 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.todo', 'sphinx.ext.mathjax']
# Add todos to the documentation
todo_include_todos = True
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
exclude_trees = ['_templates']
# The suffix of source filenames.
source_suffix = '.rst'
# The encoding of source files.
#source_encoding = 'utf-8-sig'
# The master toctree document.
master_doc = 'index'
# General information about the project.
project = u'pcigale'
author = u'The pcigale team'
copyright = u'2013, Laboratoire d\'Astrophysique de Marseille'
# 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.
import pcigale
# The short X.Y version.
version = pcigale.__version__.split('-', 1)[0]
# The full version, including alpha/beta/rc tags.
release = pcigale.__version__
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#language = None
# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
#today = ''
# Else, today_fmt is used as the format for a strftime call.
#today_fmt = '%B %d, %Y'
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
exclude_patterns = ['_build']
# The reST default role (used for this markup: `text`) to use for all documents.
#default_role = None
# If true, '()' will be appended to :func: etc. cross-reference text.
#add_function_parentheses = True
# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
#add_module_names = True
# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
#show_authors = False
# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'
# A list of ignored prefixes for module index sorting.
#modindex_common_prefix = []
# If true, keep warnings as "system message" paragraphs in the built documents.
#keep_warnings = 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 = '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
# documentation.
#html_theme_options = {}
# Add any paths that contain custom themes here, relative to this directory.
#html_theme_path = []
# The name for this set of Sphinx documents. If None, it defaults to
# "<project> v<release> documentation".
#html_title = None
# A shorter title for the navigation bar. Default is the same as html_title.
#html_short_title = None
# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
#html_logo = None
# The name of an image file (within the static path) to use as 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,
# 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']
# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.
#html_last_updated_fmt = '%b %d, %Y'
# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
#html_use_smartypants = True
# Custom sidebar templates, maps document names to template names.
#html_sidebars = {}
# Additional templates that should be rendered to pages, maps page names to
# template names.
#html_additional_pages = {}
# If false, no module index is generated.
#html_domain_indices = True
# If false, no index is generated.
#html_use_index = True
# If true, the index is split into individual pages for each letter.
#html_split_index = False
# If true, links to the reST sources are added to the pages.
#html_show_sourcelink = True
# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
#html_show_sphinx = True
# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
#html_show_copyright = True
# If true, an OpenSearch description file will be output, and all pages will
# contain a <link> tag referring to it. The value of this option must be the
# base URL from which the finished HTML is served.
#html_use_opensearch = ''
# This is the file name suffix for HTML files (e.g. ".xhtml").
#html_file_suffix = None
# Output file base name for HTML help builder.
htmlhelp_basename = 'pcigaledoc'
# -- 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': '',
}
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass [howto/manual]).
latex_documents = [
('index', 'pcigale.tex', u'pcigale Documentation',
u'pcigale team', 'manual'),
]
# The name of an image file (relative to this directory) to place at the top of
# the title page.
#latex_logo = None
# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
#latex_use_parts = False
# If true, show page references after internal links.
#latex_show_pagerefs = False
# If true, show URL addresses after external links.
#latex_show_urls = False
# Documents to append as an appendix to all manuals.
#latex_appendices = []
# If false, no module index is generated.
#latex_domain_indices = True
# -- Options for manual page output --------------------------------------------
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
('index', 'pcigale', u'pcigale Documentation',
[u'pcigale team'], 1)
]
# If true, show URL addresses after external links.
#man_show_urls = False
# -- 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 = [
('index', 'pcigale', u'pcigale Documentation',
u'pcigale team', 'pcigale', 'One line description of project.',
'Miscellaneous'),
]
# Documents to append as an appendix to all manuals.
#texinfo_appendices = []
# If false, no module index is generated.
#texinfo_domain_indices = True
# How to display URL addresses: 'footnote', 'no', or 'inline'.
#texinfo_show_urls = 'footnote'
# If true, do not generate a @detailmenu in the "Top" node's menu.
#texinfo_no_detailmenu = False
# -- Options for Epub output ---------------------------------------------------
# Bibliographic Dublin Core info.
epub_title = u'pcigale documentation'
epub_author = u'pcigale team'
epub_publisher = u'Laboratoire d\'Astrophysique de Marseille'
epub_copyright = u'Laboratoire d\'Astrophysique de Marseille'
# The language of the text. It defaults to the language option
# or en if the language is not set.
#epub_language = ''
# The scheme of the identifier. Typical schemes are ISBN or URL.
#epub_scheme = ''
# 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 tuple containing the cover image and cover page html template filenames.
#epub_cover = ()
# A sequence of (type, uri, title) tuples for the guide element of content.opf.
#epub_guide = ()
# HTML files that should be inserted before the pages created by sphinx.
# The format is a list of tuples containing the path and title.
#epub_pre_files = []
# HTML files shat should be inserted after the pages created by sphinx.
# The format is a list of tuples containing the path and title.
#epub_post_files = []
# A list of files that should not be packed into the epub file.
#epub_exclude_files = []
# The depth of the table of contents in toc.ncx.
#epub_tocdepth = 3
# Allow duplicate toc entries.
#epub_tocdup = True
# Fix unsupported image types using the PIL.
#epub_fix_images = False
# Scale large images.
#epub_max_image_width = 0
# If 'no', URL addresses will not be shown.
#epub_show_urls = 'inline'
# If false, no index is generated.
#epub_use_index = True
####################
Filter transmissions
####################
#####################################
The database distributed with pcigale
#####################################
.. toctree::
:maxdepth: 2
filters
.. pcigale documentation master file, created by
sphinx-quickstart on Wed Sep 11 16:32:56 2013.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Welcome to pcigale's documentation!
===================================
Contents:
.. toctree::
:maxdepth: 2
usage/index
sed_modules/index
stat_modules/index
database/index
programmer/index
Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
########################
Programmer documentation
########################
###########################################################
*bc03* - Bruzual & Charlot (2003) Single Stellar Population
###########################################################
#################################################################
*dh2002* - Infra-red re-emission using Dale & Helou (2002) models
#################################################################
#################################################################
*dh2002* - Infra-red re-emission using Dale & Helou (2002) models
#################################################################
##################################################################################################
*dustatt_calzleit* - Attenuation using Calzetti *et al.* (2000) and Leitherer *et al.* (2002) laws
##################################################################################################
######################################################
*dustatt_powerlaw* - Simple power law dust attenuation
######################################################
###############################################
*igmattenuation* - Redshift and IGM attenuation
###############################################
##################################
SED creation modules documentation
##################################
.. toctree::
:maxdepth: 2
sfh2exp
sfhfromfile
m2005
bc03
dustatt_calzleit
dustatt_powerlaw
dh2002
dl2007
lines
igmattenuation
############################
*lines* - Add emission lines
############################
####################################################
*m2005* - Maraston (2005) Single Stellar Populations
####################################################
##################################################
*sfh2exp* - Two exponential Star Formation History
##################################################
###########################################################
*sfhfromfile* - Read the Star Formation History from a file
###########################################################
#################################
Statistical modules documentation
#################################
.. toctree::
:maxdepth: 2
:glob:
*
####################################
*psum* - The PSUM statistical method
####################################
##################
How to use pcigale
##################
.. toctree::
:maxdepth: 2
installation
script_usage
programming
############
Installation
############
#############################
How to programme with pcigale
#############################
#########################
How to use pcigale script
#########################
pcigale comes with a script (a programme callable from the command line) that
will help you to run the complete analysis of a set of galaxy with known
redshift and fluxes in various filters.
Generation of a minimal configuration files
===========================================
First, you need a minimal configuration file. Create a directory where you
will proceed with your analysis. In a shell, go inside this directory and
launch ``pcigale init``. This will create a *pcigale.ini* file in the
directory with that content:
.. code-block:: cfg
:emphasize-lines: 4,9,14,17
# File containing the observation data to be fitted. Each flux column
# must have the name of the corresponding filter, the error columns are
# suffixed with '_err'. The values must be in mJy.
data_file =
# Order of the modules use for SED creation. Available modules : bc03,
# dh2002, dl2007, dustatt_calzleit, dustatt_powerlaw, igmattenuation,
# lines, loadfile, m2005, sfh2exp, sfhfromfile.
sed_modules = ,
# Module used to redshift the SED before the integration in the filters.
# This is a SED creation module that accepts a 'redshift' parameter (see
# the documentation).
redshift_module =
# Method used for statistical analysis. Available methods: psum.
analysis_method =
You need to edit this file to complete:
* *data_file* is the name of the file containing you observations. This is a
FITS or VO-Table file containing the observations to be analysed. It must
contain a column named *id* with an identifier for each source, a column
named *redshift* and columns containing the fluxes in *mJy* in various
filters. The flux columns must be named exactly as the corresponding filters
in the pcigale database. When a column is the error associated with a
filter, its name must prefix the filter name with *_err*.
* *sed_modules* is the list of pcigale SED creation modules, **in the right
order**, that will be used to create the theoretical SED (see the various
module documentations). The comments above the entry list the available
modules.
* *redshift_module* is the name of the module that will be used to redshift
and add IGM attenuation to the SED before computing the fluxes that will be
compared to observed ones.
* *analysis_method* is the name of the statistical analysis module that will
be used. Here again, the comments list the available modules.
Here is a sample completed minimal configuration file:
.. code-block:: cfg
# File containing the observation data to be fitted. Each flux column
# must have the name of the corresponding filter, the error columns are
# suffixed with '_err'. The values must be in mJy.
data_file = data.fits
# Order of the modules use for SED creation. Available modules : bc03,
# dh2002, dl2007, dustatt_calzleit, dustatt_powerlaw, igmattenuation,
# lines, loadfile, m2005, sfh2exp, sfhfromfile.
sed_modules = sfh2exp, m2005, dustatt_calzleit, dh2002
# Module used to redshift the SED before the integration in the filters.
# This is a SED creation module that accepts a 'redshift' parameter (see
# the documentation).
redshift_module = igmattenuation
# Method used for statistical analysis. Available methods: psum.
analysis_method = psum
Generation of the main configuration file
=========================================
You can now run the ``pcigale genconf`` command. pcigale will read the data
file to identify which columns contain filter fluxes and errors. It will then
pick each module and add their configuration section to the ini file, that
will become something like this:
.. code-block:: cfg
# File containing the observation data to be fitted. Each flux column
# must have the name of the corresponding filter, the error columns are
# suffixed with '_err'. The values must be in mJy.
data_file = data.fits
# Order of the modules use for SED creation. Available modules : bc03,
# dh2002, dl2007, dustatt_calzleit, dustatt_powerlaw, igmattenuation,
# lines, loadfile, m2005, sfh2exp, sfhfromfile.
sed_modules = sfh2exp, m2005, dustatt_calzleit, dh2002
# Module used to redshift the SED before the integration in the filters.
# This is a SED creation module that accepts a 'redshift' parameter (see
# the documentation).
redshift_module = igmattenuation
# Method used for statistical analysis. Available methods: psum.
analysis_method = psum
# List of the columns in the observation data file to use for the
# fitting.
column_list = WFI_U38, WFI_U38_err, WFI_U, WFI_U_err, WFI_B, WFI_B_err,
WFI_V, WFI_V_err, WFI_R, WFI_R_err, WFI_I, WFI_I_err, WFI_z,
WFI_z_err, IRAC1, IRAC1_err, IRAC2, IRAC2_err, IRAC3,
IRAC3_err, IRAC4, IRAC4_err, MIPS1, MIPS1_err, PACS_green,
PACS_green_err
# Configuration of the SED creation modules.
[sed_creation_modules]
[[sfh2exp]]
# Age of the oldest stars in the galaxy in Myr. The precision is 1 Myr.