more cleaning
This commit is contained in:
Celine Mercier
5
doc/.gitignore
vendored
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doc/.gitignore
vendored
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/build/
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/doxygen/
|
||||
/build_dir.txt
|
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/.DS_Store
|
||||
/.gitignore
|
||||
2432
doc/Doxyfile
2432
doc/Doxyfile
File diff suppressed because it is too large
Load Diff
203
doc/Makefile
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doc/Makefile
@ -1,203 +0,0 @@
|
||||
# Makefile for Sphinx documentation
|
||||
#
|
||||
|
||||
# You can set these variables from the command line.
|
||||
SPHINXOPTS =
|
||||
SPHINXBUILD = sphinx-build
|
||||
PAPER =
|
||||
BUILDDIR = build
|
||||
DOXYGENDIR = doxygen
|
||||
|
||||
# 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) source
|
||||
# the i18n builder cannot share the environment and doctrees with the others
|
||||
I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
|
||||
|
||||
.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest coverage 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 " applehelp to make an Apple Help Book"
|
||||
@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)"
|
||||
@echo " coverage to run coverage check of the documentation (if enabled)"
|
||||
|
||||
clean:
|
||||
rm -rf $(BUILDDIR)/*
|
||||
rm -rf $(DOXYGENDIR)/*
|
||||
|
||||
html:
|
||||
@echo "Generating Doxygen documentation..."
|
||||
doxygen Doxyfile
|
||||
@echo "Doxygen documentation generated. \n"
|
||||
$(SPHINXBUILD) -b html -c ./ $(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/OBITools-3.qhcp"
|
||||
@echo "To view the help file:"
|
||||
@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/OBITools-3.qhc"
|
||||
|
||||
applehelp:
|
||||
$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
|
||||
@echo
|
||||
@echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
|
||||
@echo "N.B. You won't be able to view it unless you put it in" \
|
||||
"~/Library/Documentation/Help or install it in your application" \
|
||||
"bundle."
|
||||
|
||||
devhelp:
|
||||
$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
|
||||
@echo
|
||||
@echo "Build finished."
|
||||
@echo "To view the help file:"
|
||||
@echo "# mkdir -p $$HOME/.local/share/devhelp/OBITools-3"
|
||||
@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/OBITools-3"
|
||||
@echo "# devhelp"
|
||||
|
||||
epub:
|
||||
$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
|
||||
@echo
|
||||
@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
|
||||
|
||||
latex:
|
||||
@echo "Generating Doxygen documentation..."
|
||||
doxygen Doxyfile
|
||||
@echo "Doxygen documentation generated. \n"
|
||||
$(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:
|
||||
@echo "Generating Doxygen documentation..."
|
||||
doxygen Doxyfile
|
||||
@echo "Doxygen documentation generated. \n"
|
||||
$(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."
|
||||
|
||||
man:
|
||||
$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
|
||||
@echo
|
||||
@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
|
||||
|
||||
texinfo:
|
||||
$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
|
||||
@echo
|
||||
@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."
|
||||
|
||||
coverage:
|
||||
$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
|
||||
@echo "Testing of coverage in the sources finished, look at the " \
|
||||
"results in $(BUILDDIR)/coverage/python.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."
|
||||
300
doc/conf.py
300
doc/conf.py
@ -1,300 +0,0 @@
|
||||
# -*- coding: utf-8 -*-
|
||||
#
|
||||
# OBITools3 documentation build configuration file, created by
|
||||
# sphinx-quickstart on Mon May 4 14:36:57 2015.
|
||||
#
|
||||
# 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
|
||||
import os
|
||||
import shlex
|
||||
|
||||
# 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.coverage',
|
||||
'sphinx.ext.imgmath',
|
||||
'sphinx.ext.ifconfig',
|
||||
'sphinx.ext.viewcode',
|
||||
'breathe',
|
||||
]
|
||||
|
||||
# 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 encoding of source files.
|
||||
#source_encoding = 'utf-8-sig'
|
||||
|
||||
# The master toctree document.
|
||||
master_doc = 'source/index'
|
||||
|
||||
# General information about the project.
|
||||
project = u'OBITools3'
|
||||
copyright = u'2015, Céline Mercier, Eric Coissac, Frédéric Boyer'
|
||||
author = u'Céline Mercier, Eric Coissac, Frédéric Boyer'
|
||||
|
||||
# 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 = '0.0'
|
||||
# The full version, including alpha/beta/rc tags.
|
||||
release = '0.0.0'
|
||||
|
||||
# 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
|
||||
|
||||
# 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 = []
|
||||
|
||||
# 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
|
||||
|
||||
# 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 = 'bizstyle'
|
||||
|
||||
# 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']
|
||||
|
||||
# Add any extra paths that contain custom files (such as robots.txt or
|
||||
# .htaccess) here, relative to this directory. These files are copied
|
||||
# directly to the root of the documentation.
|
||||
#html_extra_path = []
|
||||
|
||||
# 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
|
||||
|
||||
# Language to be used for generating the HTML full-text search index.
|
||||
# Sphinx supports the following languages:
|
||||
# 'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'
|
||||
# 'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr'
|
||||
#html_search_language = 'en'
|
||||
|
||||
# A dictionary with options for the search language support, empty by default.
|
||||
# Now only 'ja' uses this config value
|
||||
#html_search_options = {'type': 'default'}
|
||||
|
||||
# The name of a javascript file (relative to the configuration directory) that
|
||||
# implements a search results scorer. If empty, the default will be used.
|
||||
#html_search_scorer = 'scorer.js'
|
||||
|
||||
# Output file base name for HTML help builder.
|
||||
htmlhelp_basename = 'OBITools3doc'
|
||||
|
||||
# -- 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, 'OBITools3.tex', u'OBITools3 Documentation',
|
||||
u'Céline Mercier, Eric Coissac, Frédéric Boyer', '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 = [
|
||||
(master_doc, 'obitools3', u'OBITools3 Documentation',
|
||||
[author], 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 = [
|
||||
(master_doc, 'OBITools3', u'OBITools3 Documentation',
|
||||
author, 'OBITools3', '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
|
||||
|
||||
#Breathe configuration
|
||||
sys.path.append( "breathe/" )
|
||||
breathe_projects = { "OBITools3": "doxygen/xml/" }
|
||||
breathe_default_project = "OBITools3"
|
||||
#breathe_projects_source = {
|
||||
# "auto" : ( "../src", ["obidms.h", "obiavl.h"] )
|
||||
# }
|
||||
@ -1,160 +0,0 @@
|
||||
*********************************************
|
||||
The OBItools3 Data Management System (OBIDMS)
|
||||
*********************************************
|
||||
|
||||
A complete DNA metabarcoding experiment relies on several kinds of data.
|
||||
|
||||
- The sequence data resulting from the sequencing of the PCR products,
|
||||
- The description of the samples including all their metadata,
|
||||
- One or several reference databases used for the taxonomic annotation,
|
||||
- One or several taxonomy databases.
|
||||
|
||||
Up to now, each of these categories of data were stored in separate
|
||||
files, and nothing made it mandatory to keep them together.
|
||||
|
||||
|
||||
The `Data Management System` (DMS) of OBITools3 can be viewed like a basic
|
||||
database system.
|
||||
|
||||
|
||||
OBIDMS UML
|
||||
==========
|
||||
|
||||
.. image:: ./UML/OBIDMS_UML.png
|
||||
|
||||
:download:`html version of the OBIDMS UML file <UML/ObiDMS_UML.class.violet.html>`
|
||||
|
||||
|
||||
An OBIDMS directory contains :
|
||||
* one `OBIDMS history file <#obidms-history-files>`_
|
||||
* OBIDMS column directories
|
||||
|
||||
|
||||
OBIDMS column directories
|
||||
=========================
|
||||
|
||||
OBIDMS column directories contain :
|
||||
* all the different versions of one OBIDMS column, under the form of different files (`OBIDMS column files <#obidms-column-files>`_)
|
||||
* one `OBIDMS version file <#obidms-version-files>`_
|
||||
|
||||
The directory name is the column attribute with the extension ``.obicol``.
|
||||
|
||||
Example: ``count.obicol``
|
||||
|
||||
|
||||
OBIDMS column files
|
||||
===================
|
||||
|
||||
Each OBIDMS column file contains :
|
||||
* a header of a size equal to a multiple of PAGESIZE (PAGESIZE being equal to 4096 bytes
|
||||
on most systems) containing metadata
|
||||
* Lines of data with the same `OBIType <types.html#obitypes>`_
|
||||
|
||||
|
||||
Header
|
||||
------
|
||||
|
||||
The header of an OBIDMS column contains :
|
||||
|
||||
* Endian byte order
|
||||
* Header size (PAGESIZE multiple)
|
||||
* Number of lines of data
|
||||
* Number of lines of data used
|
||||
* `OBIType <types.html#obitypes>`_ (type of the data)
|
||||
* Date of creation of the file
|
||||
* Version of the OBIDMS column
|
||||
* The column name
|
||||
* Eventual comments
|
||||
|
||||
|
||||
Data
|
||||
----
|
||||
|
||||
A line of data corresponds to a vector of elements. Each element is associated with an element name.
|
||||
Elements names are stored in the header. The correspondance between an element and its name is done
|
||||
using their order in the lists of elements and elements names. This structure allows the storage of
|
||||
dictionary-like data.
|
||||
|
||||
Example: In the header, the attribute ``elements_names`` will be associated with the value ``"sample_1;
|
||||
sample_2;sample_3"``, and a line of data with the type ``OBInt_t`` will be stored as an ``OBInt_t`` vector
|
||||
of size three e.g. ``5|8|4``.
|
||||
|
||||
|
||||
Mandatory columns
|
||||
-----------------
|
||||
|
||||
Some columns must exist in an OBIDMS directory :
|
||||
* sequence identifiers column (type ``OBIStr_t``)
|
||||
|
||||
|
||||
File name
|
||||
---------
|
||||
|
||||
Each file is named with the attribute associated to the data it contains, and the number of
|
||||
its version, separated by an ``@``, and with the extension ``.odc``.
|
||||
|
||||
Example : ``count@3.odc``
|
||||
|
||||
|
||||
Modifications
|
||||
-------------
|
||||
|
||||
An OBIDMS column file can only be modified by the process that created it, and while its status is set to Open.
|
||||
|
||||
When a process wants to modify an OBIDMS column file that is closed, it must first clone it. Cloning creates a new version of the
|
||||
file that belongs to the process, i.e., only that process can modify that file, as long as its status is set to Open. Once the process
|
||||
has finished writing the new version of the column file, it sets the column file's status to Closed, and the file can never be modified
|
||||
again.
|
||||
|
||||
That means that one column is stored in one file (if there is only one version)
|
||||
or more (if there are several versions), and that there is one file per version.
|
||||
|
||||
All the versions of one column are stored in one directory.
|
||||
|
||||
|
||||
Versioning
|
||||
----------
|
||||
|
||||
The first version of a column file is numbered 0, and each new version increments that
|
||||
number by 1.
|
||||
|
||||
The number of the latest version of an OBIDMS column is stored in the `OBIDMS version file <#obidms-version-files>`_ of its directory.
|
||||
|
||||
|
||||
OBIDMS version files
|
||||
====================
|
||||
|
||||
Each OBIDMS column is associated with an OBIDMS version file in its directory, that contains the number of the latest
|
||||
version of the column.
|
||||
|
||||
File name
|
||||
---------
|
||||
|
||||
OBIDMS version files are named with the attribute associated to the data contained in the column, and
|
||||
have the extension ``.odv``.
|
||||
|
||||
Example : ``count.odv``
|
||||
|
||||
|
||||
OBIDMS views
|
||||
============
|
||||
|
||||
An OBIDMS view consists of a list of OBIDMS columns and lines. A view includes one version
|
||||
of each mandatory column. Only one version of each column is included. All the columns of
|
||||
one view contain the same number of lines in the same order.
|
||||
|
||||
|
||||
OBIDMS history file
|
||||
===================
|
||||
|
||||
An OBIDMS history file consists of an ordered list of views and commands, those commands leading
|
||||
from one view to the next one.
|
||||
|
||||
This history can be represented in the form of a ?? showing all the
|
||||
operations ever done in the OBIDMS directory and the views in between them :
|
||||
|
||||
.. image:: ./images/history.png
|
||||
:width: 150 px
|
||||
:align: center
|
||||
|
||||
|
||||
Binary file not shown.
|
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@ -1,832 +0,0 @@
|
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|
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|
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|
||||
<META name="keywords" content="Violet, UML" />
|
||||
<META charset="UTF-8" />
|
||||
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|
||||
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|
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|
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|
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|
||||
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|
||||
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|
||||
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|
||||
<SCRIPT id="content" type="text/xml"><![CDATA[<ClassDiagramGraph id="1">
|
||||
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|
||||
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|
||||
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|
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|
||||
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|
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|
||||
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|
||||
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|
||||
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|
||||
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|
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<borderColor reference="8"/>
|
||||
<textColor reference="8"/>
|
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<name id="16" justification="1" size="3" underlined="false">
|
||||
<text>OBIContainer_t</text>
|
||||
</name>
|
||||
<attributes id="17" justification="0" size="4" underlined="false">
|
||||
<text></text>
|
||||
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|
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||||
<revision>1</revision>
|
||||
<backgroundColor reference="7"/>
|
||||
<borderColor reference="8"/>
|
||||
<textColor reference="8"/>
|
||||
<name id="23" justification="1" size="3" underlined="false">
|
||||
<text>OBIElementary_t</text>
|
||||
</name>
|
||||
<attributes id="24" justification="0" size="4" underlined="false">
|
||||
<text></text>
|
||||
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|
||||
<methods id="25" justification="0" size="4" underlined="false">
|
||||
<text></text>
|
||||
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|
||||
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|
||||
<ClassNode id="26">
|
||||
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|
||||
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|
||||
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|
||||
<revision>1</revision>
|
||||
<backgroundColor reference="7"/>
|
||||
<borderColor reference="8"/>
|
||||
<textColor reference="8"/>
|
||||
<name id="30" justification="1" size="3" underlined="false">
|
||||
<text>OBIList_t</text>
|
||||
</name>
|
||||
<attributes id="31" justification="0" size="4" underlined="false">
|
||||
<text></text>
|
||||
</attributes>
|
||||
<methods id="32" justification="0" size="4" underlined="false">
|
||||
<text></text>
|
||||
</methods>
|
||||
</ClassNode>
|
||||
<ClassNode id="33">
|
||||
<children id="34"/>
|
||||
<location class="Point2D.Double" id="35" x="780.0" y="240.0"/>
|
||||
<id id="36" value="b2f4d561-0c10-4443-b8f6-d3628ab9bcfe"/>
|
||||
<revision>1</revision>
|
||||
<backgroundColor reference="7"/>
|
||||
<borderColor reference="8"/>
|
||||
<textColor reference="8"/>
|
||||
<name id="37" justification="1" size="3" underlined="false">
|
||||
<text>OBISet_t</text>
|
||||
</name>
|
||||
<attributes id="38" justification="0" size="4" underlined="false">
|
||||
<text></text>
|
||||
</attributes>
|
||||
<methods id="39" justification="0" size="4" underlined="false">
|
||||
<text></text>
|
||||
</methods>
|
||||
</ClassNode>
|
||||
<ClassNode id="40">
|
||||
<children id="41"/>
|
||||
<location class="Point2D.Double" id="42" x="890.0" y="240.0"/>
|
||||
<id id="43" value="8cc209c6-18c7-4a90-a5d4-ab7246638b2f"/>
|
||||
<revision>1</revision>
|
||||
<backgroundColor reference="7"/>
|
||||
<borderColor reference="8"/>
|
||||
<textColor reference="8"/>
|
||||
<name id="44" justification="1" size="3" underlined="false">
|
||||
<text>OBIDictionnary_t</text>
|
||||
</name>
|
||||
<attributes id="45" justification="0" size="4" underlined="false">
|
||||
<text></text>
|
||||
</attributes>
|
||||
<methods id="46" justification="0" size="4" underlined="false">
|
||||
<text></text>
|
||||
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|
||||
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|
||||
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|
||||
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|
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|
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|
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|
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|
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|
||||
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|
||||
<name id="51" justification="1" size="3" underlined="false">
|
||||
<text>OBIAtomic_t</text>
|
||||
</name>
|
||||
<attributes id="52" justification="0" size="4" underlined="false">
|
||||
<text></text>
|
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|
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|
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|
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|
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|
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|
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|
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|
||||
<revision>1</revision>
|
||||
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|
||||
<borderColor reference="8"/>
|
||||
<textColor reference="8"/>
|
||||
<name id="58" justification="1" size="3" underlined="false">
|
||||
<text>OBIComposite_t
|
||||
</text>
|
||||
</name>
|
||||
<attributes id="59" justification="0" size="4" underlined="false">
|
||||
<text></text>
|
||||
</attributes>
|
||||
<methods id="60" justification="0" size="4" underlined="false">
|
||||
<text></text>
|
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|
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|
||||
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|
||||
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|
||||
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|
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<id id="64" value="84fa636d-0c5a-4df8-bac7-79df8e546c12"/>
|
||||
<revision>1</revision>
|
||||
<backgroundColor reference="7"/>
|
||||
<borderColor reference="8"/>
|
||||
<textColor reference="8"/>
|
||||
<name id="65" justification="1" size="3" underlined="false">
|
||||
<text>OBIString_t</text>
|
||||
</name>
|
||||
<attributes id="66" justification="0" size="4" underlined="false">
|
||||
<text></text>
|
||||
</attributes>
|
||||
<methods id="67" justification="0" size="4" underlined="false">
|
||||
<text></text>
|
||||
</methods>
|
||||
</ClassNode>
|
||||
<ClassNode id="68">
|
||||
<children id="69"/>
|
||||
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|
||||
<id id="71" value="752b5f9b-0ece-4902-8de5-e2c465d281dd"/>
|
||||
<revision>1</revision>
|
||||
<backgroundColor reference="7"/>
|
||||
<borderColor reference="8"/>
|
||||
<textColor reference="8"/>
|
||||
<name id="72" justification="1" size="3" underlined="false">
|
||||
<text>OBITaxid_t
|
||||
</text>
|
||||
</name>
|
||||
<attributes id="73" justification="0" size="4" underlined="false">
|
||||
<text></text>
|
||||
</attributes>
|
||||
<methods id="74" justification="0" size="4" underlined="false">
|
||||
<text></text>
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
<revision>1</revision>
|
||||
<backgroundColor reference="7"/>
|
||||
<borderColor reference="8"/>
|
||||
<textColor reference="8"/>
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||||
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|
||||
</HTML>
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 20 KiB |
File diff suppressed because it is too large
Load Diff
@ -1,29 +0,0 @@
|
||||
===============
|
||||
Container types
|
||||
===============
|
||||
|
||||
Containers allow to manage collections of values of homogeneous type.
|
||||
Three container types exist.
|
||||
|
||||
A container is a non-mutable structure once it has been locked.
|
||||
Consequently, only insertion procedures are needed.
|
||||
|
||||
Lists
|
||||
-----
|
||||
|
||||
Correspond to an ordered collection of values belonging to an elementary type.
|
||||
|
||||
At its creation, ...
|
||||
|
||||
|
||||
Sets
|
||||
----
|
||||
|
||||
Correspond to an unordered collection of values belonging to an elementary type.
|
||||
|
||||
|
||||
Dictionaries
|
||||
------------
|
||||
|
||||
Dictionaries allow to associate a `key` to a `value`. Values can be retrieved through their associated key.
|
||||
Values must belong to an elementary type and keys must be *OBIStr_t*.
|
||||
@ -1,16 +0,0 @@
|
||||
#################
|
||||
Data in OBITools3
|
||||
#################
|
||||
|
||||
The OBITools3 introduce a new way to manage DNA metabarcoding data.
|
||||
They rely on a `Data management System` (DMS) that can be viewed like
|
||||
a simplified database system.
|
||||
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 2
|
||||
|
||||
The data management system <DMS>
|
||||
The data types <types>
|
||||
|
||||
|
||||
@ -1,40 +0,0 @@
|
||||
================
|
||||
Elementary types
|
||||
================
|
||||
|
||||
They correspond to simple values.
|
||||
|
||||
Atomic types
|
||||
------------
|
||||
|
||||
========= ========= ============ ==============================
|
||||
Type C type OBIType Definition
|
||||
========= ========= ============ ==============================
|
||||
integer int32_t OBIInt_t a signed integer value
|
||||
float double OBIFloat_t a floating value
|
||||
boolean bool OBIBool_t a boolean true/false value
|
||||
char char OBIChar_t a character
|
||||
index size_t OBIIdx_t an index in a data structure
|
||||
========= ========= ============ ==============================
|
||||
|
||||
|
||||
The composite types
|
||||
-------------------
|
||||
|
||||
Character string type
|
||||
.....................
|
||||
|
||||
================ ====== ======== ==================
|
||||
Type C type OBIType Definition
|
||||
================ ====== ======== ==================
|
||||
Character string ? OBIStr_t a character string
|
||||
================ ====== ======== ==================
|
||||
|
||||
The taxid type
|
||||
..............
|
||||
|
||||
==================== ====== ========== ======================
|
||||
Type C type OBIType Definition
|
||||
==================== ====== ========== ======================
|
||||
Taxonomic identifier size_t OBITaxid_t a taxonomic identifier
|
||||
==================== ====== ========== ======================
|
||||
@ -1,131 +0,0 @@
|
||||
######################
|
||||
Programming guidelines
|
||||
######################
|
||||
|
||||
|
||||
***************
|
||||
Version control
|
||||
***************
|
||||
|
||||
Version control is managed with `Git <http://git-scm.com/>`_.
|
||||
Issue tracking and repository management are done using `GitLab <https://about.gitlab.com/>`_
|
||||
at http://git.metabarcoding.org/.
|
||||
|
||||
|
||||
Branching strategy
|
||||
==================
|
||||
|
||||
|
||||
Master branch
|
||||
-------------
|
||||
|
||||
The master branch should only contain functional scripts.
|
||||
|
||||
|
||||
Topic branches
|
||||
--------------
|
||||
|
||||
Topic branches should correspond to development branches revolving around a topic corresponding
|
||||
to the branch's name.
|
||||
|
||||
|
||||
Release branches
|
||||
----------------
|
||||
|
||||
Release branches should start with duplicates of tags and be used to patch them.
|
||||
|
||||
|
||||
Tags
|
||||
----
|
||||
|
||||
Tags should never be committed to.
|
||||
|
||||
|
||||
Rebasing
|
||||
--------
|
||||
|
||||
Rebasing should be avoided on the distant server.
|
||||
|
||||
|
||||
Merging
|
||||
-------
|
||||
|
||||
Merging should never overwrite on a release branch or on a tag.
|
||||
|
||||
|
||||
Branching strategy diagram
|
||||
--------------------------
|
||||
|
||||
.. image:: ./images/version_control.png
|
||||
|
||||
|
||||
Issue tracking
|
||||
==============
|
||||
|
||||
Issue tracking is done using `GitLab <https://about.gitlab.com/>`_ at http://git.metabarcoding.org/.
|
||||
Tickets should always be labeled with the branches for which they are relevant.
|
||||
|
||||
|
||||
*************
|
||||
Documentation
|
||||
*************
|
||||
|
||||
C functions are documented in the header files for public functions, and in the source file for private functions.
|
||||
|
||||
|
||||
**************
|
||||
OBITools3 wiki
|
||||
**************
|
||||
|
||||
The OBITools3 wiki is managed with GitLab.
|
||||
|
||||
|
||||
*********************
|
||||
Programming languages
|
||||
*********************
|
||||
|
||||
C99 :
|
||||
* All the low-level input/output functions (e.g. all the `OBIDMS <formats.html#the-obitools3-data-management-system-obidms>`_ functions)
|
||||
* Computing-intensive code (e.g. alignment or pattern matching)
|
||||
|
||||
`Cython <cython.org>`_ :
|
||||
* Object layer
|
||||
* OBITools3 library
|
||||
|
||||
`Python 3.5 <https://www.python.org/>`_ :
|
||||
* Top layer code (scripts)
|
||||
|
||||
For the documentation, `Sphinx <http://sphinx-doc.org/>`_ should be used for both the original
|
||||
documentation and for the generation of documentation from the python code. `Doxygen <http://www.stack.nl/~dimitri/doxygen/>`_
|
||||
should be used for the generation of documentation from the C code, which should be then integrated
|
||||
in the Sphinx documentation using `Breathe <https://breathe.readthedocs.org/en/latest/>`_.
|
||||
|
||||
|
||||
******************
|
||||
Naming conventions
|
||||
******************
|
||||
|
||||
Struct, Enum: ``Title_case``
|
||||
|
||||
Enum members, macros, constants: ``ALL_CAPS``
|
||||
|
||||
Functions, local variables: ``lower_case``
|
||||
|
||||
Public functions: ``obi_lower_case``
|
||||
|
||||
Functions that shouldn't be called directly: ``_lower_case`` (``_`` prefix)
|
||||
|
||||
Global variables: ``g_lower_case`` (``g_`` prefix)
|
||||
|
||||
Pointers: ``pointer_ptr`` (``_ptr`` suffix)
|
||||
|
||||
.. note::
|
||||
Underscores are used to delimit 'words'.
|
||||
|
||||
|
||||
*****************
|
||||
Programming rules
|
||||
*****************
|
||||
|
||||
*
|
||||
|
||||
Binary file not shown.
|
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Binary file not shown.
|
Before Width: | Height: | Size: 48 KiB |
@ -1,21 +0,0 @@
|
||||
.. OBITools3 documentation master file, created by
|
||||
sphinx-quickstart on Mon May 4 14:36:57 2015.
|
||||
You can adapt this file completely to your liking, but it should at least
|
||||
contain the root `toctree` directive.
|
||||
|
||||
OBITools3 documentation
|
||||
==========================
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 2
|
||||
|
||||
Programming guidelines <guidelines>
|
||||
Data structures <data>
|
||||
Code documentation <code_doc/codedoc>
|
||||
|
||||
Indices and tables
|
||||
------------------
|
||||
|
||||
* :ref:`genindex`
|
||||
* :ref:`modindex`
|
||||
* :ref:`search`
|
||||
@ -1,55 +0,0 @@
|
||||
==============
|
||||
Special values
|
||||
==============
|
||||
|
||||
|
||||
NA values
|
||||
=========
|
||||
|
||||
All OBITypes have an associated NA (Not Available) value.
|
||||
NA values are implemented by specifying an explicit NA value for each type,
|
||||
corresponding to the R standards as much as possible:
|
||||
|
||||
* For the type ``OBIInt_t``, the NA value is ``INT_MIN``.
|
||||
|
||||
* For the type ``OBIBool_t``, the NA value is ``2``.
|
||||
|
||||
* For the type ``OBIIdx_t`` and ``OBITaxid_t``, the NA value is ``SIZE_MAX``.
|
||||
|
||||
* For the type ``OBIChar_t``: the NA value is ``\0``.
|
||||
|
||||
* For the type ``OBIFloat_t``::
|
||||
|
||||
typedef union
|
||||
{
|
||||
double value;
|
||||
unsigned int word[2];
|
||||
} ieee_double;
|
||||
|
||||
static double NA_value(void)
|
||||
{
|
||||
volatile ieee_double x;
|
||||
x.word[hw] = 0x7ff00000;
|
||||
x.word[lw] = 1954;
|
||||
return x.value;
|
||||
}
|
||||
|
||||
|
||||
Minimum and maximum values for ``OBIInt_t``
|
||||
===========================================
|
||||
|
||||
* Maximum value : ``INT_MAX``
|
||||
* Minimum value : ``INT_MIN(-1?)``
|
||||
|
||||
|
||||
Infinity values for the type ``OBIFloat_t``
|
||||
===========================================
|
||||
|
||||
* Positive infinity : ``INFINITY`` (should be defined in ``<math.h>``)
|
||||
* Negative infinity : ``-INFINITY``
|
||||
|
||||
|
||||
NaN value for the type ``OBIFloat_t``
|
||||
=====================================
|
||||
|
||||
* NaN (Not a Number) value : ``NAN`` (should be defined in ``<math.h>`` but probably needs to be tested)
|
||||
@ -1,21 +0,0 @@
|
||||
********
|
||||
OBITypes
|
||||
********
|
||||
|
||||
|
||||
.. image:: ./UML/OBITypes_UML.png
|
||||
|
||||
:download:`html version of the OBITypes UML file <UML/OBITypes_UML.class.violet.html>`
|
||||
|
||||
|
||||
.. image:: ./UML/Obicolumn_classes_UML.png
|
||||
|
||||
:download:`html version of the OBIDMS classes UML file <UML/Obicolumn_classes_UML.class.violet.html>`
|
||||
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 2
|
||||
|
||||
The elementary types <elementary>
|
||||
The containers <containers>
|
||||
Special values <specialvalues>
|
||||
2
doc/sphinx/.gitignore
vendored
2
doc/sphinx/.gitignore
vendored
@ -1,2 +0,0 @@
|
||||
.DS_Store
|
||||
/build_dir.txt
|
||||
@ -1 +0,0 @@
|
||||
build/lib.macosx-10.9-x86_64-3.7
|
||||
Reference in New Issue
Block a user