more cleaning
This commit is contained in:
Celine Mercier
5
doc/.gitignore
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doc/.gitignore
vendored
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/build/
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/doxygen/
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/build_dir.txt
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/.DS_Store
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/.gitignore
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2432
doc/Doxyfile
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doc/Doxyfile
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doc/Makefile
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doc/Makefile
@ -1,203 +0,0 @@
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|||||||
# Makefile for Sphinx documentation
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|
||||||
#
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|
||||||
|
|
||||||
# You can set these variables from the command line.
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|
||||||
SPHINXOPTS =
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|
||||||
SPHINXBUILD = sphinx-build
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|
||||||
PAPER =
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||||||
BUILDDIR = build
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|
||||||
DOXYGENDIR = doxygen
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|
||||||
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|
||||||
# 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/)
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|
||||||
endif
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|
||||||
|
|
||||||
# Internal variables.
|
|
||||||
PAPEROPT_a4 = -D latex_paper_size=a4
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|
||||||
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
|
|
||||||
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|
||||||
.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.
|
Before Width: | Height: | Size: 67 KiB |
@ -1,832 +0,0 @@
|
|||||||
<HTML>
|
|
||||||
<HEAD>
|
|
||||||
<META name="description"
|
|
||||||
content="Violet UML Editor cross format document" />
|
|
||||||
<META name="keywords" content="Violet, UML" />
|
|
||||||
<META charset="UTF-8" />
|
|
||||||
<SCRIPT type="text/javascript">
|
|
||||||
function switchVisibility() {
|
|
||||||
var obj = document.getElementById("content");
|
|
||||||
obj.style.display = (obj.style.display == "block") ? "none" : "block";
|
|
||||||
}
|
|
||||||
</SCRIPT>
|
|
||||||
</HEAD>
|
|
||||||
<BODY>
|
|
||||||
This file was generated with Violet UML Editor 2.1.0.
|
|
||||||
( <A href=# onclick="switchVisibility()">View Source</A> / <A href="http://sourceforge.net/projects/violet/files/violetumleditor/" target="_blank">Download Violet</A> )
|
|
||||||
<BR />
|
|
||||||
<BR />
|
|
||||||
<SCRIPT id="content" type="text/xml"><![CDATA[<ClassDiagramGraph id="1">
|
|
||||||
<nodes id="2">
|
|
||||||
<ClassNode id="3">
|
|
||||||
<children id="4"/>
|
|
||||||
<location class="Point2D.Double" id="5" x="520.0" y="30.0"/>
|
|
||||||
<id id="6" value="a6688f6e-9346-46c6-9cf5-4fa6148f613f"/>
|
|
||||||
<revision>1</revision>
|
|
||||||
<backgroundColor id="7">
|
|
||||||
<red>255</red>
|
|
||||||
<green>255</green>
|
|
||||||
<blue>255</blue>
|
|
||||||
<alpha>255</alpha>
|
|
||||||
</backgroundColor>
|
|
||||||
<borderColor id="8">
|
|
||||||
<red>0</red>
|
|
||||||
<green>0</green>
|
|
||||||
<blue>0</blue>
|
|
||||||
<alpha>255</alpha>
|
|
||||||
</borderColor>
|
|
||||||
<textColor reference="8"/>
|
|
||||||
<name id="9" justification="1" size="3" underlined="false">
|
|
||||||
<text>OBIType_t
|
|
||||||
</text>
|
|
||||||
</name>
|
|
||||||
<attributes id="10" justification="0" size="4" underlined="false">
|
|
||||||
<text></text>
|
|
||||||
</attributes>
|
|
||||||
<methods id="11" justification="0" size="4" underlined="false">
|
|
||||||
<text></text>
|
|
||||||
</methods>
|
|
||||||
</ClassNode>
|
|
||||||
<ClassNode id="12">
|
|
||||||
<children id="13"/>
|
|
||||||
<location class="Point2D.Double" id="14" x="780.0" y="100.0"/>
|
|
||||||
<id id="15" value="7edd4f08-c5e5-4e41-bc05-8b357cb5e629"/>
|
|
||||||
<revision>1</revision>
|
|
||||||
<backgroundColor reference="7"/>
|
|
||||||
<borderColor reference="8"/>
|
|
||||||
<textColor reference="8"/>
|
|
||||||
<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>
|
|
||||||
</attributes>
|
|
||||||
<methods id="18" justification="0" size="4" underlined="false">
|
|
||||||
<text></text>
|
|
||||||
</methods>
|
|
||||||
</ClassNode>
|
|
||||||
<ClassNode id="19">
|
|
||||||
<children id="20"/>
|
|
||||||
<location class="Point2D.Double" id="21" x="330.0" y="110.0"/>
|
|
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||||||
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<text>OBIString_t</text>
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<text>OBITaxid_t
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<text>OBIFloat_t</text>
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<text>OBIBool_t
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|
|
||||||
</BODY>
|
|
||||||
</HTML>
|
|
||||||
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|
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@ -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
|
|
||||||
*****************
|
|
||||||
|
|
||||||
*
|
|
||||||
|
|
||||||
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|
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|
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