Changeset 11706 for NEMO/trunk/doc/rst

Timestamp:

2019-10-16T10:51:40+02:00 (5 years ago)

Author:

nicolasmartin

Message:

Update files to be compliant with Python 3 (Python 2 no longer available)
The compilation of the guide is no longer easy with Python 2 with the need of virtual env to
downgrade some dependencies.
Last but not least, Python 2 support will expire by the end of the year.

Location:

NEMO/trunk/doc/rst

Files:

• Makefile (modified) (2 diffs)
• source/conf.py (modified) (4 diffs)

NEMO/trunk/doc/rst/Makefile

@@ -1 @@
-# Minimal makefile for Sphinx documentation
+# Makefile for Sphinx documentation
 #
 
@@ -5 +5 @@
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
-SPHINXPROJ    = NEMO
-SOURCEDIR     = source
+PAPER         =
 BUILDDIR      = build
 
-# Put it first so that "make" without argument is like "make help".
+# 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)) $(SPHINXOPTS) source
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
 help:
-   @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+   @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 "  livehtml   to make an autoupdate HTML export while editing"
+   @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 "  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 "  linkcheck  to check all external links for integrity"
+   @echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
 
-.PHONY: help Makefile
+clean:
+   -rm -rf $(BUILDDIR)/*
 
-# Catch-all target: route all unknown targets to Sphinx using the new
-# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
-%: Makefile
-   @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+html:
+   $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+   @echo
+   @echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
 
-# Watch source directory and rebuild the documentation when a change is detected
-# Browse to 127.0.0.1:8000/NEMO_guide.html
-htmllive:
-   sphinx-autobuild $(SPHINXOPTS) $(SOURCEDIR) $(BUILDDIR)/htmllive
+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."
+
+livehtml:
+   sphinx-autobuild -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+   @echo
+   @echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+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/NEMO.qhcp"
+   @echo "To view the help file:"
+   @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/NEMO.qhc"
+
+devhelp:
+   $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+   @echo
+   @echo "Build finished."
+   @echo "To view the help file:"
+   @echo "# mkdir -p $$HOME/.local/share/devhelp/NEMO"
+   @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/NEMO"
+   @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."
+
+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."

NEMO/trunk/doc/rst/source/conf.py

@@ -1 +1 @@
 # -*- coding: utf-8 -*-
 #
-# Configuration file for the Sphinx documentation builder.
-#
-# This file does only contain a selection of the most common options. For a
-# full list see the documentation:
-# http://www.sphinx-doc.org/en/master/config
-
-# -- Project information -----------------------------------------------------
-
-project = 'NEMO'
-author = 'NEMO System Team'
-
-# The short X.Y version
-version = 'trk'
-# The full version, including alpha/beta/rc tags
-release = 'trunk'
-
-
-# -- General configuration ---------------------------------------------------
-
-# 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.extlinks', 'sphinxcontrib.bibtex']
+# NEMO documentation build configuration file, created by
+# sphinx-quickstart on Tue Oct 15 20:13:55 2019.
+#
+# 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.extlinks', 'sphinxcontrib.bibtex', 'sphinx.ext.todo']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_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 = 'NEMO_guide'
 
+# General information about the project.
+project = u'NEMO'
+copyright = u'2019, NEMO Consortium'
+
+# 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 = 'trk'
+# The full version, including alpha/beta/rc tags.
+release = 'trunk'
+
+# 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.
-# This pattern also affects html_static_path and html_extra_path .
 exclude_patterns = ['global.rst', 'coarsening.rst']
 
+# 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'
-
-
-# -- Options for HTML output -------------------------------------------------
+pygments_style = 'emacs'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+
+# -- Options for HTML output ---------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-#
 html_theme = 'sphinx_rtd_theme'
 
@@ -50 +97 @@
 # further.  For a list of options available for each theme, see the
 # documentation.
-#
-html_theme_options = {}
+#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 = '_static/ORCA.ico'
 
 # Add any paths that contain custom static files (such as style sheets) here,
@@ -58 +123 @@
 html_static_path = ['_static']
 
-html_favicon = '_static/ORCA.ico'
-
-
-# -- Options for LaTeX output ------------------------------------------------
+# 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 = 'NEMOdoc'
+
+
+# -- 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',
+# 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, or own class]).
+# (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
-    (master_doc, 'NEMO_guide.tex', 'NEMO Quick Start Guide',
-     'NEMO System Team', 'howto'),
+  ('NEMO_guide', 'NEMO_guide.tex', u'NEMO Quick Start Guide',
+   u'NEMO Consortium', 'howto'),
 ]
 
-
-# -- Customisation -----------------------------------------------------------
+# 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 = [
+    ('NEMO_guide', 'nemo', u'NEMO Documentation',
+     [u'NEMO System 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 = [
+  ('NEMO_guide', 'NEMO', u'NEMO Documentation',
+   u'NEMO System Team', 'NEMO', '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'
+
+# -- Customisation -------------------------------------------------------------
 
 # Timestamping
@@ -99 +251 @@
 # Link aliases
 extlinks = {
-   'doi'    : ('https://doi.org/%s'                       , None),
-   'forge'  : ('https://forge.ipsl.jussieu.fr/nemo/%s'    , None),
-   'github' : ('https://github.com/%s'                    , None),
-   'xios'   : ('https://forge.ipsl.jussieu.fr/ioserver/%s', None),
-   'website': ('https://www.nemo-ocean.eu/%s'             , None),
-   'zenodo' : ('https://zenodo.org/publication/%s'        , None)
+   'doi'    : ('https://doi.org/%s'                       , None),
+   'forge'  : ('https://forge.ipsl.jussieu.fr/nemo/%s'    , None),
+   'github' : ('https://github.com/%s'                    , None),
+   'xios'   : ('https://forge.ipsl.jussieu.fr/ioserver/%s', None),
+   'website': ('https://www.nemo-ocean.eu/%s'             , None),
+   'zenodo' : ('https://zenodo.org/publication/%s'        , None)
 }