Ignore:
Timestamp:
2019-12-10T15:03:24+01:00 (22 months ago)
Author:
ayoung
Message:

Updated trunk to 12072

Location:
NEMO/branches/2019/ENHANCE-03_closea/doc
Files:
13 deleted
4 edited
20 copied

Legend:

Unmodified
Added
Removed
  • NEMO/branches/2019/ENHANCE-03_closea/doc

    • Property svn:externals set to
      ^/utils/badges badges
      ^/utils/logos logos
  • NEMO/branches/2019/ENHANCE-03_closea/doc/rst/source/_static/style.css

    r10279 r12149  
    1 .rstblue               { color: blue    ; } 
    2 .rstgrey , .rstgreysup { color: grey    ; } 
    3 .rstgreen              { color: seagreen; } 
     1.blue            { color: blue    ; } 
     2.grey , .greysup { color: grey    ; } 
     3.green           { color: seagreen; } 
    44 
    55.logo { filter: invert(1) !important; } 
  • NEMO/branches/2019/ENHANCE-03_closea/doc/rst/source/conf.py

    r10991 r12149  
    11# -*- coding: utf-8 -*- 
    22# 
    3 # Configuration file for the Sphinx documentation builder. 
    4 # 
    5 # This file does only contain a selection of the most common options. For a 
    6 # full list see the documentation: 
    7 # http://www.sphinx-doc.org/en/master/config 
    8  
    9 # -- Project information ----------------------------------------------------- 
    10  
    11 project = 'NEMO' 
    12 author = 'NEMO System Team' 
    13  
    14 # The short X.Y version 
    15 version = 'trk' 
    16 # The full version, including alpha/beta/rc tags 
    17 release = 'trunk' 
    18  
    19  
    20 # -- General configuration --------------------------------------------------- 
    21  
    22 # Add any Sphinx extension module names here, as strings. They can be 
    23 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom 
    24 # ones. 
    25 extensions = ['sphinx.ext.extlinks', 'sphinxcontrib.bibtex'] 
     3# NEMO documentation build configuration file, created by 
     4# sphinx-quickstart on Tue Oct 15 20:13:55 2019. 
     5# 
     6# This file is execfile()d with the current directory set to its containing dir. 
     7# 
     8# Note that not all possible configuration values are present in this 
     9# autogenerated file. 
     10# 
     11# All configuration values have a default; values that are commented out 
     12# serve to show the default. 
     13 
     14import sys, os 
     15 
     16# If extensions (or modules to document with autodoc) are in another directory, 
     17# add these directories to sys.path here. If the directory is relative to the 
     18# documentation root, use os.path.abspath to make it absolute, like shown here. 
     19#sys.path.insert(0, os.path.abspath('.')) 
     20 
     21# -- General configuration ----------------------------------------------------- 
     22 
     23# If your documentation needs a minimal Sphinx version, state it here. 
     24#needs_sphinx = '1.0' 
     25 
     26# Add any Sphinx extension module names here, as strings. They can be extensions 
     27# coming with Sphinx (named 'sphinx.ext.*') or your custom ones. 
     28extensions = ['sphinx.ext.extlinks', 'sphinxcontrib.bibtex', 
     29              'sphinx.ext.todo'    , 'sphinx.ext.autosectionlabel'] 
    2630 
    2731# Add any paths that contain templates here, relative to this directory. 
    2832templates_path = ['_templates'] 
    2933 
     34# The suffix of source filenames. 
     35source_suffix = '.rst' 
     36 
     37# The encoding of source files. 
     38#source_encoding = 'utf-8-sig' 
     39 
    3040# The master toctree document. 
    31 master_doc = 'NEMO_guide' 
     41master_doc = 'guide' 
     42 
     43# General information about the project. 
     44project = u'NEMO' 
     45copyright = u'2019, NEMO Consortium' 
     46 
     47# The version info for the project you're documenting, acts as replacement for 
     48# |version| and |release|, also used in various other places throughout the 
     49# built documents. 
     50# 
     51# The short X.Y version. 
     52version = 'trk' 
     53# The full version, including alpha/beta/rc tags. 
     54release = 'trunk' 
     55 
     56# The language for content autogenerated by Sphinx. Refer to documentation 
     57# for a list of supported languages. 
     58#language = None 
     59 
     60# There are two options for replacing |today|: either, you set today to some 
     61# non-false value, then it is used: 
     62#today = '' 
     63# Else, today_fmt is used as the format for a strftime call. 
     64#today_fmt = '%B %d, %Y' 
    3265 
    3366# List of patterns, relative to source directory, that match files and 
    3467# directories to ignore when looking for source files. 
    35 # This pattern also affects html_static_path and html_extra_path . 
    36 exclude_patterns = ['global.rst', 'coarsening.rst'] 
     68exclude_patterns = ['global.rst', 'readme.rst'] 
     69 
     70# The reST default role (used for this markup: `text`) to use for all documents. 
     71#default_role = None 
     72 
     73# If true, '()' will be appended to :func: etc. cross-reference text. 
     74#add_function_parentheses = True 
     75 
     76# If true, the current module name will be prepended to all description 
     77# unit titles (such as .. function::). 
     78#add_module_names = True 
     79 
     80# If true, sectionauthor and moduleauthor directives will be shown in the 
     81# output. They are ignored by default. 
     82#show_authors = False 
    3783 
    3884# The name of the Pygments (syntax highlighting) style to use. 
    39 pygments_style = 'sphinx' 
    40  
    41  
    42 # -- Options for HTML output ------------------------------------------------- 
     85pygments_style = 'emacs' 
     86 
     87# A list of ignored prefixes for module index sorting. 
     88#modindex_common_prefix = [] 
     89 
     90 
     91# -- Options for HTML output --------------------------------------------------- 
    4392 
    4493# The theme to use for HTML and HTML Help pages.  See the documentation for 
    4594# a list of builtin themes. 
    46 # 
    4795html_theme = 'sphinx_rtd_theme' 
    4896 
     
    5098# further.  For a list of options available for each theme, see the 
    5199# documentation. 
    52 # 
    53 html_theme_options = {} 
     100#html_theme_options = {} 
     101 
     102# Add any paths that contain custom themes here, relative to this directory. 
     103#html_theme_path = [] 
     104 
     105# The name for this set of Sphinx documents.  If None, it defaults to 
     106# "<project> v<release> documentation". 
     107#html_title = None 
     108 
     109# A shorter title for the navigation bar.  Default is the same as html_title. 
     110#html_short_title = None 
     111 
     112# The name of an image file (relative to this directory) to place at the top 
     113# of the sidebar. 
     114#html_logo = None 
     115 
     116# The name of an image file (within the static path) to use as favicon of the 
     117# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32 
     118# pixels large. 
     119html_favicon = '_static/ORCA.ico' 
    54120 
    55121# Add any paths that contain custom static files (such as style sheets) here, 
     
    58124html_static_path = ['_static'] 
    59125 
    60 html_favicon = '_static/ORCA.ico' 
    61  
    62  
    63 # -- Options for LaTeX output ------------------------------------------------ 
     126# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, 
     127# using the given strftime format. 
     128#html_last_updated_fmt = '%b %d, %Y' 
     129 
     130# If true, SmartyPants will be used to convert quotes and dashes to 
     131# typographically correct entities. 
     132#html_use_smartypants = True 
     133 
     134# Custom sidebar templates, maps document names to template names. 
     135#html_sidebars = {} 
     136 
     137# Additional templates that should be rendered to pages, maps page names to 
     138# template names. 
     139#html_additional_pages = {} 
     140 
     141# If false, no module index is generated. 
     142#html_domain_indices = True 
     143 
     144# If false, no index is generated. 
     145#html_use_index = True 
     146 
     147# If true, the index is split into individual pages for each letter. 
     148#html_split_index = False 
     149 
     150# If true, links to the reST sources are added to the pages. 
     151#html_show_sourcelink = True 
     152 
     153# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. 
     154#html_show_sphinx = True 
     155 
     156# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. 
     157#html_show_copyright = True 
     158 
     159# If true, an OpenSearch description file will be output, and all pages will 
     160# contain a <link> tag referring to it.  The value of this option must be the 
     161# base URL from which the finished HTML is served. 
     162#html_use_opensearch = '' 
     163 
     164# This is the file name suffix for HTML files (e.g. ".xhtml"). 
     165#html_file_suffix = None 
     166 
     167# Output file base name for HTML help builder. 
     168htmlhelp_basename = 'NEMOdoc' 
     169 
     170 
     171# -- Options for LaTeX output -------------------------------------------------- 
    64172 
    65173latex_elements = { 
    66     # The paper size ('letterpaper' or 'a4paper'). 
    67     # 
    68     # 'papersize': 'letterpaper', 
    69  
    70     # The font size ('10pt', '11pt' or '12pt'). 
    71     # 
    72     # 'pointsize': '10pt', 
    73  
    74     # Additional stuff for the LaTeX preamble. 
    75     # 
    76     # 'preamble': '', 
    77  
    78     # Latex figure (float) alignment 
    79     # 
    80     # 'figure_align': 'htbp', 
     174# The paper size ('letterpaper' or 'a4paper'). 
     175#'papersize': 'letterpaper', 
     176 
     177# The font size ('10pt', '11pt' or '12pt'). 
     178#'pointsize': '10pt', 
     179 
     180# Additional stuff for the LaTeX preamble. 
     181#'preamble': '', 
    81182} 
    82183 
    83184# Grouping the document tree into LaTeX files. List of tuples 
    84 # (source start file, target name, title, 
    85 #  author, documentclass [howto, manual, or own class]). 
     185# (source start file, target name, title, author, documentclass [howto/manual]). 
    86186latex_documents = [ 
    87     (master_doc, 'NEMO_guide.tex', 'NEMO Quick Start Guide', 
    88      'NEMO System Team', 'howto'), 
     187  ('guide', 'guide.tex', u'NEMO Quick Start Guide', 
     188   u'NEMO Consortium', 'howto'), 
    89189] 
    90190 
    91  
    92 # -- Customisation ----------------------------------------------------------- 
     191# The name of an image file (relative to this directory) to place at the top of 
     192# the title page. 
     193#latex_logo = None 
     194 
     195# For "manual" documents, if this is true, then toplevel headings are parts, 
     196# not chapters. 
     197#latex_use_parts = False 
     198 
     199# If true, show page references after internal links. 
     200#latex_show_pagerefs = False 
     201 
     202# If true, show URL addresses after external links. 
     203#latex_show_urls = False 
     204 
     205# Documents to append as an appendix to all manuals. 
     206#latex_appendices = [] 
     207 
     208# If false, no module index is generated. 
     209#latex_domain_indices = True 
     210 
     211 
     212# -- Options for manual page output -------------------------------------------- 
     213 
     214# One entry per manual page. List of tuples 
     215# (source start file, name, description, authors, manual section). 
     216man_pages = [ 
     217    ('guide', 'nemo', u'NEMO Documentation', 
     218     [u'NEMO System Team'], 1) 
     219] 
     220 
     221# If true, show URL addresses after external links. 
     222#man_show_urls = False 
     223 
     224 
     225# -- Options for Texinfo output ------------------------------------------------ 
     226 
     227# Grouping the document tree into Texinfo files. List of tuples 
     228# (source start file, target name, title, author, 
     229#  dir menu entry, description, category) 
     230texinfo_documents = [ 
     231  ('guide', 'NEMO', u'NEMO Documentation', 
     232   u'NEMO System Team', 'NEMO', 'Community Ocean Model', 
     233   'Miscellaneous'), 
     234] 
     235 
     236# Documents to append as an appendix to all manuals. 
     237#texinfo_appendices = [] 
     238 
     239# If false, no module index is generated. 
     240#texinfo_domain_indices = True 
     241 
     242# How to display URL addresses: 'footnote', 'no', or 'inline'. 
     243#texinfo_show_urls = 'footnote' 
     244 
     245# -- Customisation ------------------------------------------------------------- 
    93246 
    94247# Timestamping 
     
    99252# Link aliases 
    100253extlinks = { 
    101    'doi'    : ('https://doi.org/%s'                       , None), 
    102    'forge'  : ('https://forge.ipsl.jussieu.fr/nemo/%s'    , None), 
    103    'github' : ('https://github.com/%s'                    , None), 
    104    'xios'   : ('https://forge.ipsl.jussieu.fr/ioserver/%s', None), 
    105    'website': ('https://www.nemo-ocean.eu/%s'             , None), 
    106    'zenodo' : ('https://zenodo.org/publication/%s'        , None) 
     254   'doi'    : ('https://doi.org/%s'                                                    , 'doi:'), 
     255   'manhtml': ('https://forge.ipsl.jussieu.fr/nemo/chrome/site/doc/NEMO/manual/html/%s', None  ), 
     256   'forge'  : ('https://forge.ipsl.jussieu.fr/nemo/%s'                                 , None  ), 
     257   'gmd'    : ('https://www.geosci-model-dev.net/%s'                                   , None  ), 
     258   'github' : ('https://github.com/NEMO-ocean/%s'                                      , None  ), 
     259   'xios'   : ('https://forge.ipsl.jussieu.fr/ioserver/%s'                             , None  ), 
     260   'website': ('https://www.nemo-ocean.eu/%s'                                          , None  ), 
     261   'zenodo' : ('https://zenodo.org/publication/%s'                                     , None  ) 
    107262} 
    108263 
     
    112267# SVN revision 
    113268import subprocess 
    114 revision = subprocess.check_output("svnversion").decode("utf-8") 
    115 rst_prolog = '.. |revision| replace:: %s' % revision 
     269rev = subprocess.check_output("svnversion").decode("utf-8") 
     270rst_prolog = '.. |revision| replace:: %s' % rev 
     271 
     272# 'draft' build tag: DRAFT watermark and TODO list 
     273if tags.has('draft'): 
     274   todo_include_todos = True 
     275   todo_emit_warnings = True 
     276else: 
     277   exclude_patterns = ['global.rst', 'readme.rst', 'todos.rst', 'unpub*'] 
     278 
     279# Default language to highlight set to fortran 
     280highlight_language = 'fortran' 
  • NEMO/branches/2019/ENHANCE-03_closea/doc/rst/source/global.rst

    r10605 r12149  
    1 .. Roles (custom styles related to CSS classes in 'source/_static/style.css') 
     1.. Roles 
    22 
    3 .. role:: rstblue 
    4 .. role:: rstgreen 
    5 .. role:: rstgrey 
    6 .. role:: rstgreysup(sup) 
    7 .. role:: underline  
    8    :class: underline 
     3.. custom styles related to CSS classes in './_static/style.css' 
     4 
     5.. role:: blue 
     6.. role:: green 
     7.. role:: grey 
     8.. role:: greysup(sup) 
     9 
     10.. inline code snippets 
     11 
     12.. role:: python(code) 
     13   :language: python 
     14   :class: highlight 
     15 
     16.. role:: fortran(code) 
     17   :language: fortran 
     18   :class: highlight 
     19 
     20.. role:: console(code) 
     21   :language: console 
     22   :class: highlight 
    923 
    1024.. Substitutions 
    1125 
    12 .. |OPA| replace:: :rstblue:`NEMO-OPA` 
    13 .. |SI3| replace:: :rstgrey:`NEMO-SI`\ :rstgreysup:`3` 
    14 .. |TOP| replace:: :rstgreen:`NEMO-TOP/PISCES` 
     26.. |NEMO-OCE| replace::  :blue:`NEMO-OCE (Ocean dynamics)` 
     27.. |OCE|      replace::  :blue:`NEMO-OCE` 
     28.. |NEMO-ICE| replace::  :grey:`NEMO-SI`\ :greysup:`3`  :grey:`(Sea Ice)` 
     29.. |ICE|      replace::  :grey:`NEMO-SI`\ :greysup:`3` 
     30.. |NEMO-MBG| replace:: :green:`NEMO-TOP/PISCES (Tracers)` 
     31.. |MBG|      replace:: :green:`NEMO-TOP/PISCES` 
    1532 
    16 .. Institutes 
     33.. External links 
    1734 
    18 .. _CMCC:           https://www.cmcc.it  
    19 .. _CNRS:           https://www.cnrs.fr 
    20 .. _Mercator Ocean: https://www.mercator-ocean.fr 
    21 .. _Met Office:     https://www.metoffice.gov.uk 
    22 .. _MOI:            https://www.mercator-ocean.fr 
    23 .. _NERC:           https://nerc.ukri.org 
     35   .. Consortium institutes 
    2436 
    25 .. Models / Softwares 
     37.. _CMCC:       https://www.cmcc.it 
     38.. _CNRS:       https://www.cnrs.fr 
     39.. _Met Office: https://www.metoffice.gov.uk 
     40.. _MOI:        https://www.mercator-ocean.fr 
     41.. _NERC:       https://nerc.ukri.org 
     42 
     43   .. Models / Libraries / Dependencies 
    2644 
    2745.. _AGRIF:  http://agrif.imag.fr 
    28 .. _FCM:    https://metomi.github.io/fcm/doc/ 
     46.. _BFM:    http://www.bfm-community.eu 
     47.. _FCM:    https://metomi.github.io/fcm 
    2948.. _IOIPSL: https://forge.ipsl.jussieu.fr/igcmg/browser/IOIPSL 
     49.. _NEMO:   https://www.nemo-ocean.eu 
    3050.. _OASIS:  https://portal.enes.org/oasis 
     51.. _XIOS:   https://forge.ipsl.jussieu.fr/ioserver 
    3152 
    32 .. NEMO 
     53   .. Misc. 
    3354 
    34 .. _NEMO:          https://www.nemo-ocean.eu 
    35 .. _NEMO strategy: https://doi.org/10.5281/zenodo.1471663 
    36 .. _NEMO guide:    :samp: https://doi.org/10.5281/zenodo.1475325 
    37 .. _NEMO manual:   https://doi.org/10.5281/zenodo.1464816 
    38 .. _SI3 manual:    :samp: https://doi.org/10.5281/zenodo.1471689 
    39 .. _TOP manual:    :samp: https://doi.org/10.5281/zenodo.1471700 
     55.. _EGU: http://www.egu.eu 
     56.. _Special Issue: https://www.geosci-model-dev.net/special_issue40.html 
     57.. _BFM man: https://cmcc-foundation.github.io/www.bfm-community.eu/files/bfm-nemo-manual_r1.0_201508.pdf 
     58.. _RST man: https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html 
     59.. _PAPA station: http://www.pmel.noaa.gov/OCS/Papa/index-Papa.shtml 
     60.. _ISOMIP: http://staff.acecrc.org.au/~bkgalton/ISOMIP/test_cavities.pdf 
     61 
     62.. DOI 
     63 
     64   .. Publications (`:samp:` to deactivate link for unpublished documents) 
     65 
     66.. _DOI man OCE:          https://doi.org/10.5281/zenodo.1464816 
     67.. _DOI man ICE:   :samp: https://doi.org/10.5281/zenodo.1471689 
     68.. _DOI man MBG:   :samp: https://doi.org/10.5281/zenodo.1471700 
     69.. _DOI qsg:       :samp: https://doi.org/10.5281/zenodo.1475325 
     70.. _DOI dev  stgy:        https://doi.org/10.5281/zenodo.1471663 
     71.. _DOI data:             https://doi.org/10.5281/zenodo.1472245 
     72 
     73   .. Badges (same labels as previously, substitution to link images) 
     74 
     75.. |DOI man OCE| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1464816.svg 
     76.. |DOI man ICE| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1471689.svg 
     77.. |DOI man MBG| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1471700.svg 
     78.. |DOI qsg|     image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1475325.svg 
     79.. |DOI data|    image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1472245.svg 
Note: See TracChangeset for help on using the changeset viewer.