Changeset 11713 for NEMO/trunk/doc/rst
- Timestamp:
- 2019-10-17T17:49:19+02:00 (5 years ago)
- Location:
- NEMO/trunk/doc/rst
- Files:
-
- 1 added
- 7 edited
Legend:
- Unmodified
- Added
- Removed
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NEMO/trunk/doc/rst/Makefile
r11706 r11713 15 15 I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source 16 16 17 .PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext17 .PHONY: help clean html dirhtml drafthtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext 18 18 19 19 help: … … 21 21 @echo " html to make standalone HTML files" 22 22 @echo " dirhtml to make HTML files named index.html in directories" 23 @echo " drafthtml to make an autoupdate HTML export while editing (todo list included)" 23 24 @echo " singlehtml to make a single large HTML file" 24 @echo " livehtml to make an autoupdate HTML export while editing"25 25 @echo " pickle to make pickle files" 26 26 @echo " json to make JSON files" … … 44 44 45 45 html: 46 $(SPHINXBUILD) -b html$(ALLSPHINXOPTS) $(BUILDDIR)/html46 $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html 47 47 @echo 48 48 @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." 49 49 50 50 dirhtml: 51 $(SPHINXBUILD) -b dirhtml$(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml51 $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml 52 52 @echo 53 53 @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." 54 54 55 drafthtml: 56 sphinx-autobuild -b html -t draft $(ALLSPHINXOPTS) $(BUILDDIR)/drafthtml 57 @echo 58 @echo "Build finished. The HTML pages are in $(BUILDDIR)/drafthtml." 59 55 60 singlehtml: 56 $(SPHINXBUILD) -b singlehtml$(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml61 $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml 57 62 @echo 58 63 @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." 59 64 60 livehtml:61 sphinx-autobuild -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html62 @echo63 @echo "Build finished. The HTML pages are in $(BUILDDIR)/html."64 65 65 pickle: 66 $(SPHINXBUILD) -b pickle$(ALLSPHINXOPTS) $(BUILDDIR)/pickle66 $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle 67 67 @echo 68 68 @echo "Build finished; now you can process the pickle files." 69 69 70 70 json: 71 $(SPHINXBUILD) -b json$(ALLSPHINXOPTS) $(BUILDDIR)/json71 $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json 72 72 @echo 73 73 @echo "Build finished; now you can process the JSON files." 74 74 75 75 htmlhelp: 76 $(SPHINXBUILD) -b htmlhelp$(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp76 $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp 77 77 @echo 78 78 @echo "Build finished; now you can run HTML Help Workshop with the" \ … … 80 80 81 81 qthelp: 82 $(SPHINXBUILD) -b qthelp$(ALLSPHINXOPTS) $(BUILDDIR)/qthelp82 $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp 83 83 @echo 84 84 @echo "Build finished; now you can run "qcollectiongenerator" with the" \ … … 89 89 90 90 devhelp: 91 $(SPHINXBUILD) -b devhelp$(ALLSPHINXOPTS) $(BUILDDIR)/devhelp91 $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp 92 92 @echo 93 93 @echo "Build finished." … … 98 98 99 99 epub: 100 $(SPHINXBUILD) -b epub$(ALLSPHINXOPTS) $(BUILDDIR)/epub100 $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub 101 101 @echo 102 102 @echo "Build finished. The epub file is in $(BUILDDIR)/epub." 103 103 104 104 latex: 105 $(SPHINXBUILD) -b latex$(ALLSPHINXOPTS) $(BUILDDIR)/latex105 $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex 106 106 @echo 107 107 @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." … … 110 110 111 111 latexpdf: 112 $(SPHINXBUILD) -b latex$(ALLSPHINXOPTS) $(BUILDDIR)/latex112 $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex 113 113 @echo "Running LaTeX files through pdflatex..." 114 114 $(MAKE) -C $(BUILDDIR)/latex all-pdf … … 116 116 117 117 text: 118 $(SPHINXBUILD) -b text$(ALLSPHINXOPTS) $(BUILDDIR)/text118 $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text 119 119 @echo 120 120 @echo "Build finished. The text files are in $(BUILDDIR)/text." 121 121 122 122 man: 123 $(SPHINXBUILD) -b man$(ALLSPHINXOPTS) $(BUILDDIR)/man123 $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man 124 124 @echo 125 125 @echo "Build finished. The manual pages are in $(BUILDDIR)/man." 126 126 127 127 texinfo: 128 $(SPHINXBUILD) -b texinfo$(ALLSPHINXOPTS) $(BUILDDIR)/texinfo128 $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo 129 129 @echo 130 130 @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo." … … 133 133 134 134 info: 135 $(SPHINXBUILD) -b texinfo$(ALLSPHINXOPTS) $(BUILDDIR)/texinfo135 $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo 136 136 @echo "Running Texinfo files through makeinfo..." 137 137 make -C $(BUILDDIR)/texinfo info … … 139 139 140 140 gettext: 141 $(SPHINXBUILD) -b gettext$(I18NSPHINXOPTS) $(BUILDDIR)/locale141 $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale 142 142 @echo 143 143 @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale." 144 144 145 145 changes: 146 $(SPHINXBUILD) -b changes$(ALLSPHINXOPTS) $(BUILDDIR)/changes146 $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes 147 147 @echo 148 148 @echo "The overview file is in $(BUILDDIR)/changes." 149 149 150 150 linkcheck: 151 $(SPHINXBUILD) -b linkcheck$(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck151 $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck 152 152 @echo 153 153 @echo "Link check complete; look for any errors in the above output " \ … … 155 155 156 156 doctest: 157 $(SPHINXBUILD) -b doctest$(ALLSPHINXOPTS) $(BUILDDIR)/doctest157 $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest 158 158 @echo "Testing of doctests in the sources finished, look at the " \ 159 159 "results in $(BUILDDIR)/doctest/output.txt." -
NEMO/trunk/doc/rst/source/NEMO_guide.rst
r11707 r11713 12 12 ", for paragraphs 13 13 14 'global.rst' contains a list of common directives (roles, substitutions and URL links)15 It is loaded for each file thanks to'rst_epilog' setting in 'conf.py'14 'global.rst' contains a list of roles, substitutions and URL links for the guide. 15 It is loaded for each file with the 'rst_epilog' setting in 'conf.py' 16 16 17 17 .. toctree:: … … 49 49 glossary 50 50 51 :Release: |release| 52 53 .. only:: draft 54 55 .. include:: todos.rst 56 51 57 .. include:: readme.rst 52 53 .. Next headings markup acording to readme.rst54 55 Disclaimer56 ==========57 58 The NEMO source code is freely available and distributed under CeCILL license59 (GNU GPL compatible - see ``./LICENSE``).60 61 You can use, modify and/or redistribute the software under its terms,62 but users are provided only with a limited warranty and the software's authors and63 the successive licensor's have only limited liability. -
NEMO/trunk/doc/rst/source/citations.rst
r11707 r11713 1 *********** *****2 How to cite NEMO3 *********** *****1 *********** 2 How to cite 3 *********** 4 4 5 6 |NEMO-OCE| :cite:`NEMO_manual` 7 8 | "**NEMO ocean engine**" 9 | Gurvan Madec and NEMO System Team 10 | *Scientific Notes of Climate Modelling Center*, **27** 11 | ISSN 1288-1619 Institut Pierre-Simon Laplace (IPSL) 12 | |DOI man OCE|_ 5 |NEMO-OCE| 6 :title:`NEMO ocean engine`, 7 NEMO System Team, 8 Scientific Notes of Climate Modelling Center, 27, 9 ISSN 1288-1619 Institut Pierre-Simon Laplace (IPSL), 10 :doi:`10.5281/zenodo.1464816` 13 11 14 12 .. literalinclude:: references.bib 15 13 :language: bibtex 16 :lines: 1- 1514 :lines: 1-9 17 15 :caption: BibTeX source for NEMO manual 18 16 19 |NEMO-ICE| :cite:`SI3_manual`20 21 | "**Sea Ice modelling Integrated Initiative (SI** :sup:`3` **) -- The NEMO sea ice engine**"22 | NEMO Sea Ice Working Group23 | *Scientific Notes of Climate Modelling Center*, **31**24 | ISSN 1288-1619 Institut Pierre-Simon Laplace (IPSL)25 | |DOI man ICE|17 |NEMO-ICE| 18 :title:`Sea Ice modelling Integrated Initiative (SI`\ :sup:`3`\ :title:`) -- 19 The NEMO sea ice engine`, 20 NEMO Sea Ice Working Group, 21 Scientific Notes of Climate Modelling Center, 31, 22 ISSN 1288-1619 Institut Pierre-Simon Laplace (IPSL), 23 :doi:`10.5281/zenodo.1471689` 26 24 27 25 .. warning:: No official publication yet … … 29 27 .. literalinclude:: references.bib 30 28 :language: bibtex 31 :lines: 1 7-3329 :lines: 13-21 32 30 :caption: BibTeX source for SI\ :sup:`3` manual 33 31 34 |NEMO-MBG| :cite:`TOP_manual` 35 36 | "**Tracer in Ocean Paradigm (TOP) -- The NEMO passive tracer engine**" 37 | NEMO TOP Working Group 38 | *Scientific Notes of Climate Modelling Center*, **28** 39 | ISSN 1288-1619 Institut Pierre-Simon Laplace (IPSL) 40 | |DOI man MBG| 32 |NEMO-MBG| 33 :title:`Tracer in Ocean Paradigm (TOP) -- The NEMO passive tracer engine`, 34 NEMO TOP Working Group, 35 Scientific Notes of Climate Modelling Center, 28, 36 ISSN 1288-1619 Institut Pierre-Simon Laplace (IPSL), 37 :doi:`10.5281/zenodo.1471700` 41 38 42 39 .. warning:: No official publication yet … … 44 41 .. literalinclude:: references.bib 45 42 :language: bibtex 46 :lines: 37-4943 :lines: 25-33 47 44 :caption: BibTeX source for TOP manual 48 49 References50 ==========51 52 .. bibliography:: references.bib53 :style: unsrt54 :labelprefix: R -
NEMO/trunk/doc/rst/source/conf.py
r11706 r11713 26 26 # Add any Sphinx extension module names here, as strings. They can be extensions 27 27 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones. 28 extensions = ['sphinx.ext.extlinks', 'sphinxcontrib.bibtex', 'sphinx.ext.todo' ]28 extensions = ['sphinx.ext.extlinks', 'sphinxcontrib.bibtex', 'sphinx.ext.todo', 'sphinxmark'] 29 29 30 30 # Add any paths that contain templates here, relative to this directory. … … 251 251 # Link aliases 252 252 extlinks = { 253 'doi' : ('https://doi.org/%s' , None),254 'forge' : ('https://forge.ipsl.jussieu.fr/nemo/%s' , None),255 'github' : ('https://github.com/%s' , None),256 'xios' : ('https://forge.ipsl.jussieu.fr/ioserver/%s', None),257 'website': ('https://www.nemo-ocean.eu/%s' , None),258 'zenodo' : ('https://zenodo.org/publication/%s' , None)253 'doi' : ('https://doi.org/%s' , 'doi:'), 254 'forge' : ('https://forge.ipsl.jussieu.fr/nemo/%s' , None), 255 'github' : ('https://github.com/%s' , None), 256 'xios' : ('https://forge.ipsl.jussieu.fr/ioserver/%s', None), 257 'website': ('https://www.nemo-ocean.eu/%s' , None), 258 'zenodo' : ('https://zenodo.org/publication/%s' , None) 259 259 } 260 260 … … 266 266 revision = subprocess.check_output("svnversion").decode("utf-8") 267 267 rst_prolog = '.. |revision| replace:: %s' % revision 268 269 # Todo 270 if tags.has('draft'): 271 sphinxmark_enable = True 272 todo_include_todos = True 273 todo_emit_warnings = True -
NEMO/trunk/doc/rst/source/data_assimilation.rst
r11707 r11713 40 40 To build the SAO use makenemo. 41 41 This means compiling NEMO once (in the normal way) for the chosen configuration. 42 Then include ``SAO`` at the end of the relevant line in ``cfg.txt`` file.43 Then recompile with the replacement main program in ``./src/SAO``.44 This is a special version of ``nemogcm.F90`` (which doesn't run the model,42 Then include ``SAO`` at the end of the relevant line in :file:`cfg.txt` file. 43 Then recompile with the replacement main program in :file:`./src/SAO`. 44 This is a special version of :file:`nemogcm.F90` (which doesn't run the model, 45 45 but reads in the model fields, and observations and runs the OBS code. 46 46 See "Standalone observation operator (``SAO``)" section in |DOI man OCE|_. -
NEMO/trunk/doc/rst/source/global.rst
r11707 r11713 5 5 .. role:: grey 6 6 .. role:: greysup(sup) 7 .. role: underline8 .. :class: underline9 7 10 8 .. Substitutions 11 9 12 .. |NEMO-OCE| replace:: :blue:`NEMO-OCE (Ocean dynamics)` 13 .. |NEMO-ICE| replace:: :grey:`NEMO-SI`\ :greysup:`3`\ :grey:`(Sea Ice)` 14 .. |NEMO-MBG| replace:: :green:`NEMO-TOP/PISCES (Biogeochemistry)` 10 .. |NEMO-OCE| replace:: :blue:`NEMO-OCE (Ocean dynamics)` 11 .. |OCE| replace:: :blue:`NEMO-OCE` 12 .. |NEMO-ICE| replace:: :grey:`NEMO-SI`\ :greysup:`3` :grey:`(Sea Ice)` 13 .. |ICE| replace:: :grey:`NEMO-SI`\ :greysup:`3` 14 .. |NEMO-MBG| replace:: :green:`NEMO-TOP/PISCES (Tracers)` 15 .. |MBG| replace:: :green:`NEMO-TOP/PISCES` 15 16 16 17 .. External links … … 37 38 .. _EGU: http://www.egu.eu 38 39 .. _Special Issue: https://www.geosci-model-dev.net/special_issue40.html 40 .. _BFM man: https://cmcc-foundation.github.io/www.bfm-community.eu/files/bfm-nemo-manual_r1.0_201508.pdf 39 41 40 42 .. DOI -
NEMO/trunk/doc/rst/source/glossary.rst
r11707 r11713 3 3 ******** 4 4 5 `AGRIF`_ 6 *Adaptive Grid Refinement In Fortran*, 7 package for the integration of full adaptive mesh refinement features within 8 an existing multidimensional finite difference model 5 .. glossary:: 9 6 10 SI\ :sup:`3`\ 11 *Sea Ice Integrated Initiative*, 12 unified sea ice model merging functionalities from CICE, GELATO and LIM into the NEMO framework 7 `AGRIF`_ 8 *Adaptive Grid Refinement In Fortran*, 9 package for the integration of full adaptive mesh refinement features within 10 an existing multidimensional finite difference model 13 11 14 `OASIS`_ 15 *Ocean Atmosphere Sea Ice Soil*,16 coupling software to synchronise numerical codes representing different components of the climate system 12 SI\ :sup:`3`\ 13 *Sea Ice Integrated Initiative*, 14 unified sea ice model merging functionalities from CICE, GELATO and LIM into the NEMO framework 17 15 18 PISCES 19 *Pelagic Interactions Scheme for Carbon and Ecosystem Studies*,20 biogeochemical model simulating marine ecosystems, cycles of carbon and the main nutrients 16 `OASIS`_ 17 *Ocean Atmosphere Sea Ice Soil*, 18 coupling software to synchronise numerical codes representing different components of the climate system 21 19 22 TAM 23 *Tangent linear and Adjoint Model*, 24 tools to analyse and control the NEMO dynamical core for a wide range of applications such as 25 sensitivity analysis, parameter estimation, vectors computation or data assimilation. 20 PISCES 21 *Pelagic Interactions Scheme for Carbon and Ecosystem Studies*, 22 biogeochemical model simulating marine ecosystems, cycles of carbon and the main nutrients 26 23 27 TOP 28 *Tracers in Ocean Paradigm*, 29 on/off-line oceanic tracers transport and biogeochemistry models 24 TAM 25 *Tangent linear and Adjoint Model*, 26 tools to analyse and control the NEMO dynamical core for a wide range of applications such as 27 sensitivity analysis, parameter estimation, vectors computation or data assimilation. 30 28 31 `XIOS`_ 32 *XML Input Output Server*, 33 library dedicated to input/output management of climate code 29 TOP 30 *Tracers in Ocean Paradigm*, 31 on/off-line oceanic tracers transport and biogeochemistry models 32 33 `XIOS`_ 34 *XML Input Output Server*, 35 library dedicated to input/output management of climate code
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