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Commit e3c35821 authored by Nicolas Martin's avatar Nicolas Martin :speech_balloon:
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Makefile 0 → 100644
# Makefile for Sphinx documentation
#
# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build
PAPER =
BUILDDIR = build
# 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 drafthtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest 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 " drafthtml to make an autoupdate HTML export while editing (todo list included)"
@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 " 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)"
clean:
-rm -rf $(BUILDDIR)/*
html:
$(SPHINXBUILD) -b html $(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."
drafthtml:
sphinx-autobuild -b html -t draft $(ALLSPHINXOPTS) $(BUILDDIR)/drafthtml
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/drafthtml."
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/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 Quick Start Guide
**********************
| The NEMO guide is made up of several files written in
`ReStructuredText <http://docutils.sourceforge.net/rst.html>`_ (`.rst` extension),
a WYSIWYG markup language used in the Python community, and scattered all over the NEMO sources.
| You can view them one by one in plain text from `./source` folder, or export all to a user-friendly guide under `./build` (only HTML format at the moment, PDF expected later).
Build and export the guide in HTML
==================================
1. Install Sphinx documentation generator, its BibTeX extension and "Read The Docs" theme thanks to `pip` packages tool
.. code-block:: console
$ pip install sphinx sphinxcontrib.bibtex sphinx_rtd_theme
2. Build the HTML export with `make` in `./build/html`
.. code-block:: console
$ make html
3. Finally browse the guide by opening `./build/html/NEMO_guide.html`
Edit the sources and check the output in real time
==================================================
| To facilitate the update of the guide, editors can install a useful package that will automatically trigger a new build and the reload of the HTML page for every recorded change in the sources.
| So the reviewer saves time by controlling on-line their modifications almost as it types and also by avoiding repeated interactive rebuilds.
Install `sphinx-autobuild` package
.. code-block:: console
$ pip install sphinx-autobuild
Launch a local web server hosting a draft export of the guide (build this time in `./build/livehtml`)
.. code-block:: console
$ make livehtml
| Open in the same time the 2 formats of the content to review: the source file and the web page by browsing from the new guide hosted by your local server on `<http://127.0.0.1:8000/NEMO_guide.html>`_.
| Start the update, save your changes and verify instantly the HTML export in your browser.
.. warning::
| Your modifications are not taken into account?
| For symlink file, you will have to close it to update the HTML export. Otherwise look at the log of the Sphinx build, you probably made a typo!
.. hint::
Are there broken links? Fix "Page not found" errors by running `make linkcheck`
source/_static/AGRIF_DEMO.jpg

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source/_static/AGRIF_DEMO_no_cap.jpg

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source/_static/AMM_domain.png

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source/_static/ISOMIP_moc.png

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source/_static/LOCK-FCT4_flux_ubs.gif

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source/_static/NEMO_grey.png

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source/_static/ORCA.ico

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source/_static/OVF-sco_FCT4_flux_cen-ahm1000.gif

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source/_static/Papa2015.jpg

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source/_static/VORTEX_anim.gif

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source/_static/agrif_grid_position.jpg

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File added
<!--
============================================================================================================
= output files definition =
= Define your own files =
= put the variables you want... =
============================================================================================================
-->
<file_definition type="multiple_file" name="PATH_OUT/@expname@_@freq@" sync_freq="1d" min_digits="4">
<file_group id="1d" output_freq="1d" split_freq="1d" output_level="10" enabled=".TRUE."> <!-- 1d files -->
<file id="file1" name_suffix="_gcrsT" description="ocean T grid variables" >
<field field_ref="e3t" name="e3t" />
<field field_ref="toce" name="votemper" operation="instant" freq_op="1d" > @toce_e3t / @e3t </field>
<field field_ref="soce" name="vosaline" operation="instant" freq_op="1d" > @soce_e3t / @e3t </field>
<field field_ref="mldkz5" name="somixhgt" />
</file>
<file id="file2" name_suffix="_gcrsU" description="ocean T grid variables" >
<field field_ref="e3u" name="e3u" />
<field field_ref="uoce" name="uo" operation="instant" freq_op="1d" > @uoce_e3u / @e3u </field>
</file>
<file id="file3" name_suffix="_gcrsV" description="ocean T grid variables" >
<field field_ref="e3v" name="e3v" />
<field field_ref="voce" name="vo" operation="instant" freq_op="1d" > @voce_e3v / @e3v </field>
</file>
<file id="file4" name_suffix="_gcrsW" description="ocean T grid variables" >
<field field_ref="woce" name="woce" />
<field field_ref="avt" name="difvho" />
</file>
<file id="file5" name_suffix="_gcrsC" description="ocean T grid variables" >
<field field_ref="Alkalini" operation="instant" freq_op="1d" > @Alkalini_E3T / @e3t </field>
<field field_ref="O2" operation="instant" freq_op="1d" > @O2_E3T / @e3t </field>
<field field_ref="Si" operation="instant" freq_op="1d" > @Si_E3T / @e3t </field>
<field field_ref="PHY" operation="instant" freq_op="1d" > @PHY_E3T / @e3t </field>
<field field_ref="ZOO" operation="instant" freq_op="1d" > @ZOO_E3T / @e3t </field>
<field field_ref="DOC" operation="instant" freq_op="1d" > @DOC_E3T / @e3t </field>
<field field_ref="NCHL" operation="instant" freq_op="1d" > @NCHL_E3T / @e3t </field>
<field field_ref="DCHL" operation="instant" freq_op="1d" > @DCHL_E3T / @e3t </field>
<field field_ref="NO3" operation="instant" freq_op="1d" > @NO3_E3T / @e3t </field>
</file>
</file_group>
<file_group id="1mo" output_freq="1mo" split_freq="1mo" output_level="10" enabled=".TRUE."> <!-- 1d files -->
<file id="file6" name_suffix="_gcrsC" description="ocean T grid variables" >
<field field_ref="DIC" operation="instant" freq_op="1mo" > @DIC_E3T / @e3t </field>
<field field_ref="Alkalini" operation="instant" freq_op="1mo" > @Alkalini_E3T / @e3t </field>
<field field_ref="O2" operation="instant" freq_op="1mo" > @O2_E3T / @e3t </field>
<field field_ref="CaCO3" operation="instant" freq_op="1mo" > @CaCO3_E3T / @e3t </field>
<field field_ref="PO4" operation="instant" freq_op="1mo" > @PO4_E3T / @e3t </field>
<field field_ref="POC" operation="instant" freq_op="1mo" > @POC_E3T / @e3t </field>
<field field_ref="Si" operation="instant" freq_op="1mo" > @Si_E3T / @e3t </field>
<field field_ref="PHY" operation="instant" freq_op="1mo" > @PHY_E3T / @e3t </field>
<field field_ref="ZOO" operation="instant" freq_op="1mo" > @ZOO_E3T / @e3t </field>
<field field_ref="DOC" operation="instant" freq_op="1mo" > @DOC_E3T / @e3t </field>
<field field_ref="PHY2" operation="instant" freq_op="1mo" > @PHY2_E3T / @e3t </field>
<field field_ref="ZOO2" operation="instant" freq_op="1mo" > @ZOO2_E3T / @e3t </field>
<field field_ref="DSi" operation="instant" freq_op="1mo" > @DSi_E3T / @e3t </field>
<field field_ref="Fer" operation="instant" freq_op="1mo" > @Fer_E3T / @e3t </field>
<field field_ref="BFe" operation="instant" freq_op="1mo" > @BFe_E3T / @e3t </field>
<field field_ref="GOC" operation="instant" freq_op="1mo" > @GOC_E3T / @e3t </field>
<field field_ref="SFe" operation="instant" freq_op="1mo" > @SFe_E3T / @e3t </field>
<field field_ref="DFe" operation="instant" freq_op="1mo" > @DFe_E3T / @e3t </field>
<field field_ref="GSi" operation="instant" freq_op="1mo" > @GSi_E3T / @e3t </field>
<field field_ref="NFe" operation="instant" freq_op="1mo" > @NFe_E3T / @e3t </field>
<field field_ref="NCHL" operation="instant" freq_op="1mo" > @NCHL_E3T / @e3t </field>
<field field_ref="DCHL" operation="instant" freq_op="1mo" > @DCHL_E3T / @e3t </field>
<field field_ref="NO3" operation="instant" freq_op="1mo" > @NO3_E3T / @e3t </field>
<field field_ref="NH4" operation="instant" freq_op="1mo" > @NH4_E3T / @e3t </field>
</file>
</file_group>
</file_definition>
<!--
============================================================================================================
= output files definition =
= Define your own files default value="9.96921e+36" =
= put the variables you want... =
============================================================================================================
-->
<file_definition type="multiple_file" name="PATH_OUT/@expname@_@freq@" sync_freq="1d" min_digits="4" >
<file_group id="1d" output_freq="1d" split_freq="1d" output_level="10" enabled=".TRUE." > <!-- 5d files -->
<file id="file1" name_suffix="_gridT" description="ocean T grid variables" >
<field field_ref="e3t" name="e3t" />
<field field_ref="toce" name="votemper" operation="instant" freq_op="1d" > @toce_e3t / @e3t </field>
</file>
<file id="file2" name_suffix="_gridS" description="ocean T grid variables" >
<field field_ref="soce" name="vosaline" operation="instant" freq_op="1d" > @soce_e3t / @e3t </field>
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<file id="file3" name_suffix="_grid2D" description="ocean T grid variables" >
<field field_ref="mldkz5" name="somixhgt" />
<field field_ref="empmr" name="sowaflup" />
<field field_ref="empbmr" name="sowaflupb" />
<field field_ref="fmmflx" name="iowaflup" />
<field field_ref="ice_cover" name="soicecov" />
<field field_ref="qsr" name="soceshwf" />
<field field_ref="taum" name="sowindsp" />
<field field_ref="runoffs" name="runoffs" />
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<file id="file4" name_suffix="_gridU" description="ocean U grid variables" >
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<field field_ref="utau" name="tauuo" />
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<file id="file5" name_suffix="_gridV" description="ocean V grid variables" >
<field field_ref="e3v" name="e3v" />
<field field_ref="vocetr_eff" name="vocetr_eff" />
<field field_ref="vtau" name="tauvo" />
</file>
<file id="file6" name_suffix="_gridW" description="ocean W grid variables" >
<field field_ref="e3w" name="e3w" />
<field field_ref="wocetr_eff" name="wocetr_eff" />
</file>
<file id="file7" name_suffix="_gridKZ" description="ocean W grid variables" >
<field field_ref="avt" name="voddmavs" />
</file>
<file id="file8" name_suffix="_gridH" description="ocean W grid variables" >
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<field field_ref="e3t" name="e3t" />
<field field_ref="toce" name="votemper" operation="instant" freq_op="1d" > @toce_e3t / @e3t </field>
</file>
<file id="file11" name_suffix="_gridS" description="ocean T grid variables" >
<field field_ref="soce" name="vosaline" operation="instant" freq_op="1d" > @soce_e3t / @e3t </field>
</file>
<file id="file12" name_suffix="_grid2D" description="ocean T grid variables" >
<field field_ref="mldkz5" name="somixhgt" />
<field field_ref="empmr" name="sowaflup" />
<field field_ref="empbmr" name="sowaflupb" />
<field field_ref="fmmflx" name="iowaflup" />
<field field_ref="ice_cover" name="soicecov" />
<field field_ref="qsr" name="soceshwf" />
<field field_ref="taum" name="sowindsp" />
<field field_ref="runoffs" name="runoffs" />
</file>
<file id="file13" name_suffix="_gridU" description="ocean U grid variables" >
<field field_ref="e3u" name="e3u" />
<field field_ref="uocetr_eff" name="uocetr_eff" />
<field field_ref="utau" name="tauuo" />
</file>
<file id="file14" name_suffix="_gridV" description="ocean V grid variables" >
<field field_ref="e3v" name="e3v" />
<field field_ref="vocetr_eff" name="vocetr_eff" />
<field field_ref="vtau" name="tauvo" />
</file>
<file id="file15" name_suffix="_gridW" description="ocean W grid variables" >
<field field_ref="e3w" name="e3w" />
<field field_ref="wocetr_eff" name="wocetr_eff" />
</file>
<file id="file16" name_suffix="_gridKZ" description="ocean W grid variables" >
<field field_ref="avt" name="voddmavs" />
</file>
<file id="file17" name_suffix="_gridH" description="ocean W grid variables" >
<field field_ref="hdiv" name="hdivtr" long_name="horizontal divergence transport" operation="average" freq_op="1d" > @hdiv * @e3t </field>
</file>
</file_group>
</file_definition>
source/_static/frames/VORTEX_anim-00.png

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source/_static/frames/VORTEX_anim-01.png

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source/_static/frames/VORTEX_anim-02.png

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