Changeset 10279 for NEMO/trunk/doc/rst
- Timestamp:
- 2018-11-07T12:04:15+01:00 (6 years ago)
- Location:
- NEMO/trunk/doc/rst/source
- Files:
-
- 3 added
- 1 deleted
- 5 edited
- 4 moved
Legend:
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NEMO/trunk/doc/rst/source/NEMO_guide.rst
r10201 r10279 1 .. NEMO documentation master file, created by2 sphinx-quickstart on Tue Oct 9 18:14:01 2018.3 You can adapt this file completely to your liking, but it should at least4 contain the root `toctree` directive.5 6 1 ################# 7 2 Quick Start Guide … … 9 4 10 5 .. 11 A hidden .global.rst should be included in every subfiles with `include` directive 12 It contains a list of common URL links 13 14 .. include:: .global.rst 15 16 .. include:: readme.rst 17 18 Summary 19 ======= 20 21 .. toctree:: 22 :maxdepth: 1 23 :titlesonly: 24 25 release_notes.rst 26 install.rst 27 reference_configurations.rst 28 test_cases.rst 29 setup_configuration.rst 30 interfacing_options.rst 31 definitions.rst 32 33 .. 34 For headings markup, this convention is recommended from Python’s Style Guide 6 For headings markup, this convention is recommended from Python’s Style Guide 35 7 # with overline, for parts 36 8 * with overline, for chapters … … 40 12 ", for paragraphs 41 13 42 .. 43 Indices and tables 44 ================== 45 * :ref:`genindex` 46 * :ref:`modindex` 47 * :ref:`search` 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' 16 17 .. toctree:: 18 :hidden: 19 20 release_notes.rst 21 22 .. toctree:: 23 :hidden: 24 :caption: Getting started 25 26 install 27 configurations 28 test_cases 29 30 .. toctree:: 31 :hidden: 32 :caption: Setup your configuration 33 34 setup 35 diagnostics 36 tools 37 38 .. toctree:: 39 :hidden: 40 :caption: Advanced use 41 42 zooms 43 coarsening 44 coupling 45 assimilation 46 tracers 47 48 .. toctree:: 49 :hidden: 50 :caption: Glossary 51 52 definitions 53 54 .. include:: readme.rst 55 56 .. Next headings markup acording to readme.rst 57 58 How to cite NEMO 59 ================ 60 61 .. bibliography:: references.bib 62 :all: 63 :style: unsrt 64 :labelprefix: R 65 66 Disclaimer 67 ========== 68 69 The NEMO source code is freely available and distributed under CeCILL license 70 (GNU GPL compatible - see ``./LICENSE``). 71 72 You can use, modify and/or redistribute the software under its terms, 73 but users are provided only with a limited warranty and the software's authors and 74 the successive licensor's have only limited liability. -
NEMO/trunk/doc/rst/source/assimilation.rst
r10258 r10279 1 Data assimilation 2 ================= 3 4 .. include:: .global.rst 1 ************************************** 2 Data assimilation (OBS/SAO, ASM & TAM) 3 ************************************** 5 4 6 5 .. contents:: … … 12 11 - TAM the tangent linear and adjoint model. 13 12 14 Please see the `NEMO referencemanual`_ for more details including information about the input file formats and13 Please see the `NEMO manual`_ for more details including information about the input file formats and 15 14 the namelist settings. 16 15 17 --------------------------------------18 16 Observation and model comparison (OBS) 19 -------------------------------------- 17 ====================================== 20 18 21 19 The observation and model comparison code (OBS) reads in observation files (profile temperature and salinity, … … 28 26 To build with the OBS code active ``key_diaobs`` must be set. 29 27 30 More details in the `NEMO referencemanual`_ chapter 12.28 More details in the `NEMO manual`_ chapter 12. 31 29 32 30 Standalone observation operator (SAO) … … 43 41 This is a special version of ``nemogcm.F90`` (which doesn't run the model, but reads in the model fields, and 44 42 observations and runs the OBS code. 45 See section 12.4 of the `NEMO referencemanual`_.43 See section 12.4 of the `NEMO manual`_. 46 44 47 -----------------------------------48 45 Apply assimilation increments (ASM) 49 ----------------------------------- 46 =================================== 50 47 51 48 The ASM code adds the functionality to apply increments to the model variables: … … 56 53 To build the ASM code ``key asminc`` must be set. 57 54 58 More details in the `NEMO referencemanual`_ chapter 13.55 More details in the `NEMO manual`_ chapter 13. 59 56 60 --------------------------------61 57 Tangent linear and adjoint (TAM) 62 -------------------------------- 58 ================================ 63 59 64 60 This is the tangent linear and adjoint code of NEMO which is useful to 4D VAR assimilation. 65 66 .. _NEMO reference manual: http://doi.org/10.5281/zenodo. -
NEMO/trunk/doc/rst/source/conf.py
r10201 r10279 21 21 22 22 project = 'NEMO' 23 copyright = ' 2018, NEMO System Team'23 copyright = '' 24 24 author = 'NEMO System Team' 25 25 … … 39 39 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom 40 40 # ones. 41 extensions = ['sphinx contrib.bibtex']41 extensions = ['sphinx.ext.extlinks', 'sphinxcontrib.bibtex'] 42 42 43 43 # Add any paths that contain templates here, relative to this directory. … … 63 63 # directories to ignore when looking for source files. 64 64 # This pattern also affects html_static_path and html_extra_path . 65 exclude_patterns = [ ]65 exclude_patterns = ['global.rst'] 66 66 67 67 # The name of the Pygments (syntax highlighting) style to use. … … 74 74 # a list of builtin themes. 75 75 # 76 html_theme = 'alabaster' 76 #html_theme = 'alabaster' 77 html_theme = 'sphinx_rtd_theme' 77 78 78 79 # Theme options are theme-specific and customize the look and feel of a theme … … 81 82 # 82 83 html_theme_options = { 83 'logo': 'NEMO_grey.png', 84 'description': 'Community ocean model for multifarious space and time scales', 85 'fixed_sidebar': 'true', 86 # 'github_user': 'NEMO-ocean', 87 # 'github_repo': 'NEMO-examples', 88 # 'github_button': 'true', 89 # 'github_banner': 'true' 84 # Alabaster theme options 85 # 'logo': 'NEMO_grey.png', 86 # 'description': 'Community ocean model for multifarious space and time scales', 87 # 'fixed_sidebar': True, 90 88 } 91 89 … … 162 160 'Miscellaneous'), 163 161 ] 162 163 164 # -- Customisation ----------------------------------------------------------- 165 166 import datetime 167 year = datetime.date.today().year 168 copyright = '2008-' + str( year ) + ', NEMO Consortium' 169 170 # Link aliases 171 extlinks = { 172 'doi' : ('http://doi.org/%s' , None), 173 'forge' : ('http://forge.ipsl.jussieu.fr/nemo/%s' , None), 174 'github' : ('http://github.com/%s' , None), 175 'xios' : ('http://forge.ipsl.jussieu.fr/ioserver/%s', None), 176 'website': ('http://www.nemo-ocean.eu/%s' , None), 177 'zenodo' : ('http://zenodo.org/publication/%s' , None) 178 } 179 180 # Include common directives for every rst file 181 rst_epilog = open('global.rst', 'r').read() -
NEMO/trunk/doc/rst/source/coupling.rst
r10201 r10279 1 Coupling with other models (OASIS, SAS, ...) 2 ============================================ 3 4 .. include:: .global.rst 1 ********************** 2 Coupling (OASIS & SAS) 3 ********************** 5 4 6 5 NEMO currently exploits OASIS-3-MCT to implement a generalised coupled interface -
NEMO/trunk/doc/rst/source/definitions.rst
r10201 r10279 1 =========== 1 *********** 2 2 Definitions 3 =========== 3 *********** 4 4 5 .. include:: .global.rst 6 7 AGRIF 5 `AGRIF`_ 8 6 *Adaptive Grid Refinement In Fortran*, 9 7 package for the integration of full adaptive mesh refinement features within … … 14 12 unified sea ice model merging functionalities from CICE, GELATO and LIM into the NEMO framework 15 13 16 OASIS 14 `OASIS`_ 17 15 *Ocean Atmosphere Sea Ice Soil*, 18 16 coupling software to synchronise numerical codes representing different components of the climate system … … 31 29 on/off-line oceanic tracers transport and biogeochemistry models 32 30 33 XIOS 31 `XIOS`_ 34 32 *XML Input Output Server*, 35 33 library dedicated to input/output management of climate code -
NEMO/trunk/doc/rst/source/global.rst
r10277 r10279 1 .. Roles (custom styles related to CSS classes )1 .. Roles (custom styles related to CSS classes in 'source/_static/style.css') 2 2 3 3 .. role:: rstblue … … 5 5 .. role:: rstgrey 6 6 .. role:: rstgreysup(sup) 7 .. role:: underline 8 :class: underline 7 9 8 .. Links10 .. Substitutions 9 11 10 .. Institutes 12 .. |OPA| replace:: :rstblue:`NEMO-OPA` 13 .. |SI3| replace:: :rstgrey:`NEMO-SI`\ :rstgreysup:`3` 14 .. |TOP| replace:: :rstgreen:`NEMO-TOP/PISCES` 15 16 .. Institutes 11 17 12 18 .. _CMCC: http://www.cmcc.it … … 17 23 .. _NERC: http://nerc.ukri.org 18 24 19 25 .. Models / Softwares 20 26 21 27 .. _AGRIF: http://agrif.imag.fr 22 28 .. _OASIS: http://verc.enes.org/oasis 29 .. _XIOS: http://forge.ipsl.jussieu.fr/ioserver 23 30 24 31 .. NEMO 25 32 26 .. _NEMO: http://www.nemo-ocean.eu 27 .. _Reference Manual: http://doi.org/10.5281/zenodo.1137733 28 .. _Special Issue: http://www.geosci-model-dev.net/special_issue40.html 29 .. _Working Groups: http://forge.ipsl.jussieu.fr/nemo/wiki/WorkingGroups 30 31 .. XIOS 32 33 .. _XIOS: http://forge.ipsl.jussieu.fr/ioserver 34 .. _XIOS documentation: http://forge.ipsl.jussieu.fr/ioserver/wiki/documentation 35 .. _XIOS users mailing list: http://forge.ipsl.jussieu.fr/mailman/listinfo.cgi/xios-users 33 .. _NEMO: http://www.nemo-ocean.eu 34 .. _NEMO strategy: http://doi.org/10.5281/zenodo.1471663 35 .. _NEMO guide: http://doi.org/10.5281/zenodo.1475325 36 .. _NEMO manual: http://doi.org/10.5281/zenodo.1464816 37 .. _SI3 manual: http://doi.org/10.5281/zenodo.1471689 38 .. _TOP manual: http://doi.org/10.5281/zenodo.1471700 -
NEMO/trunk/doc/rst/source/interfacing_options.rst
r10201 r10279 3 3 =================== 4 4 5 .. include:: .global.rst 6 7 .. contents:: 5 .. 6 contents:: 8 7 :local: 9 8 :depth: 1 10 9 11 10 .. include:: zooms.rst 11 12 .. bibliography:: zooms.bib 13 :all: 14 :style: unsrt 15 :labelprefix: A 16 :keyprefix: a- 12 17 13 18 ---- … … 21 26 ---- 22 27 23 .. include:: data_assimilation.rst28 .. include:: assimilation.rst 24 29 25 30 ----
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