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Commit b2981577 authored by James Harle's avatar James Harle
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Add the beginnings of RST documentation

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docs/Makefile 0 → 100644
View file @ b2981577
# Makefile for Sphinx documentation
#
# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build
PAPER =
BUILDDIR = build
# User-friendly check for sphinx-build
ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
endif
# 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:
@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 " 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 " latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
@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 " xml to make Docutils-native XML files"
@echo " pseudoxml to make pseudoxml-XML files for display purposes"
@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."
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/pyNEMO.qhcp"
@echo "To view the help file:"
@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/pyNEMO.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/pyNEMO"
@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/pyNEMO"
@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."
latexpdfja:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@echo "Running LaTeX files through platex and dvipdfmx..."
$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
@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."
xml:
$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
@echo
@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
pseudoxml:
$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
@echo
@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
docs/make.bat 0 → 100644
View file @ b2981577
@ECHO OFF
REM Command file for Sphinx documentation
if "%SPHINXBUILD%" == "" (
set SPHINXBUILD=sphinx-build
)
set BUILDDIR=build
set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% source
set I18NSPHINXOPTS=%SPHINXOPTS% source
if NOT "%PAPER%" == "" (
set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS%
)
if "%1" == "" goto help
if "%1" == "help" (
: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. 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. text to make text files
echo. man to make manual pages
echo. texinfo to make Texinfo files
echo. gettext to make PO message catalogs
echo. changes to make an overview over all changed/added/deprecated items
echo. xml to make Docutils-native XML files
echo. pseudoxml to make pseudoxml-XML files for display purposes
echo. linkcheck to check all external links for integrity
echo. doctest to run all doctests embedded in the documentation if enabled
goto end
)
if "%1" == "clean" (
for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i
del /q /s %BUILDDIR%\*
goto end
)
%SPHINXBUILD% 2> nul
if errorlevel 9009 (
echo.
echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
echo.installed, then set the SPHINXBUILD environment variable to point
echo.to the full path of the 'sphinx-build' executable. Alternatively you
echo.may add the Sphinx directory to PATH.
echo.
echo.If you don't have Sphinx installed, grab it from
echo.http://sphinx-doc.org/
exit /b 1
)
if "%1" == "html" (
%SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The HTML pages are in %BUILDDIR%/html.
goto end
)
if "%1" == "dirhtml" (
%SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml.
goto end
)
if "%1" == "singlehtml" (
%SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml.
goto end
)
if "%1" == "pickle" (
%SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle
if errorlevel 1 exit /b 1
echo.
echo.Build finished; now you can process the pickle files.
goto end
)
if "%1" == "json" (
%SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json
if errorlevel 1 exit /b 1
echo.
echo.Build finished; now you can process the JSON files.
goto end
)
if "%1" == "htmlhelp" (
%SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp
if errorlevel 1 exit /b 1
echo.
echo.Build finished; now you can run HTML Help Workshop with the ^
.hhp project file in %BUILDDIR%/htmlhelp.
goto end
)
if "%1" == "qthelp" (
%SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp
if errorlevel 1 exit /b 1
echo.
echo.Build finished; now you can run "qcollectiongenerator" with the ^
.qhcp project file in %BUILDDIR%/qthelp, like this:
echo.^> qcollectiongenerator %BUILDDIR%\qthelp\pyNEMO.qhcp
echo.To view the help file:
echo.^> assistant -collectionFile %BUILDDIR%\qthelp\pyNEMO.ghc
goto end
)
if "%1" == "devhelp" (
%SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp
if errorlevel 1 exit /b 1
echo.
echo.Build finished.
goto end
)
if "%1" == "epub" (
%SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The epub file is in %BUILDDIR%/epub.
goto end
)
if "%1" == "latex" (
%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
if errorlevel 1 exit /b 1
echo.
echo.Build finished; the LaTeX files are in %BUILDDIR%/latex.
goto end
)
if "%1" == "latexpdf" (
%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
cd %BUILDDIR%/latex
make all-pdf
cd %BUILDDIR%/..
echo.
echo.Build finished; the PDF files are in %BUILDDIR%/latex.
goto end
)
if "%1" == "latexpdfja" (
%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
cd %BUILDDIR%/latex
make all-pdf-ja
cd %BUILDDIR%/..
echo.
echo.Build finished; the PDF files are in %BUILDDIR%/latex.
goto end
)
if "%1" == "text" (
%SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The text files are in %BUILDDIR%/text.
goto end
)
if "%1" == "man" (
%SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The manual pages are in %BUILDDIR%/man.
goto end
)
if "%1" == "texinfo" (
%SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo.
goto end
)
if "%1" == "gettext" (
%SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The message catalogs are in %BUILDDIR%/locale.
goto end
)
if "%1" == "changes" (
%SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes
if errorlevel 1 exit /b 1
echo.
echo.The overview file is in %BUILDDIR%/changes.
goto end
)
if "%1" == "linkcheck" (
%SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck
if errorlevel 1 exit /b 1
echo.
echo.Link check complete; look for any errors in the above output ^
or in %BUILDDIR%/linkcheck/output.txt.
goto end
)
if "%1" == "doctest" (
%SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest
if errorlevel 1 exit /b 1
echo.
echo.Testing of doctests in the sources finished, look at the ^
results in %BUILDDIR%/doctest/output.txt.
goto end
)
if "%1" == "xml" (
%SPHINXBUILD% -b xml %ALLSPHINXOPTS% %BUILDDIR%/xml
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The XML files are in %BUILDDIR%/xml.
goto end
)
if "%1" == "pseudoxml" (
%SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml.
goto end
)
:end
docs/source/_static/add-variable.jpg 0 → 100644
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docs/source/_static/add-variable.jpg

62.5 KB

docs/source/_static/eg2.png 0 → 100644
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docs/source/_static/eg2.png

373 KB

docs/source/_static/generator-gui.jpg 0 → 100644
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docs/source/_static/generator-gui.jpg

52.5 KB

docs/source/conf.py 0 → 100644
View file @ b2981577
# -*- coding: utf-8 -*-
#
# pyNEMO documentation build configuration file, created by
# sphinx-quickstart on Thu Jun 25 15:08:06 2015.
#
# 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
import 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.autodoc', 'sphinx.ext.napoleon', 'sphinx.ext.todo'
]
# Napoleon settings
napoleon_google_docstring = True
napoleon_numpy_docstring = True
napoleon_include_init_with_doc = False
napoleon_include_private_with_doc = False
napoleon_include_special_with_doc = False
napoleon_use_admonition_for_examples = False
napoleon_use_admonition_for_notes = False
napoleon_use_admonition_for_references = False
napoleon_use_ivar = False
napoleon_use_param = True
napoleon_use_rtype = True
napoleon_use_keyword = True
# 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 = 'index'
# General information about the project.
project = u'pyNEMO'
copyright = u'2015, James Harle, Srikanth Nagella, Shirley Crompton'
# 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 = '0.1'
# The full version, including alpha/beta/rc tags.
release = '0.1'
# 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.
exclude_patterns = []
# 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'
# A list of ignored prefixes for module index sorting.
#modindex_common_prefix = []
# If true, keep warnings as "system message" paragraphs in the built documents.
#keep_warnings = False
# -- 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'
# Theme options are theme-specific and customize the look and feel of a theme
# further. For a list of options available for each theme, see the
# documentation.
#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 = None
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_static']
# Add any extra paths that contain custom files (such as robots.txt or
# .htaccess) here, relative to this directory. These files are copied
# directly to the root of the documentation.
#html_extra_path = []
# 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 = 'pyNEMOdoc'
# -- 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': '',
}
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
# author, documentclass [howto, manual, or own class]).
latex_documents = [
('index', 'pyNEMO.tex', u'pyNEMO Documentation',
u'James Harle, Srikanth Nagella, Shirley Crompton', 'manual'),
]
# 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 = [
('index', 'pynemo', u'pyNEMO Documentation',
[u'James Harle, Srikanth Nagella, Shirley Crompton'], 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 = [
('index', 'pyNEMO', u'pyNEMO Documentation',
u'James Harle, Srikanth Nagella, Shirley Crompton', 'pyNEMO', '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'
# If true, do not generate a @detailmenu in the "Top" node's menu.
#texinfo_no_detailmenu = False
docs/source/examples.rst 0 → 100644
View file @ b2981577
Examples
========
Here we provide two worked examples using pyNEMO. The first is a setup of the Northwest European Shelf using
a remote dataset. The second is an end-to-end setup of a small regional model in the tropics.
Example 1: Northwest European Shelf
===================================
.. figure:: _static/eg1.png
:align: center
Northwest European Shelf Bathymetry
This example has been tested on the ARCHER HPC facillity *(22 Feb 2017)*.
First, create a working directory into which the code can
run. All the data required for this example are held on a
THREDDS server so no addtional data are required.
.. note:: make sure cray-netcdf-hdf5parallel cray-hdf5-parallel are loaded.
This example has been consructed under PrgEnv-intel. e.g.
::
module swap PrgEnv-cray PrgEnv-intel
module load cray-netcdf-hdf5parallel
module load cray-hdf5-parallel
.. note:: Be careful to avoid symbolic links in NEMO control files.
::
cd $WDIR
mkdir OUTPUT
Now we're ready to generate the boundary conditions using pyNEMO.
If this is not installed follow the `installation guide` or a quick
setup could be as follows:
::
cd ~
module load anaconda
conda create --name pynemo_env scipy=0.16.0 numpy matplotlib=1.5.1 basemap netcdf4 libgfortran=1.0.0
source activate pynemo_env
conda install -c conda-forge seawater=3.3.4
conda install -c https://conda.anaconda.org/srikanthnagella thredds_crawler
conda install -c https://conda.anaconda.org/srikanthnagella pyjnius
export LD_LIBRARY_PATH=/opt/java/jdk1.7.0_45/jre/lib/amd64/server:$LD_LIBRARY_PATH
svn checkout https://ccpforge.cse.rl.ac.uk/svn/pynemo
cd pynemo/trunk/Python
python setup.py build
export PYTHONPATH=~/.conda/envs/pynemo/lib/python2.7/site-packages/:$PYTHONPATH
python setup.py install --prefix ~/.conda/envs/pynemo
cp data/namelist.bdy $WDIR
cd $WDIR
Next we need to modify the namelist.bdy file to point it to the correct
data sources. First we need to create an ncml file to gather input data
and map variable names. First we update *sn_src_dir*, *sn_dst_dir* and
*cn_mask_file* to reflect the working path (e.g. sn_src_dir = '$WDIR/test.ncml',
sn_dst_dir = '$WDIR/OUTPUT' and cn_mask_file = '$WDIR/mask.nc').
Explicitly write out $WDIR. Next we need to generate test.ncml.
.. note:: pynemo may have to be run on either espp1 or espp2 (e.g. ssh -Y espp1)
as the JVM doesn't have sufficient memory on the login nodes.
::
ssh -Y espp1
module load anaconda
source activate pynemo_env
cd $WDIR
pynemo_ncml_generator
For each of the tracer and dynamics variables enter the following URL as
the source directory:
http://esurgeod.noc.soton.ac.uk:8080/thredds/dodsC/PyNEMO/data
Add a regular expression for each (Temperature, Salinity and Sea Surface
Height each use: .\*T\\.nc$ and the velocities use .\*V\\.nc$ and .\*V\\.nc$)
After each entry click the Add button. Finally fill in the output file
including directory path (this should match *sn_src_dir*). Once this is complete
click on the generate button and an ncml file should be written to $WDIR.
Then using pynemo we define the area we want to model and generate some
boundary conditions:
.. note:: I've had to add the conda env path to the $PYTHONPATH as python does
seem to be able to pick up pyjnius!?
::
export LD_LIBRARY_PATH=/opt/java/jdk1.7.0_45/jre/lib/amd64/server:$LD_LIBRARY_PATH
export PYTHONPATH=~/.conda/envs/pynemo_env/lib/python2.7/site-packages:$PYTHONPATH
pynemo -g -s namelist.bdy
Once the area of interest is selected and the close button is clicked,
open boundary data should be generated in $WDIR/OUTPUT.
Example 2: Lighthouse Reef
==========================
.. figure:: _static/eg2.png
:align: center
Regional Mask / SSH after 1 day / SST after 1 day
This example has been tested on the ARCHER HPC facillity.
First, create a working directory into which the NEMO
source code can be checked out. Create an inputs directory
to unpack the forcing tar ball.
.. note:: make sure cray-netcdf-hdf5parallel cray-hdf5-parallel are loaded.
This example has been consructed under PrgEnv-intel.
::
cd $WDIR
mkdir INPUTS
cd INPUTS
wget ftp.nerc-liv.ac.uk:/pub/general/jdha/inputs.tar.gz
tar xvfz inputs.tar.gz
rm inputs.tar.gz
cd ../
svn co http://forge.ipsl.jussieu.fr/nemo/svn/branches/2014/dev_r4621_NOC4_BDY_VERT_INTERP@5709
svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-1.0@629
cd xios-1.0
cp $WDIR/INPUTS/arch-XC30_ARCHER.* ./arch
./make_xios --full --prod --arch XC30_ARCHER --netcdf_lib netcdf4_par
Next we setup our experiment directory and drop an updated
dtatsd.F90 into MY_SRC to allow the vertical interpolation
of initial conditions on to the new verictal coordinates.
We also apply several patches for bugs in the code.
.. note:: when executing ./makenemo for the first time only choose OPA_SRC.
For some reason even though LIM_2 is not chosen key_lim2 is
in the cpp keys. This means the first call to ./makenemo will fail.
Just vi LH_REEF/cpp_LH_REEF.fcm and remove key_lim2 and re-issue
the make command.
::
export CDIR=$WDIR/dev_r4621_NOC4_BDY_VERT_INTERP/NEMOGCM/CONFIG
export TDIR=$WDIR/dev_r4621_NOC4_BDY_VERT_INTERP/NEMOGCM/TOOLS
cd $CDIR/../NEMO/OPA_SRC/SBC
patch -b < $WDIR/INPUTS/fldread.patch
cd ../DOM
patch -b < $WDIR/INPUTS/dommsk.patch
cd ../BDY
patch -b < $WDIR/INPUTS/bdyini.patch
cd $CDIR
rm $CDIR/../NEMO/OPA_SRC/TRD/trdmod.F90
cp $WDIR/INPUTS/arch-* ../ARCH
./makenemo -n LH_REEF -m XC_ARCHER_INTEL -j 10
cp $WDIR/INPUTS/cpp_LH_REEF.fcm ./LH_REEF
cp $WDIR/INPUTS/dtatsd.F90 LH_REEF/MY_SRC/
To generate bathymetry, initial conditions and grid information
we first need to compile some of the NEMO TOOLS (after a small
bugfix - and to allow direct passing of arguments). For some
reason GRIDGEN doesn't like INTEL:
::
cd $WDIR/dev_r4621_NOC4_BDY_VERT_INTERP/NEMOGCM/TOOLS/WEIGHTS/src
patch -b < $WDIR/INPUTS/scripinterp_mod.patch
patch -b < $WDIR/INPUTS/scripinterp.patch
patch -b < $WDIR/INPUTS/scrip.patch
patch -b < $WDIR/INPUTS/scripshape.patch
patch -b < $WDIR/INPUTS/scripgrid.patch
cd ../../
./maketools -n WEIGHTS -m XC_ARCHER_INTEL
./maketools -n REBUILD_NEMO -m XC_ARCHER_INTEL
module unload cray-netcdf-hdf5parallel cray-hdf5-parallel
module swap PrgEnv-intel PrgEnv-cray
module load cray-netcdf cray-hdf5
./maketools -n GRIDGEN -m XC_ARCHER
module swap PrgEnv-cray PrgEnv-intel
export TDIR=$WDIR/dev_r4621_NOC4_BDY_VERT_INTERP/NEMOGCM/TOOLS
.. note:: my standard ARCHER ENV is intel with parallel netcdf you may need to edit accordingly
Back in $WDIR/INPUTS, create a new coordinates file from the
existing global 1/12 mesh and refine to 1/84 degree resolution:
::
cd $TDIR/GRIDGEN
cp $WDIR/INPUTS/namelist_R12 ./
ln -s namelist_R12 namelist.input
./create_coordinates.exe
cp 1_coordinates_ORCA_R12.nc $WDIR/INPUTS/coordinates.nc
To create the bathymetry we use the gebco dataset. On ARCHER I
had to use a non-default nco module for netcdf operations to work.
I also had to cut down the gebco data as the SCRIP routines failed
for some unknown reason.
::
cd $WDIR/INPUTS
module load nco/4.5.0
ncap2 -s 'where(topo > 0) topo=0' gebco_1_cutdown.nc tmp.nc
ncflint --fix_rec_crd -w -1.0,0.0 tmp.nc tmp.nc gebco_in.nc
rm tmp.nc
module unload nco cray-netcdf cray-hdf5
module load cray-netcdf-hdf5parallel cray-hdf5-parallel
$TDIR/WEIGHTS/scripgrid.exe namelist_reshape_bilin_gebco
$TDIR/WEIGHTS/scrip.exe namelist_reshape_bilin_gebco
$TDIR/WEIGHTS/scripinterp.exe namelist_reshape_bilin_gebco
We perform a similar operation to create the initial conditions:
.. note:: I've put a sosie pre-step in here to flood fill the land.
I tried using sosie for 3D intepolation, but not convinced.
::
cd ~
mkdir local
svn co svn://svn.code.sf.net/p/sosie/code/trunk sosie
cd sosie
cp $WDIR/INPUTS/make.macro ./
make
make install
export PATH=~/local/bin:$PATH
cd $WDIR/INPUTS
sosie.x -f initcd_votemper.namelist
sosie.x -f initcd_vosaline.namelist
$TDIR/WEIGHTS/scripgrid.exe namelist_reshape_bilin_initcd_votemper
$TDIR/WEIGHTS/scrip.exe namelist_reshape_bilin_initcd_votemper
$TDIR/WEIGHTS/scripinterp.exe namelist_reshape_bilin_initcd_votemper
$TDIR/WEIGHTS/scripinterp.exe namelist_reshape_bilin_initcd_vosaline
Finally we setup weights files for the atmospheric forcing:
::
$TDIR/WEIGHTS/scripgrid.exe namelist_reshape_bilin_atmos
$TDIR/WEIGHTS/scrip.exe namelist_reshape_bilin_atmos
$TDIR/WEIGHTS/scripshape.exe namelist_reshape_bilin_atmos
$TDIR/WEIGHTS/scrip.exe namelist_reshape_bicubic_atmos
$TDIR/WEIGHTS/scripshape.exe namelist_reshape_bicubic_atmos
Next step is to create the mesh and mask files that will be used
in the generation of the open boundary conditions:
::
cd $CDIR
cp $WDIR/INPUTS/cpp_LH_REEF.fcm LH_REEF/
ln -s $WDIR/INPUTS/bathy_meter.nc $CDIR/LH_REEF/EXP00/bathy_meter.nc
ln -s $WDIR/INPUTS/coordinates.nc $CDIR/LH_REEF/EXP00/coordinates.nc
cp $WDIR/INPUTS/runscript $CDIR/LH_REEF/EXP00
cp $WDIR/INPUTS/namelist_cfg $CDIR/LH_REEF/EXP00/namelist_cfg
cp $WDIR/INPUTS/namelist_ref $CDIR/LH_REEF/EXP00/namelist_ref
./makenemo clean
./makenemo -n LH_REEF -m XC_ARCHER_INTEL -j 10
cd LH_REEF/EXP00
ln -s $WDIR/xios-1.0/bin/xios_server.exe xios_server.exe
qsub -q short runscript
If that works, we then need to rebuild the mesh and mask files in
to single files for the next step:
::
$TDIR/REBUILD_NEMO/rebuild_nemo -t 24 mesh_zgr 96
$TDIR/REBUILD_NEMO/rebuild_nemo -t 24 mesh_hgr 96
$TDIR/REBUILD_NEMO/rebuild_nemo -t 24 mask 96
mv mesh_zgr.nc mesh_hgr.nc mask.nc $WDIR/INPUTS
rm mesh_* mask_* LH_REEF_0000*
cd $WDIR/INPUTS
Now we're ready to generate the boundary conditions using pyNEMO.
If this is not installed follow the `installation guide` or a quick
setup could be as follows:
::
cd ~
module load anaconda
conda create --name pynemo_env scipy=0.16.0 numpy matplotlib=1.5.1 basemap netcdf4 libgfortran=1.0.0
source activate pynemo_env
conda install -c conda-forge seawater=3.3.4
conda install -c https://conda.anaconda.org/srikanthnagella thredds_crawler
conda install -c https://conda.anaconda.org/srikanthnagella pyjnius
export LD_LIBRARY_PATH=/opt/java/jdk1.7.0_45/jre/lib/amd64/server:$LD_LIBRARY_PATH
svn checkout https://ccpforge.cse.rl.ac.uk/svn/pynemo
cd pynemo/trunk/Python
python setup.py build
export PYTHONPATH=~/.conda/envs/pynemo/lib/python2.7/site-packages/:$PYTHONPATH
python setup.py install --prefix ~/.conda/envs/pynemo
cd $WDIR/INPUTS
Start up pynemo and generate boundary conditions. First we need to
create a few ncml files to gather input data and map variable names.
Then using pynemo we define the area we want to model:
.. note:: pynemo may have to be run on either espp1 or espp2 (e.g. ssh -Y espp1)
as the JVM doesn't have sufficient memory on the login nodes.
::
ssh -Y espp1
module load anaconda
source activate pynemo_env
cd $WDIR/INPUTS
pynemo_ncml_generator
.. note:: The ncml files already exist in the INPUTS directory. There is no need
generate them. It's a little tricky at the momment as the ncml generator
doesn't have all the functionality required for this example. Next step
is to fire up pynemo. You can change the mask or accept the default by just
hitting the close button (that really should say 'build' or 'go' or such like).
Also I've had to add the conda env path to the $PYTHONPATH as python does
seem to be able to pick up pyjnius!?
::
export LD_LIBRARY_PATH=/opt/java/jdk1.7.0_45/jre/lib/amd64/server:$LD_LIBRARY_PATH
export PYTHONPATH=~/.conda/envs/pynemo_env/lib/python2.7/site-packages:$PYTHONPATH
pynemo -g -s namelist.bdy
Let's have a go at running the model after exiting espp1 (after a few variable
renamings, due to inconsistencies to be ironed out):
::
exit
cd $WDIR/INPUTS
module unload cray-netcdf-hdf5parallel cray-hdf5-parallel
module load nco/4.5.0
ncrename -v deptht,gdept LH_REEF_bdyT_y1980m01.nc
ncrename -v depthu,gdepu LH_REEF_bdyU_y1980m01.nc
ncrename -v depthv,gdepv LH_REEF_bdyV_y1980m01.nc
module unload nco
module load cray-netcdf-hdf5parallel cray-hdf5-parallel
cd $CDIR/LH_REEF/EXP00
ln -s $WDIR/INPUTS/coordinates.bdy.nc $CDIR/LH_REEF/EXP00/coordinates.bdy.nc
sed -e 's/nn_msh = 3/nn_msh = 0/' namelist_cfg > tmp
sed -e 's/nn_itend = 1/nn_itend = 1440 /' tmp > namelist_cfg
cp $WDIR/INPUTS/*.xml ./
qsub -q short runscript
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NRCT User Guide
=================
Contents:
.. toctree::
:maxdepth: 3
intro
installation
usage
ncml_generator_usage
examples
troubleshooting
Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
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Installation
============
This page provides a guide to installing pyNEMO.
Dependencies
^^^^^^^^^^^^
1. Python 2.7 (Not tested with 3.x)
2. scipy
3. netCDF4-python
4. numpy
5. matplotlib
6. basemap
7. thredds_crawler
8. seawater
9. pyjnius (optional)
Anaconda
^^^^^^^^
Using conda: pyNEMO supports Win64, OSX and Linux. for other operating systems please build from source.
.. note:: It is recommended to create a seperate virtual environment for pyNEMO.
Please follow the instructions on doing this at http://www.continuum.io/blog/conda
::
conda install -c https://conda.anaconda.org/srikanthnagella pynemo
This will install pynemo and its dependencies. This build is generally outdated as development and
bug fixes to the source are a regular occurrence. It may be better to install from source until a beta
release is available.
From Source
^^^^^^^^^^^
Installing pyNEMO using other flavours of software or from source. Install all the dependencies and
download the source code from svn and install.
::
svn checkout http://ccpforge.cse.rl.ac.uk/svn/pynemo/trunk/Python/
python setup.py install
.. note:: If building from source in the Anaconda environment all dependencies can
be installed using conda apart from thredds_crawler and pyjnius which can
be installed using the following Anaconda channel:
::
conda install -c https://conda.anaconda.org/srikanthnagella thredds_crawler
conda install -c https://conda.anaconda.org/srikanthnagella pyjnius
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Introduction
============
The NRCT is a tool to set up the lateral boundary conditions for a regional `NEMO <http://www.nemo-ocean.eu>`_
model configuration. The tool is written in Python, largely within the
`Anaconda <https://store.continuum.io/cshop/anaconda/>`_ environment to aid
wider distribution and to facilitate development. In their current form these
tools are by no means generic and polished, but it is hoped will form a foundation
from which something more formal can be developed. The following sections provide a quick-start guide with
worked examples to help the user get up and running with the tool.
The tool essentially uses geographical and depth information from the source
data (e.g. a global ocean simulation) and destination simulation (i.e. the
proposed regional NEMO model configuration) to determine which source points are required
for data extraction. This is done using a kdtree approximate nearest neighbour
algorithm. The idea behind this targetted method is that it provides a generic
method of interpolation for any flavour of ocean model in order to set up a
regional NEMO model configuration. At present (alpha release) the tools do not
contain many options, but those that exist are accessed either through a NEMO style
namelist or a convient GUI.
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pyNEMO NcML Generator Usage
===========================
This GUI tool facilitates the creation of a virtual dataset for input into pyNEMO. The virtual dataset is defined using NetCDF Markup Language (`NcML <http://www.unidata.ucar.edu/software/thredds/current/netcdf-java/ncml/Tutorial.html>`_ ).
Using NcML, it is possible to:
1. modify metadata
2. modify and restructure variables
3. combine or aggregate data from multiple datasets. The datasets may reside in the local file system or in a remote OPeNDAP (http://www.opendap.org/) server.
Generator GUI
^^^^^^^^^^^^^
.. _NcML_gui:
.. figure:: _static/generator-gui.jpg
:align: center
Overview of the NcML Generator GUI.
Users need to follow three distinct steps when using the GUI to generate the virtual dataset:
1. Define a target output NcML file
2. Define the individal variable
3. Generate the NcML file
Define a Target Output File
---------------------------
User should provide the path and name of the target NcML file. The convention is to use *.ncml* as the file suffix. The target file can be specified manually using the input text box or visually using the *Select file* button. Clicking the button will bring up a file dialogue.
Define the Individual Data Variable
-----------------------------------
The nemo data variables are grouped into the following types :
1. Tracer (temperature, salinity)
2. Dynamics (zonal velocity, meridian velocity, sea surface height)
3. Ice (ice thickness, leads fraction, snow thickness)
4. Ecosystem (reserved for future use)
5. Grid (reserved for future use)
Users can access the required variable by selecting the tab widget and the variable from the *Variable* dropdown list.
.. _NcML_gui_completed:
.. figure:: _static/add-variable.jpg
:align: center
Example definition of the *Ice thickness variable*.
For each variable, users must provide information for:
* Source directory - the location of the folder containing the input datasets. User can provide an absolute path to a local file folder or an OPeNDAP endpoint, e.g. http://esurgeod.noc.soton.ac.uk:8080/thredds/dodsC/PyNEMO/data/
* Existing variable name - name used in the source datasets
Users may further filter the source datasets using:
* Include subdirs - check the box to include contents in the sub directories under the specified *Source directory*
* Regular expression - provides a search pattern for filtering the files. See the **Regex** section below for more information.
After completing the variable form, users should click the *Add* button to store the input value. Alternatively, users can use the *Reset* button to reset the input to the previously saved values. If there are no existing values, the variable tab will be reset to the default state.
Generate the NcML file
----------------------
After adding all the variables, users can generate the NcML file by clicking the *Generate* button. If the operation is successful, a pop-up confirmation dialogue will appear. The generated NcML file can then be used in the bdy file to set up the NEMO simulation.
Regular Expression (Regex)
^^^^^^^^^^^^^^^^^^^^^^^^^^
Regular expression is a special text string for describing a search pattern to match against some text. You may compare using regex to filter what files to include in your datasets against using wildcard (*) to specify a file search pattern in your computer.
A detailed description of how to define regular expression for filtering datasets in NcML is available at http://www.unidata.ucar.edu/software/thredds/current/netcdf-java/ncml/AnnotatedSchema4.html#regexp.
The following table provides some typical examples of regex:
+---------------+------------------------+---------------------------+
| Regex | Matching File Path | Description |
+===============+========================+===========================+
| .*V\\.nc$ | c:/dir/dir/dir/abcV.nc | The file path ends in |
+---------------+------------------------+---------------------------+
| | d:/muV.nc | V.nc |
+---------------+------------------------+---------------------------+
| .*\\.nc$ | c:/dir/dir/dir/\*.nc | The file suffix is nc |
+---------------+------------------------+---------------------------+
| | d:/\*.nc | |
+---------------+------------------------+---------------------------+
|.*/2015.*\\.nc$| c:/dir/2015_01_16.nc | The file path contains |
+---------------+------------------------+---------------------------+
| | d:/2015*.nc | 2015 and the file suffix |
+---------------+------------------------+---------------------------+
| | e:/a/b/c/20151106T.nc | is nc |
+---------------+------------------------+---------------------------+
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Troubleshooting
===============
1. pyNEMO crashing in MacOSX (Yosemite)?
* Downgrade the scipy package to 0.15
2. How to make pyNEMO to work behind firewall/proxy?
* Set the environment variable http_proxy. eg. in Linux export http_proxy=<proxy-server>:<proxy-port>
3. Getting this error 'Warning: Please make sure pyjnius is installed and jvm.dll/libjvm.so/libjvm.dylib is in the path' ?
* This error is displayed when the application cannot find the java installation on the local machine. please install a java 7.x runtime from http://www.oracle.com/technetwork/java/javase/downloads/jre7-downloads-1880261.html and append the path to the library in the system path. eg. on windows SET PATH="C:\\Program Files (x86)\\Java\\jre1.7\\bin\\client" on Linux in shell export LD_LIBRARY_PATH=/opt/java/jdk1.7.0_45/jre/lib/amd64/server:$LD_LIBRARY_PATH in osx export DYLD_LIBRARY_PATH=/System/Library/Java/JavaVirtualMachines/jdk1.7.0_09.jdk/Contents/Home/jre/lib/server:$DYLD_LIBRARY_PATH
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Usage
=====
There are two tools available in pyNEMO. They are described in detail below.
pynemo
------
This command line tool reads a BDY file, extracts boundary data and prepares
the data for a NEMO simulation. The bdy file is a plain text file containing
key value pairs. Please look at the sample `namelist.bdy
<http://ccpforge.cse.rl.ac.uk/gf/project/pynemo/scmsvn/?action=browse&path=%2Ftrunk%2FPython%2Fdata%2Fnamelist.bdy&view=markup>`_
file, which shares common syntax with the NEMO simulation namelist input file.
.. note:: Directory paths in bdy file can be relative or absolute.
The application picks the relative path from the current working
directory.
Syntax for pynemo command is
::
> pynemo [-g] -s <bdy file>
For help
::
> pynemo -h
> usage: pynemo [-g] -s <namelist.bdy>
> -g (optional) will open settings editor before extracting the data
> -s <bdy filename> file to use
Example comamnd
::
> pynemo -g -s namelist.bdy
pynemo_settings_editor
----------------------
This tool will open a window where you can edit the mask and change the values of bdy parameters.
Syntax for pynemo_settings_editor command is
::
> pynemo_settings_editor [-s <bdy filename>]
.. note:: If no file name is specified then a file dialog box will open to select a file.
For help
::
> pynemo_settings_editor -h
> usage: pynemo_settings_editor -s <namelist.bdy>
Example:
::
pynemo_settings_editor -s namelist.bdy
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