Start of documentation for system, in sphinx

da/doc/Makefile

+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build-2.6
+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
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest
+
+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 "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@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."
+
+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/CarbonTrackerDataAssimilationShell.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/CarbonTrackerDataAssimilationShell.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/CarbonTrackerDataAssimilationShell"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/CarbonTrackerDataAssimilationShell"
+	@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."
+
+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."

da/doc/build/html/.buildinfo

+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 29c2fd345d748612ee705cfd9e89ed06
+tags: fbb0d17656682115ca4d033fb2f83ba1

da/doc/build/html/_sources/contents.txt

+.. _contents:
+
+Contents
+========
+
+.. toctree::
+   :maxdepth: 2
+
+   System Requirements <systemrequirements>
+   Installing CTDAS <installing>
+   CTDAS Overview <overview>
+   CTDAS Tutorial <tutorial>
+   CTDAS Documentation <documentation>

da/doc/build/html/_sources/documentation.txt

+.. _documentation:
+
+Documentation
+======================
+

da/doc/build/html/_sources/gettingstarted.txt

+.. _gettingstarted:
+
+Getting Started with CTDAS
+==========================
+
+.. automodule:: da.ct.obs
+   :members: CtObservations

da/doc/build/html/_sources/index.txt

+.. CarbonTracker Data Assimilation Shell documentation master file, created by
+   sphinx-quickstart on Sun Sep 26 13:39:23 2010.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to the CTDAS documentation!
+===================================
+
+This is the starting page for the documentation of the CarbonTracker Data Assimilation Shell (CTDAS).
+
+.. sidebar:: What is CTDAS?
+
+    CTDAS is short for "CarbonTracker Data Assimilation Shell". 
+    This is the implementation of an extendible data assimilation framework for CarbonTracker,
+    developed by NOAA ESRL & Wageningen University, in close cooperation with many partners around the world.
+
+The aim of the CTDAS system is to facilitate the use of CarbonTracker, and to 
+foster its development by its many international partners. At its most basic, the CTDAS is a simple 
+control system for CarbonTracker that deals with the running, optimization, analysis, and time stepping of the system. 
+For advanced users, the CTDAS provides an easy way to extend or modify the system by introducing new configurations 
+for the state vector, for the observations, or even for the transport model or optimization method.
+
+The CarbonTracker development team welcomes suggestions and feedback on the CTDAS system, and its documentation.
+
+Follow the link below to start navigating, or use the "next topic" button in the right-hand-side menu.    
+
+.. toctree::
+   :maxdepth: 1
+
+   List of contents <contents>

da/doc/build/html/_sources/overview.txt

+.. _overview:
+
+.. index:: overview, philosophy, development centers
+
+Overview
+========
+
+This page gives a brief overview of CTDAS, with the intention to provide background information for (potential) new users. Afer reading the information below we recommend contacting one of the CTDAS development centers (Wageningen University and NOAA ESRL), or proceed to the :doc:`tutorial`.
+
+What is CTDAS?
+--------------
+
+How can you use CTDAS?
+----------------------
+
+CTDAS Design philosophy
+-----------------------
+
+Extending CTDAS
+---------------
+
+
+

da/doc/build/html/_sources/systemrequirements.txt

+.. _systemrequirements:
+
+System Requirements
+======================
+
+The CarbonTracker DAS is programmed in python and uses it built-in functionality for many of its tasks.
+Users of CTDAS are required to have a python installation on their system, with a small set of 
+open source add-ons. The minimum requirements are listed below, categorized by functionality.
+
+Getting the CTDAS code
+----------------------
+
+* A working ``subversion`` (SVN) installation is needed, to check your system type::
+
+     $ svn --version
+
+  if the system returns an error, or a version < 1.5.0, please obtain svn from <http://subversion.tigris.org/>
+
+
+Running CTDAS 
+-------------
+
+* A ``python2.4`` or later installation.  
+
+.. note:: ``python3`` is not supported, one needs a python2.x version. To check your python version type::
+
+    $ python --version
+
+* The python module ``numpy``, not included with a standard installation. You can obtain numpy from <http://numpy.scipy.org>
+
+* The python module ``Nio`` created by NCAR/UCAR. This package is freely available as a binary download from UCAR's Earth System Grid at <http://www.earthsystemgrid.org>
+
+.. note:: Registration is required at NCAR/UCAR, their software is free for academic users.
+
+
+Performing inversions
+---------------------
+
+* An important component of the CTDAS system is the observation operator, usually in the form of an atmospheric
+  transport model. This model is a stand-alone piece of code that can subsample your state vector, and return a 
+  set of observations. **You therefore require an atmospheric transport model that can run indepently on your 
+  platform.**
+
+.. note:: If you do not currently have access to such a transport model, or have no resources to run such a model
+   for long periods of time and for many ensemble configurations, you have probably stumbled onto this page not
+   understanding exactly what CTDAS is. We refer you to the :ref:`overview` for a more elaborate description.
+
+* An actual CarbonTracker inversion requires a large collection of input datasets, including
+    * Observations to be assimilated
+    * a-priori surface fluxes for your trace components
+    * a-priori uncertainty distributions for your unknowns
+    * ... and a few more items
+

da/doc/build/html/_sources/tutorial.txt

+.. _tutorial:
+
+Tutorial
+======================
+

da/doc/build/html/_static/basic.css

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