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Ernesto Rodriguez
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‎InstallBinary.md

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To create an anaconda virtual environment in a preselected directory
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(here, pointed by the environment variable RIVER_DIR):
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cd $RIVER_DIR
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conda create -p $RIVER_DIR/anaconda numpy ipython ipython-notebook
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matplotlib gdal scipy pip scikit-image statsmodels pysal pandas
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pytables shapely netcdf4 sphinx numpydoc cython
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or, to create an environment in the user's anaconda distribution (Simplest)
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conda create -n RiverObsBinary numpy ipython ipython-notebook matplotlib
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gdal scipy pip scikit-image statsmodels pysal pandas pytables
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shapely netcdf4 sphinx numpydoc cython
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conda create -p $RIVER_DIR/RiverObsBinary --file RiverObsSetupPackages.txt
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To activate this environment, type
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source activate $RIVER_DIR/anaconda
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or
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source activate RiverObsBinary
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if anaconda/bin is in your path. Otherwise, use /path/to/anaconda/bin/source.
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source activate $RIVER_DIR/RiverObsBinary
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To deactivate this environment, type
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source deactivate
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Equivalnetly, one can set
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export PATH=$RIVER_DIR/anaconda/bin:$PATH
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export PATH=$RIVER_DIR/RiverObsBinary/bin:$PATH
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##Build additional package requirements
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conda install -c https://conda.binstar.org/dougal libspatialindex
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conda install -c https://conda.binstar.org/dougal rtree
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###Install Using pip and brew or manual compilation
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However, it has been reported that, depending of the linux
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distribution, these packages may have problems of library
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dependency. If these installations have problems, remove them using
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conda remove libspatialindex
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conda remove rtree
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and use the manual installation methods below.
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###Install Using pip and brew (OSX) or manual compilation
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Working inside the virtual environment, the following command:
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pip install pyproj
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pip install rtree
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In addition, [rtree](https://github.com/Toblerity/rtree) requires the
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[Rtree](https://github.com/Toblerity/rtree) requires the
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[libspatialindex](http://libspatialindex.github.io) library. On a Mac with
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[brew](http://brew.sh) this can be done easily:
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brew install spatialindex
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On a generic Unix system, this can be done by downloading the code from
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[osgeo](http://download.osgeo.org/libspatialindex), and following the
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usual Unix install process. To avoid pat/ownership conflict, one can install into the
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anaconda installation:
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usual Unix install process. To avoid ownership conflict, one can install into the
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RiverObsBinary installation (e.g.):
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tar xvzf spatialindex-src-1.8.1.tar.gz
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cd spatialindex-src-1.8.1
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./configure --prefix=~/anaconda
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tar xvzf spatialindex-src-1.8.5.tar.gz
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cd spatialindex-src-1.8.5
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./configure --prefix=$RIVER_DIR/RiverObsBinary
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make
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make install
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###Install numpydoc for sphinx documentation (Optional)
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This should put the library in $RIVER_DIR/RiverObsBinary/lib and the
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includes in $RIVER_DIR/RiverObsBinary/include. To make sure they are
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in the load path, you may have to do the following in *nix systems:
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This is only required if you want to build the sphinx documentation:
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export LD_LIBRARY_PATH=$RIVER_DIR/RiverObsBinary/lib
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pip install numpydoc
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To install rtree, it should just be possible to issue the following
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command from within the virtual environment:
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##Install the binary package
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pip install rtree
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Unfortunately, this does not always work because in some systems
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ctypes.util.find_library fails to find the libspatialindex
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libraries. If you do have problems, you will have to download and
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install the riverobs branch of rtree as follows:
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git clone https://github.com/skinkpad/rtree.git
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cd rtree
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git checkout riverobs
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pip install .
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If for some reason that still does not work, point to the location of the libspatialindex_c library as follows
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(modify according to your system and installation):
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export LIBSPATIALINDEX=$RIVER_DIR/RiverObsBinary/lib/libspatialindex_c.so
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before installing with pip as above.
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##Install the binary package
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For release 1.0.0, RiverObs packages for OSX and 64-bit linux
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architectures are provided. Once the appropriate package has been
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obtained, the RiverObs binary installation is completed by
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cd $RIVER_DIR
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tar xvzf RiverObsBinary_ARCH_version1.0.0.tgz
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where ARCH is either linux64 or OSX. The packages can the be accessed
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while working in the RiverObsBinary environment. The the actual
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packages provided are:
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tar tzf RiverObsBinary_linux64_version1.0.0.tgz
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RiverObsBinary/bin/estimate_swot_river.py
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RiverObsBinary/lib/python2.7/site-packages/Centerline/
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RiverObsBinary/lib/python2.7/site-packages/Centerline/__init__.py
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RiverObsBinary/lib/python2.7/site-packages/Centerline/__init__.pyc
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RiverObsBinary/lib/python2.7/site-packages/Centerline/version.py
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RiverObsBinary/lib/python2.7/site-packages/Centerline/Centerline.so
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RiverObsBinary/lib/python2.7/site-packages/Centerline/version.pyc
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RiverObsBinary/lib/python2.7/site-packages/GDALOGRUtilities/
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RiverObsBinary/lib/python2.7/site-packages/GDALOGRUtilities/GDALWriter.so
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RiverObsBinary/lib/python2.7/site-packages/GDALOGRUtilities/__init__.py
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RiverObsBinary/lib/python2.7/site-packages/GDALOGRUtilities/__init__.pyc
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RiverObsBinary/lib/python2.7/site-packages/GDALOGRUtilities/GDALutilities.so
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RiverObsBinary/lib/python2.7/site-packages/GDALOGRUtilities/GeodeticPath.so
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RiverObsBinary/lib/python2.7/site-packages/GDALOGRUtilities/CoordinateTransformations.so
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RiverObsBinary/lib/python2.7/site-packages/GDALOGRUtilities/OGRWriter.so
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RiverObsBinary/lib/python2.7/site-packages/GDALOGRUtilities/version.py
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RiverObsBinary/lib/python2.7/site-packages/GDALOGRUtilities/GDALLatLonLayer.so
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RiverObsBinary/lib/python2.7/site-packages/GDALOGRUtilities/OGR2Shapely.so
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RiverObsBinary/lib/python2.7/site-packages/GDALOGRUtilities/GDALInfo.so
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RiverObsBinary/lib/python2.7/site-packages/GDALOGRUtilities/version.pyc
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RiverObsBinary/lib/python2.7/site-packages/GeometryDataBase/
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RiverObsBinary/lib/python2.7/site-packages/GeometryDataBase/__init__.py
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RiverObsBinary/lib/python2.7/site-packages/GeometryDataBase/__init__.pyc
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RiverObsBinary/lib/python2.7/site-packages/GeometryDataBase/version.py
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RiverObsBinary/lib/python2.7/site-packages/GeometryDataBase/GeometryDataBase.so
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RiverObsBinary/lib/python2.7/site-packages/GeometryDataBase/version.pyc
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RiverObsBinary/lib/python2.7/site-packages/GWDLR/
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RiverObsBinary/lib/python2.7/site-packages/GWDLR/__init__.py
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RiverObsBinary/lib/python2.7/site-packages/GWDLR/__init__.pyc
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RiverObsBinary/lib/python2.7/site-packages/GWDLR/GWDLR2shape.so
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RiverObsBinary/lib/python2.7/site-packages/GWDLR/version.py
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RiverObsBinary/lib/python2.7/site-packages/GWDLR/GWDLR.so
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RiverObsBinary/lib/python2.7/site-packages/GWDLR/version.pyc
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RiverObsBinary/lib/python2.7/site-packages/RDF/
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RiverObsBinary/lib/python2.7/site-packages/RDF/__init__.py
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RiverObsBinary/lib/python2.7/site-packages/RDF/__init__.pyc
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RiverObsBinary/lib/python2.7/site-packages/RDF/RDF_to_class.so
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RiverObsBinary/lib/python2.7/site-packages/RDF/version.py
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RiverObsBinary/lib/python2.7/site-packages/RDF/MRDF.so
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RiverObsBinary/lib/python2.7/site-packages/RDF/ExecuteRDF.so
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RiverObsBinary/lib/python2.7/site-packages/RDF/RDF.so
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RiverObsBinary/lib/python2.7/site-packages/RDF/version.pyc
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RiverObsBinary/lib/python2.7/site-packages/RiverObs/
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RiverObsBinary/lib/python2.7/site-packages/RiverObs/__init__.py
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RiverObsBinary/lib/python2.7/site-packages/RiverObs/__init__.pyc
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RiverObsBinary/lib/python2.7/site-packages/RiverObs/LatLonRegion.so
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RiverObsBinary/lib/python2.7/site-packages/RiverObs/RiverNode.so
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RiverObsBinary/lib/python2.7/site-packages/RiverObs/version.py
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RiverObsBinary/lib/python2.7/site-packages/RiverObs/ReachPreProcessor.so
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RiverObsBinary/lib/python2.7/site-packages/RiverObs/RiverReach.so
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RiverObsBinary/lib/python2.7/site-packages/RiverObs/IteratedRiverObs.so
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RiverObsBinary/lib/python2.7/site-packages/RiverObs/ReachExtractor.so
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RiverObsBinary/lib/python2.7/site-packages/RiverObs/RiverObs.so
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RiverObsBinary/lib/python2.7/site-packages/RiverObs/WidthDataBase.so
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RiverObsBinary/lib/python2.7/site-packages/RiverObs/FitRiver.so
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RiverObsBinary/lib/python2.7/site-packages/RiverObs/RiverReachWriter.so
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RiverObsBinary/lib/python2.7/site-packages/RiverObs/version.pyc
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RiverObsBinary/lib/python2.7/site-packages/SWOTRiver/
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RiverObsBinary/lib/python2.7/site-packages/SWOTRiver/__init__.py
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RiverObsBinary/lib/python2.7/site-packages/SWOTRiver/__init__.pyc
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RiverObsBinary/lib/python2.7/site-packages/SWOTRiver/SWOTL2.so
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RiverObsBinary/lib/python2.7/site-packages/SWOTRiver/version.py
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RiverObsBinary/lib/python2.7/site-packages/SWOTRiver/version.pyc
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RiverObsBinary/lib/python2.7/site-packages/SWOTRiver/EstimateSWOTRiver.so
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RiverObsBinary/lib/python2.7/site-packages/SWOTRiver/SWOTRiverEstimator.so
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RiverObsBinary/lib/python2.7/site-packages/toggle_input/
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RiverObsBinary/lib/python2.7/site-packages/toggle_input/__init__.py
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RiverObsBinary/lib/python2.7/site-packages/toggle_input/__init__.pyc
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RiverObsBinary/lib/python2.7/site-packages/toggle_input/toggle_input.so
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RiverObsBinary/lib/python2.7/site-packages/toggle_input/version.py
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RiverObsBinary/lib/python2.7/site-packages/toggle_input/version.pyc
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The files are owned by erodrigu. To correct this (which should
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not matter) you can do
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chown -R user RiverObsBinary
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where user is your user name.

‎doc/sphinx/RiverObs/API.rst

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GDALOGRUtilities
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GWDLR
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GeometryDataBase
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PyRivWidth
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RDF
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RiverObs
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SWOTRiver
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Indices and tables
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==================
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‎doc/sphinx/RiverObs/Centerline.rst

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Centerline Package
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Centerline package
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==================
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:mod:`Centerline` Package
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-------------------------
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Submodules
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----------
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.. automodule:: Centerline
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Centerline.Centerline module
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----------------------------
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.. automodule:: Centerline.Centerline
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`Centerline` Module
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------------------------
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Centerline.version module
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-------------------------
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.. automodule:: Centerline.Centerline
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.. automodule:: Centerline.version
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`version` Module
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---------------------
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.. automodule:: Centerline.version
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Module contents
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---------------
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.. automodule:: Centerline
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:members:
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:undoc-members:
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:show-inheritance:
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