Merge pull request #56 from UW-Hydro/develop

RVIC 1.1 release merge from develop

.gitattributes

@@ -0,0 +1,2 @@
+*.nc filter=lfs diff=lfs merge=lfs -text
+*.csv filter=lfs diff=lfs merge=lfs -text

.gitignore

@@ -21,6 +21,7 @@ rvic.egg-info
 # Configuration Files #
 #######################
 *cfg
+samples/cases/*
 
 # Packages #
 ############

.travis.yml

@@ -1,31 +1,35 @@
 language: python
+sudo: false # use container based build
+notifications:
+  email: false
+
+matrix:
+  fast_finish: true
+  include:
+    - python: 2.7
+    - python: 3.4
+    - python: 3.5
 
-python:
-  - "2.7"
 # Setup anaconda
 before_install:
-  - wget http://repo.continuum.io/miniconda/Miniconda-2.2.2-Linux-x86_64.sh -O miniconda.sh
-  - chmod +x miniconda.sh
-  - ./miniconda.sh -b
-  - export PATH=/home/travis/anaconda/bin:$PATH
-  # Update conda itself
-  - conda update --yes conda
-  # The next couple lines fix a crash with multiprocessing on Travis and are not specific to using Miniconda
-  - sudo rm -rf /dev/shm
-  - sudo ln -s /run/shm /dev/shm
+  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
+      wget http://repo.continuum.io/miniconda/Miniconda-3.16.0-Linux-x86_64.sh -O miniconda.sh;
+    else
+      wget http://repo.continuum.io/miniconda/Miniconda3-3.16.0-Linux-x86_64.sh -O miniconda.sh;
+    fi
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
+  - hash -r
+  - conda config --set always_yes yes --set changeps1 no
+  - conda update -q conda
+  - conda info -a
 # Install packages
 install:
-  - conda create --yes --name=rvic_test_env python=$TRAVIS_PYTHON_VERSION --file=ci/requirements-2.7.txt
-  - source activate rvic_test_env
+  - conda create --yes --name=test python=$TRAVIS_PYTHON_VERSION numpy scipy pandas netcdf4 matplotlib pytest
+  - source activate test
+  # - conda install -c https://conda.anaconda.org/ioos cdo
+  # - pip install cdo
   - python setup.py install
 # Run test
 script:
-  - which python
-  - python --version
-  - conda list
-  - pip freeze
-  - echo $PATH
-  - python -c 'import rvic; print rvic.__file__'
-  - cd tests
-  - pwd
-  - python run_tests.py unit
+  - py.test

docs/development/whats_new.md

@@ -0,0 +1,16 @@
+# What's New
+
+v1.1.0 (25 October 2015)
+
+This release contains a number of bug and compatibility fixes.
+
+### Enhancements
+
+- Compatibility with Python 3.4 and 3.5 ([GH38](https://github.com/UW-Hydro/RVIC/pull/38)).
+- Simplified multiprocessing in `parameters` which should improve stability ([GH60](https://github.com/UW-Hydro/RVIC/pull/60)).
+
+### Bug Fixes
+
+- Fixed bug that caused `REMAP=False` to fail ([GH60](https://github.com/UW-Hydro/RVIC/pull/60)).
+- Improvements were made to the `SEARCH_FOR_CHANNEL` option in `parameters`.
+- Fixed bug where last timestep of history output was not populated ([GH71](https://github.com/UW-Hydro/RVIC/pull/71)).

docs/support/faq.md

@@ -4,7 +4,7 @@
 At the moment, no.  However, many of the pieces needed to support this feature are already included in RVIC.  This is a feature that has been identified for a future version of RVIC.
 
 ### Can route flows to every grid cell in my domain using RVIC?
-Yes, it is possible to route to every grid cell in the RVIC domain.  That said, it may not be the most efficent way to use RVIC.  RVIC is a source to sink routing model which means it doesn't track where streamflow is along its flow path.  When you route to every grid cell in the domain, you are duplicating a lot of calculations.  There are other routing models that route flow from grid cell to grid cell.
+Yes, it is possible to route to every grid cell in the RVIC domain.  That said, it may not be the most efficient way to use RVIC.  RVIC is a source to sink routing model which means it doesn't track where streamflow is along its flow path.  When you route to every grid cell in the domain, you are duplicating a lot of calculations.  There are other routing models that route flow from grid cell to grid cell.
 
 ### Is there a C or Fortran Version of RVIC?
-RVIC has been coupled in the Community Earth System Model (CESM) as the streamflow routing model.  For that project, a Fortran version of the "convolution" step was written.  At this time, there is not a C version of this routing model.  In the future, a C binding may be created to coupled with the stand-alone VIC model version 5.
+RVIC has been coupled in the Community Earth System Model (CESM) as the streamflow routing model.  For that project, a Fortran version of the "convolution" step was written.  Work is currently underway to couple RVIC to the stand-alone image driver in VIC 5.0 ([VIC231](https://github.com/UW-Hydro/VIC/pull/231)).

docs/user-guide/convolution.md

@@ -28,9 +28,6 @@ The flux file(s) must be in netCDF format and have a `time` dimension as well as
 3.  **CASE_DIR**
     - Description: case run directory
     - Type: char
-4.  **RVIC_TAG**
-    - Description: RVIC Tag
-    - Type: char
 5.  **CASEID**
     - Description: Case ID
     - Type: char

docs/user-guide/install.md

@@ -1,16 +1,31 @@
 # Installing RVIC
 
 ## Dependencies
-- [Python 2.7](http://www.python.org/)
-- [Numpy](http://www.numpy.org)
-- [Scipy](http://www.scipy.org/)
-- [netcdf4-python](https://code.google.com/p/netcdf4-python/)
+- [Python 2.7 or later including Python3](http://www.python.org)
+- [NumPy](http://www.numpy.org)
+- [SciPy](http://www.scipy.org)
+- [netcdf4-python](https://code.google.com/p/netcdf4-python)
+- [pandas](http://pandas.pydata.org)
 
 If using `REMAP=True`:
 
-- [cdo](https://code.zmaw.de/projects/cdo)
+- [CDO](https://code.zmaw.de/projects/cdo)
 - [cdo.py](https://github.com/Try2Code/cdo-bindings)
 
+## Installing using a package manager
+
+RVIC is available via [PyPi](https://pypi.python.org/pypi/rvic):
+
+```
+pip install rvic
+```
+
+or Anaconda via the UW-Hydro channel:
+
+```
+conda install --channel https://conda.anaconda.org/UW-Hydro rvic
+```
+
 ## Building RVIC
 
 ### Option 1:  Using Anaconda

docs/user-guide/parameters.md

@@ -58,6 +58,8 @@ For irregular grids, you need to come up with a netCDF file that contains these
 - area (in m2 or rad2 or similar)
 - coordinate vars (lon and lat or similar)
 
+*Note: If `REMAP==False`, the resolution of the routing data grid and domain grid must be the same.  Furthermore, the domain grid must be a subset of the routing grid.  RVIC will raise an error if either of these conditions is not met.*
+
 ## Pour Points File
 A pour points CSV is needed to develop the parameter file.  This is simply a csv file containing a list of the pour point locations with 2 or 3 columns (required: lons, lats; optional: names/contributing area/etc).  One header row is required.
 

rvic/__init__.py

@@ -0,0 +1 @@
+from .version import short_version as __version__

rvic/clib/rvic_convolution.c

@@ -1,40 +1,40 @@
 #include <stdlib.h>
 
-void convolve(const int nsources,               /*scalar - number of sources*/
-                const int noutlets,             /*scalar - length of subset*/
-                const int subset_length,        /*scalar - length of subset*/
-                const int x_size,
-                const int* source2outlet_ind,   /*1d array - source to outlet mapping*/
-                const int* source_y_ind,        /*1d array - source y location*/
-                const int* source_x_ind,        /*1d array - source x location*/
-                const int* source_time_offset,  /*1d array - source time offset*/
-                const double* unit_hydrograph,  /*2d array[times][sources] - unit hydrographs*/
-                const double* aggrunin,         /*2d array[ysize][xsize] - vic runoff flux*/
-                double* ring)                   /*2d array[times][outlets] - convolution ring*/
+void
+convolve(const int     nsources,               /*scalar - number of sources*/
+         const int     noutlets,               /*scalar - length of subset*/
+         const int     subset_length,          /*scalar - length of subset*/
+         const int     x_size,
+         const int    *source2outlet_ind,      /*1d array - source to outlet mapping*/
+         const int    *source_y_ind,           /*1d array - source y location*/
+         const int    *source_x_ind,           /*1d array - source x location*/
+         const int    *source_time_offset,     /*1d array - source time offset*/
+         const double *unit_hydrograph,        /*2d array[times][sources] - unit hydrographs*/
+         const double *aggrunin,               /*2d array[ysize][xsize] - vic runoff flux*/
+         double       *ring)                   /*2d array[times][outlets] - convolution ring*/
 {
     int s, i, j;                                /*counters*/
     int y, x, offset, outlet;                   /*2d indicies*/
     int xyind, rind, uhind;                     /*1d indicies*/
 
     /*Loop through all sources*/
     for (s = 0; s < nsources; s++) {
-
         outlet = source2outlet_ind[s];
         y = source_y_ind[s];
         x = source_x_ind[s];
         offset = source_time_offset[s];
 
-        //1d index location
-        //2d-->1d indexing goes like this:  ind = y*x_size + x
-        xyind = y*x_size + x;
+        // 1d index location
+        // 2d-->1d indexing goes like this:  ind = y*x_size + x
+        xyind = y * x_size + x;
 
         /* Do the convolution */
         // i is the position in the unit hydrograph
         // j is the position in the ring
         for (i = 0; i < subset_length; i++) {
             j = i + offset;
 
-            //1d index locations
+            // 1d index locations
             rind = j * noutlets + outlet;
             uhind = i * nsources + s;