Merge pull request #83 from UW-Hydro/develop

RVIC 1.1.1

.travis.yml

@@ -9,6 +9,7 @@ matrix:
     - python: 2.7
     - python: 3.4
     - python: 3.5
+    - python: 3.6
 
 # Setup anaconda
 before_install:
@@ -23,13 +24,13 @@ before_install:
   - conda config --set always_yes yes --set changeps1 no
   - conda update -q conda
   - conda info -a
+
 # Install packages
 install:
-  - conda create --yes --name=test python=$TRAVIS_PYTHON_VERSION numpy scipy pandas netcdf4 matplotlib pytest
+  - conda create --yes --name=test python=$TRAVIS_PYTHON_VERSION numpy scipy pandas netcdf4 matplotlib pytest -c conda-forge
   - source activate test
-  # - conda install -c https://conda.anaconda.org/ioos cdo
-  # - pip install cdo
   - python setup.py install
+
 # Run test
 script:
   - py.test

README.md

@@ -1,15 +1,12 @@
 # RVIC Streamflow Routing Model
 
-
-
 | VIC Links & Badges              |                                                                             |
 |------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
 | VIC Documentation      | [![Documentation Status](https://readthedocs.org/projects/rvic/badge/?version=latest)](https://readthedocs.org/projects/rvic/?badge=latest)                                                              |
 | Travis Build           | [![Build Status](https://travis-ci.org/UW-Hydro/RVIC.svg?branch=master)](https://travis-ci.org/UW-Hydro/RVIC)                                                                                            |
 | Code Health            | [![Code Health](https://landscape.io/github/UW-Hydro/RVIC/master/landscape.svg?style=flat)](https://landscape.io/github/UW-Hydro/RVIC/master)                                                            |
 | License                | [![GitHub license](https://img.shields.io/badge/license-GPLv3-blue.svg)](https://raw.githubusercontent.com/UW-Hydro/RVIC/master/LICENSE.txt)                                                              |
-| Current Release DOI    | [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.32620.svg)](http://dx.doi.org/10.5281/zenodo.32620) |
-
+| Current Release DOI    | [![DOI](https://zenodo.org/badge/11590212.svg)](https://zenodo.org/badge/latestdoi/11590212) |
 
 The RVIC streamflow routing model is an adapted version of the model the model typically used as a post-processor with the Variable Infiltration Capacity (VIC) hydrology model. The routing model is a source-to-sink model that solves a linearized version of the Saint-Venant equations. This model, developed by Lohmann et al. (1996, 1998a, 1998b), has been used in many offline studies at a variety of spatial scales. Furthermore, the development of the impulse response functions (IRFs) is done as a preprocessing step, which considerably reduces the computation time in subsequent routing steps.
 

docs/development/whats_new.md

@@ -1,5 +1,18 @@
 # What's New
 
+v1.1.1 (7 February 2017
+
+This release contains a number of bug and compatibility fixes.
+
+### Enhancements
+
+- Ability to pass a dictionary to top level RVIC functions (instead of only a file path). This allows for the generation of large ensembles of RVIC simulations in an interactive environment ([GH78](https://github.com/UW-Hydro/RVIC/pull/78)).
+
+### Bug Fixes
+
+- Fixed bug that in `tools/fraction2domain.bash` by using a temporary variable name ([GH88](https://github.com/UW-Hydro/RVIC/pull/88)).
+- Fixed off-by-one error in `history.py` ([GH86](https://github.com/UW-Hydro/RVIC/pull/86)).
+
 v1.1.0 (25 October 2015)
 
 This release contains a number of bug and compatibility fixes.

docs/user-guide/api.md

@@ -6,6 +6,8 @@ Almost all of RVIC is available via a public API.
 import rvic
 ```
 
+`rvic.parameters.parameters` and `rvic.convolution.convolution` both support either a path (string) to an INI style configuration file or a dictionary including configuration options. This feature is quite useful when generating ensembles of RVIC simulations.
+
 Most of the internals of RVIC are stored int the `rvic.core` module:
 
 ```Python

mkdocs.yml

@@ -1,7 +1,7 @@
 site_name: RVIC
 site_description: RVIC Streamflow Routing Model
 site_author: UW Hydro | Computational Hydrology
-copyright: 'Copyright &copy; 2015, <a href="www.hydro.washington.edu/">University of Washington Computational Hydrology Group</a>.'
+copyright: 'Copyright &copy; 2017, <a href="http://uw-hydro.github.io/">University of Washington Computational Hydrology Group</a>.'
 repo_url: https://github.com/UW-Hydro/RVIC
 theme: readthedocs
 

rvic/convolution.py

@@ -31,26 +31,21 @@
 
 # -------------------------------------------------------------------- #
 # Top Level Driver
-def convolution(config_file):
+def convolution(config):
     '''
     Top level driver for RVIC convolution model.
 
     Parameters
     ----------
-    config_file : str
-        Path to RVIC convolution configuration file.
+    config : str or dict.
+        Path to RVIC convolution configuration file or dictionary of
+        configuration options.
     '''
 
     # ---------------------------------------------------------------- #
     # Initilize
     hist_tapes, data_model, rout_var, \
-        time_handle, directories = convolution_init(config_file)
-    # ---------------------------------------------------------------- #
-
-    # ---------------------------------------------------------------- #
-    # Setup the pool of processors
-    # if numofproc > 1:
-    #     pool = LoggingPool(processes=numofproc)
+        time_handle, directories = convolution_init(config)
     # ---------------------------------------------------------------- #
 
     # ---------------------------------------------------------------- #
@@ -69,7 +64,7 @@ def convolution(config_file):
 
 # -------------------------------------------------------------------- #
 # Initialize RVIC
-def convolution_init(config_file):
+def convolution_init(config):
     '''
     Initialize the RVIC convolution routine
 
@@ -85,8 +80,9 @@ def convolution_init(config_file):
 
     Parameters
     ----------
-    config_file : str
-        Path to RVIC convolution configuration file.
+    config : str or dict
+        Path to RVIC convolution configuration file or dictionary of
+        configuration options.
 
     Returns
     ----------
@@ -109,7 +105,10 @@ def convolution_init(config_file):
 
     # ---------------------------------------------------------------- #
     # Read Configuration files
-    config_dict = read_config(config_file)
+    if isinstance(config, dict):
+        config_dict = config
+    else:
+        config_dict = read_config(config)
     # ---------------------------------------------------------------- #
 
     # ---------------------------------------------------------------- #

rvic/core/history.py

@@ -518,7 +518,7 @@ def __write_grid(self):
         f.createDimension('time', None)
 
         time = f.createVariable('time', self._ncprec, ('time',))
-        time[:] = self._out_times[:self._out_data_i + 1]
+        time[:] = self._out_times[:self._out_data_i]
         for key, val in iteritems(share.time):
             if val:
                 setattr(time, key, val.encode())
@@ -531,7 +531,7 @@ def __write_grid(self):
 
             time_bnds = f.createVariable('time_bnds', self._ncprec,
                                          ('time', 'nv',), **self.ncvaropts)
-            time_bnds[:, :] = self._out_time_bnds[:self._out_data_i + 1]
+            time_bnds[:, :] = self._out_time_bnds[:self._out_data_i]
         # ------------------------------------------------------------ #
 
         # ------------------------------------------------------------ #
@@ -585,7 +585,7 @@ def __write_grid(self):
         for field in self._fincl:
             var = f.createVariable(field, self._ncprec, tcoords,
                                    **self.ncvaropts)
-            var[:, :] = self._out_data[field][:self._out_data_i + 1]
+            var[:, :] = self._out_data[field][:self._out_data_i]
 
             for key, val in iteritems(getattr(share, field)):
                 if val:

rvic/core/make_uh.py

@@ -192,8 +192,8 @@ def read_direction(fdr, dy, dx):
     '''
     log.debug('Reading direction input and finding target row/columns')
 
-    to_y = np.zeros_like(fdr, dtype=np.int16)
-    to_x = np.zeros_like(fdr, dtype=np.int16)
+    to_y = np.zeros_like(fdr, dtype=np.int32)
+    to_x = np.zeros_like(fdr, dtype=np.int32)
 
     valid_dirs = list(dy.keys())
 
@@ -238,7 +238,7 @@ def search_catchment(to_y, to_x, pour_point, basin_ids, basin_id):
     # -1 - not in catchment
     # 0 - unknown
     # 1 - in catchment
-    in_catch = np.zeros_like(to_x, dtype=np.int16) - 1
+    in_catch = np.zeros_like(to_x, dtype=np.int32) - 1
     in_catch[byinds, bxinds] = 0  # set basin inds as 0
 
     # temporary variables for tracking flow path

rvic/core/param_file.py

@@ -73,7 +73,7 @@ def finish_params(outlets, dom_data, config_dict, directories):
                  'SUBSET_DAYS<BASIN_FLOWDAYS')
         for key, outlet in iteritems(outlets):
             outlet.offset = np.zeros(outlet.unit_hydrograph.shape[1],
-                                     dtype=np.int16)
+                                     dtype=np.int32)
         full_time_length = outlet.unit_hydrograph.shape[0]
         subset_length = full_time_length
     # ---------------------------------------------------------------- #
@@ -125,6 +125,10 @@ def finish_params(outlets, dom_data, config_dict, directories):
     outlet_name = grouped_data['outlet_name']
     outlet_upstream_area = grouped_data['outlet_upstream_area']
     outlet_upstream_gridcells = grouped_data['outlet_upstream_gridcells']
+
+    # Make sure the inds are all greater than zero, ref: Github #79
+    assert source_decomp_ind.min() >= 0, source_decomp_ind
+    assert outlet_decomp_ind.min() >= 0, outlet_decomp_ind
     # ---------------------------------------------------------------- #
 
     # ---------------------------------------------------------------- #
@@ -322,7 +326,7 @@ def subset(outlets, subset_length=None):
                                axis=1)
 
         outlet.offset = np.empty(outlet.unit_hydrograph.shape[1],
-                                 dtype=np.int16)
+                                 dtype=np.int32)
         out_uh = np.zeros((subset_length, outlet.unit_hydrograph.shape[1]),
                           dtype=np.float64)
 
@@ -402,23 +406,23 @@ def group(outlets, subset_length):
     gd['frac_sources'] = np.empty(n_sources, dtype=np.float64)
     gd['source_lon'] = np.empty(n_sources, dtype=np.float64)
     gd['source_lat'] = np.empty(n_sources, dtype=np.float64)
-    gd['source_x_ind'] = np.empty(n_sources, dtype=np.int16)
-    gd['source_y_ind'] = np.empty(n_sources, dtype=np.int16)
-    gd['source_decomp_ind'] = np.empty(n_sources, dtype=np.int16)
-    gd['source_time_offset'] = np.empty(n_sources, dtype=np.int16)
-    gd['source2outlet_ind'] = np.empty(n_sources, dtype=np.int16)
+    gd['source_x_ind'] = np.empty(n_sources, dtype=np.int32)
+    gd['source_y_ind'] = np.empty(n_sources, dtype=np.int32)
+    gd['source_decomp_ind'] = np.empty(n_sources, dtype=np.int32)
+    gd['source_time_offset'] = np.empty(n_sources, dtype=np.int32)
+    gd['source2outlet_ind'] = np.empty(n_sources, dtype=np.int32)
     # ---------------------------------------------------------------- #
 
     # ---------------------------------------------------------------- #
     # outlet specific inputs
     gd['outlet_lon'] = np.empty(n_outlets, dtype=np.float64)
     gd['outlet_lat'] = np.empty(n_outlets, dtype=np.float64)
-    gd['outlet_x_ind'] = np.empty(n_outlets, dtype=np.int16)
-    gd['outlet_y_ind'] = np.empty(n_outlets, dtype=np.int16)
-    gd['outlet_decomp_ind'] = np.empty(n_outlets, dtype=np.int16)
-    gd['outlet_number'] = np.empty(n_outlets, dtype=np.int16)
+    gd['outlet_x_ind'] = np.empty(n_outlets, dtype=np.int32)
+    gd['outlet_y_ind'] = np.empty(n_outlets, dtype=np.int32)
+    gd['outlet_decomp_ind'] = np.empty(n_outlets, dtype=np.int32)
+    gd['outlet_number'] = np.empty(n_outlets, dtype=np.int32)
     gd['outlet_name'] = np.empty(n_outlets, dtype='S{0}'.format(MAX_NC_CHARS))
-    gd['outlet_upstream_gridcells'] = np.empty(n_outlets, dtype=np.int16)
+    gd['outlet_upstream_gridcells'] = np.empty(n_outlets, dtype=np.int32)
     gd['outlet_upstream_area'] = np.empty(n_outlets, dtype=np.float64)
     # ---------------------------------------------------------------- #
 

rvic/core/plots.py

@@ -40,7 +40,7 @@ def uhs(data, title, case_id, plot_dir):
     plt.xlabel('timesteps')
     plt.ylabel('unit-hydrograph')
     fig.savefig(pfname)
-
+    plt.close()
     return pfname
 # -------------------------------------------------------------------- #
 
@@ -71,6 +71,7 @@ def _fractions_grid(data, dom_x, dom_y, title, case_id, plot_dir):
     plt.ylim([0, dom_y.shape[0]])
     plt.xlim([0, dom_x.shape[1]])
     fig.savefig(pfname)
+    plt.close()
     # ---------------------------------------------------------------- #
     return pfname
 # -------------------------------------------------------------------- #
@@ -129,6 +130,7 @@ def _fractions_map(data, dom_x, dom_y, title, case_id, plot_dir):
     m.colorbar(cs, location='right', pad='5%')
     plt.title(title)
     fig.savefig(pfname)
+    plt.close()
     # ---------------------------------------------------------------- #
     return pfname
 # -------------------------------------------------------------------- #

rvic/core/utilities.py

@@ -320,8 +320,10 @@ def read_domain(domain_dict, lat0_is_min=False):
     # ---------------------------------------------------------------- #
     # Create the cell_ids variable
     dom_mask = domain_dict['LAND_MASK_VAR']
-    temp = np.arange(dom_data[dom_mask].size)
-    dom_data['cell_ids'] = temp.reshape(dom_data[dom_mask].shape)
+    dom_data['cell_ids'] = np.arange(
+        dom_data[dom_mask].size).reshape(dom_data[dom_mask].shape)
+    # Make sure the inds are all greater than zero, ref: Github #79
+    assert dom_data['cell_ids'].min() >= 0
     # ---------------------------------------------------------------- #
 
     # ---------------------------------------------------------------- #

rvic/parameters.py

@@ -33,22 +33,23 @@
 
 # -------------------------------------------------------------------- #
 # Top level driver
-def parameters(config_file, numofproc=1):
+def parameters(config, numofproc=1):
     '''
     Top level function for RVIC parameter generation function.
 
     Parameters
     ----------
-    config_file : str
-        Path to RVIC parameters configuration file.
+    config : str or dict
+        Path to RVIC parameters configuration file or dictionary of
+        configuration options.
     numofproc : int
         Number of processors to use when developing RVIC parameters.
     '''
 
     # ---------------------------------------------------------------- #
     # Initilize
     uh_box, fdr_data, fdr_vatts, dom_data, \
-        outlets, config_dict, directories = gen_uh_init(config_file)
+        outlets, config_dict, directories = gen_uh_init(config)
     # ---------------------------------------------------------------- #
 
     # ---------------------------------------------------------------- #
@@ -100,7 +101,7 @@ def parameters(config_file, numofproc=1):
 # -------------------------------------------------------------------- #
 
 
-def gen_uh_init(config_file):
+def gen_uh_init(config):
     '''Initialize RVIC parameters script.
 
     This function:
@@ -113,8 +114,9 @@ def gen_uh_init(config_file):
 
     Parameters
     ----------
-    config_file : str
-        Path to RVIC parameters configuration file.
+    config : str or dict
+        Path to RVIC parameters configuration file or dictionary of
+        configuration options.
 
     Returns
     ----------
@@ -138,7 +140,10 @@ def gen_uh_init(config_file):
 
     # ---------------------------------------------------------------- #
     # Read Configuration files
-    config_dict = read_config(config_file)
+    if isinstance(config, dict):
+        config_dict = config
+    else:
+        config_dict = read_config(config)
     # ---------------------------------------------------------------- #
 
     # ---------------------------------------------------------------- #
@@ -158,7 +163,8 @@ def gen_uh_init(config_file):
 
     # ---------------------------------------------------------------- #
     # copy inputs to $case_dir/inputs and update configuration
-    config_dict = copy_inputs(config_file, directories['inputs'])
+    if not isinstance(config, dict):
+        config_dict = copy_inputs(config, directories['inputs'])
     options = config_dict['OPTIONS']
     # ---------------------------------------------------------------- #
 
@@ -570,6 +576,11 @@ def gen_uh_run(uh_box, fdr_data, fdr_vatts, dom_data, outlet, config_dict,
     outlet.cell_id_source = dom_data['cell_ids'][y, x]
     outlet.x_source = x
     outlet.y_source = y
+
+    # Make sure the inds are all greater than zero, ref: Github #79
+    assert all(outlet.cell_id_source >= 0)
+    assert all(outlet.x_source >= 0)
+    assert all(outlet.y_source >= 0)
     # ---------------------------------------------------------------- #
     return outlet
 # -------------------------------------------------------------------- #

setup.py

@@ -12,7 +12,7 @@
 
 MAJOR = 1
 MINOR = 1
-MICRO = 0
+MICRO = 1
 ISRELEASED = True
 VERSION = '%d.%d.%d' % (MAJOR, MINOR, MICRO)
 QUALIFIER = ''