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Added ability to convert VIC 4.2 ascii state files to VIC 5.0 netcdf #66

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Added ability to convert VIC 4.2 ascii state files to VIC 5.0 netcdf #66

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a9b8812
Added ability to convert VIC 4.2 ascii state files to VIC 5.0 netcdf.…
tbohn Jul 13, 2017
609d03c
Reformatted to make vim/syntastic happy.
tbohn Jul 13, 2017
4af7e58
Updates to addressing pull request comments.
tbohn Aug 5, 2017
e74712a
Removed extraneous file.
tbohn Aug 5, 2017
fdc8543
Fix small typo.
tbohn Aug 5, 2017
f48e7dd
Test
tbohn Aug 5, 2017
5d19c03
Test
tbohn Aug 5, 2017
7a380dc
Test
tbohn Aug 6, 2017
583f5a7
Test
tbohn Aug 6, 2017
3acd668
Test
tbohn Aug 6, 2017
1f6d73d
Fixed unhashable list error.
tbohn Aug 6, 2017
f67d3fc
Misc updates in response to review comments.
tbohn Aug 27, 2017
59c4f52
Rolled back the change in the order of arguments in the parser.add_ar…
tbohn Aug 27, 2017
7549df5
Added the action='store_true' arguments back in, and eliminated type=…
tbohn Aug 28, 2017
1bc1bc3
Made depth a 3-column variable.
tbohn Aug 28, 2017
8d1cef4
Removed unnecessary '+' line continuation symbols.
tbohn Aug 28, 2017
42e40fc
Removed more unnecessary '+' line continuation symbols.
tbohn Aug 28, 2017
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24 changes: 17 additions & 7 deletions .travis.yml
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -6,15 +6,25 @@ python:
- "2.7"
- "3.4"

# Setup anaconda
# Set up 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:$PATH
# Example yml file didn't set sudo to false above,
# and had the next line uncommented
# - sudo apt-get update
- if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
else
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
fi
- bash miniconda.sh -b -p $HOME/miniconda
# - chmod +x miniconda.sh
# - ./miniconda.sh -b -p $HOME/miniconda
- export PATH=$HOME/miniconda/bin:$PATH
- hash -r
# Update conda itself
- conda update --yes conda

- conda config --set always_yes yes --set changeps1 no
- conda update -q conda
- conda info -a
install:
- conda create --yes --name=tonic_test_env python=$TRAVIS_PYTHON_VERSION --file=ci/requirements-$TRAVIS_PYTHON_VERSION.txt
- source activate tonic_test_env
Expand Down
206 changes: 182 additions & 24 deletions scripts/vic_utils
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Original file line number Diff line number Diff line change
Expand Up @@ -30,9 +30,10 @@ def main():

# ---------------------------------------------------------------- #
# create the parser for the "netcdf2vic" command
netcdf2vic_parser = subparsers.add_parser('netcdf2vic',
help=netcdf2vic.help,
description=netcdf2vic.description)
netcdf2vic_parser \
= subparsers.add_parser('netcdf2vic',
help=netcdf2vic.help,
description=netcdf2vic.description)
netcdf2vic_parser.set_defaults(func=netcdf2vic._run)
netcdf2vic_parser.add_argument("config",
type=str,
Expand All @@ -41,9 +42,10 @@ def main():

# ---------------------------------------------------------------- #
# create the parser for the "grid_params" command
grid_params_parser = subparsers.add_parser('grid_params',
help=grid_params.help,
description=grid_params.description)
grid_params_parser \
= subparsers.add_parser('grid_params',
help=grid_params.help,
description=grid_params.description)
grid_params_parser.set_defaults(func=grid_params._run)
grid_params_parser.add_argument("soil_file",
type=str,
Expand All @@ -59,37 +61,190 @@ def main():
"elevation band data in standard VIC "
"format",
default=None)
grid_params_parser.add_argument("-b", "--vegl_file",
type=str,
help="Input file containing vegetation "
"library data in"
" standard VIC format",
default=None)
grid_params_parser.add_argument("-v", "--veg_file",
type=str,
help="Input file containing vegitation "
help="Input file containing vegetation "
"parameter data "
"in standard VIC format",
default=None)
grid_params_parser.add_argument("-l", "--vegl_file",
grid_params_parser.add_argument("-l", "--lake_file",
type=str,
help="Input file containing vegitation "
"library data in"
" standard VIC format",
help="Input file containing lake "
"parameter data "
"in standard VIC format",
default=None)
grid_params_parser.add_argument("-s", "--state_file",
type=str,
help="Input file containing model "
"state data "
"in standard VIC format",
default=None)
grid_params_parser.add_argument("-o", "--out_file",
type=str,
help="Output file name, "
help="Output file name "
"(default=/params.nc)",
default='params.nc')

grid_params_parser.add_argument("-t", "--out_state_file",
type=str,
help="Output state file name "
"(default=/state.nc)",
default=None)
grid_params_parser.add_argument("--VIC_version",
type=str,
help="VIC version to write parameter file "
"for",
choices=['4.1.2', '5.0.dev'],
default='4.1.2')
choices=['4.1.2', '4.2', '5.0.dev'],
default='4.2')
grid_params_parser.add_argument("-d", "--grid_decimal",
type=str,
help="Number of decimal places in "
"grid cell center lat/lon "
"coordinates (default=4)",
default=4)
grid_params_parser.add_argument("--nlayers",
type=str,
help="Number of soil layers "
"(default=3)",
default=3)
grid_params_parser.add_argument("--snow_bands",
type=str,
help="Number of snow bands "
"(default=1)",
default=1)
grid_params_parser.add_argument("--veg_classes",
type=str,
help="Number of veg classes "
"(default=11)",
default=11)
grid_params_parser.add_argument("--max_roots",
type=str,
help="Number of root zones "
"(default=3)",
default=3)
grid_params_parser.add_argument("--max_numnod",
type=str,
help="Max number of lake nodes "
"(default=10)",
default=10)
grid_params_parser.add_argument("--soil_nodes",
type=str,
help="Number of soil thermal nodes "
"(default=3)",
default=3)
grid_params_parser.add_argument("--nfrost",
type=str,
help="Number of spatial frost "
"zones (default=1)",
default=1)
grid_params_parser.add_argument("--cells",
type=str,
help="Number of cells "
"(default=determine from "
"input files)",
default=None)
grid_params_parser.add_argument("--organic_fract",
action='store_true',
help="Flag indicating whether soil "
"parameter file contains organic "
"fractions (default=False)")
grid_params_parser.add_argument("--spatial_frost",
action='store_true',
help="Flag indicating whether soil "
"parameter file contains spatial "
"frost parameters (default=False)")
grid_params_parser.add_argument("--spatial_snow",
action='store_true',
help="Flag indicating whether soil "
"parameter file contains spatial "
"snow parameters (default=False)")
grid_params_parser.add_argument("--july_tavg_supplied",
action='store_true',
help="Flag indicating whether soil "
"parameter file contains July "
"average temperature "
"(default=False)")
grid_params_parser.add_argument("--veglib_photo",
action='store_true',
help="Flag indicating whether veg "
"library file contains photo-"
"synthesis parameters "
"(default=False)")
grid_params_parser.add_argument("--veglib_fcan",
action='store_true',
help="Flag indicating whether veg "
"library file contains fcanopy "
"values (default=False)")
grid_params_parser.add_argument("--blowing_snow",
action='store_true',
help="Flag indicating whether veg "
"parameter file contains blowing "
"snow parameters (default=False)")
grid_params_parser.add_argument("--vegparam_lai",
action='store_true',
help="Flag indicating whether veg "
"parameter file contains lai "
"values (default=False)")
grid_params_parser.add_argument("--vegparam_fcan",
action='store_true',
help="Flag indicating whether veg "
"parameter file contains fcanopy "
"values (default=False)")
grid_params_parser.add_argument("--vegparam_albedo",
action='store_true',
help="Flag indicating whether veg "
"parameter file contains albedo "
"values (default=False)")
grid_params_parser.add_argument("--lai_src",
type=str,
help="Where to take lai values from; "
"can be one of: \'FROM_VEGLIB\', "
"\'FROM_VEGPARAM\' "
"(default=\'FROM_VEGLIB\')",
choices=['FROM_VEGLIB', 'FROM_VEGPARAM'],
default="FROM_VEGLIB")
grid_params_parser.add_argument("--fcan_src",
type=str,
help="Where to take fcanopy values from; "
"can be one of: \'FROM_DEFAULT\', "
"\'FROM_VEGLIB\', \'FROM_VEGPARAM\'; "
"\'FROM_DEFAULT\' = set them to 1.0; "
"(default=\'FROM_DEFAULT\')",
choices=['FROM_DEFAULT',
'FROM_VEGLIB', 'FROM_VEGPARAM'],
default="FROM_DEFAULT")
grid_params_parser.add_argument("--alb_src",
type=str,
help="Where to take albedo values from; "
"can be one of: \'FROM_VEGLIB\', "
"\'FROM_VEGPARAM\' "
"(default=\'FROM_VEGLIB\')",
choices=['FROM_VEGLIB', 'FROM_VEGPARAM'],
default="FROM_VEGLIB")
grid_params_parser.add_argument("--lake_profile",
action='store_true',
help="Flag indicating whether lake "
"parameter file contains lake "
"depth-area relationship "
"(default=False)")
grid_params_parser.add_argument("--carbon",
action='store_true',
help="Flag indicating whether state "
"file contains carbon-cycle "
"variables (default=False)")
# ---------------------------------------------------------------- #

# ---------------------------------------------------------------- #
# create the parser for the "ncparam2ascii" command
ncparam2ascii_parser = subparsers.add_parser('ncparam2ascii',
help=ncparam2ascii.help,
description=ncparam2ascii.description)
ncparam2ascii_parser \
= subparsers.add_parser('ncparam2ascii',
help=ncparam2ascii.help,
description=ncparam2ascii.description)
ncparam2ascii_parser.set_defaults(func=ncparam2ascii._run)
ncparam2ascii_parser.add_argument("nc_params",
type=str,
Expand Down Expand Up @@ -139,9 +294,10 @@ def main():

# ---------------------------------------------------------------- #
# create the parser for the "compare_soil_params" command
compare_soil_params_parser = subparsers.add_parser('compare_soil_params',
help=compare_soil_params.help,
description=compare_soil_params.description)
compare_soil_params_parser \
= subparsers.add_parser('compare_soil_params',
help=compare_soil_params.help,
description=compare_soil_params.description)
compare_soil_params_parser.set_defaults(func=compare_soil_params._run)

compare_soil_params_parser.add_argument("-d", "--domain_file",
Expand Down Expand Up @@ -175,9 +331,10 @@ def main():

# ---------------------------------------------------------------- #
# create the parser for the "vic2netcdf" command
vic2netcdf_parser = subparsers.add_parser('vic2netcdf',
help=vic2netcdf.help,
description=vic2netcdf.description)
vic2netcdf_parser \
= subparsers.add_parser('vic2netcdf',
help=vic2netcdf.help,
description=vic2netcdf.description)
vic2netcdf_parser.set_defaults(func=vic2netcdf._run)
vic2netcdf_parser.add_argument("config_file",
type=str,
Expand Down Expand Up @@ -216,6 +373,7 @@ def complete_subparser_action(prefix, **kwargs):
return internal_actions + external_actions
# -------------------------------------------------------------------- #


# -------------------------------------------------------------------- #
if __name__ == "__main__":
main()
Expand Down
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