added bias calc to main cli

setup.py

@@ -54,6 +54,7 @@ def run(self):
  "sup3r-batch=sup3r.batch.batch_cli:main",
  "sup3r-qa=sup3r.qa.qa_cli:main",
  "sup3r-windstats=sup3r.qa.windstats_cli:main",
+ "sup3r-bias-calc=sup3r.bias.bias_calc_cli:main",
  "sup3r-solar=sup3r.solar.solar_cli:main",
  ("sup3r-forward-pass=sup3r.pipeline."
  "forward_pass_cli:main"),

sup3r/bias/bias_calc.py

@@ -81,7 +81,8 @@ def __init__(self, base_fps, bias_fps, base_dset, bias_features,
  logger.error(msg)
  raise RuntimeError(msg)
 
- elif 'windspeed' not in self.base_dset and len(self.bias_features) != 1:
+ elif ('windspeed' not in self.base_dset
+ and len(self.bias_features) != 1):
  msg = ('If base dataset is not windspeed, cannot handle more than '
  'one feature from the bias data, but received: {}'
  .format(self.bias_features))
@@ -158,6 +159,7 @@ def get_node_cmd(cls, config):
  logger.error(msg)
  raise NotImplementedError(msg)
 
+ # pylint: disable=E1101
  init_str = get_fun_call_str(cls, config)
  fun_str = get_fun_call_str(cls.run, config)
 
@@ -366,6 +368,7 @@ def write_outputs(self, fp_out):
  """
  if fp_out is not None:
  with h5py.File(fp_out, 'a') as f:
+ # pylint: disable=E1136
  lat = self.bias_dh.lat_lon[..., 0]
  lon = self.bias_dh.lat_lon[..., 1]
  f.create_dataset('latitude', data=lat)

sup3r/cli.py

@@ -15,6 +15,7 @@
 from sup3r.pipeline.pipeline_cli import from_config as pipe_cli
 from sup3r.pipeline.pipeline_cli import valid_config_keys as pipeline_keys
 from sup3r.batch.batch_cli import from_config as batch_cli
+from sup3r.bias.bias_calc_cli import from_config as bias_calc_cli
 
 
 logger = logging.getLogger(__name__)
@@ -143,7 +144,7 @@ def solar(ctx, verbose):
  :meth:`sup3r.solar.solar.Solar.run_temporal_chunk` method. You do not need
  to include the ``i_t_chunk`` input, this is added by the CLI. The config
  also has several optional arguments: ``log_pattern``, ``log_level``, and
- ``execution_control``. Here's a small example forward pass config::
+ ``execution_control``. Here's a small example solar config::
 
  {
  "fp_pattern": "./chunks/sup3r*.h5",
@@ -167,6 +168,70 @@ def solar(ctx, verbose):
  ctx.invoke(solar_cli, config_file=config_file, verbose=verbose)
 
 
+@main.command()
+@click.option('-v', '--verbose', is_flag=True,
+ help='Flag to turn on debug logging.')
+@click.pass_context
+def bias_calc(ctx, verbose):
+ """Sup3r bias correction calculation module to create bias correction
+ factors for low res input data.
+
+ This is typically used to understand and correct the biases in global
+ climate model (GCM) data from CMIP. Bias correcting GCM data is a very
+ common process when dealing with climate data and this helps automate that
+ process prior to passing GCM data through sup3r generative models. This is
+ typically the first step in a GCM downscaling pipeline.
+
+ You can call the bias calc module via the sup3r-pipeline CLI, or call it
+ directly with either of these equivelant commands::
+
+ $ sup3r -c config_bias.json bias-calc
+
+ $ sup3r-bias-calc from-config -c config_bias.json
+
+ A sup3r bias calc config.json file can contain any arguments or keyword
+ arguments required to call the
+
+ The config has high level ``bias_calc_class`` and ``jobs`` keys. The
+ ``bias_calc_class`` is a class name from the :mod:`sup3r.bias.bias_calc`
+ module, and the ``jobs`` argument is a list of kwargs required to
+ initialize the ``bias_calc_class`` and run the ``bias_calc_class.run()``
+ method (for example, see
+ :meth:`sup3r.bias.bias_calc.LinearCorrection.run`). There are also has
+ several optional arguments: ``log_pattern``, ``log_level``, and
+ ``execution_control``. Here's a small example bias calc config::
+
+ {
+ "bias_calc_class": "LinearCorrection",
+ "jobs": [
+ {
+ "base_fps" : ["/datasets/WIND/HRRR/HRRR_2015.h5"],
+ "bias_fps": ["./ta_day_EC-Earth3-Veg_ssp585.nc"],
+ "base_dset": "windspeed_100m",
+ "bias_features": ["U_100m", "V_100m"],
+ "target": [20, -130],
+ "shape": [48, 95]
+ }
+ ],
+ "execution_control": {
+ "option": "local"
+ },
+ "execution_control_eagle": {
+ "option": "eagle",
+ "walltime": 4,
+ "alloc": "sup3r"
+ }
+ }
+
+ Note that the ``execution_control`` block will run the job locally, while
+ the ``execution_control_eagle`` block are kwargs that would be required to
+ distribute the job on multiple nodes on the NREL HPC.
+ """
+ config_file = ctx.obj['CONFIG_FILE']
+ verbose = any([verbose, ctx.obj['VERBOSE']])
+ ctx.invoke(bias_calc_cli, config_file=config_file, verbose=verbose)
+
+
 @main.command()
 @click.option('-v', '--verbose', is_flag=True,
  help='Flag to turn on debug logging.')