Added config params for estimate to cli

src/rail/cli/commands.py

@@ -1,5 +1,7 @@
 import os
 import click
+import pprint
+import yaml
 
 from rail.core import __version__
 from rail.cli import options, scripts
@@ -85,22 +87,46 @@ def get_data(verbose, **kwargs):
 @options.stage_name()
 @options.stage_class()
 @options.stage_module()
+@options.stages_config()
 @options.model_file()
 @options.catalog_tag()
 @options.dry_run()
 @options.input_file()
-def estimate(stage_name, stage_class, stage_module, model_file, catalog_tag, dry_run, input_file):
+@options.params()
+def estimate(stage_name, stage_class, stage_module, stages_config, model_file, catalog_tag, dry_run, input_file, params):
     """Run a pz estimation stage"""
     if catalog_tag:
         catalog_utils.apply_defaults(catalog_tag)
+
+    if stages_config not in [None, 'none', 'None']:
+        with open(stages_config) as fin:
+            config_data = yaml.safe_load(fin)
+            if stage_name in config_data:
+                kwargs = config_data[stage_name]
+            elif isinstance(config_data, dict):
+                kwargs = config_data
+            else:
+                raise ValueError(f"Config file {stages_config} is not properly constructed")                
+    else:
+        kwargs = {}
+
+    kwargs.update(**options.args_to_dict(params))
+
     stage = PZFactory.build_cat_estimator_stage(
         stage_name=stage_name,
         class_name=stage_class,
         module_name=stage_module,
         model_path=model_file,
         data_path='dummy.in',
+        **kwargs,
     )
 
+    if dry_run:
+        print(f"Running stage {stage.name} of type {type(stage)} on {input_file}")
+        print("Stage config:   ")
+        pprint.pprint(stage.config.to_dict())
+        return 0
+
     output = PZFactory.run_cat_estimator_stage(
         stage,
         data_path=input_file,

src/rail/cli/options.py

@@ -5,6 +5,7 @@
 import click
 
 __all__ = [
+    "args_to_dict",
     "clear_output",
     "bpz_demo_data",
     "catalog_tag",
@@ -14,6 +15,7 @@
     "from_source",
     "model_file",
     "git_mode",
+    "params",
     "pipeline_class",
     "pipeline_yaml",
     "print_all",
@@ -58,6 +60,18 @@ def convert(self, value: Any, param, ctx) -> EnumType_co:  # pragma: no cover
         return self._enum.__members__[converted_str]
 
 
+def args_to_dict(args):
+    """Convert a series of command line key=value statements
+    to a dict"""    
+    out_dict = {}
+    for arg_ in args:
+        tokens = arg_.split('=')
+        if len(tokens) != 2:
+            raise ValueError(f"Poorly formed argument {arg_}.  Should by key=value")
+        out_dict[tokens[0]] = tokens[1]
+    return out_dict
+
+
 class PartialOption:
     """Wraps click.option with partial arguments for convenient reuse"""
 
@@ -237,6 +251,8 @@ def __call__(self, *args: Any, **kwargs: Any) -> Any:  # pragma: no cover
 
 inputs = PartialArgument("inputs", nargs=-1)
 
+params = PartialArgument("params", nargs=-1)
+
 verbose_download = PartialOption(
     "-v", "--verbose", help="Verbose output when downloading", is_flag=True
 )