allow user to specify config values to overwrite in run_stardis function

stardis/base.py

@@ -8,7 +8,9 @@
 import logging
 
 
-def run_stardis(config_fname, tracing_lambdas_or_nus):
+def run_stardis(
+    config_fname, tracing_lambdas_or_nus, add_config_keys=None, add_config_vals=None
+):
     """
     Runs a STARDIS simulation.
 
@@ -20,6 +22,10 @@ def run_stardis(config_fname, tracing_lambdas_or_nus):
         Numpy array of the frequencies or wavelengths to calculate the
         spectrum for. Must have units attached to it, with dimensions
         of either length or inverse time.
+    add_config_keys : list, optional
+        List of additional keys to add or overwrite for the configuration file.
+    add_config_vals : list, optional
+        List of corresponding additional values to add to the configuration file.
 
     Returns
     -------
@@ -29,7 +35,9 @@ def run_stardis(config_fname, tracing_lambdas_or_nus):
 
     tracing_nus = tracing_lambdas_or_nus.to(u.Hz, u.spectral())
 
-    config, adata, stellar_model = parse_config_to_model(config_fname)
+    config, adata, stellar_model = parse_config_to_model(
+        config_fname, add_config_keys, add_config_vals
+    )
     set_num_threads(config.n_threads)
     stellar_plasma = create_stellar_plasma(stellar_model, adata, config)
     stellar_radiation_field = create_stellar_radiation_field(

stardis/io/base.py

@@ -3,7 +3,7 @@
 import numpy as np
 
 from tardis.io.atom_data import AtomData
-from tardis.io.configuration.config_validator import validate_yaml
+from tardis.io.configuration.config_validator import validate_yaml, validate_dict
 from tardis.io.configuration.config_reader import Configuration
 
 from stardis.io.model.marcs import read_marcs_model
@@ -15,14 +15,18 @@
 SCHEMA_PATH = BASE_DIR / "config_schema.yml"
 
 
-def parse_config_to_model(config_fname):
+def parse_config_to_model(config_fname, add_config_keys=None, add_config_vals=None):
     """
     Parses the config and model files and outputs python objects to be passed into run stardis so they can be individually modified in python.
 
     Parameters
     ----------
     config_fname : str
         Filepath to the STARDIS configuration. Must be a YAML file.
+        add_config_keys : list, optional
+        List of additional keys to add or overwrite for the configuration file.
+    add_config_vals : list, optional
+        List of corresponding additional values to add to the configuration file.
 
     Returns
     -------
@@ -40,6 +44,23 @@ def parse_config_to_model(config_fname):
     except:
         raise ValueError("Config failed to validate. Check the config file.")
 
+    if (
+        not add_config_keys
+    ):  # If a dictionary was passed, update the config with the dictionary
+        pass
+    else:
+        print("Updating config with additional keys and values")
+        try:
+            for key, val in zip(add_config_keys, add_config_vals):
+                config.set_config_item(key, val)
+        except:
+            config.set_config_item(add_config_keys, add_config_vals)
+
+        try:
+            config_dict = validate_dict(config, schemapath=SCHEMA_PATH)
+        except:
+            raise ValueError("Additional config keys and values failed to validate.")
+
     adata = AtomData.from_hdf(config.atom_data)
 
     # model

stardis/io/model/__init__.py

@@ -1 +1 @@
-from stardis.io.model.marcs import read_marcs_model
+from stardis.io.model.marcs import *