Merge branch 'main' into remove_wavelength_bounds_from_config

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 *

stardis/io/model/marcs.py

@@ -167,43 +167,43 @@ def read_marcs_metadata(fpath, gzipped=True):
     """
 
     METADATA_RE_STR = [
-        ("(.+)\\n", "fname"),
+        (r"(.+)\n", "fname"),
         (
-            "  (\d+\.)\s+Teff \[(.+)\]\.\s+Last iteration; yyyymmdd=\d+",
+            r"  (\d+\.)\s+Teff \[(.+)\]\.\s+Last iteration; yyyymmdd=\d+",
             "teff",
             "teff_units",
         ),
-        ("  (\d+\.\d+E\+\d+) Flux \[(.+)\]", "flux", "flux_units"),
+        (r"  (\d+\.\d+E\+\d+) Flux \[(.+)\]", "flux", "flux_units"),
         (
-            "  (\d+.\d+E\+\d+) Surface gravity \[(.+)\]",
+            r"  (\d+.\d+E\+\d+) Surface gravity \[(.+)\]",
             "surface_grav",
             "surface_grav_units",
         ),
         (
-            "  (\d+\.\d+)\W+Microturbulence parameter \[(.+)\]",
+            r"  (\d+\.\d+)\W+Microturbulence parameter \[(.+)\]",
             "microturbulence",
             "microturbulence_units",
         ),
-        ("  (\d+\.\d+)\s+(No mass for plane-parallel models)", "plane_parallel_mass"),
+        (r"  (\d+\.\d+)\s+(No mass for plane-parallel models)", "plane_parallel_mass"),
         (
-            " (\+?\-?\d+.\d+) (\+?\-?\d+.\d+) Metallicity \[Fe\/H] and \[alpha\/Fe\]",
+            r" (\+?\-?\d+.\d+) (\+?\-?\d+.\d+) Metallicity \[Fe\/H] and \[alpha\/Fe\]",
             "feh",
             "afe",
         ),
         (
-            "  (\d+\.\d+E\+00) (1 cm radius for plane-parallel models)",
+            r"  (\d+\.\d+E\+00) (1 cm radius for plane-parallel models)",
             "radius for plane-parallel model",
         ),
-        ("  (\d.\d+E-\d+) Luminosity \[(.+)\]", "luminosity", "luminosity_units"),
+        (r"  (\d.\d+E-\d+) Luminosity \[(.+)\]", "luminosity", "luminosity_units"),
         (
-            "  (\d+.\d+) (\d+.\d+) (\d+.\d+) (\d+.\d+) are the convection parameters: alpha, nu, y and beta",
+            r"  (\d+.\d+) (\d+.\d+) (\d+.\d+) (\d+.\d+) are the convection parameters: alpha, nu, y and beta",
             "conv_alpha",
             "conv_nu",
             "conv_y",
             "conv_beta",
         ),
         (
-            "  (0.\d+) (0.\d+) (\d.\d+E-\d+) are X, Y and Z, 12C\/13C=(\d+.?\d+)",
+            r"  (0.\d+) (0.\d+) (\d.\d+E-\d+) are X, Y and Z, 12C\/13C=(\d+.?\d+)",
             "x",
             "y",
             "z",
@@ -276,15 +276,15 @@ def read_marcs_data(fpath, gzipped=True):
         fpath,
         skiprows=LINES_BEFORE_UPPER_TABLE,
         nrows=MARCS_MODEL_SHELLS,
-        delim_whitespace=True,
+        sep=r"\s+",
         index_col="k",
     )
     marcs_model_data_lower_split = pd.read_csv(
         fpath,
         skiprows=LINES_BEFORE_LOWER_TABLE,
         nrows=MARCS_MODEL_SHELLS,
         index_col="k",
-        sep="(?:\s+)|(?<=\+\d{2})(?=-)",
+        sep=r"(?:\s+)|(?<=\+\d{2})(?=-)",
         engine="python",
     )
 

stardis/io/model/mesa.py

@@ -218,7 +218,7 @@ def read_mesa_data(fpath, mesa_shells):
     mesa_model = pd.read_csv(
         fpath,
         skiprows=ROWS_TO_SKIP,
-        delim_whitespace=True,
+        sep=r"\s+",
         nrows=mesa_shells,
         index_col=0,
         comment="!",