Started work on inform stage and yaml config stuff

src/lephare/__init__.py

@@ -24,6 +24,7 @@
 from .data_retrieval import *
 from .filter import *
 from .filterSvc import *
+from .inform import *
 from .mag_gal import *
 from .magSvc import *
 from .sedtolib import *

src/lephare/inform.py

@@ -0,0 +1,94 @@
+import os
+
+import yaml
+
+import lephare as lp
+
+
+def inform(config, star_config=None, gal_config=None, qso_config=None):
+    """Run the inform stages of LePHARE
+
+    We overide the config for each type if distinct config set.
+
+    Parameters
+    ==========
+    config : dict of lephare.keyword
+        The config base to run all tasks
+    star_config : dict of lephare.keyword or None
+        Config values to override for stars
+    gal_config : dict of lephare.keyword or None
+        Config values to override for galaxies
+    qso_config : dict of lephare.keyword or None
+        Config values to override for QSO.
+    """
+    object_types = {"STAR": star_config, "GAL": gal_config, "QSO": qso_config}
+    # Run the filter command
+    # load filters from config file
+    filter_lib = lp.FilterSvc.from_config(config)
+    # Get location to store filter files
+    filter_output = os.path.join(os.environ["LEPHAREWORK"], "filt", config["FILTER_FILE"].value)
+    # Write filter files
+    lp.write_output_filter(filter_output + ".dat", filter_output + ".doc", filter_lib)
+    # Write config to work directory
+    write_yaml_config(config, f"{filter_output}_config.yaml")
+
+    for object_type in object_types:
+        updated_config = overwrite_config(config, object_types[object_type])
+        # Run sedtolib
+        sedlib = lp.Sedtolib(config_keymap=updated_config)
+        sedlib.run(typ=object_type)
+        # Write config
+        sed_output = os.environ["LEPHAREWORK"] + "sedtolib"
+        write_yaml_config(updated_config, f"{sed_output}_config.yaml")
+        # Run mag_gal
+        maglib = lp.MagGal(config_keymap=updated_config)
+        maglib.run(typ=object_type)
+        # Write config
+        mag_output = os.environ["LEPHAREWORK"] + "mag_gal"
+        write_yaml_config(updated_config, f"{mag_output}_config.yaml")
+
+
+def overwrite_config(c1, c2):
+    """Check that two config can be safely broadcast for a joint run"""
+    if c2 is None:
+        return c1
+    config = c1
+    # Redshift grid must be idenitical
+    # assert True
+    # filters must be indentical
+    # assert True
+    for k in c2:
+        config[k] = config[k]
+    return config
+
+
+def read_yaml_config(yaml_file_path):
+    """Open a standard yaml file and render it as a dictionary of keywords
+
+    Parameters
+    ==========
+    yaml_file_path : str
+        Path to input yaml file.
+    """
+    with open(yaml_file_path, "r") as file:
+        config = yaml.safe_load(file)
+    for key in config:
+        config[key] = lp.keyword(key, config[key])
+    return config
+
+
+def write_yaml_config(keymap, yaml_file_path):
+    """Write a dictionary of keywords to a yaml file
+
+    Parameters
+    ==========
+    keymap : dict of lephare.keyword
+        The dictionary of keywords to be written to yaml.
+    yaml_file_path : str
+        Path to output yaml file.
+    """
+    config_dict = {}
+    for k in keymap:
+        config_dict[keymap[k].name] = keymap[k].value
+    with open(yaml_file_path, "w") as yaml_file:
+        yaml.dump(config_dict, yaml_file)