Clean up config_keywords

Use "BASE_BIO_ON == FALSE" instead of "EXCLUDE_BASE_BIO" and "ABIO_DIC_ON == TRUE" instead of "INCLUDE_ABIO_DIC". Note that, when appropriate, "BASE_BIO_ON == TRUE" and "ABIO_DIC_ON == FALSE" are available in _config_keywords so it will be easy to do things like change the default value of abio_dic_on to .true. Also cleaned up comments in _parse_args() for generating the settings file.
mnlevy1981 · Mar 7, 2024 · 644cadc · 644cadc
1 parent 13d30c6
commit 644cadc
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Showing 14 changed files with 32 additions and 30 deletions.
diff --git a/MARBL_tools/MARBL_generate_settings_file.py b/MARBL_tools/MARBL_generate_settings_file.py
@@ -81,11 +81,11 @@ def _parse_args(marbl_root):
                         default='settings_file', choices = set(('settings_file', 'GCM')),
                         help="Source of initial value for saved state vars that can come from GCM or settings file")
 
-    # Command line argument to specify resolution (default is None)
+    # Command line flag to turn off the base biotic tracers
     parser.add_argument('--disable-base-bio', action='store_false', dest='base_bio_on',
                         help='Turn off base biotic tracer module (default is on)')
 
-    # Command line argument to specify resolution (default is None)
+    # Command line flag to turn on the abiotic DIC tracers
     parser.add_argument('--enable-abio-dic', action='store_true', dest='abio_dic_on',
                         help='Turn on abiotic DIC tracer module (default is off)')
 

diff --git a/MARBL_tools/MARBL_settings_file_class.py b/MARBL_tools/MARBL_settings_file_class.py
@@ -23,12 +23,14 @@ def __init__(self, default_settings_file, saved_state_vars_source="settings_file
 
         logger = logging.getLogger(__name__)
 
+        # Check argument types
+        if not (type(base_bio_on) == bool and type(abio_dic_on == bool)):
+          raise ValueError("base_bio_on and abio_dic_on must be type bool")
+
         # 1. List of configuration keywords to match in JSON if default_default is a dictionary
         self._config_keyword = []
-        if not base_bio_on:
-            self._config_keyword.append('EXCLUDE_BASE_BIO')
-        if abio_dic_on:
-            self._config_keyword.append('INCLUDE_ABIO_DIC')
+        self._config_keyword.append(f'BASE_BIO_ON == {str(base_bio_on).upper()}')
+        self._config_keyword.append(f'ABIO_DIC_ON == {str(abio_dic_on).upper()}')
         if grid != None:
             self._config_keyword.append('GRID == "%s"' % grid)
         self._config_keyword.append('SAVED_STATE_VARS_SOURCE == "%s"' % saved_state_vars_source)

diff --git a/defaults/json/settings_cesm2.0.json b/defaults/json/settings_cesm2.0.json
@@ -1520,7 +1520,7 @@
          "_append_to_config_keywords": true,
          "datatype": "logical",
          "default_value": {
-            "INCLUDE_ABIO_DIC": ".true.",
+            "ABIO_DIC_ON == TRUE": ".true.",
             "default": ".false."
          },
          "longname": "Control whether abiotic carbon tracer module is active",
@@ -1531,7 +1531,7 @@
          "_append_to_config_keywords": true,
          "datatype": "logical",
          "default_value": {
-            "EXCLUDE_BASE_BIO": ".false.",
+            "BASE_BIO_ON == FALSE": ".false.",
             "default": ".true."
          },
          "longname": "Control whether the base ecosystem tracer module is active",

diff --git a/defaults/json/settings_cesm2.1+cocco.json b/defaults/json/settings_cesm2.1+cocco.json
@@ -1565,7 +1565,7 @@
          "_append_to_config_keywords": true,
          "datatype": "logical",
          "default_value": {
-            "INCLUDE_ABIO_DIC": ".true.",
+            "ABIO_DIC_ON == TRUE": ".true.",
             "default": ".false."
          },
          "longname": "Control whether abiotic carbon tracer module is active",
@@ -1576,7 +1576,7 @@
          "_append_to_config_keywords": true,
          "datatype": "logical",
          "default_value": {
-            "EXCLUDE_BASE_BIO": ".false.",
+            "BASE_BIO_ON == FALSE": ".false.",
             "default": ".true."
          },
          "longname": "Control whether the base ecosystem tracer module is active",

diff --git a/defaults/json/settings_cesm2.1.json b/defaults/json/settings_cesm2.1.json
@@ -1523,7 +1523,7 @@
          "_append_to_config_keywords": true,
          "datatype": "logical",
          "default_value": {
-            "INCLUDE_ABIO_DIC": ".true.",
+            "ABIO_DIC_ON == TRUE": ".true.",
             "default": ".false."
          },
          "longname": "Control whether abiotic carbon tracer module is active",
@@ -1534,7 +1534,7 @@
          "_append_to_config_keywords": true,
          "datatype": "logical",
          "default_value": {
-            "EXCLUDE_BASE_BIO": ".false.",
+            "BASE_BIO_ON == FALSE": ".false.",
             "default": ".true."
          },
          "longname": "Control whether the base ecosystem tracer module is active",

diff --git a/defaults/json/settings_latest+4p2z.json b/defaults/json/settings_latest+4p2z.json
@@ -1618,7 +1618,7 @@
          "_append_to_config_keywords": true,
          "datatype": "logical",
          "default_value": {
-            "INCLUDE_ABIO_DIC": ".true.",
+            "ABIO_DIC_ON == TRUE": ".true.",
             "default": ".false."
          },
          "longname": "Control whether abiotic carbon tracer module is active",
@@ -1629,7 +1629,7 @@
          "_append_to_config_keywords": true,
          "datatype": "logical",
          "default_value": {
-            "EXCLUDE_BASE_BIO": ".false.",
+            "BASE_BIO_ON == FALSE": ".false.",
             "default": ".true."
          },
          "longname": "Control whether the base ecosystem tracer module is active",

diff --git a/defaults/json/settings_latest+cocco.json b/defaults/json/settings_latest+cocco.json
@@ -1565,7 +1565,7 @@
          "_append_to_config_keywords": true,
          "datatype": "logical",
          "default_value": {
-            "INCLUDE_ABIO_DIC": ".true.",
+            "ABIO_DIC_ON == TRUE": ".true.",
             "default": ".false."
          },
          "longname": "Control whether abiotic carbon tracer module is active",
@@ -1576,7 +1576,7 @@
          "_append_to_config_keywords": true,
          "datatype": "logical",
          "default_value": {
-            "EXCLUDE_BASE_BIO": ".false.",
+            "BASE_BIO_ON == FALSE": ".false.",
             "default": ".true."
          },
          "longname": "Control whether the base ecosystem tracer module is active",

diff --git a/defaults/json/settings_latest.json b/defaults/json/settings_latest.json
@@ -1529,7 +1529,7 @@
          "_append_to_config_keywords": true,
          "datatype": "logical",
          "default_value": {
-            "INCLUDE_ABIO_DIC": ".true.",
+            "ABIO_DIC_ON == TRUE": ".true.",
             "default": ".false."
          },
          "longname": "Control whether abiotic carbon tracer module is active",
@@ -1540,7 +1540,7 @@
          "_append_to_config_keywords": true,
          "datatype": "logical",
          "default_value": {
-            "EXCLUDE_BASE_BIO": ".false.",
+            "BASE_BIO_ON == FALSE": ".false.",
             "default": ".true."
          },
          "longname": "Control whether the base ecosystem tracer module is active",

diff --git a/defaults/settings_cesm2.0.yaml b/defaults/settings_cesm2.0.yaml
@@ -257,7 +257,7 @@ tracer_modules :
       datatype : logical
       default_value :
          default : .true.
-         EXCLUDE_BASE_BIO : .false.
+         BASE_BIO_ON == FALSE : .false.
       _append_to_config_keywords : true
    abio_dic_on :
       longname : Control whether abiotic carbon tracer module is active
@@ -266,7 +266,7 @@ tracer_modules :
       datatype : logical
       default_value :
          default : .false.
-         INCLUDE_ABIO_DIC : .true.
+         ABIO_DIC_ON == TRUE : .true.
       _append_to_config_keywords : true
    ciso_on :
       longname : Control whether CISO tracer module is active

diff --git a/defaults/settings_cesm2.1+cocco.yaml b/defaults/settings_cesm2.1+cocco.yaml
@@ -257,7 +257,7 @@ tracer_modules :
       datatype : logical
       default_value :
          default : .true.
-         EXCLUDE_BASE_BIO : .false.
+         BASE_BIO_ON == FALSE : .false.
       _append_to_config_keywords : true
    abio_dic_on :
       longname : Control whether abiotic carbon tracer module is active
@@ -266,7 +266,7 @@ tracer_modules :
       datatype : logical
       default_value :
          default : .false.
-         INCLUDE_ABIO_DIC : .true.
+         ABIO_DIC_ON == TRUE : .true.
       _append_to_config_keywords : true
    ciso_on :
       longname : Control whether CISO tracer module is active

diff --git a/defaults/settings_cesm2.1.yaml b/defaults/settings_cesm2.1.yaml
@@ -257,7 +257,7 @@ tracer_modules :
       datatype : logical
       default_value :
          default : .true.
-         EXCLUDE_BASE_BIO : .false.
+         BASE_BIO_ON == FALSE : .false.
       _append_to_config_keywords : true
    abio_dic_on :
       longname : Control whether abiotic carbon tracer module is active
@@ -266,7 +266,7 @@ tracer_modules :
       datatype : logical
       default_value :
          default : .false.
-         INCLUDE_ABIO_DIC : .true.
+         ABIO_DIC_ON == TRUE : .true.
       _append_to_config_keywords : true
    ciso_on :
       longname : Control whether CISO tracer module is active

diff --git a/defaults/settings_latest+4p2z.yaml b/defaults/settings_latest+4p2z.yaml
@@ -268,7 +268,7 @@ tracer_modules :
       datatype : logical
       default_value :
          default : .true.
-         EXCLUDE_BASE_BIO : .false.
+         BASE_BIO_ON == FALSE : .false.
       _append_to_config_keywords : true
    abio_dic_on :
       longname : Control whether abiotic carbon tracer module is active
@@ -277,7 +277,7 @@ tracer_modules :
       datatype : logical
       default_value :
          default : .false.
-         INCLUDE_ABIO_DIC : .true.
+         ABIO_DIC_ON == TRUE : .true.
       _append_to_config_keywords : true
    ciso_on :
       longname : Control whether CISO tracer module is active

diff --git a/defaults/settings_latest+cocco.yaml b/defaults/settings_latest+cocco.yaml
@@ -257,7 +257,7 @@ tracer_modules :
       datatype : logical
       default_value :
          default : .true.
-         EXCLUDE_BASE_BIO : .false.
+         BASE_BIO_ON == FALSE : .false.
       _append_to_config_keywords : true
    abio_dic_on :
       longname : Control whether abiotic carbon tracer module is active
@@ -266,7 +266,7 @@ tracer_modules :
       datatype : logical
       default_value :
          default : .false.
-         INCLUDE_ABIO_DIC : .true.
+         ABIO_DIC_ON == TRUE : .true.
       _append_to_config_keywords : true
    ciso_on :
       longname : Control whether CISO tracer module is active

diff --git a/defaults/settings_latest.yaml b/defaults/settings_latest.yaml
@@ -257,7 +257,7 @@ tracer_modules :
       datatype : logical
       default_value :
          default : .true.
-         EXCLUDE_BASE_BIO : .false.
+         BASE_BIO_ON == FALSE : .false.
       _append_to_config_keywords : true
    abio_dic_on :
       longname : Control whether abiotic carbon tracer module is active
@@ -266,7 +266,7 @@ tracer_modules :
       datatype : logical
       default_value :
          default : .false.
-         INCLUDE_ABIO_DIC : .true.
+         ABIO_DIC_ON == TRUE : .true.
       _append_to_config_keywords : true
    ciso_on :
       longname : Control whether CISO tracer module is active