ENH: Run config files through jinja, so we can inject variables (e.g. FSLDIR,

BIPDIR, etc)

bip/utils/config.py

@@ -26,6 +26,8 @@ import              os
 import os.path   as op
 import              operator
 
+import jinja2    as j2
+
 
 # python >= 3.11
 try:
@@ -321,7 +323,7 @@ class Config:
 
 
     @staticmethod
-    def load_config_file(cfgfile, selectors=None):
+    def load_config_file(cfgfile, selectors=None, env=None):
         """Load a BIP configuration file. The file is assumed to be a TOML
         file, named as described in the config_file_identifier documentation.
 
@@ -337,16 +339,27 @@ class Config:
             'T1_struct_bet_f'        : 0.5
             'T1_struct_fast_classes' : 3
 
-        Re-labelling is not applied to the main "config.toml" configuration
-        file.
+        This re-labelling is not applied to the main "config.toml"
+        configuration file.
+
+        If selectors are provided, alternate values stored in the file may be
+        used - refer to the resolve_selectors method.
+
+        Configuration files may contain variables using Jinja2 syntax - if
+        an "env" dictionary is provided, the file contents are passed through
+        Jinja2 to resolve these variable references.
         """
 
         if selectors is None:
             selectors = {}
 
-        with open(cfgfile, 'rb') as f:
-            settings = tomllib.load(f)
+        with open(cfgfile, 'rt') as f:
+            settings = f.read()
+
+        if env is not None:
+            settings = j2.Template(settings).render(**env)
 
+        settings  = tomllib.loads(settings)
         ident     = Config.config_file_identifier(cfgfile)
         selectors = {k : selectors[k] for k in sorted(selectors.keys())}
         settings  = Config.resolve_selectors(settings, selectors)
@@ -378,6 +391,7 @@ class Config:
         return settings
 
 
+    # env=None - run all files through equivalent of op.expandvars
     def __init__(self, cfgdir=None, selectors=None, overrides=None):
         """Create a Config object. Read configuration files from cfgdir.