wip

augur/export_v2.py

@@ -365,10 +365,6 @@ def _add_title_and_type(coloring):
         return coloring
 
     def _add_coloring(colorings, key):
-        # handle deprecations
-        if key == "authors":
-            deprecated("[colorings] The 'authors' key is now called 'author'")
-            key = "author"
         # check if the key has already been added by another part of the color-creating logic
         if key not in {x['key'] for x in colorings}:
             colorings.append({"key": key})
@@ -1151,7 +1147,7 @@ def get_additional_metadata_columns(config, command_line_metadata_columns, metad
                   "It will be ignored during export, please rename field if you would like to include as a metadata field.")
             continue
         # Match the column names corrected within parse_node_data_and_metadata
-        corrected_col = update_deprecated_names(col)
+        # corrected_col = update_deprecated_names(col)
         if corrected_col not in metadata_names:
             warn(f"Requested metadata column {col!r} does not exist and will not be exported")
             continue

augur/util_support/auspice_config.py

@@ -88,6 +88,20 @@ def _rename_display_keys(display: dict) -> dict:
     return defaults
 
 
+def _update_deprecated_values(config):
+    # The 'authors' coloring is now called 'author' (and remapped as such)
+    author  = [[idx, c] for [idx, c] in enumerate(config.get('colorings', [])) if c['key']=='author' ]
+    authors = [[idx, c] for [idx, c] in enumerate(config.get('colorings', [])) if c['key']=='authors']
+    if authors:
+        if author:
+            deprecated("[config file] coloring 'authors' has been renamed 'author', however a " +
+                       "coloring for 'author' already exists. 'authors' will be ignored")
+            config['colorings'] = [c for [idx, c] in enumerate(config['colorings']) if idx!=authors[0][0]]
+        else:
+            deprecated("[config file] renaming coloring 'authors' to 'author'")
+            config['colorings'][authors[0][0]]['key'] = "author"
+
+
 TOP_LEVEL_DEPRECATED_KEYS = [
     # [ <old key>, <new key>, <modify func>] #
     ["defaults", "display_defaults", _rename_display_keys],
@@ -106,5 +120,8 @@ def read_auspice_config(fname):
         _replace_deprecated(config, *keys)
     for key in TOP_LEVEL_UNUSED_KEYS:
         _remove_deprecated(config, key)
+    _update_deprecated_values(config)
+
+    import pprint; pprint.pp(config)
 
     return config