Restore clades to top entry in colorings

The intention of the coloring logic is that if an auspice-config provides
the clade_membership key then it is exported at that position in the
colorings list. If clade_membership is not explicitly set in the config
(but is present in a node-data file) then we have (for a very long time)
added it as the very first entry in the colorings list.

PR #728 (augur v22.0.0) erroneously modified the behavior of the second
case described above, which has now been restored by this commit.

Author: jameshadfield

augur/export_v2.py

@@ -361,10 +361,8 @@ def _add_coloring(colorings, key):
             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 in {x['key'] for x in colorings}:
-            return False
-        colorings.append({"key": key})
-        return True
+        if key not in {x['key'] for x in colorings}:
+            colorings.append({"key": key})
 
     def _is_valid(coloring):
         key = coloring["key"]
@@ -798,8 +796,9 @@ def node_data_prop_is_normal_trait(name):
         "authors",          # authors are set as a node property, not a trait property
         "author",           # see above
         "vaccine",          # vaccine info is stored as a "special" node prop
+        'clade_membership', # explicitly set as a coloring if present
         'branch_length',
-        'num_date',
+        'num_date',         # explicitly set as a coloring if present
         'raw_date',
         'numdate',
         'clock_length',

tests/functional/export_v2/dataset-with-branch-labels.json

@@ -25,13 +25,13 @@
     },
     "colorings": [
       {
-        "key": "gt",
-        "title": "Genotype",
+        "key": "clade_membership",
+        "title": "Clade",
         "type": "categorical"
       },
       {
-        "key": "clade_membership",
-        "title": "Clade",
+        "key": "gt",
+        "title": "Genotype",
         "type": "categorical"
       }
     ],