mpxv temporal colouring scale

Snakefile

@@ -1,3 +1,13 @@
+from packaging import version
+from augur.__version__ import __version__ as augur_version
+import sys
+
+min_version = "16.0.0"
+if version.parse(augur_version) < version.parse(min_version):
+  print("This pipeline needs a newer version of augur than you currently have...")
+  print(f"Current augur version: {augur_version}. Minimum required: {min_version}")
+  sys.exit(1)
+
 if not config:
     configfile: "config/config_hmpxv1.yaml"
 

config/auspice_config_mpxv.json

@@ -17,9 +17,9 @@
       "type": "categorical"
     },
     {
-      "key": "date",
-      "title": "Date",
-      "type": "categorical"
+      "key": "sample_date",
+      "title": "Sample Date",
+      "type": "temporal"
     },
     {
       "key": "region",

scripts/remove_timeinfo.py

@@ -1,6 +1,16 @@
 from collections import defaultdict
 import json, argparse
 
+def sample_date(node):
+    """
+    Returns the sample date in numeric form.
+    In the future, we could examine the 'raw_date' attr here to decide whether to ignore
+    some sequences, as 'numdate' is the inferred (timetree) date which can hide
+    uncertainty in actual sampling date,
+    """
+    if "raw_date" not in node: # internal node or tip with no date info
+        return
+    return node['numdate']
 
 
 
@@ -25,8 +35,9 @@
             "mutation_length": node["mutation_length"],
             "branch_length": node["branch_length"]
         }
-        if "raw_date" in node:
-            new_node_data[name]["date"] = node["raw_date"]
+        sdate = sample_date(node)
+        if sdate:
+            new_node_data[name]["sample_date"] = sdate
 
     data["nodes"] = new_node_data
     with open(args.output_node_data, 'w') as fh: