Merge pull request #979: Use pandas.DataFrame.at instead of .loc for …

…single values
nextstrain · Aug 15, 2022 · f97b1cb · f97b1cb
2 parents f148234 + 740fc85
commit f97b1cb
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diff --git a/CHANGES.md b/CHANGES.md
@@ -6,6 +6,12 @@
 
 * Upgrade treetime from 0.8.6 to >= 0.9.2 which enables a speedup of timetree inference in marginal mode due to the use of Fast Fourier Transforms [#1018][]. (@rneher and @anna-parker)
 
+### Bug Fixes
+
+* refine, export v1: Use pandas.DataFrame.at instead of .loc for single values [#979][]. (@victorlin)
+
+[#979]: https://github.com/nextstrain/augur/pull/979
+
 ## 17.0.0 (9 August 2022)
 
 ### Major Changes

diff --git a/augur/export_v1.py b/augur/export_v1.py
@@ -269,8 +269,8 @@ def add_tsv_metadata_to_nodes(nodes, meta_tsv, meta_json, extra_fields=['authors
             continue
         for field in fields:
             # Allow fields to have value of 0! - but prevent from having value of "" (breaks auspice v1)
-            if field not in node and field in meta_tsv.columns and (meta_tsv.loc[strain, field] or meta_tsv.loc[strain, field]==0):
-                node[field] = meta_tsv.loc[strain, field]
+            if field not in node and field in meta_tsv.columns and (meta_tsv.at[strain, field] or meta_tsv.at[strain, field]==0):
+                node[field] = meta_tsv.at[strain, field]
 
 
 def get_root_sequence(root_node, ref=None, translations=None):

diff --git a/augur/refine.py b/augur/refine.py
@@ -211,7 +211,7 @@ def run(args):
         # save input state string for later export
         for n in T.get_terminals():
             if n.name in metadata.index and 'date' in metadata.columns:
-                n.raw_date = metadata.loc[n.name, 'date']
+                n.raw_date = metadata.at[n.name, 'date']
 
         if args.date_confidence:
             time_inference_mode = 'always' if args.date_inference=='marginal' else 'only-final'