From 8e43773628dee5bf8ae662e8ab3a0a9f33101f0f Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Fri, 17 Jun 2022 21:42:00 +0000
Subject: [PATCH 1/2] Use pandas.DataFrame.at instead of .loc for single values

This is the recommended way by pandas [1].

[1]: https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.at.html
---
 augur/export_v1.py | 4 ++--
 augur/refine.py    | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/augur/export_v1.py b/augur/export_v1.py
index 9f9fcc180..7ab3d1bdd 100644
--- 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
index a1c176a78..9becce2d9 100644
--- 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'

From 740fc85374c1810720eaf06cc1c690ce0fd45a43 Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Mon, 15 Aug 2022 12:25:29 -0700
Subject: [PATCH 2/2] Add changelog entry

---
 CHANGES.md | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/CHANGES.md b/CHANGES.md
index 997574c66..d85de5696 100644
--- 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