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 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'