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Use pandas.DataFrame.at instead of .loc for single values #979

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merged 2 commits into from
Aug 15, 2022
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Use pandas.DataFrame.at instead of .loc for single values #979

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8e43773
Use pandas.DataFrame.at instead of .loc for single values
victorlin Jun 17, 2022
740fc85
Add changelog entry
victorlin Aug 15, 2022
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6 changes: 6 additions & 0 deletions CHANGES.md
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Expand Up @@ -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
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4 changes: 2 additions & 2 deletions augur/export_v1.py
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Expand Up @@ -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):
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2 changes: 1 addition & 1 deletion augur/refine.py
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Expand Up @@ -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'
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