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Fix failing tests: Add compatibility with pandas 2 #85

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01e6456
Fix failing tests: Add compatibility with pandas 2
Jul 23, 2024
d977fb2
Update tox settings
Jul 23, 2024
6e0e357
Minimize diffs to simplify the review
Jul 27, 2024
9110266
Minimize diffs to simplify the review
Jul 27, 2024
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4 changes: 2 additions & 2 deletions src/GEOparse/GEOTypes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -432,7 +432,7 @@ def annotate_and_average(
if merge_on_column:
logger.info("merge_on_column is not None. Using this option.")
tmp_data = self.table.merge(gpl.table, on=merge_on_column, how="outer")
tmp_data = tmp_data.groupby(group_by_column).mean()[[expression_column]]
tmp_data = tmp_data.groupby(group_by_column)[[expression_column]].mean()
else:
if gpl_on is None or gsm_on is None:
raise Exception(
Expand All @@ -442,7 +442,7 @@ def annotate_and_average(
tmp_data = self.table.merge(
gpl.table, left_on=gsm_on, right_on=gpl_on, how="outer"
)
tmp_data = tmp_data.groupby(group_by_column).mean()[[expression_column]]
tmp_data = tmp_data.groupby(group_by_column)[[expression_column]].mean()
if rename:
tmp_data.columns = [self.name]
return tmp_data
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3 changes: 2 additions & 1 deletion tox.ini
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Expand Up @@ -6,7 +6,8 @@ envlist = py38,
changedir = tests
basepython =
py38: python3.8
passenv = GEOPARSE_USE_HTTP_FOR_FTP *_proxy *_PROXY USER
passenv = GEOPARSE_USE_HTTP_FOR_FTP,*_proxy,*_PROXY,USER
commands = pytest {posargs}
deps = -r{toxinidir}/requirements.txt
lxml
commands-pre = pip install ..