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pandas 3.0 compatibility #471

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7ff4a96
pandas 3.0 compatibility
dweindl Jan 26, 2026
b2e9810
..
dweindl Jan 26, 2026
b58dfda
Merge branch 'main' into pandas3
dweindl Jan 26, 2026
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2 changes: 1 addition & 1 deletion petab/v1/conditions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -111,7 +111,7 @@ def get_parametric_overrides(condition_df: pd.DataFrame) -> list[str]:
result = []

for column in constant_parameters:
if np.issubdtype(condition_df[column].dtype, np.number):
if not pd.api.types.is_string_dtype(condition_df[column].dtype):
continue

floatified = condition_df.loc[:, column].apply(core.to_float_if_float)
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16 changes: 8 additions & 8 deletions petab/v1/lint.py
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@dilpath dilpath Jan 26, 2026

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All edits in this file are in repeated code but fine as is

Original file line number Diff line number Diff line change
Expand Up @@ -129,7 +129,7 @@ def check_condition_df(
)

for column_name in req_cols:
if not np.issubdtype(df[column_name].dtype, np.number):
if pd.api.types.is_string_dtype(df[column_name].dtype):
assert_no_leading_trailing_whitespace(
df[column_name].values, column_name
)
Expand Down Expand Up @@ -173,14 +173,14 @@ def check_measurement_df(
_check_df(df, MEASUREMENT_DF_REQUIRED_COLS, "measurement")

for column_name in MEASUREMENT_DF_REQUIRED_COLS:
if not np.issubdtype(df[column_name].dtype, np.number):
if pd.api.types.is_string_dtype(df[column_name].dtype):
assert_no_leading_trailing_whitespace(
df[column_name].values, column_name
)

for column_name in MEASUREMENT_DF_OPTIONAL_COLS:
if column_name in df and not np.issubdtype(
df[column_name].dtype, np.number
if column_name in df and pd.api.types.is_string_dtype(
df[column_name].dtype
):
assert_no_leading_trailing_whitespace(
df[column_name].values, column_name
Expand Down Expand Up @@ -243,7 +243,7 @@ def check_parameter_df(
check_ids(df.index.values, kind="parameter")

for column_name in PARAMETER_DF_REQUIRED_COLS[1:]: # 0 is PARAMETER_ID
if not np.issubdtype(df[column_name].dtype, np.number):
if pd.api.types.is_string_dtype(df[column_name].dtype):
assert_no_leading_trailing_whitespace(
df[column_name].values, column_name
)
Expand Down Expand Up @@ -304,14 +304,14 @@ def check_observable_df(observable_df: pd.DataFrame) -> None:
check_ids(observable_df.index.values, kind="observable")

for column_name in OBSERVABLE_DF_REQUIRED_COLS[1:]:
if not np.issubdtype(observable_df[column_name].dtype, np.number):
if pd.api.types.is_string_dtype(observable_df[column_name].dtype):
assert_no_leading_trailing_whitespace(
observable_df[column_name].values, column_name
)

for column_name in OBSERVABLE_DF_OPTIONAL_COLS:
if column_name in observable_df and not np.issubdtype(
observable_df[column_name].dtype, np.number
if column_name in observable_df and pd.api.types.is_string_dtype(
observable_df[column_name].dtype
):
assert_no_leading_trailing_whitespace(
observable_df[column_name].values, column_name
Expand Down
2 changes: 1 addition & 1 deletion petab/v1/visualize/data_overview.py
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Original file line number Diff line number Diff line change
Expand Up @@ -69,7 +69,7 @@ def get_data_per_observable(measurement_df: pd.DataFrame) -> pd.DataFrame:
my_measurements[PREEQUILIBRATION_CONDITION_ID] = (
my_measurements[PREEQUILIBRATION_CONDITION_ID]
.astype("object")
.fillna("", inplace=True)
.fillna("")
)
index.append(PREEQUILIBRATION_CONDITION_ID)

Expand Down
2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ description = "Parameter estimation tabular data"
requires-python = ">=3.11"
dependencies = [
"numpy>=1.15.1",
"pandas>=1.2.0,<3",
"pandas>=1.2.0",
"python-libsbml>=5.17.0",
"sympy",
"colorama",
Expand Down
2 changes: 1 addition & 1 deletion tests/v1/test_petab.py
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Original file line number Diff line number Diff line change
Expand Up @@ -508,7 +508,7 @@ def test_flatten_timepoint_specific_output_overrides():
)

pd.testing.assert_frame_equal(
problem.observable_df, observable_df_expected
problem.observable_df, observable_df_expected, check_dtype=False
)
Comment on lines 510 to 512
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@dilpath dilpath Jan 26, 2026

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Why False? Could add a brief comment.

pd.testing.assert_frame_equal(
problem.measurement_df, measurement_df_expected
Expand Down