suppress openpyxl user warning

CHANGELOG.md

@@ -17,6 +17,7 @@ Code freeze date: YYYY-MM-DD
 - Adds `MeasureConfig` and related dataclasses for new `Measure` object retrocompatibility and (de)serialization capabilities [#1276](https://github.com/CLIMADA-project/climada_python/pull/1276)
 - Add inter- and extrapolation options to `ImpactFreqCurve` with method `interpolate` [#1252](https://github.com/CLIMADA-project/climada_python/pull/1252)
 - Add `trajectory` module to ease the handling of multiple risk assessment at different point in time, and enable interpolation in between. [#1197](https://github.com/CLIMADA-project/climada_python/pull/1197), [#1198](https://github.com/CLIMADA-project/climada_python/pull/1198), [#1199](https://github.com/CLIMADA-project/climada_python/pull/1199), [#1200](https://github.com/CLIMADA-project/climada_python/pull/1197), [#1201](https://github.com/CLIMADA-project/climada_python/pull/1197)
+- `climada.util.dataframe_handling.read_excel` a wrapper around `pandas.read_excel` that suppresses unrelated user-warnings [#1335](https://github.com/CLIMADA-project/climada_python/issues/1335)
 
 ### Changed
 

climada/engine/impact.py

@@ -26,21 +26,21 @@
 import datetime as dt
 import logging
 import warnings
-from collections.abc import Collection
+from collections.abc import Collection, Iterable
 from dataclasses import dataclass, field
 from itertools import zip_longest
 from pathlib import Path
-from typing import Any, Iterable, Union
+from typing import Any, Union
 
 import contextily as ctx
 import geopandas as gpd
 import h5py
-import matplotlib.animation as animation
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
 import xlsxwriter
 from deprecation import deprecated
+from matplotlib import animation
 from matplotlib.colors import Normalize
 from pandas.api.types import is_string_dtype
 from pyproj import CRS as pyprojCRS
@@ -49,6 +49,7 @@
 from tqdm import tqdm
 
 import climada.util.coordinates as u_coord
+import climada.util.dataframe_handling as u_pd
 import climada.util.dates_times as u_dt
 import climada.util.interpolation as u_interp
 import climada.util.plot as u_plot
@@ -1567,7 +1568,7 @@ def from_excel(cls, file_name):
             Impact from excel file
         """
         LOGGER.info("Reading %s", file_name)
-        imp_df = pd.read_excel(file_name)
+        imp_df = u_pd.read_excel(file_name)
         imp = cls(haz_type=str(imp_df["haz_type"][0]))
 
         imp.unit = imp_df["unit"][0]

climada/entity/_legacy_measures/measure_set.py

@@ -24,13 +24,12 @@
 import ast
 import copy
 import logging
-from typing import List, Optional
 
 import numpy as np
-import pandas as pd
 import xlsxwriter
 from matplotlib import colormaps as cm
 
+import climada.util.dataframe_handling as u_pd
 import climada.util.hdf5_handler as u_hdf5
 
 from .base import Measure
@@ -99,7 +98,7 @@ class MeasureSet:
         Use the available methods instead.
     """
 
-    def __init__(self, measure_list: Optional[List[Measure]] = None):
+    def __init__(self, measure_list: list[Measure] | None = None):
         """Initialize a new MeasureSet object with specified data.
 
         Parameters
@@ -130,7 +129,7 @@ def __init__(self, measure_list: Optional[List[Measure]] = None):
             for meas in measure_list:
                 self.append(meas)
 
-    def clear(self, _data: Optional[dict] = None):
+    def clear(self, _data: dict | None = None):
         """Reinitialize attributes.
 
         Parameters
@@ -544,7 +543,7 @@ def read_att_excel(measures, dfr, var_names):
 
                 measures.append(Measure(**meas_kwargs))
 
-        dfr = pd.read_excel(file_name, var_names["sheet_name"])
+        dfr = u_pd.read_excel(file_name, var_names["sheet_name"])
         dfr = dfr.fillna("")
         meas_set = cls()
         try:

climada/entity/disc_rates/base.py

@@ -32,6 +32,7 @@
 import xlsxwriter
 
 import climada.util.checker as u_check
+import climada.util.dataframe_handling as u_pd
 import climada.util.finance as u_fin
 import climada.util.hdf5_handler as u_hdf5
 
@@ -293,7 +294,7 @@ def from_excel(cls, file_name, var_names=None):
         """
         if var_names is None:
             var_names = DEF_VAR_EXCEL
-        dfr = pd.read_excel(file_name, var_names["sheet_name"])
+        dfr = u_pd.read_excel(file_name, var_names["sheet_name"])
         try:
             years = dfr[var_names["col_name"]["year"]].values.astype(int, copy=False)
             rates = dfr[var_names["col_name"]["disc"]].values

climada/entity/entity_def.py

@@ -24,9 +24,8 @@
 import logging
 from typing import Optional
 
-import pandas as pd
-
-from climada.entity._legacy_measures.measure_set import Measure, MeasureSet
+import climada.util.dataframe_handling as u_pd
+from climada.entity._legacy_measures.measure_set import MeasureSet
 from climada.entity.disc_rates.base import DiscRates
 from climada.entity.exposures.base import Exposures
 from climada.entity.impact_funcs.impact_func_set import ImpactFuncSet
@@ -128,7 +127,7 @@ def from_excel(cls, file_name):
             The entity from excel file
         """
 
-        exp = Exposures(pd.read_excel(file_name))
+        exp = Exposures(u_pd.read_excel(file_name))
 
         disc_rates = DiscRates.from_excel(file_name)
         impf_set = ImpactFuncSet.from_excel(file_name)

climada/entity/exposures/litpop/litpop.py

@@ -31,6 +31,7 @@
 from shapefile import Shape
 
 import climada.util.coordinates as u_coord
+import climada.util.dataframe_handling as u_pd
 import climada.util.finance as u_fin
 from climada import CONFIG
 from climada.entity.exposures.base import DEF_REF_YEAR, INDICATOR_IMPF, Exposures
@@ -1493,7 +1494,7 @@ def _grp_read(country_iso3, admin1_info=None, data_dir=SYSTEM_DIR):
     )
     if file_name is not None:
         # open spreadsheet and identify relevant columns:
-        admin1_xls_data = pd.read_excel(file_name)
+        admin1_xls_data = u_pd.read_excel(file_name)
         if admin1_xls_data.get("State_Province") is None:
             admin1_xls_data = admin1_xls_data.rename(
                 columns={admin1_xls_data.columns[0]: "State_Province"}

climada/entity/exposures/test/test_base.py

@@ -31,6 +31,7 @@
 from sklearn.metrics import DistanceMetric
 
 import climada.util.coordinates as u_coord
+import climada.util.dataframe_handling as u_pd
 from climada import CONFIG
 from climada.entity import LitPop
 from climada.entity.exposures.base import (
@@ -425,7 +426,7 @@ class TestIO(unittest.TestCase):
 
     def test_read_template_pass(self):
         """Wrong exposures definition"""
-        df = pd.read_excel(ENT_TEMPLATE_XLS)
+        df = u_pd.read_excel(ENT_TEMPLATE_XLS)
         exp_df = Exposures(df)
         # set metadata
         exp_df.ref_year = 2020
@@ -434,7 +435,7 @@ def test_read_template_pass(self):
 
     def test_handling_unit_conflicts_pass(self):
         """Check that the value_unit is correctly set when there are conflicting value_unit definitions in the data frame and the meta attribute."""
-        df = pd.read_excel(ENT_TEMPLATE_XLS)
+        df = u_pd.read_excel(ENT_TEMPLATE_XLS)
         exp_df = Exposures(df, meta={"value_unit": "XSD"}, value_unit="XSD")
         exp_df.check()
         self.assertEqual(exp_df.value_unit, "XSD")
@@ -444,7 +445,7 @@ def test_handling_unit_conflicts_pass(self):
     def test_io_hdf5_pass(self):
         """write and read hdf5"""
         exp = Exposures(
-            pd.read_excel(ENT_TEMPLATE_XLS), crs="epsg:32632", ref_year=2020
+            u_pd.read_excel(ENT_TEMPLATE_XLS), crs="epsg:32632", ref_year=2020
         )
 
         # add another geometry column

climada/entity/impact_funcs/impact_func_set.py

@@ -23,14 +23,15 @@
 
 import copy
 import logging
+from collections.abc import Iterable
 from itertools import repeat
-from typing import Iterable, Optional, Union, overload
+from typing import Optional, Union, overload
 
 import matplotlib.pyplot as plt
 import numpy as np
-import pandas as pd
 import xlsxwriter
 
+import climada.util.dataframe_handling as u_pd
 import climada.util.hdf5_handler as u_hdf5
 import climada.util.plot as u_plot
 from climada.entity.impact_funcs.base import ImpactFunc
@@ -424,7 +425,7 @@ def from_excel(cls, file_name, var_names=None):
         """
         if var_names is None:
             var_names = DEF_VAR_EXCEL
-        dfr = pd.read_excel(file_name, var_names["sheet_name"])
+        dfr = u_pd.read_excel(file_name, var_names["sheet_name"])
 
         imp_func_set = cls()
         imp_func_set._fill_dfr(dfr, var_names)

climada/hazard/centroids/centr.py

@@ -39,6 +39,7 @@
 from shapely.geometry.point import Point
 
 import climada.util.coordinates as u_coord
+import climada.util.dataframe_handling as u_pd
 from climada.util.constants import DEF_CRS
 
 __all__ = ["Centroids"]
@@ -882,7 +883,7 @@ def from_excel(cls, file_path, sheet_name=None):
         """
         if sheet_name is None:
             sheet_name = "centroids"
-        df = pd.read_excel(file_path, sheet_name)
+        df = u_pd.read_excel(file_path, sheet_name)
         return cls._from_dataframe(df)
 
     def write_excel(self, file_path):
@@ -1053,7 +1054,7 @@ def _gdf_from_legacy_hdf5(data):
     def _legacy_from_excel(cls, file_name, var_names):
         LOGGER.info("Reading %s", file_name)
         try:
-            df = pd.read_excel(file_name, var_names["sheet_name"])
+            df = u_pd.read_excel(file_name, var_names["sheet_name"])
             df = df.rename(columns=var_names["col_name"])
         except KeyError as err:
             raise KeyError("Not existing variable: %s" % str(err)) from err

climada/hazard/io.py

@@ -25,18 +25,18 @@
 import pathlib
 import warnings
 from collections.abc import Collection
-from typing import Any, Dict, Optional, Union
+from typing import Any, Union
 
 import h5py
 import numpy as np
-import pandas as pd
 import rasterio
 import xarray as xr
 from deprecation import deprecated
 from scipy import sparse
 
 import climada.util.constants as u_const
 import climada.util.coordinates as u_coord
+import climada.util.dataframe_handling as u_pd
 import climada.util.hdf5_handler as u_hdf5
 from climada.hazard.centroids.centr import Centroids
 
@@ -317,8 +317,8 @@ def from_xarray_raster(
         intensity_unit: str,
         *,
         intensity: str = "intensity",
-        coordinate_vars: Optional[Dict[str, str]] = None,
-        data_vars: Optional[Dict[str, str]] = None,
+        coordinate_vars: dict[str, str] | None = None,
+        data_vars: dict[str, str] | None = None,
         crs: str = u_const.DEF_CRS,
         rechunk: bool = False,
         open_dataset_kws: dict[str, Any] | None = None,
@@ -604,7 +604,7 @@ def from_xarray_raster(
         return cls(**cls._check_and_cast_attrs(kwargs))
 
     @staticmethod
-    def _check_and_cast_attrs(attrs: Dict[str, Any]) -> Dict[str, Any]:
+    def _check_and_cast_attrs(attrs: dict[str, Any]) -> dict[str, Any]:
         """Check the validity of the hazard attributes given and cast to correct type if required
         and possible.
 
@@ -731,7 +731,7 @@ def _check_and_cast_elements(
         return attrs
 
     @staticmethod
-    def _attrs_to_kwargs(attrs: Dict[str, Any], num_events: int) -> Dict[str, Any]:
+    def _attrs_to_kwargs(attrs: dict[str, Any], num_events: int) -> dict[str, Any]:
         """Transform attributes to init kwargs or use default values
 
         If attributes are missing from ``attrs``, this method will use a sensible default
@@ -1092,7 +1092,7 @@ def _read_att_mat(data, file_name, var_names, centroids):
     @staticmethod
     def _read_att_excel(file_name, var_names, centroids):
         """Read Excel hazard's attributes."""
-        dfr = pd.read_excel(file_name, var_names["sheet_name"]["freq"])
+        dfr = u_pd.read_excel(file_name, var_names["sheet_name"]["freq"])
 
         num_events = dfr.shape[0]
         attrs = dict()
@@ -1106,7 +1106,7 @@ def _read_att_excel(file_name, var_names, centroids):
         )
         attrs["event_name"] = dfr[var_names["col_name"]["even_name"]].values.tolist()
 
-        dfr = pd.read_excel(file_name, var_names["sheet_name"]["inten"])
+        dfr = u_pd.read_excel(file_name, var_names["sheet_name"]["inten"])
         # number of events (ignore centroid_ID column)
         # check the number of events is the same as the one in the frequency
         if dfr.shape[1] - 1 is not num_events:

climada/hazard/test/test_tc_tracks_synth.py

@@ -434,6 +434,7 @@ def test_wrong_decay_pass(self):
             4: (1.0714354641894077, 0.002783787561718677),
         }
         track_gen.attrs["orig_event_flag"] = False
+
         # the reference central pressure may need to be updated when IBTrACS change their files,
         # which may happen even without an apparent version change
         cp_ref = np.array([1013.0, 1012.0] + [1011.0] * 6 + [1010.0] * 10)

climada/test/test_plot.py

@@ -21,14 +21,13 @@
 
 import copy
 import unittest
-import urllib
 from pathlib import Path
 
 import contextily as ctx
 import matplotlib.pyplot as plt
 import numpy as np
-import pandas as pd
 
+import climada.util.dataframe_handling as u_pd
 from climada.engine import CostBenefit, ImpactCalc, ImpactFreqCurve
 from climada.engine.unsequa import UncOutput
 from climada.entity import (
@@ -40,7 +39,7 @@
     Measure,
     MeasureSet,
 )
-from climada.hazard import Centroids, Hazard
+from climada.hazard import Hazard
 from climada.test import get_test_file
 from climada.util.api_client import Client
 from climada.util.constants import ENT_DEMO_TODAY, HAZ_DEMO_FL, TEST_UNC_OUTPUT_COSTBEN
@@ -117,7 +116,7 @@ def test_hazard_rp_intensity(self):
 
     def test_exposures_value_pass(self):
         """Plot exposures values."""
-        myexp = pd.read_excel(ENT_DEMO_TODAY)
+        myexp = u_pd.read_excel(ENT_DEMO_TODAY)
         myexp = Exposures(myexp)
         myexp.check()
         myexp.description = "demo_today"

climada/util/dataframe_handling.py

@@ -19,6 +19,8 @@
 Define functions to handle with coordinates
 """
 
+import warnings
+
 import pandas as pd
 
 
@@ -63,3 +65,30 @@ def reorder_dataframe_columns(
         new_column_order.extend(remaining_columns)
 
     return dataframe[new_column_order]
+
+
+def read_excel(*args, **kwargs):
+    """A wrapper around pandas.read_excel that suppresses the openpyxl warning
+    'Unknown extension is not supported and will be removed', from openpyxl.worksheet._read_only
+
+    Parameters
+    ----------
+    *args
+        Positional arguments forwarded to :func:`pandas.read_excel`. The first
+        argument is typically the path to an Excel file or a file-like object.
+    **kwargs
+        Keyword arguments forwarded unchanged to :func:`pandas.read_excel`,
+        such as ``sheet_name``, ``header``, and ``usecols``.
+
+    Returns
+    -------
+    pandas.DataFrame
+    """
+    with warnings.catch_warnings():
+        warnings.filterwarnings(
+            "ignore",
+            message="Unknown extension is not supported and will be removed",
+            category=UserWarning,
+            module="openpyxl.worksheet._reader",
+        )
+        return pd.read_excel(*args, **kwargs)