Merge pull request #3255 from dopplershift/silence-warnings

Cleanup warnings from tests

.github/actions/install-pypi/action.yml

@@ -44,6 +44,12 @@ runs:
       shell: bash
       run: echo "PIP_NO_BINARY=shapely" >> $GITHUB_ENV
 
+    - name: Upgrade pip and setuptools
+      shell: bash
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install --upgrade setuptools
+
     - name: Set dependency groups for install
       shell: bash
       run: |

ci/download_cartopy_maps.py

@@ -21,9 +21,6 @@ def grab_ne(category, feature, res):
         for r in ['110m', '50m', '10m']:
             grab_ne('cultural', feat, r)
 
-    for feat, r in [('coastline', '10m'), ('coastline', '50m'), ('coastline', '110m'),
-                    ('lakes', '10m'), ('lakes', '50m'),
-                    ('land', '10m'), ('land', '50m'), ('land', '110m'),
-                    ('ocean', '110m'), ('ocean', '50m'),
-                    ('rivers_lake_centerlines', '10m'), ('rivers_lake_centerlines', '110m')]:
-        grab_ne('physical', feat, r)
+    for feat in ['coastline', 'lakes', 'land', 'ocean', 'rivers_lake_centerlines']:
+        for r in ['110m', '50m', '10m']:
+            grab_ne('physical', feat, r)

conftest.py

@@ -111,9 +111,8 @@ def test_da_xy():
          'lambert_conformal': ([], '')},
         coords={
             'time': xarray.DataArray(
-                numpy.array([numpy.datetime64('2018-07-01T00:00'),
-                             numpy.datetime64('2018-07-01T06:00'),
-                             numpy.datetime64('2018-07-01T12:00')]),
+                numpy.array(['2018-07-01T00:00', '2018-07-01T06:00', '2018-07-01T12:00'],
+                            dtype='datetime64[ns]'),
                 name='time',
                 dims=['time']
             ),
@@ -153,17 +152,6 @@ def test_da_xy():
     return ds.metpy.parse_cf('temperature')
 
 
-@pytest.fixture()
-def set_agg_backend():
-    """Fixture to ensure the Agg backend is active."""
-    prev_backend = matplotlib.pyplot.get_backend()
-    try:
-        matplotlib.pyplot.switch_backend('agg')
-        yield
-    finally:
-        matplotlib.pyplot.switch_backend(prev_backend)
-
-
 @pytest.fixture(params=['dask', 'xarray', 'masked', 'numpy'])
 def array_type(request):
     """Return an array type for testing calc functions."""

docs/conf.py

@@ -9,7 +9,7 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-from datetime import datetime
+from datetime import datetime, timezone
 import inspect
 import os
 from pathlib import Path
@@ -129,7 +129,7 @@
 
 # The encoding of source files.
 # source_encoding = 'utf-8-sig'
-cur_date = datetime.utcnow()
+cur_date = datetime.now(timezone.utc)
 
 # The main toctree document.
 master_doc = 'index'

examples/meteogram_metpy.py

@@ -46,7 +46,7 @@ def __init__(self, fig, dates, probeid, time=None, axis=0):
             axis: number that controls the new axis to be plotted (FOR FUTURE)
         """
         if not time:
-            time = dt.datetime.utcnow()
+            time = dt.datetime.now(dt.timezone.utc)
         self.start = dates[0]
         self.fig = fig
         self.end = dates[-1]

pyproject.toml

@@ -28,13 +28,13 @@ requires-python = ">=3.9"
 dependencies = [
     "matplotlib>=3.5.0",
     "numpy>=1.20.0",
-    "pandas>=1.2.0",
-    "pint>=0.15",
+    "pandas>=1.4.0",
+    "pint>=0.17",
     "pooch>=1.2.0",
     "pyproj>=3.0.0",
-    "scipy>=1.6.0",
+    "scipy>=1.8.0",
     "traitlets>=5.0.5",
-    "xarray>=0.18.0"
+    "xarray>=0.21.0"
 ]
 
 [project.entry-points."xarray.backends"]
@@ -103,6 +103,18 @@ norecursedirs = "build docs .idea"
 doctest_optionflags = "NORMALIZE_WHITESPACE"
 mpl-results-path = "test_output"
 xfail_strict = true
+filterwarnings = [
+    "error",
+    "ignore:numpy.ndarray size changed:RuntimeWarning",
+    # To be removed in the next python-dateutil release.
+    # See: https://github.com/dateutil/dateutil/issues/1314
+    'ignore:datetime.datetime.utcfromtimestamp\(\) is deprecated:DeprecationWarning:dateutil.tz.tz:37',
+    # Numpy deprecation triggered by Pint: https://github.com/hgrecco/pint/pull/1880
+    "ignore:Conversion of an array with ndim > 0 to a scalar is deprecated:DeprecationWarning:pint.facets.plain.quantity:575",
+    # PyProj automatically dispatching for single point, will be waiting for NumPy 2.0 to address
+    # See: https://github.com/pyproj4/pyproj/issues/1309
+    "ignore:Conversion of an array with ndim > 0 to a scalar is deprecated:DeprecationWarning:pyproj.geod:404"
+]
 
 [tool.ruff]
 line-length = 95

src/metpy/calc/basic.py

@@ -93,7 +93,7 @@ def wind_direction(u, v, convention='from'):
     origshape = wdir.shape
     wdir = np.atleast_1d(wdir)
 
-    # Handle oceanographic convection
+    # Handle oceanographic convention
     if convention == 'to':
         wdir -= units.Quantity(180., 'deg')
     elif convention not in ('to', 'from'):
@@ -405,8 +405,8 @@ def apparent_temperature(temperature, relative_humidity, speed, face_level_winds
     # NB: older numpy.ma.where does not return a masked array
     app_temperature = masked_array(
         np.ma.where(masked_array(wind_chill_temperature).mask,
-                    heat_index_temperature.to(temperature.units),
-                    wind_chill_temperature.to(temperature.units)
+                    heat_index_temperature.m_as(temperature.units),
+                    wind_chill_temperature.m_as(temperature.units)
                     ), temperature.units)
 
     # If mask_undefined is False, then set any masked values to the temperature
@@ -829,6 +829,9 @@ def smooth_gaussian(scalar_grid, n):
     num_ax = len(scalar_grid.shape)
     # Assume the last two axes represent the horizontal directions
     sgma_seq = [sgma if i > num_ax - 3 else 0 for i in range(num_ax)]
+    # Drop units as necessary to avoid warnings from scipy doing so--units will be reattached
+    # if necessary by wrapper
+    scalar_grid = getattr(scalar_grid, 'magnitude', scalar_grid)
 
     filter_args = {'sigma': sgma_seq, 'truncate': 2 * np.sqrt(2)}
     if hasattr(scalar_grid, 'mask'):
@@ -1104,6 +1107,8 @@ def zoom_xarray(input_field, zoom, output=None, order=3, mode='constant', cval=0
         available.
 
     """
+    # Dequantify input to avoid warnings and make sure units propagate
+    input_field = input_field.metpy.dequantify()
     # Zoom data
     zoomed_data = scipy_zoom(
         input_field.data, zoom, output=output, order=order, mode=mode, cval=cval,

src/metpy/calc/cross_sections.py

@@ -123,8 +123,8 @@ def unit_vectors_from_cross_section(cross, index='index'):
 
     """
     x, y = distances_from_cross_section(cross)
-    dx_di = first_derivative(x, axis=index).values
-    dy_di = first_derivative(y, axis=index).values
+    dx_di = first_derivative(x, axis=index).data
+    dy_di = first_derivative(y, axis=index).data
     tangent_vector_mag = np.hypot(dx_di, dy_di)
     unit_tangent_vector = np.vstack([dx_di / tangent_vector_mag, dy_di / tangent_vector_mag])
     unit_normal_vector = np.vstack([-dy_di / tangent_vector_mag, dx_di / tangent_vector_mag])

src/metpy/calc/thermo.py

@@ -1638,7 +1638,7 @@ def saturation_equivalent_potential_temperature(pressure, temperature):
     e = saturation_vapor_pressure(temperature).to('hPa').magnitude
     r = saturation_mixing_ratio(pressure, temperature).magnitude
 
-    th_l = t * (1000 / (p - e)) ** mpconsts.kappa
+    th_l = t * (1000 / (p - e)) ** mpconsts.nounit.kappa
     th_es = th_l * np.exp((3036. / t - 1.78) * r * (1 + 0.448 * r))
 
     return units.Quantity(th_es, units.kelvin)

src/metpy/calc/tools.py

@@ -25,19 +25,19 @@
 
 UND = 'UND'
 UND_ANGLE = -999.
-DIR_STRS = (
+DIR_STRS = [
     'N', 'NNE', 'NE', 'ENE',
     'E', 'ESE', 'SE', 'SSE',
     'S', 'SSW', 'SW', 'WSW',
     'W', 'WNW', 'NW', 'NNW',
     UND
-)  # note the order matters!
+]  # note the order matters!
 
 MAX_DEGREE_ANGLE = units.Quantity(360, 'degree')
 BASE_DEGREE_MULTIPLIER = units.Quantity(22.5, 'degree')
 
 DIR_DICT = {dir_str: i * BASE_DEGREE_MULTIPLIER for i, dir_str in enumerate(DIR_STRS)}
-DIR_DICT[UND] = np.nan
+DIR_DICT[UND] = units.Quantity(np.nan, 'degree')
 
 
 @exporter.export
@@ -1773,16 +1773,15 @@ def parse_angle(input_dir):
 
     """
     if isinstance(input_dir, str):
-        # abb_dirs = abbrieviated directions
-        abb_dirs = _clean_direction([_abbrieviate_direction(input_dir)])
+        abb_dir = _clean_direction([_abbreviate_direction(input_dir)])[0]
+        return DIR_DICT[abb_dir]
     elif hasattr(input_dir, '__len__'):  # handle np.array, pd.Series, list, and array-like
         input_dir_str = ','.join(_clean_direction(input_dir, preprocess=True))
-        abb_dir_str = _abbrieviate_direction(input_dir_str)
+        abb_dir_str = _abbreviate_direction(input_dir_str)
         abb_dirs = _clean_direction(abb_dir_str.split(','))
+        return units.Quantity.from_list(itemgetter(*abb_dirs)(DIR_DICT))
     else:  # handle unrecognizable scalar
-        return np.nan
-
-    return itemgetter(*abb_dirs)(DIR_DICT)
+        return units.Quantity(np.nan, 'degree')
 
 
 def _clean_direction(dir_list, preprocess=False):
@@ -1795,7 +1794,7 @@ def _clean_direction(dir_list, preprocess=False):
                 for the_dir in dir_list]
 
 
-def _abbrieviate_direction(ext_dir_str):
+def _abbreviate_direction(ext_dir_str):
     """Convert extended (non-abbreviated) directions to abbreviation."""
     return (ext_dir_str
             .upper()
@@ -1846,11 +1845,10 @@ def angle_to_direction(input_angle, full=False, level=3):
 
     # clean any numeric strings, negatives, and None does not handle strings with alphabet
     input_angle = units.Quantity(np.array(input_angle).astype(float), origin_units)
-    input_angle[input_angle < 0] = units.Quantity(np.nan, origin_units)
+    input_angle[input_angle < 0] = np.nan
 
-    # normalizer used for angles > 360 degree to normalize between 0 - 360
-    normalizer = np.array(input_angle.m / MAX_DEGREE_ANGLE.m, dtype=int)
-    norm_angles = abs(input_angle - MAX_DEGREE_ANGLE * normalizer)
+    # Normalize between 0 - 360
+    norm_angles = input_angle % MAX_DEGREE_ANGLE
 
     if level == 3:
         nskip = 1
@@ -1889,12 +1887,12 @@ def angle_to_direction(input_angle, full=False, level=3):
         return dir_str_arr
 
     dir_str_arr = ','.join(dir_str_arr)
-    dir_str_arr = _unabbrieviate_direction(dir_str_arr)
+    dir_str_arr = _unabbreviate_direction(dir_str_arr)
     return dir_str_arr.replace(',', ' ') if scalar else dir_str_arr.split(',')
 
 
-def _unabbrieviate_direction(abb_dir_str):
-    """Convert abbrieviated directions to non-abbrieviated direction."""
+def _unabbreviate_direction(abb_dir_str):
+    """Convert abbreviated directions to non-abbreviated direction."""
     return (abb_dir_str
             .upper()
             .replace(UND, 'Undefined ')

src/metpy/interpolate/points.py

@@ -8,7 +8,7 @@
 
 import numpy as np
 from scipy.interpolate import griddata, Rbf
-from scipy.spatial import cKDTree, ConvexHull, Delaunay, qhull
+from scipy.spatial import cKDTree, ConvexHull, Delaunay, QhullError
 
 from . import geometry, tools
 from ..package_tools import Exporter
@@ -153,7 +153,7 @@ def natural_neighbor_point(xp, yp, variable, grid_loc, tri, neighbors, circumcen
 
             area_list.append(cur_area * value[0])
 
-        except (ZeroDivisionError, qhull.QhullError) as e:
+        except (ZeroDivisionError, QhullError) as e:
             message = ('Error during processing of a grid. '
                        'Interpolation will continue but be mindful '
                        f'of errors in output. {e}')

src/metpy/interpolate/slices.py

@@ -7,7 +7,6 @@
 import xarray as xr
 
 from ..package_tools import Exporter
-from ..units import is_quantity, units
 from ..xarray import check_axis
 
 exporter = Exporter(globals())
@@ -50,17 +49,14 @@ def interpolate_to_slice(data, points, interp_type='linear'):
                          'your data has been parsed by MetPy with proper x and y '
                          'dimension coordinates.') from None
 
+    data = data.metpy.dequantify()
     data_sliced = data.interp({
         x.name: xr.DataArray(points[:, 0], dims='index', attrs=x.attrs),
         y.name: xr.DataArray(points[:, 1], dims='index', attrs=y.attrs)
     }, method=interp_type)
     data_sliced.coords['index'] = range(len(points))
 
-    # Bug in xarray: interp strips units
-    if is_quantity(data.data) and not is_quantity(data_sliced.data):
-        data_sliced.data = units.Quantity(data_sliced.data, data.data.units)
-
-    return data_sliced
+    return data_sliced.metpy.quantify()
 
 
 @exporter.export

src/metpy/io/nexrad.py

@@ -6,7 +6,7 @@
 import bz2
 from collections import defaultdict, namedtuple, OrderedDict
 import contextlib
-import datetime
+from datetime import datetime, timezone
 import logging
 import pathlib
 import re
@@ -75,7 +75,8 @@ def bzip_blocks_decompress_all(data):
 def nexrad_to_datetime(julian_date, ms_midnight):
     """Convert NEXRAD date time format to python `datetime.datetime`."""
     # Subtracting one from julian_date is because epoch date is 1
-    return datetime.datetime.utcfromtimestamp((julian_date - 1) * day + ms_midnight * milli)
+    return datetime.fromtimestamp((julian_date - 1) * day + ms_midnight * milli,
+                                  tz=timezone.utc).replace(tzinfo=None)
 
 
 def remap_status(val):

src/metpy/io/text.py

@@ -4,7 +4,7 @@
 """Support reading information from various text file formats."""
 
 import contextlib
-from datetime import datetime
+from datetime import datetime, timezone
 import re
 import string
 
@@ -95,7 +95,7 @@ def parse_wpc_surface_bulletin(bulletin, year=None):
         text = file.read().decode('utf-8')
 
     parsed_text = []
-    valid_time = datetime.utcnow()
+    valid_time = datetime.now(timezone.utc).replace(tzinfo=None)
     for parts in _regroup_lines(text.splitlines()):
         # A single file may have multiple sets of data that are valid at different times. Set
         # the valid_time string that will correspond to all the following lines parsed, until

src/metpy/plots/_util.py

@@ -3,7 +3,7 @@
 # SPDX-License-Identifier: BSD-3-Clause
 """Utilities for use in making plots."""
 
-from datetime import datetime
+from datetime import datetime, timezone
 
 from matplotlib.collections import LineCollection
 import matplotlib.patheffects as mpatheffects
@@ -24,7 +24,7 @@ def add_timestamp(ax, time=None, x=0.99, y=-0.04, ha='right', high_contrast=Fals
     ax : `matplotlib.axes.Axes`
         The `Axes` instance used for plotting
     time : `datetime.datetime` (or any object with a compatible ``strftime`` method)
-        Specific time to be plotted - datetime.utcnow will be use if not specified
+        Specific time to be plotted - ``datetime.now(UTC)`` will be use if not specified
     x : float
         Relative x position on the axes of the timestamp
     y : float
@@ -52,7 +52,7 @@ def add_timestamp(ax, time=None, x=0.99, y=-0.04, ha='right', high_contrast=Fals
         text_args = {}
     text_args.update(**kwargs)
     if not time:
-        time = datetime.utcnow()
+        time = datetime.now(timezone.utc)
     timestr = time.strftime(time_format)
     # If we don't have a time string after that, assume xarray/numpy and see if item
     if not isinstance(timestr, str):