Merge pull request #1937 from dopplershift/cleanup

Cleaning up analysis warnings

conftest.py

@@ -151,3 +151,14 @@ 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)

docs/conf.py

@@ -10,7 +10,6 @@
 # serve to show the default.
 
 from datetime import datetime
-import os
 from pathlib import Path
 import re
 import sys

setup.cfg

@@ -57,7 +57,7 @@ where = src
 [options.extras_require]
 doc = sphinx; sphinx-gallery>=0.4; myst-parser; netCDF4
 examples = cartopy>=0.15.0; matplotlib>=2.2.0
-test = pytest>=2.4; pytest-mpl; cartopy>=0.16.0; netCDF4
+test = pytest>=2.4; pytest-mpl; cartopy>=0.17.0; netCDF4
 
 [build_sphinx]
 source-dir = docs/source

src/metpy/io/metar.py

@@ -4,6 +4,7 @@
 """Parse METAR-formatted data."""
 # Import the necessary libraries
 from collections import namedtuple
+import contextlib
 from datetime import datetime
 import warnings
 
@@ -521,11 +522,9 @@ def merge(x, key='     '):
         if len(tmp):
             yield ' '.join(tmp)
 
-    # Open the file
-    myfile = open_as_needed(filename, 'rt')
-
-    # Clean up the file and take out the next line (\n)
-    value = myfile.read().rstrip()
+    # Open the file and clean up and take out the next line (\n)
+    with contextlib.closing(open_as_needed(filename, 'rt')) as myfile:
+        value = myfile.read().rstrip()
     list_values = value.split('\n')
     list_values = list(filter(None, list_values))
 

src/metpy/io/nexrad.py

@@ -964,7 +964,7 @@ def __init__(self, prod):
         offset = prod.thresholds[1] / 1000.
         leading_flags = prod.thresholds[3]
         for i in range(leading_flags, data_levels):
-            self.lut = scale * i + offset
+            self.lut[i] = scale * i + offset
 
 
 class LegacyMapper(DataMapper):

src/metpy/plots/cartopy_utils.py

@@ -27,7 +27,7 @@ def geometries(self):
             # Ensure that the associated files are in the cache
             fname = f'{self.name}_{self.scaler.scale}'
             for extension in ['.dbf', '.shx']:
-                get_test_data(fname + extension)
+                get_test_data(fname + extension, as_file_obj=False)
             path = get_test_data(fname + '.shp', as_file_obj=False)
             return iter(tuple(shapereader.Reader(path).geometries()))
 

src/metpy/testing.py

@@ -7,6 +7,7 @@
 * unit-aware test functions
 * code for testing matplotlib figures
 """
+import contextlib
 import functools
 
 import numpy as np
@@ -57,30 +58,28 @@ def get_upper_air_data(date, station):
                       '2002-11-11T00Z_BNA': 'nov11_sounding.txt',
                       '2010-12-09T12Z_BOI': 'dec9_sounding.txt'}
 
-    fname = sounding_files[sounding_key]
-    fobj = get_test_data(fname)
+    # Initiate lists for variables
+    arr_data = []
 
     def to_float(s):
         # Remove all whitespace and replace empty values with NaN
         if not s.strip():
             s = 'nan'
         return float(s)
 
-    # Skip dashes, column names, units, and more dashes
-    for _ in range(4):
-        fobj.readline()
-
-    # Initiate lists for variables
-    arr_data = []
+    with contextlib.closing(get_test_data(sounding_files[sounding_key])) as fobj:
+        # Skip dashes, column names, units, and more dashes
+        for _ in range(4):
+            fobj.readline()
 
-    # Read all lines of data and append to lists only if there is some data
-    for row in fobj:
-        level = to_float(row[0:7])
-        values = (to_float(row[7:14]), to_float(row[14:21]), to_float(row[21:28]),
-                  to_float(row[42:49]), to_float(row[49:56]))
+        # Read all lines of data and append to lists only if there is some data
+        for row in fobj:
+            level = to_float(row[0:7])
+            values = (to_float(row[7:14]), to_float(row[14:21]), to_float(row[21:28]),
+                      to_float(row[42:49]), to_float(row[49:56]))
 
-        if any(np.invert(np.isnan(values[1:]))):
-            arr_data.append((level,) + values)
+            if any(np.invert(np.isnan(values[1:]))):
+                arr_data.append((level,) + values)
 
     p, z, t, td, direc, spd = np.array(arr_data).T
 
@@ -200,18 +199,6 @@ def assert_xarray_allclose(actual, desired):
     assert desired.attrs == actual.attrs
 
 
-@pytest.fixture(scope='module', autouse=True)
-def set_agg_backend():
-    """Fixture to ensure the Agg backend is active."""
-    import matplotlib.pyplot as plt
-    prev_backend = plt.get_backend()
-    try:
-        plt.switch_backend('agg')
-        yield
-    finally:
-        plt.switch_backend(prev_backend)
-
-
 def check_and_silence_warning(warn_type):
     """Decorate a function to swallow some warning type, making sure they are present.
 

tests/interpolate/test_grid.py

@@ -164,6 +164,7 @@ def test_inverse_distance_to_grid(method, test_data, test_grid):
     xg, yg = test_grid
 
     extra_kw = {}
+    test_file = ''
     if method == 'cressman':
         extra_kw['r'] = 20
         extra_kw['min_neighbors'] = 1

tests/interpolate/test_points.py

@@ -119,27 +119,28 @@ def test_inverse_distance_to_points(method, test_data, test_points):
     obs_points = np.vstack([xp, yp]).transpose()
 
     extra_kw = {}
-    if method == 'cressman':
-        extra_kw['r'] = 20
-        extra_kw['min_neighbors'] = 1
-        test_file = 'cressman_r20_mn1.npz'
-    elif method == 'barnes':
-        extra_kw['r'] = 40
-        extra_kw['kappa'] = 100
-        test_file = 'barnes_r40_k100.npz'
-    elif method == 'shouldraise':
+    if method == 'shouldraise':
         extra_kw['r'] = 40
         with pytest.raises(ValueError):
             inverse_distance_to_points(
                 obs_points, z, test_points, kind=method, **extra_kw)
-        return
-
-    img = inverse_distance_to_points(obs_points, z, test_points, kind=method, **extra_kw)
-
-    with get_test_data(test_file) as fobj:
-        truth = np.load(fobj)['img'].reshape(-1)
-
-    assert_array_almost_equal(truth, img)
+    else:
+        test_file = ''
+        if method == 'cressman':
+            extra_kw['r'] = 20
+            extra_kw['min_neighbors'] = 1
+            test_file = 'cressman_r20_mn1.npz'
+        elif method == 'barnes':
+            extra_kw['r'] = 40
+            extra_kw['kappa'] = 100
+            test_file = 'barnes_r40_k100.npz'
+
+        img = inverse_distance_to_points(obs_points, z, test_points, kind=method, **extra_kw)
+
+        with get_test_data(test_file) as fobj:
+            truth = np.load(fobj)['img'].reshape(-1)
+
+        assert_array_almost_equal(truth, img)
 
 
 @pytest.mark.parametrize('method', ['natural_neighbor', 'cressman', 'barnes', 'linear',

tests/io/test_nexrad.py

@@ -2,7 +2,7 @@
 # Distributed under the terms of the BSD 3-Clause License.
 # SPDX-License-Identifier: BSD-3-Clause
 """Test the `nexrad` module."""
-
+import contextlib
 from datetime import datetime
 from io import BytesIO
 import logging
@@ -76,7 +76,8 @@ def read(self, n=None):
 
 def test_doubled_file():
     """Test for #489 where doubled-up files didn't parse at all."""
-    data = get_test_data('Level2_KFTG_20150430_1419.ar2v').read()
+    with contextlib.closing(get_test_data('Level2_KFTG_20150430_1419.ar2v')) as infile:
+        data = infile.read()
     fobj = BytesIO(data + data)
     f = Level2File(fobj)
     assert len(f.sweeps) == 12

tests/plots/test_cartopy_utils.py

@@ -7,9 +7,6 @@
 import pytest
 
 import metpy.plots as mpplots
-from metpy.plots import cartopy_utils
-# Fixture to make sure we have the right backend
-from metpy.testing import set_agg_backend  # noqa: F401, I202
 
 MPL_VERSION = matplotlib.__version__[:3]
 
@@ -79,15 +76,15 @@ def test_cartopy_stub(monkeypatch):
     # This makes sure that cartopy is not found
     monkeypatch.setitem(sys.modules, 'cartopy.crs', None)
 
-    ccrs = cartopy_utils.import_cartopy()
+    ccrs = mpplots.cartopy_utils.import_cartopy()
     with pytest.raises(AttributeError, match='without Cartopy'):
         ccrs.PlateCarree()
 
 
 def test_plots_getattr(monkeypatch):
     """Ensure the module-level getattr works."""
     # Make sure the feature is missing
-    monkeypatch.delattr(cartopy_utils, 'USSTATES', raising=False)
+    monkeypatch.delattr(mpplots.cartopy_utils, 'USSTATES', raising=False)
     with pytest.raises(AttributeError, match='Cannot use USSTATES without Cartopy'):
         assert not mpplots.USSTATES  # Should fail on attribute lookup before assert
 

tests/plots/test_declarative.py

@@ -19,8 +19,7 @@
 from metpy.io.metar import parse_metar_file
 from metpy.plots import (BarbPlot, ContourPlot, FilledContourPlot, ImagePlot, MapPanel,
                          PanelContainer, PlotObs)
-# Fixtures to make sure we have the right backend
-from metpy.testing import needs_cartopy, set_agg_backend  # noqa: F401, I202
+from metpy.testing import needs_cartopy
 from metpy.units import units
 
 
@@ -1357,7 +1356,7 @@ def test_save():
     assert fobj.read()
 
 
-def test_show():
+def test_show(set_agg_backend):
     """Test that show works properly."""
     pc = PanelContainer()
 

tests/plots/test_mapping.py

@@ -136,14 +136,13 @@ def test_mercator():
     assert crs.proj4_params['lon_0'] == -100
 
 
-# This won't work until at least CartoPy > 0.16.0
-# def test_mercator_scale_factor():
-#     """Test handling a mercator projection with a scale factor."""
-#     attrs = {'grid_mapping_name': 'mercator', 'scale_factor_at_projection_origin': 0.9}
-#     crs = CFProjection(attrs).to_cartopy()
-#
-#     assert isinstance(crs, ccrs.Mercator)
-#     assert crs.proj4_params['k_0'] == 0.9
+def test_mercator_scale_factor():
+    """Test handling a mercator projection with a scale factor."""
+    attrs = {'grid_mapping_name': 'mercator', 'scale_factor_at_projection_origin': 0.9}
+    crs = CFProjection(attrs).to_cartopy()
+
+    assert isinstance(crs, ccrs.Mercator)
+    assert crs.proj4_params['k_0'] == 0.9
 
 
 def test_geostationary():

tests/plots/test_mpl.py

@@ -11,8 +11,6 @@
 
 # Needed to trigger scattertext monkey-patching
 import metpy.plots  # noqa: F401, I202
-# Fixture to make sure we have the right backend
-from metpy.testing import set_agg_backend  # noqa: F401, I202
 
 
 # Avoiding an image-based test here since that would involve text, which can be tricky

tests/plots/test_skewt.py

@@ -10,8 +10,6 @@
 import pytest
 
 from metpy.plots import Hodograph, SkewT
-# Fixtures to make sure we have the right backend and consistent round
-from metpy.testing import set_agg_backend  # noqa: F401, I202
 from metpy.units import units
 
 

tests/plots/test_station_plot.py

@@ -11,8 +11,6 @@
 
 from metpy.plots import (current_weather, high_clouds, nws_layout, simple_layout,
                          sky_cover, StationPlot, StationPlotLayout)
-# Fixtures to make sure we have the right backend and consistent round
-from metpy.testing import set_agg_backend  # noqa: F401, I202
 from metpy.units import units
 
 

tests/plots/test_util.py

@@ -11,8 +11,6 @@
 import pytest
 
 from metpy.plots import add_metpy_logo, add_timestamp, add_unidata_logo, convert_gempak_color
-# Fixture to make sure we have the right backend
-from metpy.testing import set_agg_backend  # noqa: F401, I202
 
 MPL_VERSION = matplotlib.__version__[:3]
 

tests/units/test_units.py

@@ -9,7 +9,7 @@
 import pytest
 
 from metpy.testing import assert_array_almost_equal, assert_array_equal
-from metpy.testing import assert_nan, set_agg_backend  # noqa: F401
+from metpy.testing import assert_nan
 from metpy.units import check_units, concatenate, pandas_dataframe_to_unit_arrays, units