Merge pull request #849 from dopplershift/masked-gradient

Fix mask propagation in gradient

.circleci/config.yml

@@ -26,7 +26,8 @@ jobs:
             sudo apt-get install libgeos-dev libproj-dev
             python3 -m venv venv
             . venv/bin/activate
-            pip install ".[test,cdm]" "shapely<1.5.17.post1" -f https://unidata-python.s3.amazonaws.com/wheelhouse/index.html
+            pip install --upgrade pytest
+            pip install ".[test,cdm]" "shapely<1.5.17.post1" --upgrade --upgrade-strategy=eager -f https://unidata-python.s3.amazonaws.com/wheelhouse/index.html
 
       - save_cache:
           paths:
@@ -43,4 +44,3 @@ jobs:
       - store_artifacts:
           path: test-reports
           destination: test-reports
-

.mailmap

@@ -8,3 +8,5 @@ Brian Mapes <[email protected]>
 Kristen Pozsonyi <[email protected]>
 Daryl Herzmann <[email protected]>
 Kishan Mehta <[email protected]>
+Matt Wilson <[email protected]>
+Andrew Huang <[email protected]>

.travis.yml

@@ -103,7 +103,7 @@ before_install:
   - touch $WHEELDIR/download_marker && ls -lrt $WHEELDIR;
   - travis_wait pip wheel -w $WHEELDIR $EXTRA_PACKAGES -f $WHEELHOUSE $PRE $VERSIONS;
   - pip install $EXTRA_PACKAGES --upgrade --upgrade-strategy=eager --no-index -f file://$PWD/$WHEELDIR $VERSIONS;
-  - travis_wait pip wheel -w $WHEELDIR ".[$EXTRA_INSTALLS]" $EXTRA_PACKAGES -f $WHEELHOUSE $PRE $VERSIONS;
+  - travis_wait 30 pip wheel -w $WHEELDIR ".[$EXTRA_INSTALLS]" $EXTRA_PACKAGES -f $WHEELHOUSE $PRE $VERSIONS;
   - rm -f $WHEELDIR/MetPy*.whl;
 
 install:

AUTHORS.txt

@@ -3,8 +3,12 @@ UCAR/Unidata
 Aaron Hill
 Abby Kenyon
 Alex Haberlie
+Andrew Huang
+Assela Pathirana
 Brian Mapes
 Bryan Guarente
+Claude Dicaire
+Dan Dawson
 Daryl Herzmann
 Denis Sergeev
 Eric Bruning

metpy/calc/tests/test_tools.py

@@ -614,6 +614,18 @@ def test_first_derivative_scalar_delta():
     assert_array_almost_equal(df_dx, np.array([1., 1., 1.]), 6)
 
 
+def test_first_derivative_masked():
+    """Test that first_derivative properly propagates masks."""
+    data = np.ma.arange(7)
+    data[3] = np.ma.masked
+    df_dx = first_derivative(data, delta=1)
+
+    truth = np.ma.array([1., 1., 1., 1., 1., 1., 1.],
+                        mask=[False, False, True, True, True, False, False])
+    assert_array_almost_equal(df_dx, truth)
+    assert_array_equal(df_dx.mask, truth.mask)
+
+
 def test_second_derivative(deriv_1d_data):
     """Test second_derivative with a simple 1D array."""
     d2v_dx2 = second_derivative(deriv_1d_data.values, x=deriv_1d_data.x)

metpy/tests/test_units.py

@@ -11,14 +11,34 @@
 import pandas as pd
 import pytest
 
-from metpy.testing import assert_array_equal, set_agg_backend  # noqa: F401
-from metpy.units import (atleast_1d, atleast_2d, check_units, diff,
+from metpy.testing import assert_array_almost_equal, assert_array_equal
+from metpy.testing import set_agg_backend  # noqa: F401
+from metpy.units import (atleast_1d, atleast_2d, check_units, concatenate, diff,
                          pandas_dataframe_to_unit_arrays, units)
 
 
 warnings.filterwarnings('ignore', 'Pandas doesn\'t allow columns to be created', UserWarning)
 
 
+def test_concatenate():
+    """Test basic functionality of unit-aware concatenate."""
+    result = concatenate((3 * units.meter, 400 * units.cm))
+    assert_array_equal(result, np.array([3, 4]) * units.meter)
+    assert not isinstance(result.m, np.ma.MaskedArray)
+
+
+def test_concatenate_masked():
+    """Test concatenate preserves masks."""
+    d1 = units.Quantity(np.ma.array([1, 2, 3], mask=[False, True, False]), 'degC')
+    result = concatenate((d1, 32 * units.degF))
+
+    truth = np.ma.array([1, np.inf, 3, 0])
+    truth[1] = np.ma.masked
+
+    assert_array_almost_equal(result, units.Quantity(truth, 'degC'), 6)
+    assert_array_equal(result.mask, np.array([False, True, False, False]))
+
+
 @pytest.mark.mpl_image_compare(tolerance=0, remove_text=True)
 def test_axhline():
     r"""Ensure that passing a quantity to axhline does not error."""

metpy/units.py

@@ -101,7 +101,13 @@ def concatenate(arrs, axis=0):
             a = a.to(dest).magnitude
         data.append(np.atleast_1d(a))
 
-    return units.Quantity(np.concatenate(data, axis=axis), dest)
+    # Use masked array concatenate to ensure masks are preserved, but convert to an
+    # array if there are no masked values.
+    data = np.ma.concatenate(data, axis=axis)
+    if not np.any(data.mask):
+        data = np.asarray(data)
+
+    return units.Quantity(data, dest)
 
 
 def diff(x, **kwargs):

setup.py

@@ -59,7 +59,7 @@
                 'netCDF4'],
         'examples': ['cartopy>=0.13.1'],
         'test': ['pytest>=2.4', 'pytest-runner', 'pytest-mpl', 'pytest-flake8',
-                 'cartopy>=0.13.1', 'flake8>3.2.0', 'flake8-builtins!=1.4.0',
+                 'cartopy>=0.16.0', 'flake8>3.2.0', 'flake8-builtins!=1.4.0',
                  'flake8-comprehensions', 'flake8-copyright',
                  'flake8-docstrings', 'flake8-import-order', 'flake8-mutable',
                  'flake8-pep3101', 'flake8-print', 'flake8-quotes',