Merge pull request #15 from earthlab/master

Update jlpalomino fork from earthpy master

CHANGELOG.md

@@ -5,7 +5,9 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [unreleased]
+
+## [0.6.8]
+* Add multi-panel plotting to plot_bands (@lwasser, #316)
 * Fix bug in plot_rgb where multipanel plots are blank (@lwasser, #313)
 * Add example vignette for calculating and classifying NDVI with EarthPy (@jlpalomino, #266)
 

docs/conf.py

@@ -24,9 +24,9 @@
 author = "Earth Lab"
 
 # The short X.Y version
-version = "0.6.7"
+version = "0.6.8"
 # The full version, including alpha/beta/rc tags
-release = "0.6.7"
+release = "0.6.8"
 
 
 # -- General configuration ---------------------------------------------------

earthpy/plot.py

@@ -71,6 +71,61 @@ def colorbar(mapobj, size="3%", pad=0.09):
     return fig.colorbar(mapobj, cax=cax)
 
 
+def _plot_image(
+    arr_im,
+    cmap="Greys_r",
+    title=None,
+    extent=None,
+    cbar=True,
+    scale=True,
+    vmin=None,
+    vmax=None,
+    ax=None,
+):
+
+    """
+    Create a matplotlib figure with an image axis and associated extent.
+
+    Parameters
+    ----------
+    arr_im : numpy array
+        An n-dimensional numpy array to plot.
+    cmap : str (default = "Greys_r")
+        Colormap name for plots.
+    title : str or list (optional)
+        Title of one band or list of titles with one title per band.
+    extent : tuple (optional)
+        Bounding box that the data will fill: (minx, miny, maxx, maxy).
+    cbar : Boolean (default = True)
+        Turn off colorbar if needed.
+    scale : Boolean (Default = True)
+        Turn off bytescale scaling if needed.
+    vmin : Int (Optional)
+        Specify the vmin to scale imshow() plots.
+    vmax : Int (Optional)
+        Specify the vmax to scale imshow() plots.
+    ax : Matplotlib axes object (Optional)
+        Matplotlib axis object to plot image.
+
+    Returns
+    ----------
+    ax : axes object
+        The axes object(s) associated with the plot.
+    """
+
+    if scale:
+        arr_im = es.bytescale(arr_im)
+
+    im = ax.imshow(arr_im, cmap=cmap, vmin=vmin, vmax=vmax, extent=extent)
+    if title:
+        ax.set(title=title)
+    if cbar:
+        colorbar(im)
+    ax.set(xticks=[], yticks=[])
+
+    return ax
+
+
 def plot_bands(
     arr,
     cmap="Greys_r",
@@ -82,6 +137,7 @@ def plot_bands(
     scale=True,
     vmin=None,
     vmax=None,
+    ax=None,
 ):
     """Plot each band in a numpy array in its own axis.
 
@@ -112,11 +168,8 @@ def plot_bands(
 
     Returns
     ----------
-    tuple
-        fig : figure object
-            The figure of the plotted band(s).
-        ax or axs : axes object(s)
-            The axes object(s) associated with the plot.
+    ax or axs : matplotlib.axes._subplots.AxesSubplot object(s)
+        The axes object(s) associated with the plot.
 
     Example
     -------
@@ -133,7 +186,7 @@ def plot_bands(
         ...                   figsize=(8, 3))
         array([<matplotlib.axes._subplots.AxesSubplot object at 0x...
     """
-
+    show = False
     try:
         arr.ndim
     except AttributeError:
@@ -171,19 +224,23 @@ def plot_bands(
             band = i + 1
 
             arr_im = arr[i]
-            if scale:
-                arr_im = es.bytescale(arr_im)
 
-            im = ax.imshow(
-                arr_im, cmap=cmap, vmin=vmin, vmax=vmax, extent=extent
-            )
             if title:
-                ax.set(title=title[i])
+                the_title = title[i]
             else:
-                ax.set(title="Band %i" % band)
-            if cbar:
-                colorbar(im)
-            ax.set(xticks=[], yticks=[])
+                the_title = "Band {}".format(band)
+
+            _plot_image(
+                arr_im,
+                cmap=cmap,
+                cbar=cbar,
+                scale=scale,
+                vmin=vmin,
+                vmax=vmax,
+                extent=extent,
+                title=the_title,
+                ax=ax,
+            )
         # This loop clears out the plots for axes which are empty
         # A matplotlib axis grid is always uniform with x cols and x rows
         # eg: an 8 band plot with 3 cols will always be 3 x 3
@@ -198,17 +255,26 @@ def plot_bands(
         # If it's a 2 dimensional array with a 3rd dimension
         arr = np.squeeze(arr)
 
-        fig, ax = plt.subplots(figsize=figsize)
-        if scale:
-            arr = es.bytescale(arr)
+        if ax is None:
+            fig, ax = plt.subplots(figsize=figsize)
+            show = True
 
-        im = ax.imshow(arr, cmap=cmap, vmin=vmin, vmax=vmax, extent=extent)
         if title:
-            ax.set(title=title[0])
-        ax.set(xticks=[], yticks=[])
-        if cbar:
-            colorbar(im)
-        plt.show()
+            title = title[0]
+
+        _plot_image(
+            arr,
+            cmap=cmap,
+            scale=scale,
+            cbar=cbar,
+            vmin=vmin,
+            vmax=vmax,
+            extent=extent,
+            title=title,
+            ax=ax,
+        )
+        if show:
+            plt.show()
         return ax
 
 
@@ -269,14 +335,12 @@ def plot_rgb(
         The intended title of the plot.
     stretch : Boolean (optional)
         Application of a linear stretch. If set to True, a linear stretch will be applied.
+
     Returns
     ----------
-    tuple
-        fig : figure object
-            The figure object associated with the 3 band image. If the
-            ax keyword is specified, the figure return will be None.
-        ax : axes object
-            The axes object associated with the 3 band image.
+    ax : axes object
+        The axes object associated with the 3 band image.
+
     Example
     -------
 

earthpy/tests/test_io.py

@@ -9,6 +9,16 @@
 import earthpy.io as eio
 
 
+RUNNING_ON_CI = False
+if "CI" in os.environ:
+    if os.environ["CI"]:
+        RUNNING_ON_CI = True
+
+skip_on_ci = pytest.mark.skipif(
+    RUNNING_ON_CI, reason="Test fails intermittently on CI systems."
+)
+
+
 @pytest.fixture
 def eld(tmpdir):
     return eio.Data(path=tmpdir)
@@ -87,6 +97,7 @@ def test_continental_divide_trail():
 ]
 
 
+@skip_on_ci
 @pytest.mark.vcr()
 def test_urls_are_valid():
     """ Test responses for each dataset to ensure valid URLs. """
@@ -125,13 +136,15 @@ def test_invalid_dataset_key(eld):
         eld.get_data(key="some non-existent key")
 
 
+@skip_on_ci
 @pytest.mark.vcr()
 def test_valid_download_file(eld):
     """ Test that single files get downloaded. """
     file = eld.get_data("little-text-file")
     assert os.path.isfile(file)
 
 
+@skip_on_ci
 @pytest.mark.vcr()
 def test_valid_download_zip(eld):
     """ Test that zipped files get downloaded and extracted. """
@@ -140,6 +153,7 @@ def test_valid_download_zip(eld):
     assert path_has_contents
 
 
+@skip_on_ci
 @pytest.mark.parametrize("replace_arg_value", [True, False])
 @pytest.mark.vcr()
 def test_replace_arg_controle_overwrite(eld, replace_arg_value):
@@ -154,6 +168,7 @@ def test_replace_arg_controle_overwrite(eld, replace_arg_value):
         assert mtime1 == mtime2
 
 
+@skip_on_ci
 @pytest.mark.vcr()
 def test_arbitrary_url_file_download(eld):
     """ Verify that arbitrary URLs work for data file downloads. """
@@ -170,6 +185,7 @@ def test_invalid_data_type(eld):
         eld.get_data("invalid-data-type")
 
 
+@skip_on_ci
 @pytest.mark.vcr()
 def test_arbitrary_url_zip_download(eld):
     """ Verify that aribitrary URLs work for zip file downloads. """
@@ -180,27 +196,31 @@ def test_arbitrary_url_zip_download(eld):
     assert path_has_contents
 
 
+@skip_on_ci
 @pytest.mark.vcr()
 def test_url_download_tar_file(eld):
     """ Ensure that tar files are downloaded and extracted. """
     path = eld.get_data(url="https://ndownloader.figshare.com/files/14615411")
     assert "abc.txt" in os.listdir(path)
 
 
+@skip_on_ci
 @pytest.mark.vcr()
 def test_url_download_tar_gz_file(eld):
     """ Ensure that tar.gz files are downloaded and extracted. """
     path = eld.get_data(url="https://ndownloader.figshare.com/files/14615414")
     assert "abc.txt" in os.listdir(path)
 
 
+@skip_on_ci
 @pytest.mark.vcr()
 def test_url_download_txt_file_with_content_disposition(eld):
     """ Test arbitrary URL download with content-disposition. """
     path = eld.get_data(url="https://ndownloader.figshare.com/files/14555681")
     assert path.endswith("abc.txt") and os.path.isfile(path)
 
 
+@skip_on_ci
 @pytest.mark.parametrize("verbose_arg_value", [True, False])
 @pytest.mark.vcr()
 def test_verbose_arg_works(eld, verbose_arg_value, capsys):

earthpy/tests/test_plot_bands.py

@@ -224,3 +224,20 @@ def test_extent(one_band_3dims):
     # Cbar should be scaled between the vmin and vmax vals
     assert pl_extent == ext
     plt.close()
+
+
+def test_multi_panel_single_band(one_band_3dims):
+    """Test that multi panel works with single band arr."""
+
+    title1 = "Title axis one"
+    title2 = "Title axis two"
+    f, (ax1, ax2) = plt.subplots(2, 1)
+    ep.plot_bands(one_band_3dims, title=title1, ax=ax1)
+    ep.plot_bands(one_band_3dims, title=title2, ax=ax2)
+
+    # get all axis subplot elements - note this returns subplots and axes
+    all_axes = f.axes
+
+    assert len(all_axes) == 4
+    assert all_axes[0].get_title() == title1
+    assert all_axes[1].get_title() == title2

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.6.7
+current_version = 0.6.8
 commit = True
 tag = True
 

setup.py

@@ -22,7 +22,7 @@
         description=DESCRIPTION,
         long_description=LONG_DESCRIPTION,
         long_description_content_type="text/markdown",
-        version="0.6.7",
+        version="0.6.8",
         packages=["earthpy"],
         install_requires=[
             "geopandas",