AttributeError: module 'matplotlib.cm' has no attribute 'get_cmap' with Matplotlib 3.9

[QuLogic]

The matplotlib.cm.get_cmap function was deprecated in Matplotlib 3.7: https://matplotlib.org/stable/api/prev_api_changes/api_changes_3.7.0.html#deprecation-of-top-level-cmap-registration-and-access-functions-in-mpl-cm

It is being removed in 3.9, which causes a test failure:

___________________________ test_example[filepath1] ____________________________

filepath = PosixPath('/builddir/build/BUILD/NeuroM-3.2.10/examples/density_plot.py')

    @pytest.mark.parametrize("filepath", EXAMPLES_DIR.glob("*.py"))
    def test_example(filepath):
    
        spec = importlib.util.spec_from_file_location(filepath.stem, filepath)
        module = spec.loader.load_module()
    
        with tempfile.TemporaryDirectory() as tempdir:
    
            # change directory to avoid creating files in the root folder
            try:
                cwd = os.getcwd()
                os.chdir(tempdir)
>               module.main()

tests/test_examples.py:25: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
examples/density_plot.py:117: in main
    plot_density(neurons)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

population = <neurom.core.population.Population object at 0x7fdf028645f0>
bins = 100, new_fig = True, subplot = 111, levels = None, plane = 'xy'
colorlabel = 'Nodes per unit area', labelfontsize = 16, color_map = 'Reds'
no_colorbar = False, threshold = 0.01
neurite_type = <NeuriteType.basal_dendrite: 3>, kwargs = {}
fig = <Figure size 640x480 with 1 Axes>, ax = <Axes: >
H1 = array([[0., 0., 0., ..., 0., 0., 0.],
       [0., 0., 0., ..., 0., 0., 0.],
       [0., 0., 0., ..., 0., 0., 0.],
       ...,
       [0., 0., 0., ..., 0., 0., 0.],
       [0., 0., 0., ..., 0., 0., 0.],
       [0., 0., 0., ..., 0., 0., 0.]])
xedges1 = array([-150.66921768, -147.69081765, -144.71241761, -141.73401757,
       -138.75561753, -135.77721749, -132.79881745,... 129.30038604,  132.27878608,
        135.25718612,  138.23558616,  141.2139862 ,  144.19238624,
        147.17078628])
yedges1 = array([-150.48435587, -147.43490588, -144.38545588, -141.33600588,
       -138.28655589, -135.23710589, -132.18765589,... 136.16394384,  139.21339384,
        142.26284383,  145.31229383,  148.36174383,  151.41119382,
        154.46064382])
mask = array([[ True,  True,  True, ...,  True,  True,  True],
       [ True,  True,  True, ...,  True,  True,  True],
      ...True],
       [ True,  True,  True, ...,  True,  True,  True],
       [ True,  True,  True, ...,  True,  True,  True]])
H2 = masked_array(
  data=[[--, --, --, ..., --, --, --],
        [--, --, --, ..., --, --, --],
        [--, --, --, ..., ...  True,  True, ...,  True,  True,  True],
        [ True,  True,  True, ...,  True,  True,  True]],
  fill_value=1e+20)

    def plot_density(population,  # pylint: disable=too-many-arguments, too-many-locals
                     bins=100, new_fig=True, subplot=111, levels=None, plane='xy',
                     colorlabel='Nodes per unit area', labelfontsize=16,
                     color_map='Reds', no_colorbar=False, threshold=0.01,
                     neurite_type=NeuriteType.basal_dendrite, **kwargs):
        """Plots the 2d histogram of the center
           coordinates of segments in the selected plane.
        """
        fig, ax = matplotlib_utils.get_figure(new_fig=new_fig, subplot=subplot)
    
        H1, xedges1, yedges1 = extract_density(population, plane=plane, bins=bins,
                                               neurite_type=neurite_type)
    
        mask = H1 < threshold  # mask = H1==0
        H2 = np.ma.masked_array(H1, mask)
    
>       colormap = mpl.cm.get_cmap(color_map).copy()
E       AttributeError: module 'matplotlib.cm' has no attribute 'get_cmap'

examples/density_plot.py:73: AttributeError

[QuLogic]

You can fix it by using matplotlib.pyplot .get_cmap instead (and while at it, you really should replace import pylab as plt with import matplotlib.pyplot as plt).

[eleftherioszisis]

Thank you for catching that. I merged a fix with your suggestion.