MNT,FIX test code on python 3.11, fix matplotlib register cmap (#536)

Author: mvdoc

.github/workflows/install_from_wheel.yml

@@ -35,7 +35,7 @@ jobs:
         sudo apt-get update
         sudo apt-get install -y inkscape
         pip install --upgrade pip
-        pip install wheel numpy "cython<3.0"
+        pip install build wheel numpy "cython<3.0"
 
     - name: Create the wheel
       run: python setup.py bdist_wheel

.github/workflows/run_tests.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9, "3.10"]
+        python-version: [3.7, 3.8, 3.9, "3.10", "3.11"]
       max-parallel: 5
 
     steps:
@@ -35,7 +35,7 @@ jobs:
         sudo apt-get update
         sudo apt-get install -y inkscape
         pip install --upgrade pip
-        pip install wheel numpy "cython<3.0"
+        pip install wheel setuptools numpy "cython<3.0"
         # force using latest nibabel
         pip install -U nibabel
         pip install -e . --no-build-isolation

cortex/dataset/views.py

@@ -1,14 +1,23 @@
-import os
 import glob
 import json
+import os
+
 import h5py
 import numpy as np
 
 from .. import options
-from .braindata import BrainData, VolumeData, VertexData
+from .braindata import BrainData, VertexData, VolumeData
 
 default_cmap = options.config.get("basic", "default_cmap")
 
+# register_cmap is deprecated in matplotlib > 3.7.0 and replaced by colormaps.register
+try:
+    from matplotlib import colormaps as cm
+    def register_cmap(cmap):
+        return cm.register(cmap)
+except ImportError:
+    from matplotlib.cm import register_cmap
+
 
 def normalize(data):
     if isinstance(data, tuple):
@@ -193,7 +202,8 @@ def _write_hdf(self, h5, name="data", data=None, xfmname=None):
     def get_cmapdict(self):
         """Returns a dictionary with cmap information."""
 
-        from matplotlib import colors, pyplot as plt
+        from matplotlib import colors
+        from matplotlib import pyplot as plt
 
         try:
             # plt.get_cmap accepts:
@@ -206,18 +216,19 @@ def get_cmapdict(self):
             cmapdir = options.config.get('webgl', 'colormaps')
             colormaps = glob.glob(os.path.join(cmapdir, "*.png"))
             colormaps = dict(((os.path.split(c)[1][:-4], c) for c in colormaps))
-            if not self.cmap in colormaps:
+            if self.cmap not in colormaps:
                 raise ValueError('Unkown color map %s' % self.cmap)
             I = plt.imread(colormaps[self.cmap])
-            cmap = colors.ListedColormap(np.squeeze(I))
+            name = self.cmap if isinstance(self.cmap, str) else self.cmap.name
+            cmap = colors.ListedColormap(np.squeeze(I), name=name)
             # Register colormap to matplotlib to avoid loading it again
-            plt.register_cmap(self.cmap, cmap)
+            register_cmap(cmap)
 
         return dict(cmap=cmap, vmin=self.vmin, vmax=self.vmax)
 
     @property
     def raw(self):
-        from matplotlib import colors, cm
+        from matplotlib import cm, colors
 
         cmap = self.get_cmapdict()['cmap']
         # Normalize colors according to vmin, vmax
@@ -398,5 +409,5 @@ def u(s, encoding='utf8'):
         return s
 
 
-from .viewRGB import VolumeRGB, VertexRGB, Colors
-from .view2D import Volume2D, Vertex2D
+from .viewRGB import Colors, VertexRGB, VolumeRGB
+from .view2D import Vertex2D, Volume2D

cortex/utils.py

@@ -23,6 +23,14 @@
 from .testing_utils import INKSCAPE_VERSION
 from .volume import anat2epispace
 
+# register_cmap is deprecated in matplotlib > 3.7.0 and replaced by colormaps.register
+try:
+    from matplotlib import colormaps as cm
+    def register_cmap(cmap):
+        return cm.register(cmap)
+except ImportError:
+    from matplotlib.cm import register_cmap
+
 
 class DocLoader(object):
     def __init__(self, func, mod, package):
@@ -1000,9 +1008,9 @@ def get_cmap(name):
     colormaps = dict((c[:-4], os.path.join(cmapdir, c)) for c in colormaps)
     if name in colormaps:
         I = plt.imread(colormaps[name])
-        cmap = colors.ListedColormap(np.squeeze(I))
+        cmap = colors.ListedColormap(np.squeeze(I), name=name)
         try:
-            plt.cm.register_cmap(name,cmap)
+            register_cmap(cmap)
         except:
             print(f"Color map {name} is already registered.")
     else:

pyproject.toml

@@ -1,7 +1,8 @@
 [build-system]
 # Minimum requirements for the build system to execute, according to PEP518
 # specification.
-requires = ["numpy", "cython<3.0", "setuptools", "wheel"]
+requires = ["setuptools", "build", "numpy", "cython<3.0", "wheel"]
+build-backend = "setuptools.build_meta"
 
 [tool.codespell]
 skip = '.git,*.pdf,*.svg,*.css,*.min.*,*.gii,resources,OpenCTM-1.0.3,filestore,build,_build'

requirements.txt

@@ -1,3 +1,4 @@
+setuptools
 future
 numpy
 scipy