fix(grid, plotting): bugfixes for all grid instances and plotting code (

#1174)

* grid fix iverts and verts; expose laycbd for use in utilities
* plotting add RuntimeError exception to matplotlib imports to fix Condor containerization issues with flopy

flopy/discretization/grid.py

@@ -180,6 +180,7 @@ def __init__(
 
         self._iverts = None
         self._verts = None
+        self._laycbd = None
 
     ###################################
     # access to basic grid properties
@@ -285,6 +286,13 @@ def botm(self):
     def top_botm(self):
         raise NotImplementedError("must define top_botm in child class")
 
+    @property
+    def laycbd(self):
+        if self._laycbd is None:
+            return None
+        else:
+            return self._laycbd
+
     @property
     def thick(self):
         """

flopy/discretization/structuredgrid.py

@@ -195,9 +195,9 @@ def __init__(
         else:
             self.__nlay = nlay
         if laycbd is not None:
-            self.__laycbd = laycbd
+            self._laycbd = laycbd
         else:
-            self.__laycbd = np.zeros(self.__nlay or (), dtype=int)
+            self._laycbd = np.zeros(self.__nlay or (), dtype=int)
 
     ####################
     # Properties
@@ -464,7 +464,7 @@ def xyzcellcenters(self):
                 z = np.empty((self.__nlay, self.__nrow, self.__ncol))
                 z[0, :, :] = (self._top[:, :] + self._botm[0, :, :]) / 2.0
                 ibs = np.arange(self.__nlay)
-                quasi3d = [cbd != 0 for cbd in self.__laycbd]
+                quasi3d = [cbd != 0 for cbd in self._laycbd]
                 if np.any(quasi3d):
                     ibs[1:] = ibs[1:] + np.cumsum(quasi3d)[: self.__nlay - 1]
                 for l, ib in enumerate(ibs[1:], 1):

flopy/discretization/unstructuredgrid.py

@@ -208,7 +208,7 @@ def verts(self):
         if self._vertices is None:
             return self._vertices
         else:
-            return np.array([t[1:] for t in self._vertices], dtype=float)
+            return np.array([list(t)[1:] for t in self._vertices], dtype=float)
 
     @property
     def ia(self):

flopy/discretization/vertexgrid.py

@@ -4,7 +4,7 @@
 
 try:
     from matplotlib.path import Path
-except ImportError:
+except (ImportError, RuntimeError):
     Path = None
 
 from .grid import Grid, CachedData
@@ -128,11 +128,11 @@ def nvert(self):
 
     @property
     def iverts(self):
-        return [[t[0]] + t[4:] for t in self._cell2d]
+        return [[t[0]] + list(t)[4:] for t in self._cell2d]
 
     @property
     def verts(self):
-        return np.array([t[1:] for t in self._vertices], dtype=float)
+        return np.array([list(t)[1:] for t in self._vertices], dtype=float)
 
     @property
     def shape(self):

flopy/plot/crosssection.py

@@ -4,7 +4,7 @@
     import matplotlib.pyplot as plt
     import matplotlib.colors
     from matplotlib.patches import Polygon
-except (ImportError, ModuleNotFoundError):
+except (ImportError, ModuleNotFoundError, RuntimeError):
     plt = None
 
 from flopy.plot import plotutil

flopy/plot/map.py

@@ -7,7 +7,7 @@
     import matplotlib.colors
     from matplotlib.collections import PathCollection, LineCollection
     from matplotlib.path import Path
-except (ImportError, ModuleNotFoundError):
+except (ImportError, ModuleNotFoundError, RuntimeError):
     plt = None
 
 from . import plotutil

flopy/plot/plotutil.py

@@ -20,7 +20,7 @@
 
 try:
     import matplotlib.pyplot as plt
-except ImportError:
+except (ImportError, RuntimeError):
     plt = None
 
 warnings.simplefilter("ignore", RuntimeWarning)

flopy/plot/styles.py

@@ -1,7 +1,7 @@
 try:
     import matplotlib.pyplot as plt
     import matplotlib as mpl
-except (ImportError, ModuleNotFoundError):
+except (ImportError, ModuleNotFoundError, RuntimeError):
     plt = None
 
 import os

flopy/utils/check.py

@@ -437,7 +437,7 @@ def get_active(self, include_cbd=False):
         """
         mg = self.model.modelgrid
         if mg.grid_type == "structured":
-            nlaycbd = mg._StructuredGrid__laycbd.sum() if include_cbd else 0
+            nlaycbd = mg.laycbd.sum() if include_cbd else 0
             inds = (mg.nlay + nlaycbd, mg.nrow, mg.ncol)
         elif mg.grid_type == "vertex":
             inds = (mg.nlay, mg.ncpl)

flopy/utils/gridintersect.py

@@ -2,7 +2,7 @@
 
 try:
     import matplotlib.pyplot as plt
-except ImportError:
+except (ImportError, RuntimeError):
     plt = None
 
 from .geometry import transform

flopy/utils/voronoi.py

@@ -1,5 +1,4 @@
 import numpy as np
-import matplotlib.pyplot as plt
 from scipy.spatial import Voronoi
 from .cvfdutil import get_disv_gridprops
 
@@ -282,6 +281,8 @@ def plot(self, ax=None, plot_title=True, **kwargs):
             axes that contains the voronoi model grid
 
         """
+        import matplotlib.pyplot as plt
+
         if ax is None:
             ax = plt.subplot(1, 1, 1, aspect="equal")
         pc = self.get_patch_collection(ax, **kwargs)