observations code updated

dependencies/flopy/datbase.py

@@ -18,43 +18,43 @@ class DataInterface:
     @abc.abstractmethod
     def data_type(self):
         raise NotImplementedError(
-            "must define dat_type in child " "class to use this base class"
+            "must define dat_type in child class to use this base class"
         )
 
     @property
     @abc.abstractmethod
     def dtype(self):
         def dtype(self):
             raise NotImplementedError(
-                "must define dtype in child " "class to use this base class"
+                "must define dtype in child class to use this base class"
             )
 
     @property
     @abc.abstractmethod
     def array(self):
         raise NotImplementedError(
-            "must define array in child " "class to use this base class"
+            "must define array in child class to use this base class"
         )
 
     @property
     @abc.abstractmethod
     def name(self):
         raise NotImplementedError(
-            "must define name in child " "class to use this base class"
+            "must define name in child class to use this base class"
         )
 
     @property
     @abc.abstractmethod
     def model(self):
         raise NotImplementedError(
-            "must define name in child " "class to use this base class"
+            "must define name in child class to use this base class"
         )
 
     @property
     @abc.abstractmethod
     def plottable(self):
         raise NotImplementedError(
-            "must define plottable in child " "class to use this base class"
+            "must define plottable in child class to use this base class"
         )
 
 
@@ -63,15 +63,15 @@ class DataListInterface:
     @abc.abstractmethod
     def package(self):
         raise NotImplementedError(
-            "must define package in child " "class to use this base class"
+            "must define package in child class to use this base class"
         )
 
     @property
     @abc.abstractmethod
     def to_array(self, kper=0, mask=False):
         def to_array(self):
             raise NotImplementedError(
-                "must define to_array in child " "class to use this base class"
+                "must define to_array in child class to use this base class"
             )
 
     @abc.abstractmethod

dependencies/flopy/discretization/grid.py

@@ -180,6 +180,7 @@ def __init__(
 
         self._iverts = None
         self._verts = None
+        self._laycbd = None
 
     ###################################
     # access to basic grid properties
@@ -192,16 +193,16 @@ def __repr__(self):
             and self.angrot is not None
         ):
             items += [
-                "xll:" + str(self.xoffset),
-                "yll:" + str(self.yoffset),
-                "rotation:" + str(self.angrot),
+                f"xll:{self.xoffset!s}",
+                f"yll:{self.yoffset!s}",
+                f"rotation:{self.angrot!s}",
             ]
         if self.proj4 is not None:
-            items.append("proj4_str:" + str(self.proj4))
+            items.append(f"proj4_str:{self.proj4}")
         if self.units is not None:
-            items.append("units:" + str(self.units))
+            items.append(f"units:{self.units}")
         if self.lenuni is not None:
-            items.append("lenuni:" + str(self.lenuni))
+            items.append(f"lenuni:{self.lenuni}")
         return "; ".join(items)
 
     @property
@@ -258,7 +259,7 @@ def proj4(self):
             else:
                 proj4 = self._proj4
         elif self.epsg is not None:
-            proj4 = "epsg:{}".format(self.epsg)
+            proj4 = f"epsg:{self.epsg}"
         return proj4
 
     @proj4.setter
@@ -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):
         """
@@ -317,6 +325,11 @@ def saturated_thick(self, array, mask=None):
         thick = self.thick
         top = self.top_botm[:-1].reshape(thick.shape)
         bot = self.top_botm[1:].reshape(thick.shape)
+        thick = self.remove_confining_beds(thick)
+        top = self.remove_confining_beds(top)
+        bot = self.remove_confining_beds(bot)
+        array = self.remove_confining_beds(array)
+
         idx = np.where((array < top) & (array > bot))
         thick[idx] = array[idx] - bot[idx]
         idx = np.where(array <= bot)
@@ -443,6 +456,32 @@ def xyzvertices(self):
     def cross_section_vertices(self):
         return self.xyzvertices[0], self.xyzvertices[1]
 
+    def remove_confining_beds(self, array):
+        """
+        Method to remove confining bed layers from an array
+
+        Parameters
+        ----------
+        array : np.ndarray
+            array to remove quasi3d confining bed data from. Shape of axis 0
+            should be (self.lay + ncb) to remove beds
+        Returns
+        -------
+            np.ndarray
+        """
+        if self.laycbd is not None:
+            ncb = np.count_nonzero(self.laycbd)
+            if ncb > 0:
+                if array.shape[0] == self.shape[0] + ncb:
+                    cb = 0
+                    idx = []
+                    for ix, i in enumerate(self.laycbd):
+                        idx.append(ix + cb)
+                        if i > 0:
+                            cb += 1
+                    array = array[idx]
+        return array
+
     def cross_section_lay_ncpl_ncb(self, ncb):
         """
         Get PlotCrossSection compatible layers, ncpl, and ncb
@@ -706,19 +745,11 @@ def attribs_from_namfile_header(self, namefile):
             elif "xul" in item.lower():
                 try:
                     xul = float(item.split(":")[1])
-                    warnings.warn(
-                        "xul/yul have been deprecated. Use xll/yll instead.",
-                        DeprecationWarning,
-                    )
                 except:
                     pass
             elif "yul" in item.lower():
                 try:
                     yul = float(item.split(":")[1])
-                    warnings.warn(
-                        "xul/yul have been deprecated. Use xll/yll instead.",
-                        DeprecationWarning,
-                    )
                 except:
                     pass
             elif "rotation" in item.lower():

dependencies/flopy/discretization/structuredgrid.py

@@ -4,34 +4,6 @@
 import numpy as np
 from .grid import Grid, CachedData
 
-try:
-    from numpy.lib import NumpyVersion
-
-    numpy115 = NumpyVersion(np.__version__) >= "1.15.0"
-except ImportError:
-    numpy115 = False
-
-if not numpy115:
-
-    def flip_numpy115(m, axis=None):
-        """Provide same behavior for np.flip since numpy 1.15.0."""
-        import numpy.core.numeric as _nx
-        from numpy.core.numeric import asarray
-
-        if not hasattr(m, "ndim"):
-            m = asarray(m)
-        if axis is None:
-            indexer = (np.s_[::-1],) * m.ndim
-        else:
-            axis = _nx.normalize_axis_tuple(axis, m.ndim)
-            indexer = [np.s_[:]] * m.ndim
-            for ax in axis:
-                indexer[ax] = np.s_[::-1]
-            indexer = tuple(indexer)
-        return m[indexer]
-
-    np.flip = flip_numpy115
-
 
 def array_at_verts_basic2d(a):
     """
@@ -189,15 +161,15 @@ def __init__(
                 self.__nlay = nlay
             else:
                 if laycbd is not None:
-                    self.__nlay = len(botm) - np.sum(laycbd > 0)
+                    self.__nlay = len(botm) - np.count_nonzero(laycbd)
                 else:
                     self.__nlay = len(botm)
         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 +436,7 @@ 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):
@@ -1562,7 +1534,7 @@ def get_plottable_layer_array(self, a, layer):
                 plotarray = plotarray[layer, :, :]
         else:
             raise Exception("Array to plot must be of dimension 1, 2, or 3")
-        msg = "{} /= {}".format(plotarray.shape, required_shape)
+        msg = f"{plotarray.shape} /= {required_shape}"
         assert plotarray.shape == required_shape, msg
         return plotarray
 
@@ -1643,11 +1615,10 @@ def from_binary_grid_file(cls, file_path, verbose=False):
 
         grb_obj = MfGrdFile(file_path, verbose=verbose)
         if grb_obj.grid_type != "DIS":
-            err_msg = (
-                "Binary grid file ({}) ".format(os.path.basename(file_path))
-                + "is not a structured (DIS) grid."
+            raise ValueError(
+                f"Binary grid file ({os.path.basename(file_path)}) "
+                "is not a structured (DIS) grid."
             )
-            raise ValueError(err_msg)
 
         idomain = grb_obj.idomain
         xorigin = grb_obj.xorigin

dependencies/flopy/discretization/unstructuredgrid.py

@@ -128,14 +128,13 @@ def __init__(
 
         if iverts is not None:
             if self.grid_varies_by_layer:
-                msg = "Length of iverts must equal grid nodes ({} {})".format(
-                    len(iverts), self.nnodes
+                msg = (
+                    "Length of iverts must equal grid nodes "
+                    f"({len(iverts)} {self.nnodes})"
                 )
                 assert len(iverts) == self.nnodes, msg
             else:
-                msg = "Length of iverts must equal ncpl ({} {})".format(
-                    len(iverts), self.ncpl
-                )
+                msg = f"Length of iverts must equal ncpl ({len(iverts)} {self.ncpl})"
                 assert np.all([cpl == len(iverts) for cpl in self.ncpl]), msg
 
         return
@@ -208,7 +207,7 @@ 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):
@@ -809,11 +808,10 @@ def from_binary_grid_file(cls, file_path, verbose=False):
 
         grb_obj = MfGrdFile(file_path, verbose=verbose)
         if grb_obj.grid_type != "DISU":
-            err_msg = (
-                "Binary grid file ({}) ".format(os.path.basename(file_path))
-                + "is not a vertex (DISU) grid."
+            raise ValueError(
+                f"Binary grid file ({os.path.basename(file_path)}) "
+                "is not a vertex (DISU) grid."
             )
-            raise ValueError(err_msg)
 
         iverts = grb_obj.iverts
         if iverts is not None:
@@ -842,8 +840,7 @@ def from_binary_grid_file(cls, file_path, verbose=False):
                 angrot=angrot,
             )
         else:
-            err_msg = (
-                "{} binary grid file".format(os.path.basename(file_path))
-                + " does not include vertex data"
+            raise TypeError(
+                f"{os.path.basename(file_path)} binary grid file "
+                "does not include vertex data"
             )
-            raise TypeError(err_msg)

dependencies/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):
@@ -273,7 +273,7 @@ def intersect(self, x, y, local=False, forgive=False):
         if Path is None:
             s = (
                 "Could not import matplotlib.  Must install matplotlib "
-                + " in order to use VertexGrid.intersect() method"
+                "in order to use VertexGrid.intersect() method"
             )
             raise ImportError(s)
 
@@ -314,9 +314,7 @@ def get_cell_vertices(self, cellid):
         """
         while cellid >= self.ncpl:
             if cellid > self.nnodes:
-                err = "cellid {} out of index for size {}".format(
-                    cellid, self.nnodes
-                )
+                err = f"cellid {cellid} out of index for size {self.nnodes}"
                 raise IndexError(err)
 
             cellid -= self.ncpl
@@ -491,7 +489,7 @@ def get_plottable_layer_array(self, a, layer):
                 plotarray = plotarray[layer, :]
         else:
             raise Exception("Array to plot must be of dimension 1 or 2")
-        msg = "{} /= {}".format(plotarray.shape[0], required_shape)
+        msg = f"{plotarray.shape[0]} /= {required_shape}"
         assert plotarray.shape == required_shape, msg
         return plotarray
 
@@ -518,11 +516,10 @@ def from_binary_grid_file(cls, file_path, verbose=False):
 
         grb_obj = MfGrdFile(file_path, verbose=verbose)
         if grb_obj.grid_type != "DISV":
-            err_msg = (
-                "Binary grid file ({}) ".format(os.path.basename(file_path))
-                + "is not a vertex (DISV) grid."
+            raise ValueError(
+                f"Binary grid file ({os.path.basename(file_path)}) "
+                "is not a vertex (DISV) grid."
             )
-            raise ValueError(err_msg)
 
         idomain = grb_obj.idomain
         xorigin = grb_obj.xorigin