refactor(deprecated): remove additional deprecated classes and functi…

…ons (#1204)

autotest/t042_test.py

@@ -11,7 +11,6 @@
     get_transmissivities,
     get_water_table,
     get_gradients,
-    get_saturated_thickness,
 )
 
 mf = flopy.modflow

flopy/discretization/grid.py

@@ -745,19 +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():

flopy/mbase.py

@@ -347,11 +347,6 @@ def __init__(
         yll = kwargs.pop("yll", None)
         self._xul = kwargs.pop("xul", None)
         self._yul = kwargs.pop("yul", None)
-        if self._xul is not None or self._yul is not None:
-            warnings.warn(
-                "xul/yul have been deprecated. Use xll/yll instead.",
-                DeprecationWarning,
-            )
 
         self._rotation = kwargs.pop("rotation", 0.0)
         self._proj4_str = kwargs.pop("proj4_str", None)

flopy/mf6/mfmodel.py

@@ -113,17 +113,7 @@ def __init__(
         xll = kwargs.pop("xll", None)
         yll = kwargs.pop("yll", None)
         self._xul = kwargs.pop("xul", None)
-        if self._xul is not None:
-            warnings.warn(
-                "xul/yul have been deprecated. Use xll/yll instead.",
-                DeprecationWarning,
-            )
         self._yul = kwargs.pop("yul", None)
-        if self._yul is not None:
-            warnings.warn(
-                "xul/yul have been deprecated. Use xll/yll instead.",
-                DeprecationWarning,
-            )
         rotation = kwargs.pop("rotation", 0.0)
         proj4 = kwargs.pop("proj4_str", None)
         # build model grid object

flopy/plot/plotutil.py

@@ -2529,10 +2529,6 @@ def _set_coord_info(mg, xul, yul, xll, yll, rotation):
     import warnings
 
     if xul is not None and yul is not None:
-        warnings.warn(
-            "xul/yul have been deprecated. Use xll/yll instead.",
-            DeprecationWarning,
-        )
         if rotation is not None:
             mg._angrot = rotation
 

flopy/utils/__init__.py

@@ -67,4 +67,3 @@
 from .optionblock import OptionBlock
 from .rasters import Raster
 from .gridintersect import GridIntersect, ModflowGridIndices
-from .binarygrid_util import MfGrdFile

flopy/utils/geometry.py

@@ -701,42 +701,6 @@ def transform(
     return xrot, yrot
 
 
-def shape(pyshp_shpobj):
-    """
-    Convert a pyshp geometry object to a flopy geometry object.
-
-    Parameters
-    ----------
-    pyshp_shpobj : shapefile._Shape instance
-
-    Returns
-    -------
-    shape : flopy.utils.geometry Polygon, Linestring, or Point
-
-    Notes
-    -----
-    Currently only regular Polygons, LineStrings and Points (pyshp types 5, 3, 1) supported.
-
-    Examples
-    --------
-    >>> import shapefile as sf
-    >>> from flopy.utils.geometry import shape
-    >>> sfobj = sf.Reader('shapefile.shp')
-    >>> flopy_geom = shape(list(sfobj.iterShapes())[0])
-
-    """
-    import warnings
-
-    warnings.warn(
-        "Method will be Deprecated, calling GeoSpatialUtil",
-        DeprecationWarning,
-    )
-
-    from .geospatial_utils import GeoSpatialUtil
-
-    return GeoSpatialUtil(pyshp_shpobj).flopy_geometry
-
-
 def get_polygon_area(geom):
     """
     Calculate the area of a closed polygon

flopy/utils/gridgen.py

@@ -1379,13 +1379,6 @@ def get_cellxy(self, ncells):
             cellxy[n, 1] = y
         return cellxy
 
-    def get_gridprops(self):
-        msg = (
-            "Use: "
-            "get_gridprops_disu5, get_gridprops_disu6, get_gridprops_disv"
-        )
-        raise DeprecationWarning(msg)
-
     @staticmethod
     def gridarray_to_flopyusg_gridarray(nodelay, a):
         nlay = nodelay.shape[0]
@@ -1680,16 +1673,6 @@ def get_gridprops_unstructuredgrid(self):
 
         return gridprops
 
-    def to_disu6(self, fname, writevertices=True):
-        raise DeprecationWarning(
-            "Use: flopy.mf6.ModflowGwfdisu(gwf, **g.get_gridprops_disu6())"
-        )
-
-    def to_disv6(self, fname, verbose=False):
-        raise DeprecationWarning(
-            "Use: flopy.mf6.ModflowGwfdisv(gwf, **g.get_gridprops_disv())"
-        )
-
     def intersect(self, features, featuretype, layer):
         """
         Parameters

flopy/utils/postprocessing.py

@@ -167,74 +167,6 @@ def get_water_table(heads, nodata, per_idx=None):
     return np.squeeze(wt)
 
 
-def get_saturated_thickness(heads, m, nodata, per_idx=None):
-    """
-    Calculates the saturated thickness for each cell from the heads
-    array for each stress period.
-
-    Parameters
-    ----------
-    heads : 3 or 4-D np.ndarray
-        Heads array.
-    m : flopy.modflow.Modflow object
-        Must have a flopy.modflow.ModflowDis object attached.
-    nodata : float, list
-        HDRY value indicating dry cells and/or HNOFLO values.
-    per_idx : int or sequence of ints
-        stress periods to return. If None,
-        returns all stress periods (default).
-
-    Returns
-    -------
-    sat_thickness : 3 or 4-D np.ndarray
-        Array of saturated thickness
-    """
-    warnings.warn(
-        "postprocessing.get_saturated_thickness will be deprecated and "
-        "removed in version 3.3.5.  Use grid.saturated_thick(heads).",
-        PendingDeprecationWarning,
-    )
-
-    if not isinstance(nodata, list):
-        nodata = [nodata]
-    heads = np.array(heads, ndmin=4)
-    for mv in nodata:
-        heads[heads == mv] = np.nan
-
-    top = m.dis.top.array
-    botm = m.dis.botm.array
-    top.shape = (1,) + botm.shape[1:]
-    top = np.concatenate((top, botm[0:-1]), axis=0)
-    thickness = m.modelgrid.thick
-    nper, nlay, nrow, ncol = heads.shape
-    if per_idx is None:
-        per_idx = list(range(nper))
-    elif np.isscalar(per_idx):
-        per_idx = [per_idx]
-
-    # get confined or unconfined/convertible info
-    laytyp = m.laytyp
-    if len(laytyp.shape) == 1:
-        laytyp.shape = (m.nlay, 1, 1)
-        is_conf = np.logical_and(
-            (laytyp == 0), np.full(m.modelgrid.shape, True)
-        )
-    else:
-        is_conf = laytyp == 0
-
-    # calculate saturated thickness
-    sat_thickness = []
-    for per in per_idx:
-        hds = heads[per]
-        hds = np.where(hds < botm, botm, hds)  # for NWT when hds < botm
-        unconf_thickness = np.where(hds > top, top - botm, hds - botm)
-        perthickness = np.where(is_conf, thickness, unconf_thickness)
-        sat_thickness.append(perthickness)
-    sat_thickness = np.squeeze(sat_thickness)
-
-    return sat_thickness
-
-
 def get_gradients(heads, m, nodata, per_idx=None):
     """
     Calculates the hydraulic gradients from the heads

flopy/utils/util_array.py

@@ -659,38 +659,6 @@ def export(self, f, **kwargs):
 
         return export.utils.array3d_export(f, self, **kwargs)
 
-    def to_shapefile(self, filename):
-        """
-        Export 3-D model data to shapefile (polygons).  Adds an
-            attribute for each Util2d in self.u2ds
-
-        Parameters
-        ----------
-        filename : str
-            Shapefile name to write
-
-        Returns
-        ----------
-        None
-
-        See Also
-        --------
-
-        Notes
-        -----
-
-        Examples
-        --------
-        >>> import flopy
-        >>> ml = flopy.modflow.Modflow.load('test.nam')
-        >>> ml.lpf.hk.to_shapefile('test_hk.shp')
-        """
-        warn(
-            "Deprecation warning: to_shapefile() is deprecated. use .export()",
-            DeprecationWarning,
-        )
-        self.export(filename)
-
     def plot(
         self,
         filename_base=None,
@@ -1494,38 +1462,6 @@ def get_zero_2d(self, kper):
             array_free_format=self.array_free_format,
         )
 
-    def to_shapefile(self, filename):
-        """
-        Export transient 2D data to a shapefile (as polygons). Adds an
-            attribute for each unique Util2d instance in self.data
-
-        Parameters
-        ----------
-        filename : str
-            Shapefile name to write
-
-        Returns
-        ----------
-        None
-
-        See Also
-        --------
-
-        Notes
-        -----
-
-        Examples
-        --------
-        >>> import flopy
-        >>> ml = flopy.modflow.Modflow.load('test.nam')
-        >>> ml.rch.rech.as_shapefile('test_rech.shp')
-        """
-        warn(
-            "Deprecation warning: to_shapefile() is deprecated. use .export()",
-            DeprecationWarning,
-        )
-        self.export(filename)
-
     def plot(
         self,
         filename_base=None,
@@ -2076,38 +2012,6 @@ def export(self, f, **kwargs):
 
         return export.utils.array2d_export(f, self, **kwargs)
 
-    def to_shapefile(self, filename):
-        """
-        Export 2-D model data to a shapefile (as polygons) of self.array
-
-        Parameters
-        ----------
-        filename : str
-            Shapefile name to write
-
-        Returns
-        ----------
-        None
-
-        See Also
-        --------
-
-        Notes
-        -----
-
-        Examples
-        --------
-        >>> import flopy
-        >>> ml = flopy.modflow.Modflow.load('test.nam')
-        >>> ml.dis.top.as_shapefile('test_top.shp')
-        """
-
-        warn(
-            "Deprecation warning: to_shapefile() is deprecated. use .export()",
-            DeprecationWarning,
-        )
-        self.export(filename)
-
     def set_fmtin(self, fmtin):
         self._format = ArrayFormat(
             self,