Merge pull request #112 from DOI-USGS/v0.6.1

Version 0.6.1

Author: aleaf

.github/CODEOWNERS

@@ -0,0 +1 @@
+@aleaf

ci/test_environment.yaml

@@ -27,7 +27,7 @@ dependencies:
 - coverage
 - flake8
 - pytest
-- sphinx
+- sphinx=8.1.3
 - numpydoc
 - nbsphinx  # for rendering notebooks in sphinx-generated docs
 - sphinx-copybutton

docs/source/conf.py

@@ -132,7 +132,6 @@
 # a list of builtin themes.
 #
 html_theme = 'sphinx_rtd_theme'
-import sphinx_rtd_theme
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the

docs/source/release-history.rst

@@ -2,6 +2,11 @@
 Release History
 ===============
 
+Version 0.6.1 (2025-03-17)
+----------------------------------------
+* fix 'TemporalReference' issue related to change in Flopy code
+* fix issue with Mover Package SFR connections across LGR model interfaces (mover.py::get_sfr_package_connections)); follow-up fix to fbe1bb1 to handle cases where parent model SFR reach along the LGR interface has both upstream and downstream connections to the inset model.
+
 Version 0.6.0 (2025-01-06)
 ----------------------------------------
 

mfsetup/discretization.py

@@ -249,12 +249,12 @@ def fill_cells_vertically(top, botm):
 
     Parameters
     ----------
-    top : 2D numpy array; model top elevations
+    top : 2D (nrow, ncol) array; model top elevations
     botm : 3D (nlay, nrow, ncol) array; model bottom elevations
 
     Returns
     -------
-    top, botm : filled top and botm arrays
+    botm : filled botm array
     """
     thickness = get_layer_thicknesses(top, botm)
     assert np.all(np.isnan(thickness[np.isnan(thickness)]))
@@ -333,12 +333,11 @@ def get_layer(botm_array, i, j, elev):
     k : np.ndarray (1-D) or scalar
         zero-based layer index
     """
+# convert scalars to 1D numpy arrays
     def to_array(arg):
         if np.isscalar(arg):
-            np.array([arg])
-        #if not isinstance(arg, np.ndarray):
-        #    return np.array([arg])
-        else:
+            return np.array([arg])
+        else: # if already an np.array, return as is
             return np.array(arg)
 
     i = to_array(i)

mfsetup/equality.py

@@ -8,7 +8,6 @@
 mf6 = flopy.mf6
 from flopy.datbase import DataInterface, DataType
 from flopy.mbase import ModelInterface
-from flopy.utils import TemporalReference
 
 
 def get_package_list(model):
@@ -81,8 +80,6 @@ def package_eq(pk1, pk2):
                     # TODO: this may return False if there are nans
                     elif not np.allclose(v.array, v2.array):
                         return False
-        elif isinstance(v, TemporalReference):
-            pass
         elif v != v2:
             return False
     return True

mfsetup/fileio.py

@@ -25,7 +25,7 @@
 )
 from flopy.mf6.modflow import mfims, mftdis
 from flopy.modflow.mf import ModflowGlobal
-from flopy.utils import TemporalReference, mfreadnam
+from flopy.utils import mfreadnam
 
 import mfsetup
 from mfsetup.grid import MFsetupGrid
@@ -647,25 +647,6 @@ def flopy_mf2005_load(m, load_only=None, forgive=False, check=False):
     m.setup_grid()  # reset model grid now that DIS package is loaded
     assert m.pop_key_list.pop() == dis_key
     ext_unit_dict.pop(dis_key)  #.filehandle.close()
-    #start_datetime = attribs.pop("start_datetime", "01-01-1970")
-    #itmuni = attribs.pop("itmuni", 4)
-    #ref_source = attribs.pop("source", "defaults")
-    # if m.structured:
-    #    # get model units from usgs.model.reference, if provided
-    #    if ref_source == 'usgs.model.reference':
-    #        pass
-    #    # otherwise get them from the DIS file
-    #    else:
-    #        itmuni = dis.itmuni
-    #        ref_attributes['lenuni'] = dis.lenuni
-    #    sr = SpatialReference(delr=m.dis.delr.array, delc=ml.dis.delc.array,
-    #                          **ref_attributes)
-    # else:
-    #    sr = None
-    #
-    #dis.sr = m.sr
-    #dis.tr = TemporalReference(itmuni=itmuni, start_datetime=start_datetime)
-    #dis.start_datetime = start_datetime
 
     if load_only is None:
         # load all packages/files

mfsetup/mover.py

@@ -164,18 +164,20 @@ def neighbors(i, j):
     for parent_reach, inset_reach in parent_to_inset.items():
         if parent_reach in inset_to_parent.values():
             parent_to_inset_distance = parent_to_inset_distances[parent_reach]
-            inset_to_parent_distance = inset_to_parent_distances[inset_reach]
-            if inset_to_parent_distance < parent_to_inset_distance:
-                delete_parent_to_inset_items.add(parent_reach)
-            elif parent_to_inset_distance < inset_to_parent_distance:
-                del inset_to_parent[inset_reach]
-            else:
-                raise ValueError("Circular connection between SFR Packages in the Mover Package input.\n"
-                                 f"Connection distance between the end of parent reach {parent_reach} "
-                                 f"in parent model and start of inset reach {inset_reach} in inset model "
-                                 f"is equal to\nthe distance between the end of inset reach {inset_reach} "
-                                 f"and start of parent reach {parent_reach}.\nCheck input linework."
-                                 )
+            if inset_to_parent_distances.get(inset_reach) is not None:
+                inset_to_parent_distance = inset_to_parent_distances[inset_reach]
+                if inset_to_parent_distance < parent_to_inset_distance:
+                    delete_parent_to_inset_items.add(parent_reach)
+                elif parent_to_inset_distance < inset_to_parent_distance:
+                    del inset_to_parent[inset_reach]
+                else:
+                    raise ValueError(
+                        "Circular connection between SFR Packages in the Mover Package input.\n"
+                        f"Connection distance between the end of parent reach {parent_reach} "
+                        f"in parent model and start of inset reach {inset_reach} in inset model "
+                        f"is equal to\nthe distance between the end of inset reach {inset_reach} "
+                        f"and start of parent reach {parent_reach}.\nCheck input linework."
+                        )
     for parent_reach in delete_parent_to_inset_items:
         del parent_to_inset[parent_reach]
     return parent_to_inset, inset_to_parent

pyproject.toml

@@ -66,9 +66,6 @@ docs = [
     "sphinx-rtd-theme"
 ]
 
-[project.scripts]
-get-modflow = "flopy.utils.get_modflow:cli_main"
-
 [project.urls]
 documentation = "https://doi-usgs.github.io/modflow-setup/latest/"
 repository = "https://github.com/doi-usgs/modflow-setup"