Merge pull request #2450 from modflowpy/v3.9.2

Release 3.9.2

Author: wpbonelli

.docs/Notebooks/array_output_tutorial.py

@@ -17,16 +17,13 @@
 #       - name: Jeremy White
 # ---
 
-# + [markdown] pycharm={"name": "#%% md\n"}
 # # Formatting ASCII output arrays
 #
 # ### Configuring numeric arrays written by FloPy
 
-# + [markdown] pycharm={"name": "#%% md\n"}
 # load and run the Freyberg model
 
 
-# + pycharm={"name": "#%%\n"}
 import os
 import sys
 from pathlib import Path
@@ -111,26 +108,20 @@
         errmsg = f"Error. Output file cannot be found: {f}"
         print(errmsg)
 
-# + [markdown] pycharm={"name": "#%% md\n"}
 # Each ``Util2d`` instance now has a ```.format``` attribute, which is an ```ArrayFormat``` instance:
 
-# + pycharm={"name": "#%%\n"}
 print(ml.lpf.hk[0].format)
 
-# + [markdown] pycharm={"name": "#%% md\n"}
 # The ```ArrayFormat``` class exposes each of the attributes seen in the ```ArrayFormat.___str___()``` call. ```ArrayFormat``` also exposes ``.fortran``, ``.py`` and ``.numpy`` atrributes, which are the respective format descriptors:
 
-# + pycharm={"name": "#%%\n"}
 print(ml.dis.botm[0].format.fortran)
 print(ml.dis.botm[0].format.py)
 print(ml.dis.botm[0].format.numpy)
 
-# + [markdown] pycharm={"name": "#%% md\n"}
 # #### (re)-setting ```.format```
 #
 # We can reset the format using a standard fortran type format descriptor
 
-# + pycharm={"name": "#%%\n"}
 ml.dis.botm[0].format.free = False
 ml.dis.botm[0].format.fortran = "(20f10.4)"
 print(ml.dis.botm[0].format.fortran)
@@ -147,25 +138,19 @@
 else:
     raise ValueError("Failed to run.")
 
-# + [markdown] pycharm={"name": "#%% md\n"}
 # Let's load the model we just wrote and check that the desired ```botm[0].format``` was used:
 
-# + pycharm={"name": "#%%\n"}
 ml1 = flopy.modflow.Modflow.load("freyberg.nam", model_ws=modelpth)
 print(ml1.dis.botm[0].format)
 
-# + [markdown] pycharm={"name": "#%% md\n"}
 # We can also reset individual format components (we can also generate some warnings):
 
-# + pycharm={"name": "#%%\n"}
 ml.dis.botm[0].format.width = 9
 ml.dis.botm[0].format.decimal = 1
 print(ml1.dis.botm[0].format)
 
-# + [markdown] pycharm={"name": "#%% md\n"}
 # We can also select ``free`` format.  Note that setting to free format resets the format attributes to the default, max precision:
 
-# + pycharm={"name": "#%%\n"}
 ml.dis.botm[0].format.free = True
 print(ml1.dis.botm[0].format)
 # -
@@ -178,6 +163,5 @@
 else:
     raise ValueError("Failed to run.")
 
-# + pycharm={"name": "#%%\n"}
 ml1 = flopy.modflow.Modflow.load("freyberg.nam", model_ws=modelpth)
 print(ml1.dis.botm[0].format)

.docs/Notebooks/export_vtk_tutorial.py

@@ -122,13 +122,6 @@
 model_bottom_dir = output_dir / "BOTM"
 ml.dis.botm.export(model_bottom_dir, fmt="vtk")
 
-# ### Export transient array recharge
-
-# transient 2d array
-# export recharge
-model_recharge_dir = output_dir / "RECH"
-ml.rch.rech.export(model_recharge_dir, fmt="vtk", pvd=True)
-
 # ### Export HK with point scalars
 #
 
@@ -245,7 +238,8 @@
 vtkobj = vtk.Vtk(ml, xml=True, pvd=True, vertical_exageration=10)
 
 ## add recharge to the VTK object
-recharge = ml.rch.rech.transient_2ds
+subset = list(range(10))
+recharge = {k: v for k, v in ml.rch.rech.transient_2ds.items() if k in subset}
 vtkobj.add_transient_array(recharge, "recharge", masked_values=[0])
 
 ## write vtk files
@@ -268,8 +262,8 @@
 spd = ml.wel.stress_period_data
 vtkobj.add_transient_list(spd, masked_values=[0])
 
-## write vtk files
-vtkobj.write(output_dir / "tr_list_example" / "wel_flux.vtu")
+## write vtk files (skipped, slow)
+# vtkobj.write(output_dir / "tr_list_example" / "wel_flux.vtu")
 # -
 
 # ### Adding packages to the `Vtk` object
@@ -320,7 +314,9 @@
 # create the vtk object and export heads
 vtkobj = vtk.Vtk(ml, xml=True, pvd=True, vertical_exageration=10)
 vtkobj.add_heads(hds)
-vtkobj.write(workspace / "heads_output_test" / "freyberg_head.vtu")
+
+# skipped, slow
+# vtkobj.write(workspace / "heads_output_test" / "freyberg_head.vtu")
 # -
 
 # ### Export heads as point scalar arrays

.docs/Notebooks/mt3dms_sft_lkt_uzt_tutorial.py

@@ -841,7 +841,6 @@
 
 # #### Write the MT3D-USGS input files for inspecting and running
 
-# + pycharm={"name": "#%%\n"}
 mf.write_input()
 mt.write_input()