add tests

Author: mjreno

.docs/Notebooks/netcdf01_tutorial.py .docs/Notebooks/mf6_netcdf01_tutorial.py.docs/Notebooks/netcdf01_tutorial.py renamed to .docs/Notebooks/mf6_netcdf01_tutorial.py

@@ -7,7 +7,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.17.2
+#       jupytext_version: 1.16.4
 #   kernelspec:
 #     display_name: Python 3 (ipykernel)
 #     language: python
@@ -18,13 +18,15 @@
 #
 # ## NetCDF tutorial 1: MODFLOW 6 structured input file
 #
-# This tutorial demonstrates how to generate a MODFLOW 6 NetCDF file from
-# an existing FloPy simulation. In the tutorial, candidate array data is
-# added to an xarray dataset and annotated so that the generated NetCDF
-# file can be read by MODFLOW 6 as model input.
+# This tutorial shows how to generate a MODFLOW 6 NetCDF file from
+# an existing FloPy simulation. Two methods will be demonstrated that
+# generate a simulation with package data stored in a model NetCDF
+# file. The first method is non-interactive- FloPy will generate the
+# file with a modified `write_simulation()` call.  The second method
+# is interactive, which provides an oppurtinity to modify the dataset
+# before it is written to NetCDF.
 #
-# This tutorial generates a structured NetCDF variant - for more information
-# on supported MODFLOW 6 NetCDF formats see:
+# For more information on supported MODFLOW 6 NetCDF formats see:
 # [MODFLOW NetCDF Format](https://github.com/MODFLOW-ORG/modflow6/wiki/MODFLOW-NetCDF-Format).
 #
 # Note that NetCDF is only supported by the Extended version of MODFLOW 6.
@@ -75,13 +77,13 @@
     "uzf01.uzf.obs": None,
 }
 
-# for fname, fhash in file_names.items():
-#    pooch.retrieve(
-#        url=f"https://github.com/modflowpy/flopy/raw/develop/examples/data/{sim_name}/{fname}",
-#        fname=fname,
-#        path=data_path / sim_name,
-#        known_hash=fhash,
-#    )
+for fname, fhash in file_names.items():
+    pooch.retrieve(
+        url=f"https://github.com/modflowpy/flopy/raw/develop/examples/data/{sim_name}/{fname}",
+        fname=fname,
+        path=data_path / sim_name,
+        known_hash=fhash,
+    )
 
 # ## Create simulation workspace
 
@@ -104,7 +106,44 @@
 success, buff = sim.run_simulation(silent=True, report=True)
 assert success, pformat(buff)
 
-# ## Create NetCDF based simulation
+# ## Create NetCDF based simulation method 1
+#
+# This is the most straightforward way to create a NetCDF simulation
+# from the loaded ascii input simulation. Simply define the `netcdf`
+# argument to `write_simulation()` to be either `structured` or
+# `layered`, depending on the desired format of the generated NetCDF
+# file.
+#
+# The name of the created file can be specified by first setting the
+# model `name_file.nc_filerecord` attribute to the desired name. If
+# this step is not taken, the default name of `{model_name}.input.nc`
+# is used.
+
+# create directory for netcdf sim
+sim.set_sim_path(workspace / "netcdf1")
+# set model name file nc_filerecord attribute to export name
+gwf = sim.get_model("uzf01")
+gwf.name_file.nc_filerecord = "uzf01.structured.nc"
+# write simulation with structured NetCDF file
+sim.write_simulation(netcdf="structured")
+
+# success, buff = sim.run_simulation(silent=True, report=True)
+# assert success, pformat(buff)
+
+# ## Repeat method 1 with layered mesh NetCDF format
+
+# create directory for netcdf sim
+sim.set_sim_path(workspace / "netcdf2")
+# set model name file nc_filerecord attribute to export name
+gwf = sim.get_model("uzf01")
+gwf.name_file.nc_filerecord = "uzf01.layered.nc"
+# write simulation with with layered mesh NetCDF file
+sim.write_simulation(netcdf="layered")
+
+# success, buff = sim.run_simulation(silent=True, report=True)
+# assert success, pformat(buff)
+
+# ## Create NetCDF based simulation method 2
 #
 # Reset the simulation path and set the `GWF` name file `nc_filerecord`
 # attribute to the name of the intended input NetCDF file. Display
@@ -116,21 +155,30 @@
 # and `GHBG` packages. Data will be copied from the package objects into
 # dataset arrays.
 #
-# Flopy does not currently generate the NetCDF input file. This tutorial
-# shows one way that can be accomplished.
+# Flopy will not generate the NetCDF input file when the `netcdf` argument
+# to `write_simulation()` is set to `nofile`. This step is needed, however,
+# to update ascii input with the keywords required to support the model
+# NetCDF file that we will generate.
 
 # create directory for netcdf sim
-sim.set_sim_path(workspace / "netcdf")
+sim.set_sim_path(workspace / "netcdf3")
 # set model name file nc_filerecord attribute to export name
 gwf = sim.get_model("uzf01")
 gwf.name_file.nc_filerecord = "uzf01.structured.nc"
 # write simulation with ASCII inputs tagged for NetCDF
-sim.write_simulation(netcdf=True)
+# but do not create NetCDF file
+sim.write_simulation(netcdf="nofile")
+
+# ## Show name file with NetCDF input configured
+
 # show name file with NetCDF input configured
-with open(workspace / "netcdf" / "uzf01.nam", "r") as fh:
+with open(workspace / "netcdf3" / "uzf01.nam", "r") as fh:
     print(fh.read())
+
+# ## Show example package file with NetCDF keywords
+
 # show example package file with NetCDF input configured
-with open(workspace / "netcdf" / "uzf01.ic", "r") as fh:
+with open(workspace / "netcdf3" / "uzf01.ic", "r") as fh:
     print(fh.read())
 
 # ## Create dataset
@@ -184,14 +232,15 @@
 # existing simulation objects and update the dataset.
 #
 # Default dataset variable names are defined in the package `netcdf_info()`
-# dictionary.
+# dictionary. Here we will use the info dictionary to programmatically update
+# the dataset- for remaining packages we will hardcode the variable names
+# being updated for maximum clarity.
 
-# update dataset from dis arrays
-ds["dis_delr"].values = dis.delr.get_data()
-ds["dis_delc"].values = dis.delc.get_data()
-ds["dis_top"].values = dis.top.get_data()
-ds["dis_botm"].values = dis.botm.get_data()
-ds["dis_idomain"].values = dis.idomain.get_data()
+nc_info = dis.netcdf_info()
+for v in nc_info:
+    name = nc_info[v]["attrs"]["modflow_input"].rsplit("/", 1)[1].lower()
+    d = getattr(dis, name)
+    ds[nc_info[v]["varname"]].values = d.get_data()
 
 # ## Access `NPF` package NetCDF attributes
 #
@@ -277,7 +326,7 @@
 
 # write dataset to netcdf
 ds.to_netcdf(
-    workspace / "netcdf/uzf01.structured.nc", format="NETCDF4", engine="netcdf4"
+    workspace / "netcdf3" / "uzf01.structured.nc", format="NETCDF4", engine="netcdf4"
 )
 
 # ## Run MODFLOW 6 simulation with NetCDF input