fix(quotes+exe_path+nam_file): fixes for quoted strings, exe path, and nam file (#1645)

* fix(quotes+exe_path+nam_file): Quotes properly removed when loading files with quoted strings.  If all else fails trying to find exe_path, abs_path is used.  Proper error message given when user attempts to create namefile.

* test(quotes): added test for quoting of names in spaces

Co-authored-by: jdhughes-usgs <[email protected]>

Author: spaulins-usgs

autotest/regression/test_mf6.py

@@ -1379,7 +1379,7 @@ def test005_create_tests_advgw_tidal(tmpdir, example_data_path):
 
     obs_dict = {
         ("ghb_obs.csv", "binary"): [
-            ("ghb-2-6-10", "GHB", (1, 5, 9)),
+            ("ghb- 2-6-10", "GHB", (1, 5, 9)),
             ("ghb-3-6-10", "GHB", (2, 5, 9)),
         ],
         "ghb_flows.csv": [
@@ -1743,6 +1743,7 @@ def test005_create_tests_advgw_tidal(tmpdir, example_data_path):
             # there should be only one
             assert not found_obs
             found_obs = True
+            assert value[0][0] == "ghb- 2-6-10"
     assert found_flows and found_obs
 
     # clean up

autotest/test_mf6.py

@@ -25,6 +25,7 @@
     ModflowGwflak,
     ModflowGwfmaw,
     ModflowGwfmvr,
+    ModflowGwfnam,
     ModflowGwfnpf,
     ModflowGwfoc,
     ModflowGwfrch,
@@ -41,6 +42,7 @@
     ModflowGwtoc,
     ModflowGwtssm,
     ModflowIms,
+    ModflowNam,
     ModflowTdis,
     ModflowUtllaktab,
 )
@@ -1570,3 +1572,55 @@ def test_multi_model(tmpdir):
     # save and run updated model
     sim.write_simulation()
     sim.run_simulation()
+
+
+@requires_exe("mf6")
+def test_namefile_creation(tmpdir):
+    test_ex_name = "test_namefile"
+    # build MODFLOW 6 files
+    sim = MFSimulation(
+        sim_name=test_ex_name,
+        version="mf6",
+        exe_name="mf6",
+        sim_ws=str(tmpdir),
+    )
+
+    tdis_rc = [(6.0, 2, 1.0), (6.0, 3, 1.0), (6.0, 3, 1.0), (6.0, 3, 1.0)]
+    tdis = ModflowTdis(sim, time_units="DAYS", nper=4, perioddata=tdis_rc)
+    ims_package = ModflowIms(
+        sim,
+        pname="my_ims_file",
+        filename=f"{test_ex_name}.ims",
+        print_option="ALL",
+        complexity="SIMPLE",
+        outer_dvclose=0.0001,
+        outer_maximum=50,
+        under_relaxation="NONE",
+        inner_maximum=30,
+        inner_dvclose=0.0001,
+        linear_acceleration="CG",
+        preconditioner_levels=7,
+        preconditioner_drop_tolerance=0.01,
+        number_orthogonalizations=2,
+    )
+    model = ModflowGwf(
+        sim,
+        modelname=test_ex_name,
+        model_nam_file="{}.nam".format(test_ex_name),
+    )
+
+    # try to create simulation name file
+    ex_happened = False
+    try:
+        nam = ModflowNam(sim)
+    except flopy.mf6.mfbase.FlopyException:
+        ex_happened = True
+    assert ex_happened
+
+    # try to create model name file
+    ex_happened = False
+    try:
+        nam = ModflowGwfnam(model)
+    except flopy.mf6.mfbase.FlopyException:
+        ex_happened = True
+    assert ex_happened

flopy/mbase.py

@@ -1701,6 +1701,9 @@ def run_model(
         if exe_name.lower().endswith(".exe"):
             # try removing .exe suffix
             exe = which(exe_name[:-4])
+    if exe is None:
+        # try abspath
+        exe = which(os.path.abspath(exe_name))
     if exe is None:
         raise Exception(
             f"The program {exe_name} does not exist or is not executable."

flopy/mf6/mfmodel.py

@@ -146,7 +146,10 @@ def __init__(
             raise FlopyException(excpt_str)
 
         self.name_file = package_obj(
-            self, filename=self.model_nam_file, pname=self.name
+            self,
+            filename=self.model_nam_file,
+            pname=self.name,
+            _internal_package=True,
         )
 
     def __init_subclass__(cls):
@@ -1644,7 +1647,10 @@ def register_package(
             package.package_type
         )
         if add_to_package_list and path in self._package_paths:
-            if not package_struct.multi_package_support:
+            if (
+                package_struct is not None
+                and not package_struct.multi_package_support
+            ):
                 # package of this type already exists, replace it
                 self.remove_package(package.package_type)
                 if (
@@ -1685,6 +1691,15 @@ def register_package(
         self._package_paths[path] = 1
 
         if package.package_type.lower() == "nam":
+            if not package.internal_package:
+                excpt_str = (
+                    "Unable to register nam file.  Do not create your own nam "
+                    "files.  Nam files are automatically created and managed "
+                    "for you by FloPy."
+                )
+                print(excpt_str)
+                raise FlopyException(excpt_str)
+
             return path, self.structure.name_file_struct_obj
 
         package_extension = package.package_type
@@ -1853,6 +1868,7 @@ def load_package(
             pname=dict_package_name,
             loading_package=True,
             parent_file=parent_package,
+            _internal_package=True,
         )
         try:
             package.load(strict)
@@ -1865,6 +1881,7 @@ def load_package(
                 pname=dict_package_name,
                 loading_package=True,
                 parent_file=parent_package,
+                _internal_package=True,
             )
             package.load(strict)
 

flopy/mf6/mfpackage.py

@@ -1594,6 +1594,10 @@ def __init__(
         else:
             self.model_or_sim = parent
             self.parent_file = None
+        if "_internal_package" in kwargs and kwargs["_internal_package"]:
+            self.internal_package = True
+        else:
+            self.internal_package = False
         self._data_list = []
         self._package_type = package_type
         if self.model_or_sim.type == "Model" and package_type.lower() != "nam":

flopy/mf6/modflow/mfsimulation.py

@@ -336,8 +336,7 @@ class MFSimulation(PackageContainer):
     version : str
         Version of MODFLOW 6 executable
     exe_name : str
-        Relative path to MODFLOW 6 executable from the simulation
-        working folder.
+        Path to MODFLOW 6 executable
     sim_ws : str
         Path to MODFLOW 6 simulation working folder.  This is the folder
         containing the simulation name file.
@@ -432,6 +431,7 @@ def __init__(
             continue_=continue_,
             nocheck=nocheck,
             memory_print_option=memory_print_option,
+            _internal_package=True,
         )
 
         # try to build directory structure
@@ -1902,6 +1902,14 @@ def register_package(
                 # added during ims package registration
                 self._add_package(package, path)
         if package.package_type.lower() == "nam":
+            if not package.internal_package:
+                excpt_str = (
+                    "Unable to register nam file.  Do not create your own nam "
+                    "files.  Nam files are automatically created and managed "
+                    "for you by FloPy."
+                )
+                print(excpt_str)
+                raise FlopyException(excpt_str)
             return path, self.structure.name_file_struct_obj
         elif package.package_type.lower() == "tdis":
             self._tdis_file = package

flopy/utils/datautil.py

@@ -358,8 +358,8 @@ def split_data_line(line, external_file=False, delimiter_conf_length=15):
                 if item and item[0] in PyListUtil.quote_list:
                     # starts with a quote, handle quoted text
                     if item[-1] in PyListUtil.quote_list:
-                        # if quoted on both ends, keep quotes
-                        arr_fixed_line.append(item)
+                        # if quoted on both ends, remove quotes
+                        arr_fixed_line.append(item[1:-1])
                     else:
                         arr_fixed_line.append(item[1:])
                         # loop until trailing quote found