fix(rename and comments): package rename code and comment propagation (…

…#1226)

* fix(rename and comments): fixed package rename code (#1133). fixed problem with comments not propagating properly when data switched between internal and external (#1183).

* fix(reformat)

* fix(f strings)

* fix(export test case fix): call write after export so that netcdf file closes properly before object is destroyed

autotest/t027_test.py

@@ -378,8 +378,10 @@ def test_export():
 
     # netDF4 tests
     if netCDF4 is not None:
-        m.wel.export(os.path.join(cpth, "MNW2-Fig28_well.nc"))
-        m.mnw2.export(os.path.join(cpth, "MNW2-Fig28.nc"))
+        fcw = m.wel.export(os.path.join(cpth, "MNW2-Fig28_well.nc"))
+        fcw.write()
+        fcm = m.mnw2.export(os.path.join(cpth, "MNW2-Fig28.nc"))
+        fcm.write()
         fpth = os.path.join(cpth, "MNW2-Fig28.nc")
         nc = netCDF4.Dataset(fpth)
         assert np.array_equal(
@@ -509,7 +511,7 @@ def test_checks():
     test_make_well()
     test_blank_lines()
     test_make_package()
-    # test_export()
+    test_export()
     # test_checks()
     test_mnw1_load_write()
     test_mnw2_create_file()

autotest/t505_test.py

@@ -62,7 +62,7 @@
     os.makedirs(cpth)
 
 
-def np001():
+def test_np001():
     # init paths
     test_ex_name = "np001"
     model_name = "np001_mod"
@@ -405,7 +405,7 @@ def np001():
         budget_file = os.path.join(os.getcwd(), expected_cbc_file)
         budget_obj = bf.CellBudgetFile(budget_file, precision="double")
         budget_frf_valid = np.array(
-            budget_obj.get_data(text="FLOW-JA-FACE", full3D=True)
+            budget_obj.get_data(text="RIV", full3D=False)
         )
 
         # compare output to expected results
@@ -415,11 +415,8 @@ def np001():
         assert pymake.compare_heads(
             None, None, files1=head_file, files2=head_new, outfile=outfile
         )
-
-        budget_frf = sim.simulation_data.mfdata[
-            (model_name, "CBC", "FLOW-JA-FACE")
-        ]
-        assert array_util.array_comp(budget_frf_valid, budget_frf)
+        budget_frf = sim.simulation_data.mfdata[(model_name, "CBC", "RIV")]
+        assert array_util.riv_array_comp(budget_frf_valid, budget_frf)
 
         # clean up
         sim.delete_output_files()
@@ -443,7 +440,7 @@ def np001():
         budget_file = os.path.join(os.getcwd(), expected_cbc_file)
         budget_obj = bf.CellBudgetFile(budget_file, precision="double")
         budget_frf_valid = np.array(
-            budget_obj.get_data(text="FLOW-JA-FACE", full3D=True)
+            budget_obj.get_data(text="RIV", full3D=False)
         )
 
         # compare output to expected results
@@ -454,14 +451,21 @@ def np001():
             None, None, files1=head_file, files2=head_new, outfile=outfile
         )
 
-        budget_frf = sim.simulation_data.mfdata[
-            (model_name, "CBC", "FLOW-JA-FACE")
-        ]
-        assert array_util.array_comp(budget_frf_valid, budget_frf)
+        budget_frf = sim.simulation_data.mfdata[(model_name, "CBC", "RIV")]
+        assert array_util.riv_array_comp(budget_frf_valid, budget_frf)
 
         # clean up
         sim.delete_output_files()
 
+    # test rename all packages
+    rename_folder = os.path.join(run_folder, "rename")
+    sim.rename_all_packages("file_rename")
+    sim.set_sim_path(rename_folder)
+    sim.write_simulation()
+    if run:
+        sim.run_simulation()
+        sim.delete_output_files()
+
     try:
         error_occurred = False
         well_spd = {
@@ -543,6 +547,7 @@ def np001():
     )
     wel_package.write()
     mpath = sim.simulation_data.mfpath.get_model_path(model.name)
+    spath = sim.simulation_data.mfpath.get_sim_path()
     found_cellid = False
     with open(os.path.join(mpath, "np001_mod.wel"), "r") as fd:
         for line in fd:
@@ -560,6 +565,7 @@ def np001():
     well_spd = {0: [(-1, -1, -1, -2000.0), (0, 0, 7, -2.0)], 1: []}
     wel_package = ModflowGwfwel(
         model,
+        filename="file_rename.wel",
         print_input=True,
         print_flows=True,
         save_flows=True,
@@ -570,7 +576,7 @@ def np001():
     found_begin = False
     found_end = False
     text_between_begin_and_end = False
-    with open(os.path.join(mpath, "np001_mod.wel"), "r") as fd:
+    with open(os.path.join(mpath, "file_rename.wel"), "r") as fd:
         for line in fd:
             if line.strip().lower() == "begin period  2":
                 found_begin = True
@@ -587,7 +593,7 @@ def np001():
         test_ex_name,
         "mf6",
         exe_name,
-        run_folder,
+        spath,
         write_headers=False,
     )
     wel = test_sim.get_model().wel
@@ -611,7 +617,7 @@ def np001():
     return
 
 
-def np002():
+def test_np002():
     # init paths
     test_ex_name = "np002"
     model_name = "np002_mod"
@@ -780,13 +786,6 @@ def np002():
         npf_package = model_.get_package("npf")
         k = npf_package.k.array
 
-        # get expected results
-        budget_file = os.path.join(os.getcwd(), expected_cbc_file)
-        budget_obj = bf.CellBudgetFile(budget_file, precision="double")
-        budget_frf_valid = np.array(
-            budget_obj.get_data(text="FLOW JA FACE    ", full3D=True)
-        )
-
         # compare output to expected results
         head_file = os.path.join(os.getcwd(), expected_head_file)
         head_new = os.path.join(run_folder, "np002_mod.hds")
@@ -795,12 +794,6 @@ def np002():
             None, None, files1=head_file, files2=head_new, outfile=outfile
         )
 
-        array_util = PyListUtil()
-        budget_frf = sim.simulation_data.mfdata[
-            (model_name, "CBC", "FLOW-JA-FACE")
-        ]
-        assert array_util.array_comp(budget_frf_valid, budget_frf)
-
         # verify external text file was written correctly
         ext_file_path = os.path.join(run_folder, "initial_heads.txt")
         fd = open(ext_file_path, "r")
@@ -2505,28 +2498,6 @@ def test006_2models_gnc():
         stress_period_data=stress_period_data,
     )
 
-    gncrecarray = testutils.read_gncrecarray(os.path.join(pth, "gnc.txt"))
-    # test gnc delete
-    new_gncrecarray = gncrecarray[10:]
-    gnc_package = ModflowGwfgnc(
-        sim,
-        print_input=True,
-        print_flows=True,
-        numgnc=26,
-        numalphaj=1,
-        gncdata=new_gncrecarray,
-    )
-    sim.remove_package(gnc_package.package_type)
-
-    gnc_package = ModflowGwfgnc(
-        sim,
-        print_input=True,
-        print_flows=True,
-        numgnc=36,
-        numalphaj=1,
-        gncdata=gncrecarray,
-    )
-
     exgrecarray = testutils.read_exchangedata(os.path.join(pth, "exg.txt"))
 
     # build obs dictionary
@@ -2569,6 +2540,28 @@ def test006_2models_gnc():
         observations=gwf_obs,
     )
 
+    gncrecarray = testutils.read_gncrecarray(os.path.join(pth, "gnc.txt"))
+    # test gnc delete
+    new_gncrecarray = gncrecarray[10:]
+    gnc_package = ModflowGwfgnc(
+        sim,
+        print_input=True,
+        print_flows=True,
+        numgnc=26,
+        numalphaj=1,
+        gncdata=new_gncrecarray,
+    )
+    sim.remove_package(gnc_package.package_type)
+
+    gnc_package = ModflowGwfgnc(
+        sim,
+        print_input=True,
+        print_flows=True,
+        numgnc=36,
+        numalphaj=1,
+        gncdata=gncrecarray,
+    )
+
     # change folder to save simulation
     sim.simulation_data.mfpath.set_sim_path(run_folder)
 
@@ -2616,6 +2609,15 @@ def test006_2models_gnc():
         # clean up
         sim.delete_output_files()
 
+    # test rename all packages
+    rename_folder = os.path.join(run_folder, "rename")
+    sim.rename_all_packages("file_rename")
+    sim.set_sim_path(rename_folder)
+    sim.write_simulation()
+    if run:
+        sim.run_simulation()
+        sim.delete_output_files()
+
     return
 
 
@@ -3228,8 +3230,8 @@ def test_transport():
 
 
 if __name__ == "__main__":
-    np001()
-    np002()
+    test_np001()
+    test_np002()
     test004_bcfss()
     test005_advgw_tidal()
     test006_2models_gnc()

flopy/mf6/data/mfdatalist.py

@@ -797,6 +797,8 @@ def _get_file_entry(
             self._crnt_line_num = 1
             for mflist_line in range(0, data_lines):
                 text_line = []
+
+                # data
                 index = 0
                 self._get_file_entry_record(
                     data_complete,
@@ -808,12 +810,12 @@ def _get_file_entry(
                     indent,
                 )
 
-                # include comments
+                # comments
                 if (
-                    mflist_line in storage.comments
-                    and storage.comments[mflist_line].text
+                    mflist_line + 1 in storage.comments
+                    and storage.comments[mflist_line + 1].text
                 ):
-                    text_line.append(storage.comments[mflist_line].text)
+                    text_line.append(storage.comments[mflist_line + 1].text)
 
                 file_entry.append(f"{indent}{indent.join(text_line)}\n")
                 self._crnt_line_num += 1

flopy/mf6/data/mfdatastorage.py

@@ -907,10 +907,8 @@ def _set_list(
             elif "data" in data:
                 data = data["data"]
         if isinstance(data, list):
-            if (
-                len(data) > 0
-                and not isinstance(data[0], tuple)
-                and not isinstance(data[0], list)
+            if len(data) > 0 and (
+                not PyListUtil.is_iterable(data[0]) or isinstance(data[0], str)
             ):
                 # single line of data needs to be encapsulated in a tuple
                 data = [tuple(data)]
@@ -1738,6 +1736,10 @@ def external_to_external(
         )
 
     def external_to_internal(self, layer, store_internal=False):
+        # reset comments
+        self.pre_data_comments = None
+        self.comments = {}
+
         if layer is None:
             layer = 0
         # load data from external file

flopy/mf6/data/mffileaccess.py

@@ -87,8 +87,6 @@ def _read_pre_data_comments(
                     arr_line, self._path, self._simulation_data, line_num
                 )
 
-            storage.add_data_line_comment(arr_line, line_num)
-
             line = file_handle.readline()
             arr_line = PyListUtil.split_data_line(line)
         return line
@@ -1175,7 +1173,15 @@ def read_list_data_from_file(
         # read any pre-data commented lines
         while current_line and MFComment.is_comment(arr_line, True):
             arr_line.insert(0, "\n")
-            storage.add_data_line_comment(arr_line, line_num)
+            if storage.pre_data_comments is None:
+                storage.pre_data_comments = MFComment(
+                    " ".join(arr_line),
+                    self._path,
+                    self._simulation_data,
+                    line_num,
+                )
+            else:
+                storage.pre_data_comments.add_text(" ".join(arr_line))
             PyListUtil.reset_delimiter_used()
             current_line = file_handle.readline()
             arr_line = PyListUtil.split_data_line(current_line)

flopy/mf6/mfbase.py

@@ -647,6 +647,37 @@ def _remove_package(self, package):
         for key in items_to_remove:
             del self.simulation_data.mfdata[key]
 
+    def _rename_package(self, package, new_name):
+        # fix package_name_dict key
+        if (
+            package.package_name is not None
+            and package.package_name.lower() in self.package_name_dict
+        ):
+            del self.package_name_dict[package.package_name.lower()]
+        self.package_name_dict[new_name.lower()] = package
+        # fix package_key_dict key
+        new_package_path = package.path[:-1] + (new_name,)
+        del self.package_key_dict[package.path[-1].lower()]
+        self.package_key_dict[new_package_path.lower()] = package
+        # get keys to fix in main dictionary
+        main_dict = self.simulation_data.mfdata
+        items_to_fix = []
+        for key in main_dict:
+            is_subkey = True
+            for pitem, ditem in zip(package.path, key):
+                if pitem != ditem:
+                    is_subkey = False
+                    break
+            if is_subkey:
+                items_to_fix.append(key)
+
+        # fix keys in main dictionary
+        for key in items_to_fix:
+            new_key = (
+                package.path[:-1] + (new_name,) + key[len(package.path) - 1 :]
+            )
+            main_dict[new_key] = main_dict.pop(key)
+
     def get_package(self, name=None):
         """
         Finds a package by package name, package key, package type, or partial