fix(paths): Path code made more robust so that non-standard model fol…

…der structures are supported (#1311) (#1316)

* fix(paths): Path code made more robust so that non-standard model folder structures are supported.  There are three basic path times, the path to the simulation, model relative paths to particular models in the simulation, and package/data relative paths to package or data files in a model or simulation. Model relative paths are relative to the simulation path.  Package/data relative paths are relative to the simulation path for packages/data not attached to a model and relative to model relative path for packages/data attached to a model. (#1311)

* test(paths): added more comprehensive testing of paths

Co-authored-by: Scott Paulinski <spaulinski@usgs.gov>

autotest/t505_test.py

@@ -811,6 +811,7 @@ def test_np001():
     }
     wel_package = ModflowGwfwel(
         model,
+        filename=f"well_folder\\{model_name}.wel",
         print_input=True,
         print_flows=True,
         save_flows=True,
@@ -841,7 +842,7 @@ def test_np001():
 
     riv_spd = {
         0: {
-            "filename": "riv.txt",
+            "filename": os.path.join("riv_folder", "riv.txt"),
             "data": [((0, 0, 9), 110, 90.0, 100.0, 1.0, 2.0, 3.0)],
         }
     }
@@ -914,6 +915,12 @@ def test_np001():
     assert (
         sim.simulation_data.max_columns_of_data == dis_package.ncol.get_data()
     )
+    # test package file with relative path to simulation path
+    wel_path = os.path.join(run_folder, "well_folder", f"{model_name}.wel")
+    assert os.path.exists(wel_path)
+    # test data file with relative path to simulation path
+    riv_path = os.path.join(run_folder, "riv_folder", "riv.txt")
+    assert os.path.exists(riv_path)
 
     # run simulation
     if run:
@@ -950,6 +957,17 @@ def test_np001():
     sim.set_all_data_external(external_data_folder="data")
     sim.write_simulation()
 
+    # test file with relative path to model relative path
+    wel_path = os.path.join(
+        run_folder, md_folder, "well_folder", f"{model_name}.wel"
+    )
+    assert os.path.exists(wel_path)
+    # test data file was recreated by set_all_data_external
+    riv_path = os.path.join(
+        run_folder, md_folder, "data", "np001_mod.riv_stress_period_data_1.txt"
+    )
+    assert os.path.exists(riv_path)
+
     assert (
         sim.simulation_data.max_columns_of_data == dis_package.ncol.get_data()
     )
@@ -974,7 +992,6 @@ def test_np001():
             outfile=outfile,
         )
 
-        # budget_frf = sim.simulation_data.mfdata[(model_name, "CBC", "RIV")]
         budget_frf = model.output.budget().get_data(text="RIV", full3D=False)
         assert array_util.riv_array_comp(budget_frf_valid, budget_frf)
 
@@ -1090,14 +1107,15 @@ def test_np001():
     well_spd = {0: [(-1, -1, -1, -2000.0), (0, 0, 7, -2.0)], 1: []}
     wel_package = ModflowGwfwel(
         model,
+        pname="wel_1",
         filename="file_rename.wel",
         print_input=True,
         print_flows=True,
         save_flows=True,
         maxbound=2,
         stress_period_data=well_spd,
     )
-    wel_package.write()
+    sim.write_simulation()
     found_begin = False
     found_end = False
     text_between_begin_and_end = False
@@ -1121,7 +1139,7 @@ def test_np001():
         spath,
         write_headers=False,
     )
-    wel = test_sim.get_model().wel
+    wel = test_sim.get_model().get_package("wel_1")
     wel._filename = "np001_spd_test.wel"
     wel.write()
     found_begin = False
@@ -1778,7 +1796,7 @@ def test005_advgw_tidal():
         (31.0, 0.0, -600.0, -400.0),
     ]
     ts_dict = {
-        "filename": "well-rates.ts",
+        "filename": os.path.join("well-rates", "well-rates.ts"),
         "timeseries": timeseries,
         "time_series_namerecord": [
             ("well_1_rate", "well_2_rate", "well_3_rate")
@@ -2160,6 +2178,10 @@ def test005_advgw_tidal():
     sim.set_all_data_external()
     sim.write_simulation()
 
+    # test time series data file with relative path to simulation path
+    ts_path = os.path.join(run_folder, "well-rates", "well-rates.ts")
+    assert os.path.exists(ts_path)
+
     # run simulation
     sim.run_simulation()
 
@@ -2180,22 +2202,24 @@ def test005_advgw_tidal():
     package_type_dict = {}
     for package in model.packagelist:
         if not package.package_type in package_type_dict:
-            assert package.filename == f"new_name.{package.package_type}"
+            filename = os.path.split(package.filename)[1]
+            assert filename == f"new_name.{package.package_type}"
             package_type_dict[package.package_type] = 1
     sim.write_simulation()
     name_file = os.path.join(run_folder, "new_name.nam")
     assert os.path.exists(name_file)
     dis_file = os.path.join(run_folder, "new_name.dis")
     assert os.path.exists(dis_file)
+    # test time series data file with relative path to simulation path
+    ts_path = os.path.join(run_folder, "well-rates", "new_name.ts")
+    assert os.path.exists(ts_path)
 
     sim.rename_all_packages("all_files_same_name")
     package_type_dict = {}
     for package in model.packagelist:
         if not package.package_type in package_type_dict:
-            assert (
-                package.filename
-                == f"all_files_same_name.{package.package_type}"
-            )
+            filename = os.path.split(package.filename)[1]
+            assert filename == f"all_files_same_name.{package.package_type}"
             package_type_dict[package.package_type] = 1
     assert sim._tdis_file.filename == "all_files_same_name.tdis"
     for ims_file in sim._ims_files.values():
@@ -2207,6 +2231,9 @@ def test005_advgw_tidal():
     assert os.path.exists(dis_file)
     tdis_file = os.path.join(run_folder, "all_files_same_name.tdis")
     assert os.path.exists(tdis_file)
+    # test time series data file with relative path to simulation path
+    ts_path = os.path.join(run_folder, "well-rates", "all_files_same_name.ts")
+    assert os.path.exists(ts_path)
 
     # load simulation
     sim_load = MFSimulation.load(
@@ -3073,13 +3100,14 @@ def test006_2models_gnc():
 
     # test exg delete
     newexgrecarray = exgrecarray[10:]
+    gnc_path = os.path.join("gnc", "test006_2models_gnc.gnc")
     exg_package = ModflowGwfgwf(
         sim,
         print_input=True,
         print_flows=True,
         save_flows=True,
         auxiliary="testaux",
-        gnc_filerecord="test006_2models_gnc.gnc",
+        gnc_filerecord=gnc_path,
         nexg=26,
         exchangedata=newexgrecarray,
         exgtype="gwf6-gwf6",
@@ -3094,7 +3122,7 @@ def test006_2models_gnc():
         print_flows=True,
         save_flows=True,
         auxiliary="testaux",
-        gnc_filerecord="test006_2models_gnc.gnc",
+        gnc_filerecord=gnc_path,
         nexg=36,
         exchangedata=exgrecarray,
         exgtype="gwf6-gwf6",
@@ -3108,6 +3136,7 @@ def test006_2models_gnc():
     new_gncrecarray = gncrecarray[10:]
     gnc_package = ModflowGwfgnc(
         sim,
+        filename=gnc_path,
         print_input=True,
         print_flows=True,
         numgnc=26,
@@ -3118,6 +3147,7 @@ def test006_2models_gnc():
 
     gnc_package = ModflowGwfgnc(
         sim,
+        filename=gnc_path,
         print_input=True,
         print_flows=True,
         numgnc=36,
@@ -3131,6 +3161,10 @@ def test006_2models_gnc():
     # write simulation to new location
     sim.write_simulation()
 
+    # test gnc file was created in correct location
+    gnc_full_path = os.path.join(run_folder, gnc_path)
+    assert os.path.exists(gnc_full_path)
+
     # run simulation
     if run:
         sim.run_simulation()
@@ -3172,6 +3206,9 @@ def test006_2models_gnc():
         sim_path, "model2", "data", "model2.dis_botm.txt"
     )
     assert os.path.exists(ext_file_path_2)
+    # test gnc file was created in correct location
+    gnc_full_path = os.path.join(sim_path, gnc_path)
+    assert os.path.exists(gnc_full_path)
     if run:
         sim.run_simulation()
 
@@ -3183,6 +3220,9 @@ def test006_2models_gnc():
     sim.rename_all_packages("file_rename")
     sim.set_sim_path(rename_folder)
     sim.write_simulation()
+    # test gnc file was created in correct location
+    gnc_full_path = os.path.join(rename_folder, "gnc", "file_rename.gnc")
+    assert os.path.exists(gnc_full_path)
     if run:
         sim.run_simulation()
         sim.delete_output_files()

flopy/mf6/data/mfdatastorage.py

@@ -1552,6 +1552,12 @@ def store_external(
                         precision="double",
                     )
                 else:
+                    # make sure folder exists
+                    file_path = os.path.split(fp)[0]
+                    if not os.path.exists(file_path):
+                        os.makedirs(file_path)
+
+                    # create file
                     try:
                         fd = open(fp, "w")
                     except:

flopy/mf6/mfbase.py

@@ -270,17 +270,23 @@ def _build_relative_path(self, model_name):
     def strip_model_relative_path(self, model_name, path):
         """Strip out the model relative path part of `path`.  For internal
         FloPy use, not intended for end user."""
+        new_path = path
         if model_name in self.model_relative_path:
             model_rel_path = self.model_relative_path[model_name]
-            new_path = None
-            while path:
-                path, leaf = os.path.split(path)
-                if leaf != model_rel_path:
-                    if new_path:
-                        new_path = os.path.join(leaf, new_path)
-                    else:
-                        new_path = leaf
-            return new_path
+            if (
+                model_rel_path is not None
+                and len(model_rel_path) > 0
+                and model_rel_path != "."
+            ):
+                model_rel_path_lst = model_rel_path.split(os.path.sep)
+                path_lst = path.split(os.path.sep)
+                new_path = ""
+                for i, mrp in enumerate(model_rel_path_lst):
+                    if mrp != path_lst[i]:
+                        new_path = os.path.join(new_path, path_lst[i])
+                for rp in path_lst[len(model_rel_path_lst) :]:
+                    new_path = os.path.join(new_path, rp)
+        return new_path
 
     @staticmethod
     def unique_file_name(file_name, lookup):

flopy/mf6/mfmodel.py

@@ -1045,10 +1045,24 @@ def set_model_relative_path(self, model_ws):
                 packages_data = packages.get_data()
                 if packages_data is not None:
                     for index, entry in enumerate(packages_data):
-                        old_package_name = os.path.split(entry[1])[1]
-                        packages_data[index][1] = os.path.join(
-                            path, old_package_name
-                        )
+                        # get package object associated with entry
+                        package = None
+                        if len(entry) >= 3:
+                            package = self.get_package(entry[2])
+                        if package is None:
+                            package = self.get_package(entry[0])
+                        if package is not None:
+                            # combine model relative path with package path
+                            packages_data[index][1] = os.path.join(
+                                path, package.filename
+                            )
+                        else:
+                            # package not found, create path based on
+                            # information in name file
+                            old_package_name = os.path.split(entry[1])[-1]
+                            packages_data[index][1] = os.path.join(
+                                path, old_package_name
+                            )
                     packages.set_data(packages_data)
                 # update files referenced from within packages
                 for package in self.packagelist:
@@ -1186,12 +1200,15 @@ def update_package_filename(self, package, new_name):
                 message=message,
             )
         try:
+            file_mgr = self.simulation_data.mfpath
+            model_rel_path = file_mgr.model_relative_path[self.name]
             # update namefile package data with new name
             new_rec_array = None
+            old_leaf = os.path.split(package.filename)[1]
             for item in package_data:
-                base, leaf = os.path.split(item[1])
-                if leaf == package.filename:
-                    item[1] = os.path.join(base, new_name)
+                leaf = os.path.split(item[1])[1]
+                if leaf == old_leaf:
+                    item[1] = os.path.join(model_rel_path, new_name)
 
                 if new_rec_array is None:
                     new_rec_array = np.rec.array(
@@ -1246,7 +1263,14 @@ def rename_all_packages(self, name):
         package_type_count = {}
         for package in self.packagelist:
             if package.package_type not in package_type_count:
-                package.filename = f"{name}.{package.package_type}"
+                base_filename, leaf = os.path.split(package.filename)
+                new_fileleaf = f"{name}.{package.package_type}"
+                if base_filename != "":
+                    package.filename = os.path.join(
+                        base_filename, new_fileleaf
+                    )
+                else:
+                    package.filename = new_fileleaf
                 package_type_count[package.package_type] = 1
             else:
                 package_type_count[package.package_type] += 1