feat(pathlike): support pathlike in user-facing APIs (#1730)

- support pathlike or str paths in public APIs
- add tests for supported path arguments
- update docstrings and add type hints
- update some notebooks to use pathlib
- update most autotests to use pathlib
- add verbose flag to more util functions
- add sim_path property to MFSimulation
- expand run_model() tests to cover #1633
- update resolve_exe(), add tests

autotest/regression/test_mf6_examples.py

@@ -59,7 +59,7 @@ def run_models():
 
             # load simulation
             sim = MFSimulation.load(
-                namfile_name, version="mf6", exe_name="mf6", sim_ws=str(wrkdir)
+                namfile_name, version="mf6", exe_name="mf6", sim_ws=wrkdir
             )
             assert isinstance(sim, MFSimulation)
 
@@ -68,7 +68,7 @@ def run_models():
             assert success
 
             # change to comparison workspace
-            sim.simulation_data.mfpath.set_sim_path(str(cmpdir))
+            sim.simulation_data.mfpath.set_sim_path(cmpdir)
 
             # write simulation files and rerun
             sim.write_simulation()
@@ -87,7 +87,7 @@ def run_models():
                 text="head",
                 files1=[str(p) for p in headfiles1],
                 files2=[str(p) for p in headfiles2],
-                outfile=str(cmpdir / "head_compare.dat"),
+                outfile=cmpdir / "head_compare.dat",
             )
 
     run_models()

autotest/regression/test_mfnwt.py

@@ -24,7 +24,7 @@ def get_nfnwt_namfiles():
             if "WEL" in value.filetype:
                 wel = True
         if lpf and wel:
-            namfiles.append(str(namfile))
+            namfiles.append(namfile)
     return namfiles
 
 
@@ -107,16 +107,16 @@ def test_run_mfnwt_model(function_tmpdir, namfile):
     wel.iunitramp = 2
 
     # change workspace and write MODFLOW-NWT model
-    m.change_model_ws(str(function_tmpdir))
+    m.change_model_ws(function_tmpdir)
     m.write_input()
     success, buff = m.run_model(silent=False)
     assert success, "base model run did not terminate successfully"
-    fn0 = str(function_tmpdir / namfile)
+    fn0 = function_tmpdir / namfile
 
     # reload the model just written
     m = Modflow.load(
         namfile,
-        model_ws=str(function_tmpdir),
+        model_ws=function_tmpdir,
         version="mfnwt",
         verbose=True,
         check=False,
@@ -126,17 +126,17 @@ def test_run_mfnwt_model(function_tmpdir, namfile):
     assert m.load_fail is False
 
     # change workspace and write MODFLOW-NWT model
-    pthf = str(function_tmpdir / "flopy")
+    pthf = function_tmpdir / "flopy"
     m.change_model_ws(pthf)
     m.write_input()
     success, buff = m.run_model(silent=False)
     assert success, "base model run did not terminate successfully"
     fn1 = os.path.join(pthf, namfile)
 
-    fsum = str(function_tmpdir / f"{base_name}.head.out")
+    fsum = function_tmpdir / f"{base_name}.head.out"
     assert compare_heads(fn0, fn1, outfile=fsum), "head comparison failure"
 
-    fsum = str(function_tmpdir / f"{base_name}.budget.out")
+    fsum = function_tmpdir / f"{base_name}.budget.out"
     assert compare_budget(
         fn0, fn1, max_incpd=0.1, max_cumpd=0.1, outfile=fsum
     ), "budget comparison failure"

autotest/regression/test_modflow.py

@@ -26,7 +26,7 @@ def uzf_example_path(example_data_path):
 @pytest.mark.regression
 def test_uzf_unit_numbers(function_tmpdir, uzf_example_path):
     mfnam = "UZFtest2.nam"
-    ws = str(function_tmpdir / "ws")
+    ws = function_tmpdir / "ws"
     copytree(uzf_example_path, ws)
 
     m = Modflow.load(
@@ -73,7 +73,7 @@ def test_uzf_unit_numbers(function_tmpdir, uzf_example_path):
     fn1 = join(model_ws2, mfnam)
 
     # compare budget terms
-    fsum = join(str(function_tmpdir), f"{splitext(mfnam)[0]}.budget.out")
+    fsum = join(function_tmpdir, f"{splitext(mfnam)[0]}.budget.out")
     success = compare_budget(
         fn0, fn1, max_incpd=0.1, max_cumpd=0.1, outfile=fsum
     )
@@ -85,7 +85,7 @@ def test_uzf_unit_numbers(function_tmpdir, uzf_example_path):
 @pytest.mark.regression
 def test_unitnums(function_tmpdir, mf2005_test_path):
     mfnam = "testsfr2_tab.nam"
-    ws = str(function_tmpdir / "ws")
+    ws = function_tmpdir / "ws"
     copytree(mf2005_test_path, ws)
 
     m = Modflow.load(mfnam, verbose=True, model_ws=ws, exe_name="mf2005")
@@ -125,9 +125,9 @@ def test_gage(function_tmpdir, example_data_path):
     """
     test043 load and write of MODFLOW-2005 GAGE example problem
     """
-    pth = str(example_data_path / "mf2005_test")
+    pth = example_data_path / "mf2005_test"
     fpth = join(pth, "testsfr2_tab.nam")
-    ws = str(function_tmpdir / "ws")
+    ws = function_tmpdir / "ws"
     copytree(pth, ws)
 
     # load the modflow model
@@ -169,7 +169,7 @@ def test_gage(function_tmpdir, example_data_path):
 @pytest.mark.parametrize(
     "namfile",
     [
-        str(__example_data_path / "pcgn_test" / nf)
+        __example_data_path / "pcgn_test" / nf
         for nf in ["twri.nam", "MNW2.nam"]
     ],
 )
@@ -180,7 +180,7 @@ def test_mf2005pcgn(function_tmpdir, namfile):
 
     m = Modflow.load(
         nf,
-        model_ws=str(ws),
+        model_ws=ws,
         verbose=True,
         exe_name="mf2005",
     )
@@ -192,22 +192,22 @@ def test_mf2005pcgn(function_tmpdir, namfile):
 
     success, buff = m.run_model(silent=False)
     assert success, "base model run did not terminate successfully"
-    fn0 = str(ws / nf)
+    fn0 = ws / nf
 
     # rewrite files
     ws2 = function_tmpdir / "ws2"
-    m.change_model_ws(str(ws2))
+    m.change_model_ws(ws2)
     m.write_input()
 
     success, buff = m.run_model(silent=False)
     assert success, "new model run did not terminate successfully"
-    fn1 = str(ws2 / nf)
+    fn1 = ws2 / nf
 
-    fsum = str(function_tmpdir / f"{Path(namfile).stem}.head.out")
+    fsum = function_tmpdir / f"{Path(namfile).stem}.head.out"
     success = compare_heads(fn0, fn1, outfile=fsum, htol=0.005)
     assert success, "head comparison failure"
 
-    fsum = str(function_tmpdir / f"{Path(namfile).stem}.budget.out")
+    fsum = function_tmpdir / f"{Path(namfile).stem}.budget.out"
     success = compare_budget(
         fn0, fn1, max_incpd=0.1, max_cumpd=0.1, outfile=fsum
     )
@@ -218,7 +218,7 @@ def test_mf2005pcgn(function_tmpdir, namfile):
 @pytest.mark.slow
 @pytest.mark.regression
 @pytest.mark.parametrize(
-    "namfile", [str(__example_data_path / "secp" / nf) for nf in ["secp.nam"]]
+    "namfile", [__example_data_path / "secp" / nf for nf in ["secp.nam"]]
 )
 def test_mf2005gmg(function_tmpdir, namfile):
     ws = function_tmpdir / "ws"
@@ -227,29 +227,29 @@ def test_mf2005gmg(function_tmpdir, namfile):
 
     m = Modflow.load(
         namfile,
-        model_ws=str(ws),
+        model_ws=ws,
         verbose=True,
         exe_name="mf2005",
     )
     assert m.load_fail is False
 
     success, buff = m.run_model(silent=False)
     assert success, "base model run did not terminate successfully"
-    fn0 = str(ws / nf)
+    fn0 = ws / nf
 
     # rewrite files
-    m.change_model_ws(str(function_tmpdir))
+    m.change_model_ws(function_tmpdir)
     m.write_input()
 
     success, buff = m.run_model(silent=False)
     assert success, "new model run did not terminate successfully"
-    fn1 = str(function_tmpdir / nf)
+    fn1 = function_tmpdir / nf
 
-    fsum = str(function_tmpdir / f"{Path(namfile).stem}.head.out")
+    fsum = function_tmpdir / f"{Path(namfile).stem}.head.out"
     success = compare_heads(fn0, fn1, outfile=fsum)
     assert success, "head comparison failure"
 
-    fsum = str(function_tmpdir / f"{Path(namfile).stem}.budget.out")
+    fsum = function_tmpdir / f"{Path(namfile).stem}.budget.out"
     success = compare_budget(
         fn0, fn1, max_incpd=0.1, max_cumpd=0.1, outfile=fsum
     )
@@ -260,27 +260,27 @@ def test_mf2005gmg(function_tmpdir, namfile):
 @pytest.mark.regression
 @pytest.mark.parametrize(
     "namfile",
-    [str(__example_data_path / "freyberg" / nf) for nf in ["freyberg.nam"]],
+    [__example_data_path / "freyberg" / nf for nf in ["freyberg.nam"]],
 )
 def test_mf2005(function_tmpdir, namfile):
     """
     test045 load and write of MODFLOW-2005 GMG example problem
     """
     compth = function_tmpdir / "flopy"
     ws = function_tmpdir / "ws"
-    copytree(Path(namfile).parent, str(ws))
+    copytree(Path(namfile).parent, ws)
 
     m = Modflow.load(
         Path(namfile).name,
-        model_ws=str(ws),
+        model_ws=ws,
         verbose=True,
         exe_name="mf2005",
     )
     assert m.load_fail is False
 
     success, buff = m.run_model(silent=False)
     assert success, "base model run did not terminate successfully"
-    fn0 = str(ws / Path(namfile).name)
+    fn0 = ws / Path(namfile).name
 
     # change model workspace
     m.change_model_ws(compth)
@@ -304,28 +304,28 @@ def test_mf2005(function_tmpdir, namfile):
 
     success, buff = m.run_model()
     assert success, "new model run did not terminate successfully"
-    fn1 = str(compth / Path(namfile).name)
+    fn1 = compth / Path(namfile).name
 
     # compare heads
-    fsum = str(ws / f"{Path(namfile).stem}.head.out")
+    fsum = ws / f"{Path(namfile).stem}.head.out"
     success = compare_heads(fn0, fn1, outfile=fsum)
     assert success, "head comparison failure"
 
     # compare heads
-    fsum = str(ws / f"{Path(namfile).stem}.ddn.out")
+    fsum = ws / f"{Path(namfile).stem}.ddn.out"
     success = compare_heads(fn0, fn1, outfile=fsum, text="drawdown")
     assert success, "head comparison failure"
 
     # compare budgets
-    fsum = str(ws / f"{Path(namfile).stem}.budget.out")
+    fsum = ws / f"{Path(namfile).stem}.budget.out"
     success = compare_budget(
         fn0, fn1, max_incpd=0.1, max_cumpd=0.1, outfile=fsum
     )
     assert success, "budget comparison failure"
 
 
 mf2005_namfiles = [
-    str(__example_data_path / "mf2005_test" / nf)
+    __example_data_path / "mf2005_test" / nf
     for nf in [
         "fhb.nam",
         "l1a2k.nam",
@@ -341,7 +341,7 @@ def test_mf2005(function_tmpdir, namfile):
 @pytest.mark.regression
 @pytest.mark.parametrize("namfile", mf2005_namfiles)
 def test_mf2005fhb(function_tmpdir, namfile):
-    ws = str(function_tmpdir / "ws")
+    ws = function_tmpdir / "ws"
     copytree(Path(namfile).parent, ws)
 
     m = Modflow.load(
@@ -354,12 +354,12 @@ def test_mf2005fhb(function_tmpdir, namfile):
     fn0 = join(ws, Path(namfile).name)
 
     # rewrite files
-    m.change_model_ws(str(function_tmpdir), reset_external=True)
+    m.change_model_ws(function_tmpdir, reset_external=True)
     m.write_input()
 
     success, buff = m.run_model()
     assert success, "new model run did not terminate successfully"
-    fn1 = join(str(function_tmpdir), Path(namfile).name)
+    fn1 = join(function_tmpdir, Path(namfile).name)
 
     fsum = join(ws, f"{Path(namfile).stem}.head.out")
     success = compare_heads(fn0, fn1, outfile=fsum)
@@ -377,12 +377,12 @@ def test_mf2005fhb(function_tmpdir, namfile):
 @pytest.mark.regression
 @pytest.mark.parametrize("namfile", mf2005_namfiles)
 def test_mf2005_lake(function_tmpdir, namfile, mf2005_test_path):
-    ws = str(function_tmpdir / "ws")
+    ws = function_tmpdir / "ws"
 
     copytree(mf2005_test_path, ws)
     m = Modflow.load(
         Path(namfile).name,
-        model_ws=str(ws),
+        model_ws=ws,
         verbose=True,
         forgive=False,
         exe_name="mf2005",

autotest/regression/test_str.py

@@ -21,11 +21,11 @@ def test_str_fixed_free(function_tmpdir, example_data_path):
     m = Modflow.load(
         str_items[0]["mfnam"],
         exe_name="mf2005",
-        model_ws=str(mf2005_model_path),
+        model_ws=mf2005_model_path,
         verbose=False,
         check=False,
     )
-    m.change_model_ws(str(function_tmpdir))
+    m.change_model_ws(function_tmpdir)
 
     # get pointer to str package
     mstr = m.str
@@ -81,7 +81,7 @@ def test_str_fixed_free(function_tmpdir, example_data_path):
         m2 = Modflow.load(
             str_items[0]["mfnam"],
             exe_name="mf2005",
-            model_ws=str(mf2005_model_path),
+            model_ws=mf2005_model_path,
             verbose=False,
             check=False,
         )
@@ -95,7 +95,7 @@ def test_str_fixed_free(function_tmpdir, example_data_path):
     for p in function_tmpdir.glob("*"):
         p.unlink()
 
-    m.change_model_ws(str(function_tmpdir))
+    m.change_model_ws(function_tmpdir)
     m.set_ifrefm()
     m.write_input()
 
@@ -107,7 +107,7 @@ def test_str_fixed_free(function_tmpdir, example_data_path):
         m2 = Modflow.load(
             str_items[0]["mfnam"],
             exe_name="mf2005",
-            model_ws=str(function_tmpdir),
+            model_ws=function_tmpdir,
             verbose=False,
             check=False,
         )
@@ -119,8 +119,8 @@ def test_str_fixed_free(function_tmpdir, example_data_path):
     ), "could not load the free format model with aux variables"
 
     # compare the fixed and free format head files
-    fn1 = str(function_tmpdir / "str.nam")
-    fn2 = str(function_tmpdir / "str.nam")
+    fn1 = function_tmpdir / "str.nam"
+    fn2 = function_tmpdir / "str.nam"
     assert compare_heads(
         fn1, fn2, verbose=True
     ), "fixed and free format input output head files are different"

autotest/regression/test_swi2.py

@@ -21,7 +21,7 @@ def swi_path(example_data_path):
 )
 def test_mf2005swi2(function_tmpdir, swi_path, namfile):
     name = namfile.replace(".nam", "")
-    ws = str(function_tmpdir / "ws")
+    ws = function_tmpdir / "ws"
     shutil.copytree(swi_path, ws)
 
     m = Modflow.load(namfile, model_ws=ws, verbose=True, exe_name="mf2005")