refactor(flopy_io, notebooks): update path cleaning mechanism

autotest/test_flopy_io.py

@@ -1,4 +1,15 @@
-from flopy.utils.flopy_io import line_parse
+import os
+import platform
+from os import getcwd
+from os.path import relpath, splitdrive
+from pathlib import Path
+from shutil import which
+
+import pytest
+from modflow_devtools.markers import requires_exe
+from modflow_devtools.misc import set_dir
+
+from flopy.utils.flopy_io import line_parse, relpath_safe
 
 
 def test_line_parse():
@@ -7,3 +18,36 @@ def test_line_parse():
     # comment handling
     line = line_parse("Well-A  -1                   ; 2a. WELLID,NNODES")
     assert line == ["Well-A", "-1"]
+
+
+@requires_exe("mf6")
+@pytest.mark.parametrize("scrub", [True, False])
+def test_relpath_safe(function_tmpdir, scrub):
+    if (
+        platform.system() == "Windows"
+        and splitdrive(function_tmpdir)[0] != splitdrive(getcwd())[0]
+    ):
+        assert Path(relpath_safe(function_tmpdir)) == function_tmpdir.absolute()
+        assert relpath_safe(which("mf6")) == str(Path(which("mf6")).absolute())
+    else:
+        assert Path(
+            relpath_safe(function_tmpdir, function_tmpdir.parent)
+        ) == Path(function_tmpdir.name)
+        assert (
+            Path(relpath_safe(function_tmpdir, function_tmpdir.parent.parent))
+            == Path(function_tmpdir.parent.name) / function_tmpdir.name
+        )
+
+        assert relpath_safe(which("mf6")) == relpath(which("mf6"), getcwd())
+
+        # test user login obfuscation
+        with set_dir("/"):
+            try:
+                login = os.getlogin()
+                p = relpath_safe(Path.home(), scrub=scrub)
+                if login in str(Path.home()) and scrub:
+                    assert "***" in p
+                    assert login not in p
+            except OSError:
+                # OSError is possible in CI, e.g. 'No such device or address'
+                pass

autotest/test_mf6.py

@@ -1031,13 +1031,15 @@ def test_output_add_observation(function_tmpdir, example_data_path):
         sfr_obs, Mf6Obs
     ), "remove and add observation test (Mf6Output) failed"
 
+
 @requires_exe("mf6")
 def test_sfr_connections(function_tmpdir, example_data_path):
-    '''MODFLOW just warns if any reaches are unconnected
-    flopy fails to load model if reach 1 is unconnected, fine with other unconnected'''
+    """MODFLOW just warns if any reaches are unconnected
+    flopy fails to load model if reach 1 is unconnected, fine with other unconnected
+    """
     data_path = example_data_path / "mf6" / "test666_sfrconnections"
     sim_ws = function_tmpdir
-    for test in ['sfr0', 'sfr1']:
+    for test in ["sfr0", "sfr1"]:
         sim_name = "test_sfr"
         model_name = "test_sfr"
         tdis_name = f"{sim_name}.tdis"
@@ -1079,31 +1081,34 @@ def test_sfr_connections(function_tmpdir, example_data_path):
             k=50.0,
         )
 
-        cnfile = f'mf6_{test}_connection.txt'
-        pkfile = f'mf6_{test}_package.txt'
+        cnfile = f"mf6_{test}_connection.txt"
+        pkfile = f"mf6_{test}_package.txt"
 
-        with open(data_path / pkfile, 'r') as f:
+        with open(data_path / pkfile, "r") as f:
             nreaches = len(f.readlines())
-        sfr = ModflowGwfsfr(model,
-                            packagedata={'filename': str(data_path / pkfile)},
-                            connectiondata={'filename': str(data_path / cnfile)},
-                            nreaches=nreaches,
-                            pname='sfr',
-                            unit_conversion=86400
-                            )
+        sfr = ModflowGwfsfr(
+            model,
+            packagedata={"filename": str(data_path / pkfile)},
+            connectiondata={"filename": str(data_path / cnfile)},
+            nreaches=nreaches,
+            pname="sfr",
+            unit_conversion=86400,
+        )
         sim.set_all_data_external()
         sim.write_simulation()
         success, buff = sim.run_simulation()
         assert success, f"simulation {sim.name} did not run"
 
-        #reload simulation
+        # reload simulation
         sim2 = MFSimulation.load(sim_ws=sim_ws)
         sim.set_all_data_external()
         sim.write_simulation()
         success, buff = sim.run_simulation()
-        assert success, f"simulation {sim.name} did not run after being reloaded"
-
-
+        assert (
+            success
+        ), f"simulation {sim.name} did not run after being reloaded"
+
+
 @requires_exe("mf6")
 def test_array(function_tmpdir):
     # get_data

autotest/test_mnw.py

@@ -353,9 +353,7 @@ def test_mnw2_create_file(function_tmpdir):
         mnwmax=len(wells),
         mnw=wells,
         itmp=list(
-            (np.ones(len(stress_period_data.index)) * len(wellids)).astype(
-                int
-            )
+            (np.ones(len(stress_period_data.index)) * len(wellids)).astype(int)
         ),
     )
 

examples/FAQ/load_existing_mf2005.ipynb

@@ -5,20 +5,19 @@
    "execution_count": 1,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2022-12-15T13:28:43.181355Z",
-     "iopub.status.busy": "2022-12-15T13:28:43.180716Z",
-     "iopub.status.idle": "2022-12-15T13:28:44.452726Z",
-     "shell.execute_reply": "2022-12-15T13:28:44.447102Z"
+     "iopub.execute_input": "2023-02-22T02:38:54.562417Z",
+     "iopub.status.busy": "2023-02-22T02:38:54.562015Z",
+     "iopub.status.idle": "2023-02-22T02:38:55.452558Z",
+     "shell.execute_reply": "2023-02-22T02:38:55.451685Z"
     }
    },
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "3.7.15 (default, Oct 18 2022, 09:36:49) \n",
-      "[GCC 11.2.0]\n",
-      "flopy version: 3.3.6\n"
+      "3.10.6 (main, Nov 14 2022, 16:10:14) [GCC 11.3.0]\n",
+      "flopy version: 3.3.7\n"
      ]
     }
    ],
@@ -52,10 +51,10 @@
    "execution_count": 2,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2022-12-15T13:28:44.502987Z",
-     "iopub.status.busy": "2022-12-15T13:28:44.501928Z",
-     "iopub.status.idle": "2022-12-15T13:28:44.523250Z",
-     "shell.execute_reply": "2022-12-15T13:28:44.522309Z"
+     "iopub.execute_input": "2023-02-22T02:38:55.487988Z",
+     "iopub.status.busy": "2023-02-22T02:38:55.487318Z",
+     "iopub.status.idle": "2023-02-22T02:38:55.506112Z",
+     "shell.execute_reply": "2023-02-22T02:38:55.505372Z"
     }
    },
    "outputs": [
@@ -107,20 +106,12 @@
       "   BCF6 package load...success\n",
       "loading wel package file...\n",
       "   loading <class 'flopy.modflow.mfwel.ModflowWel'> for kper     1\n",
-      "   implicit itmpp in ../data/mf2005_test/bcf2ss.wel\n",
-      "   implicit itmp_cln in ../data/mf2005_test/bcf2ss.wel\n",
       "   loading <class 'flopy.modflow.mfwel.ModflowWel'> for kper     2\n",
-      "   implicit itmpp in ../data/mf2005_test/bcf2ss.wel\n",
-      "   implicit itmp_cln in ../data/mf2005_test/bcf2ss.wel\n",
       "adding Package:  WEL\n",
       "   WEL  package load...success\n",
       "loading riv package file...\n",
       "   loading <class 'flopy.modflow.mfriv.ModflowRiv'> for kper     1\n",
-      "   implicit itmpp in ../data/mf2005_test/bcf2ss.riv\n",
-      "   implicit itmp_cln in ../data/mf2005_test/bcf2ss.riv\n",
       "   loading <class 'flopy.modflow.mfriv.ModflowRiv'> for kper     2\n",
-      "   implicit itmpp in ../data/mf2005_test/bcf2ss.riv\n",
-      "   implicit itmp_cln in ../data/mf2005_test/bcf2ss.riv\n",
       "adding Package:  RIV\n",
       "   RIV  package load...success\n",
       "loading rch package file...\n",
@@ -195,7 +186,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.15"
+   "version": "3.10.6"
   }
  },
  "nbformat": 4,

examples/FAQ/load_existing_model_wAUX.ipynb

@@ -5,20 +5,19 @@
    "execution_count": 1,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2022-12-15T13:28:47.284600Z",
-     "iopub.status.busy": "2022-12-15T13:28:47.284136Z",
-     "iopub.status.idle": "2022-12-15T13:28:48.584587Z",
-     "shell.execute_reply": "2022-12-15T13:28:48.582184Z"
+     "iopub.execute_input": "2023-02-22T02:38:57.989290Z",
+     "iopub.status.busy": "2023-02-22T02:38:57.988720Z",
+     "iopub.status.idle": "2023-02-22T02:38:58.902520Z",
+     "shell.execute_reply": "2023-02-22T02:38:58.901874Z"
     }
    },
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "3.7.15 (default, Oct 18 2022, 09:36:49) \n",
-      "[GCC 11.2.0]\n",
-      "flopy version: 3.3.6\n"
+      "3.10.6 (main, Nov 14 2022, 16:10:14) [GCC 11.3.0]\n",
+      "flopy version: 3.3.7\n"
      ]
     }
    ],
@@ -49,10 +48,10 @@
    "execution_count": 2,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2022-12-15T13:28:48.631684Z",
-     "iopub.status.busy": "2022-12-15T13:28:48.630599Z",
-     "iopub.status.idle": "2022-12-15T13:28:48.648958Z",
-     "shell.execute_reply": "2022-12-15T13:28:48.648073Z"
+     "iopub.execute_input": "2023-02-22T02:38:58.968512Z",
+     "iopub.status.busy": "2023-02-22T02:38:58.967651Z",
+     "iopub.status.idle": "2023-02-22T02:38:58.987908Z",
+     "shell.execute_reply": "2023-02-22T02:38:58.986885Z"
     }
    },
    "outputs": [],
@@ -79,10 +78,10 @@
    "execution_count": 3,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2022-12-15T13:28:48.653210Z",
-     "iopub.status.busy": "2022-12-15T13:28:48.652598Z",
-     "iopub.status.idle": "2022-12-15T13:28:48.657827Z",
-     "shell.execute_reply": "2022-12-15T13:28:48.656720Z"
+     "iopub.execute_input": "2023-02-22T02:38:58.992067Z",
+     "iopub.status.busy": "2023-02-22T02:38:58.991398Z",
+     "iopub.status.idle": "2023-02-22T02:38:58.997441Z",
+     "shell.execute_reply": "2023-02-22T02:38:58.996570Z"
     }
    },
    "outputs": [],
@@ -102,10 +101,10 @@
    "execution_count": 4,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2022-12-15T13:28:48.661328Z",
-     "iopub.status.busy": "2022-12-15T13:28:48.660925Z",
-     "iopub.status.idle": "2022-12-15T13:28:48.670325Z",
-     "shell.execute_reply": "2022-12-15T13:28:48.669141Z"
+     "iopub.execute_input": "2023-02-22T02:38:59.001461Z",
+     "iopub.status.busy": "2023-02-22T02:38:59.000710Z",
+     "iopub.status.idle": "2023-02-22T02:38:59.011006Z",
+     "shell.execute_reply": "2023-02-22T02:38:59.010185Z"
     }
    },
    "outputs": [
@@ -136,10 +135,10 @@
    "execution_count": 5,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2022-12-15T13:28:48.674398Z",
-     "iopub.status.busy": "2022-12-15T13:28:48.673839Z",
-     "iopub.status.idle": "2022-12-15T13:28:48.680585Z",
-     "shell.execute_reply": "2022-12-15T13:28:48.679578Z"
+     "iopub.execute_input": "2023-02-22T02:38:59.015980Z",
+     "iopub.status.busy": "2023-02-22T02:38:59.015391Z",
+     "iopub.status.idle": "2023-02-22T02:38:59.022103Z",
+     "shell.execute_reply": "2023-02-22T02:38:59.021231Z"
     }
    },
    "outputs": [
@@ -183,7 +182,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.15"
+   "version": "3.10.6"
   }
  },
  "nbformat": 4,