From 51d04bdcd57cc3f6b10c96438e2324bccf886245 Mon Sep 17 00:00:00 2001
From: Brioch <briochh@gmail.com>
Date: Tue, 19 Aug 2025 17:27:04 +1200
Subject: [PATCH 1/3] Refactoring text exe messes

+ Modifying bin path behaviour in tests to resolve fall back path if exe not found on PATH
---
 autotest/conftest.py           |  52 ++++++++-
 autotest/pst_from_tests.py     | 197 +++++++--------------------------
 autotest/utils_tests.py        |  40 ++-----
 examples/pstfrom_mf6.ipynb     |  63 +++++------
 examples/pstfrom_mf6_ppu.ipynb |   2 +-
 pyemu/utils/os_utils.py        |  11 +-
 6 files changed, 134 insertions(+), 231 deletions(-)

diff --git a/autotest/conftest.py b/autotest/conftest.py
index 8a6cca34d..0e7114b73 100644
--- a/autotest/conftest.py
+++ b/autotest/conftest.py
@@ -1,5 +1,7 @@
 from pathlib import Path
 import pytest
+import shutil
+import platform
 # from pst_from_tests import setup_freyberg_mf6
 
 pytest_plugins = ["modflow_devtools.fixtures"]
@@ -17,10 +19,56 @@
     # "moouu_tests.py",
     # "mat_tests.py",
     # "da_tests.py",
-    # "get_pestpp_tests.py"
+    # "get_pestpp_tests.py",
 ]
 
+def get_project_root_path():
+    """
+    Get the root path of the project.
+    """
+    return Path(__file__).parent.parent
+
+
+def get_exe_path(exe_name, forgive=True):
+    """
+    Get the absolute path to an executable in the project.
+    """
+    if shutil.which(exe_name) is not None:
+        return exe_name
+    root_path = get_project_root_path()
+    exe_path = root_path / "bin"
+    if not (exe_path / exe_name).exists():
+        if "linux" in platform.system().lower():
+            exe_path = Path(exe_path, "linux")
+        elif "darwin" in platform.system().lower():
+            exe_path = Path(exe_path, "mac")
+        else:
+            exe_path = Path(exe_path, "win")
+    if not (exe_path / exe_name).exists():
+        if forgive:
+            print(f"Executable {exe_name} not found in {exe_path}, returning None")
+        else:
+            raise FileNotFoundError(f"Executable {exe_name} not found in system PATH or fallback path:"
+                                    f" {exe_path}")
+        return None
+    return exe_path / exe_name
+
+
+def full_exe_ref_dict():
+    """
+    Get a dictionary of executable references for the project.
+    """
+    d = {}
+    for exe_name in [
+        "mfnwt", "mt3dusgs", "mfusg_gsi", "mf6",
+        "pestpp-ies", "pestpp-sen", "pestpp-opt", "pestpp-glm",
+        "pestpp-mou", "pestpp-da", "pestpp-sqp", "pestpp-swp"
+    ]:
+        d[exe_name] = get_exe_path(exe_name)
+    return d
+
+
 @pytest.fixture(autouse=True)
 def _ch2testdir(monkeypatch):
     testdir = Path(__file__).parent
-    monkeypatch.chdir(testdir)
\ No newline at end of file
+    monkeypatch.chdir(testdir)
diff --git a/autotest/pst_from_tests.py b/autotest/pst_from_tests.py
index dc916a9ba..751fc3e60 100644
--- a/autotest/pst_from_tests.py
+++ b/autotest/pst_from_tests.py
@@ -10,35 +10,14 @@
 import shutil
 import pytest
 
-ext = ''
-local_bins = False  # change if wanting to test with local binary exes
-if local_bins:
-    bin_path = os.path.join("..", "..", "bin")
-    if "linux" in platform.system().lower():
-        pass
-        bin_path = os.path.join(bin_path, "linux")
-    elif "darwin" in platform.system().lower():
-        pass
-        bin_path = os.path.join(bin_path, "mac")
-    else:
-        bin_path = os.path.join(bin_path, "win")
-        ext = '.exe'
-else:
-    bin_path = ''
-    if "windows" in platform.system().lower():
-        ext = '.exe'
-
-mf_exe_path = os.path.join(bin_path, "mfnwt")
-mt_exe_path = os.path.join(bin_path, "mt3dusgs")
-usg_exe_path = os.path.join(bin_path, "mfusg_gsi")
-mf6_exe_path = os.path.join(bin_path, "mf6")
-pp_exe_path = os.path.join(bin_path, "pestpp-glm")
-ies_exe_path = os.path.join(bin_path, "pestpp-ies")
-swp_exe_path = os.path.join(bin_path, "pestpp-swp")
-
-mf_exe_name = os.path.basename(mf_exe_path)
-mf6_exe_name = os.path.basename(mf6_exe_path)
+from autotest.conftest import full_exe_ref_dict
 
+exepath_dict = full_exe_ref_dict()
+ies_exe_path = exepath_dict['pestpp-ies']
+mf_exe_path = exepath_dict['mfnwt']
+mf6_exe_path = exepath_dict['mf6']
+pp_exe_path = exepath_dict['pestpp-glm']
+usg_exe_path = exepath_dict["mfusg_gsi"]
 
 def _get_port():
     import socket
@@ -92,104 +71,8 @@ def setup_tmp(od, tmp_d, sub=None):
     shutil.copytree(od, new_d)
     return new_d
 
-# @pytest.fixture
-# def freybergmf6_2_pstfrom(tmp_path):
-#     import numpy as np
-#     import pandas as pd
-#     pd.set_option('display.max_rows', 500)
-#     pd.set_option('display.max_columns', 500)
-#     pd.set_option('display.width', 1000)
-#     try:
-#         import flopy
-#     except:
-#         return
-#
-#     org_model_ws = os.path.join('..', 'examples', 'freyberg_mf6')
-#     tmp_model_ws = setup_tmp(org_model_ws, tmp_path)
-#     bd = Path.cwd()
-#     os.chdir(tmp_path)
-#     try:
-#         tmp_model_ws = tmp_model_ws.relative_to(tmp_path)
-#         sim = flopy.mf6.MFSimulation.load(sim_ws=str(tmp_model_ws))
-#         m = sim.get_model()
-#         sim.set_all_data_external(check_data=False)
-#         sim.write_simulation()
-#
-#         # SETUP pest stuff...
-#         os_utils.run("{0} ".format(mf6_exe_path), cwd=tmp_model_ws)
-#         template_ws = "new_temp"
-#         if os.path.exists(template_ws):
-#             shutil.rmtree(template_ws)
-#         # sr0 = m.sr
-#         # sr = pyemu.helpers.SpatialReference.from_namfile(
-#         #     os.path.join(tmp_model_ws, "freyberg6.nam"),
-#         #     delr=m.dis.delr.array, delc=m.dis.delc.array)
-#         sr = m.modelgrid
-#         # set up PstFrom object
-#         pf = PstFrom(original_d=tmp_model_ws, new_d=template_ws,
-#                      remove_existing=True,
-#                      longnames=True, spatial_reference=sr,
-#                      zero_based=False, start_datetime="1-1-2018",
-#                      chunk_len=1)
-#         yield pf
-#     except Exception as e:
-#         os.chdir(bd)
-#         raise e
-#     os.chdir(bd)
-
-
-# @pytest.fixture
-# def freybergnwt_2_pstfrom(tmp_path):
-#     import numpy as np
-#     import pandas as pd
-#     pd.set_option('display.max_rows', 500)
-#     pd.set_option('display.max_columns', 500)
-#     pd.set_option('display.width', 1000)
-#     try:
-#         import flopy
-#     except:
-#         return
-#
-#     org_model_ws = os.path.join('..', 'examples', 'freyberg_sfr_reaches')
-#     tmp_model_ws = setup_tmp(org_model_ws, tmp_path)
-#     bd = Path.cwd()
-#     os.chdir(tmp_path)
-#     nam_file = "freyberg.nam"
-#     try:
-#         tmp_model_ws = tmp_model_ws.relative_to(tmp_path)
-#         m = flopy.modflow.Modflow.load(nam_file, model_ws=tmp_model_ws,
-#                                        check=False, forgive=False,
-#                                        exe_name=mf_exe_path)
-#         flopy.modflow.ModflowRiv(m, stress_period_data={
-#             0: [[0, 0, 0, m.dis.top.array[0, 0], 1.0, m.dis.botm.array[0, 0, 0]],
-#                 [0, 0, 1, m.dis.top.array[0, 1], 1.0, m.dis.botm.array[0, 0, 1]],
-#                 [0, 0, 1, m.dis.top.array[0, 1], 1.0, m.dis.botm.array[0, 0, 1]]]})
-#
-#         m.external_path = "."
-#         m.write_input()
-#         runstr = ("{0} {1}".format(mf_exe_path, m.name + ".nam"), tmp_model_ws)
-#         print(runstr)
-#         os_utils.run(*runstr)
-#         template_ws = "template"
-#         if os.path.exists(template_ws):
-#             shutil.rmtree(template_ws)
-#         sr = pyemu.helpers.SpatialReference.from_namfile(
-#             os.path.join(m.model_ws, m.namefile),
-#             delr=m.dis.delr, delc=m.dis.delc)
-#         # set up PstFrom object
-#         pf = PstFrom(original_d=tmp_model_ws, new_d=template_ws,
-#                      remove_existing=True,
-#                      longnames=True, spatial_reference=sr,
-#                      zero_based=False, start_datetime="1-1-2018",
-#                      chunk_len=1)
-#         yield pf
-#     except Exception as e:
-#         os.chdir(bd)
-#         raise e
-#     os.chdir(bd)
-
-
-def freyberg_test(tmp_path):
+
+def test_freyberg(tmp_path):
     import numpy as np
     import pandas as pd
     from pyemu import PyemuWarning
@@ -383,7 +266,7 @@ def freyberg_test(tmp_path):
 
 
     # add model run command
-    pf.mod_sys_cmds.append("{0} {1}".format(mf_exe_name, m.name + ".nam"))
+    pf.mod_sys_cmds.append("{0} {1}".format(mf_exe_path, m.name + ".nam"))
     print(pf.mult_files)
     print(pf.org_files)
 
@@ -608,7 +491,7 @@ def test_freyberg_prior_build(tmp_path):
 
 
     # add model run command
-    pf.mod_sys_cmds.append("{0} {1}".format(mf_exe_name, m.name + ".nam"))
+    pf.mod_sys_cmds.append("{0} {1}".format(mf_exe_path, m.name + ".nam"))
     print(pf.mult_files)
     print(pf.org_files)
 
@@ -1086,7 +969,7 @@ def test_mf6_freyberg(tmp_path):
                           geostruct=rch_temporal_gs)
 
     # add model run command
-    pf.mod_sys_cmds.append("mf6")
+    pf.mod_sys_cmds.append(mf6_exe_path)
     # print(pf.mult_files)
     # print(pf.org_files)
 
@@ -1298,7 +1181,7 @@ def mf6_freyberg_shortnames_test(tmp_path):
     assert len(pdf) == 4
 
     # add model run command
-    pf.mod_sys_cmds.append("mf6")
+    pf.mod_sys_cmds.append(mf6_exe_path)
     print(pf.mult_files)
     print(pf.org_files)
 
@@ -1414,7 +1297,7 @@ def mf6_freyberg_da_test(tmp_path):
     m = sim.get_model("freyberg6")
 
     # SETUP pest stuff...
-    os_utils.run("{0} ".format("mf6"), cwd=tmp_model_ws)
+    os_utils.run("{0} ".format(mf6_exe_path), cwd=tmp_model_ws)
 
     template_ws = "new_temp_da"
     if os.path.exists(template_ws):
@@ -1485,7 +1368,7 @@ def mf6_freyberg_da_test(tmp_path):
                       par_type="grid")
 
     # add model run command
-    pf.mod_sys_cmds.append("mf6")
+    pf.mod_sys_cmds.append(mf6_exe_path)
     # print(pf.mult_files)
     # print(pf.org_files)
 
@@ -1585,7 +1468,7 @@ def setup_freyberg_mf6(wd, model="freyberg_mf6", **kwargs):
         sim.write_simulation()
 
         # SETUP pest stuff...
-        os_utils.run("{0} ".format("mf6"), cwd=tmp_model_ws)
+        os_utils.run("{0} ".format(mf6_exe_path), cwd=tmp_model_ws)
 
         template_ws = Path(wd, "template")
         if os.path.exists(template_ws):
@@ -1613,7 +1496,7 @@ def setup_freyberg_mf6(wd, model="freyberg_mf6", **kwargs):
 
 
 def build_direct(pf):
-    pf.mod_sys_cmds.append("mf6")
+    pf.mod_sys_cmds.append(mf6_exe_path)
     print(pf.mult_files)
     print(pf.org_files)
 
@@ -2071,7 +1954,7 @@ def mf6_freyberg_direct_test(tmp_path):
     sim.write_simulation()
 
     # SETUP pest stuff...
-    os_utils.run("{0} ".format("mf6"), cwd=tmp_model_ws)
+    os_utils.run("{0} ".format(mf6_exe_path), cwd=tmp_model_ws)
 
     template_ws = Path(tmp_path, "new_temp_direct")
     if os.path.exists(template_ws):
@@ -2249,7 +2132,7 @@ def mf6_freyberg_direct_test(tmp_path):
                       use_rows=[('well2', 21, 15), ('well4', 30, 7)])
     assert len(pf.par_dfs[-1]) == 2 * 2  # should be
     # add model run command
-    pf.mod_sys_cmds.append("mf6")
+    pf.mod_sys_cmds.append(mf6_exe_path)
     print(pf.mult_files)
     print(pf.org_files)
 
@@ -2497,7 +2380,7 @@ def mf6_freyberg_varying_idomain(tmp_path):
                               geostruct=gr_gs, zone_array=ib[k],ult_lbound=ult_lb,ult_ubound=ult_ub)
 
     # add model run command
-    pf.mod_sys_cmds.append("mf6")
+    pf.mod_sys_cmds.append(mf6_exe_path)
     df = pd.read_csv(os.path.join(tmp_model_ws, "heads.csv"), index_col=0)
     df = pf.add_observations("heads.csv", insfile="heads.csv.ins", index_cols="time", use_cols=list(df.columns.values),
                         prefix="hds", ofile_sep=",")
@@ -2617,7 +2500,7 @@ def mf6_freyberg_short_direct_test(tmp_path):
     sim.write_simulation()
 
     # SETUP pest stuff...
-    os_utils.run("{0} ".format("mf6"), cwd=tmp_model_ws)
+    os_utils.run("{0} ".format(mf6_exe_path), cwd=tmp_model_ws)
 
     template_ws = "new_temp_direct"
     if os.path.exists(template_ws):
@@ -2759,7 +2642,7 @@ def mf6_freyberg_short_direct_test(tmp_path):
                       transform="none")
 
     # add model run command
-    pf.mod_sys_cmds.append("mf6")
+    pf.mod_sys_cmds.append(mf6_exe_path)
     print(pf.mult_files)
     print(pf.org_files)
 
@@ -3595,7 +3478,7 @@ def mf6_freyberg_arr_obs_and_headerless_test(tmp_path):
             arr_dict[arr_file] = np.loadtxt(pf.new_d / arr_file)
 
     # add model run command
-    pf.mod_sys_cmds.append("mf6")
+    pf.mod_sys_cmds.append(mf6_exe_path)
     print(pf.mult_files)
     print(pf.org_files)
 
@@ -3642,7 +3525,7 @@ def mf6_freyberg_arr_obs_and_headerless_test(tmp_path):
     assert d.sum() == 0
 
 
-def mf6_freyberg_pp_locs_test(tmp_path):
+def test_mf6_freyberg_pp_locs(tmp_path):
     import numpy as np
     import pandas as pd
     pd.set_option('display.max_rows', 500)
@@ -3747,7 +3630,7 @@ def mf6_freyberg_pp_locs_test(tmp_path):
 
 
     # add model run command
-    pf.mod_sys_cmds.append("mf6")
+    pf.mod_sys_cmds.append(mf6_exe_path)
     print(pf.mult_files)
     print(pf.org_files)
 
@@ -4037,7 +3920,7 @@ def mf6_add_various_obs_test(tmp_path):
     pf.add_parameters(["freyberg6.npf_k_layer1.txt",
                        "freyberg6.npf_k_layer2.txt",
                        "freyberg6.npf_k_layer3.txt"],par_type='constant')
-    pf.mod_sys_cmds.append("mf6")
+    pf.mod_sys_cmds.append(mf6_exe_path)
     pf.add_py_function(
         __file__,
         f"_add_big_obsffile('.', profile=False, nchar={linelen})",
@@ -4102,11 +3985,7 @@ def mf6_subdir_test(tmp_path):
     sim.write_simulation()
 
     # SETUP pest stuff...
-    if bin_path == '':
-        exe = mf6_exe_path  # bit of flexibility for local/server run
-    else:
-        exe = os.path.join('..', mf6_exe_path)
-    os_utils.run("{0} ".format(exe), cwd=tmp2_ws)
+    os_utils.run("{0} ".format(mf6_exe_path), cwd=tmp2_ws)
     # call generic once so that the output file exists
     df = generic_function(tmp2_ws)
     template_ws = "new_temp"
@@ -4271,7 +4150,7 @@ def mf6_subdir_test(tmp_path):
     #
     # # add model run command
     pf.pre_py_cmds.append(f"os.chdir('{sd}')")
-    pf.mod_sys_cmds.append("mf6")
+    pf.mod_sys_cmds.append(mf6_exe_path)
     pf.post_py_cmds.insert(0, "os.chdir('..')")
     # print(pf.mult_files)
     # print(pf.org_files)
@@ -4584,7 +4463,7 @@ def test_vertex_grid(tmp_path):
         a = [float(i) for i in a.split()]
         np.savetxt(fname=filename, X=a)
     # run model after input file change
-    pyemu.os_utils.run('mf6', cwd=template_ws)
+    pyemu.os_utils.run(mf6_exe_path, cwd=template_ws)
 
     for f in files:
         layer = int(f.split('_layer')[-1].split('.')[0]) - 1
@@ -4635,7 +4514,7 @@ def test_vertex_grid(tmp_path):
                                 index_cols="time",
                                 use_cols=list(df.columns.values),
                                 prefix="sfr")
-    pf.mod_sys_cmds.append('mf6')
+    pf.mod_sys_cmds.append(mf6_exe_path)
     pst = pf.build_pst()
     # check_apply(pf)
     # run once
@@ -4837,7 +4716,7 @@ def mf6_freyberg_thresh_test(tmp_path):
 
 
     # SETUP pest stuff...
-    os_utils.run("{0} ".format("mf6"), cwd=tmp_model_ws)
+    os_utils.run("{0} ".format(mf6_exe_path), cwd=tmp_model_ws)
 
     template_ws = Path(tmp_path, "new_temp_thresh")
     if os.path.exists(template_ws):
@@ -4944,7 +4823,7 @@ def mf6_freyberg_thresh_test(tmp_path):
                 num_cat_arrays += 1
 
     # add model run command
-    pf.mod_sys_cmds.append("mf6")
+    pf.mod_sys_cmds.append(mf6_exe_path)
     # print(pf.mult_files)
     # print(pf.org_files)
 
@@ -5707,7 +5586,7 @@ def mf6_freyberg_ppu_hyperpars_invest(tmp_path):
 
 
     # add model run command
-    pf.mod_sys_cmds.append("mf6")
+    pf.mod_sys_cmds.append(mf6_exe_path)
     print(pf.mult_files)
     print(pf.org_files)
 
@@ -5806,7 +5685,7 @@ def mf6_freyberg_ppu_hyperpars_thresh_invest(tmp_path):
     sim.write_simulation()
 
     # SETUP pest stuff...
-    os_utils.run("{0} ".format("mf6"), cwd=tmp_model_ws)
+    os_utils.run("{0} ".format(mf6_exe_path), cwd=tmp_model_ws)
 
     template_ws = Path(tmp_path, "new_temp_thresh")
     if os.path.exists(template_ws):
@@ -5961,7 +5840,7 @@ def mf6_freyberg_ppu_hyperpars_thresh_invest(tmp_path):
                 num_cat_arrays += 1
 
     # add model run command
-    pf.mod_sys_cmds.append("mf6")
+    pf.mod_sys_cmds.append(mf6_exe_path)
     print(pf.mult_files)
     print(pf.org_files)
 
@@ -6322,7 +6201,7 @@ def invest_vertexpp_setup_speed():
     from pathlib import Path
     from shapely import Polygon
     import cProfile
-    sim = flopy.mf6.MFSimulation(sim_name="test", sim_ws="test", exe_name="mf6")
+    sim = flopy.mf6.MFSimulation(sim_name="test", sim_ws="test", exe_name=mf6_exe_path)
     gwf = flopy.mf6.ModflowGwf(sim, modelname="test")
 
     dis = flopy.mf6.ModflowGwfdis(
@@ -6418,7 +6297,7 @@ def xsec_pars_as_obs_test(tmp_path):
 
 
 if __name__ == "__main__":
-    xsec_pars_as_obs_test(".")
+    # xsec_pars_as_obs_test(".")
     #add_py_function_test('.')
     #mf6_freyberg_pp_locs_test('.')
     #mf6_subdir_test(".")
@@ -6433,7 +6312,7 @@ def xsec_pars_as_obs_test(tmp_path):
 
     # invest()
     # test_add_array_parameters_pps_grid()
-    #freyberg_test(os.path.abspath("."))
+    test_freyberg(os.path.abspath("."))
     # freyberg_prior_build_test()
     #mf6_freyberg_test(os.path.abspath("."))
     #$mf6_freyberg_da_test()
diff --git a/autotest/utils_tests.py b/autotest/utils_tests.py
index 4391c0e7c..2939c1991 100644
--- a/autotest/utils_tests.py
+++ b/autotest/utils_tests.py
@@ -11,37 +11,15 @@
 import pyemu
 from pst_from_tests import _get_port
 
-ext = ''
-local_bins = False  # change if wanting to test with local binary exes
-if local_bins:
-    bin_path = os.path.join("..", "..", "bin")
-    if "linux" in platform.system().lower():
-        pass
-        bin_path = os.path.join(bin_path, "linux")
-    elif "darwin" in platform.system().lower():
-        pass
-        bin_path = os.path.join(bin_path, "mac")
-    else:
-        bin_path = os.path.join(bin_path, "win")
-        ext = '.exe'
-else:
-    bin_path = ''
-    if "windows" in platform.system().lower():
-        ext = '.exe'
-
-mf_exe_path = os.path.join(bin_path, "mfnwt")
-mt_exe_path = os.path.join(bin_path, "mt3dusgs")
-usg_exe_path = os.path.join(bin_path, "mfusg_gsi")
-mf6_exe_path = os.path.join(bin_path, "mf6")
-pp_exe_path = os.path.join(bin_path, "pestpp-glm")
-ies_exe_path = os.path.join(bin_path, "pestpp-ies")
-mou_exe_path = os.path.join(bin_path, "pestpp-mou")
-swp_exe_path = os.path.join(bin_path, "pestpp-swp")
-
-mf_exe_name = os.path.basename(mf_exe_path)
-mf6_exe_name = os.path.basename(mf6_exe_path)
-
-
+from autotest.conftest import full_exe_ref_dict
+
+exepath_dict = full_exe_ref_dict()
+ies_exe_path = exepath_dict['pestpp-ies']
+mf_exe_path = exepath_dict['mfnwt']
+mf6_exe_path = exepath_dict['mf6']
+pp_exe_path = exepath_dict['pestpp-glm']
+usg_exe_path = exepath_dict["mfusg_gsi"]
+mou_exe_path = exepath_dict["pestpp-mou"]
 
 def add_pi_obj_func_test(tmp_path):
     import os
diff --git a/examples/pstfrom_mf6.ipynb b/examples/pstfrom_mf6.ipynb
index c043ce20c..c2e21f67a 100644
--- a/examples/pstfrom_mf6.ipynb
+++ b/examples/pstfrom_mf6.ipynb
@@ -911,10 +911,10 @@
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
    "metadata": {},
+   "cell_type": "code",
    "outputs": [],
+   "execution_count": null,
    "source": [
     "# load the mf6 model with flopy to get the spatial reference\n",
     "sim = flopy.mf6.MFSimulation.load(sim_ws=tmp_model_ws)\n",
@@ -935,13 +935,13 @@
     "\n",
     "# add observations from the sfr observation output file\n",
     "df = pd.read_csv(os.path.join(tmp_model_ws, \"sfr.csv\"), index_col=0)\n",
-    "pf.add_observations(\"sfr.csv\", insfile=\"sfr.csv.ins\", index_cols=\"time\", \n",
+    "pf.add_observations(\"sfr.csv\", insfile=\"sfr.csv.ins\", index_cols=\"time\",\n",
     "                    use_cols=list(df.columns.values),\n",
     "                    prefix=\"sfr\")\n",
     "\n",
     "# add observations for the heads observation output file\n",
     "df = pd.read_csv(os.path.join(tmp_model_ws, \"heads.csv\"), index_col=0)\n",
-    "pf.add_observations(\"heads.csv\", insfile=\"heads.csv.ins\", \n",
+    "pf.add_observations(\"heads.csv\", insfile=\"heads.csv.ins\",\n",
     "                    index_cols=\"time\", use_cols=list(df.columns.values),\n",
     "                    prefix=\"hds\")\n",
     "\n",
@@ -977,28 +977,28 @@
     "for tag,bnd in tags.items():\n",
     "    lb,ub = bnd[0],bnd[1]\n",
     "    # find all array based files that have the tag in the name\n",
-    "    arr_files = [f for f in os.listdir(template_ws) if tag in f \n",
+    "    arr_files = [f for f in os.listdir(template_ws) if tag in f\n",
     "\t\t\t\t and f.endswith(\".txt\")]\n",
     "\n",
     "    if len(arr_files) == 0:\n",
     "        print(\"warning: no array files found for \",tag)\n",
     "        continue\n",
-    "    \n",
+    "\n",
     "    # make sure each array file in nrow X ncol dimensions (not wrapped, sigh)\n",
     "    for arr_file in arr_files:\n",
     "        arr = np.loadtxt(os.path.join(template_ws,arr_file)).reshape(ib.shape)\n",
     "        np.savetxt(os.path.join(template_ws,arr_file),arr,fmt=\"%15.6E\")\n",
-    "    \n",
+    "\n",
     "    # if this is the recharge tag\n",
     "    if \"rch\" in tag:\n",
     "        # add one set of grid-scale parameters for all files\n",
-    "        pf.add_parameters(filenames=arr_files, par_type=\"grid\", \n",
-    "        \t\t\t\t  par_name_base=\"rch_gr\",pargp=\"rch_gr\", \n",
-    "        \t\t\t\t  zone_array=ib, upper_bound=ub, \n",
+    "        pf.add_parameters(filenames=arr_files, par_type=\"grid\",\n",
+    "        \t\t\t\t  par_name_base=\"rch_gr\",pargp=\"rch_gr\",\n",
+    "        \t\t\t\t  zone_array=ib, upper_bound=ub,\n",
     "        \t\t\t\t  lower_bound=lb,geostruct=rch_gs)\n",
     "\n",
-    "        # add one constant parameter for each array, and \n",
-    "        # assign it a datetime so we can work out the \n",
+    "        # add one constant parameter for each array, and\n",
+    "        # assign it a datetime so we can work out the\n",
     "        # temporal correlation\n",
     "        for arr_file in arr_files:\n",
     "            kper = int(arr_file.split('.')[1].split('_')[-1]) - 1\n",
@@ -1016,40 +1016,40 @@
     "                              pargp=arr_file.split('.')[1]+\"_gr\",zone_array=ib,\n",
     "                              upper_bound=ub,lower_bound=lb,\n",
     "                              geostruct=grid_gs)\n",
-    "            pf.add_parameters(filenames=arr_file, par_type=\"pilotpoints\", \n",
+    "            pf.add_parameters(filenames=arr_file, par_type=\"pilotpoints\",\n",
     "                              par_name_base=arr_file.split('.')[1]+\"_pp\",\n",
-    "                              pargp=arr_file.split('.')[1]+\"_pp\", \n",
+    "                              pargp=arr_file.split('.')[1]+\"_pp\",\n",
     "                              zone_array=ib,upper_bound=ub,lower_bound=lb,\n",
     "                              pp_space=int(5 * redis_fac),geostruct=pp_gs)\n",
     "\n",
     "\n",
     "# get all the list-type files associated with the wel package\n",
-    "list_files = [f for f in os.listdir(tmp_model_ws) if \n",
-    "\t\t\t  \"freyberg6.wel_stress_period_data_\" \n",
+    "list_files = [f for f in os.listdir(tmp_model_ws) if\n",
+    "\t\t\t  \"freyberg6.wel_stress_period_data_\"\n",
     "              in f and f.endswith(\".txt\")]\n",
-    "# for each wel-package list-type file \n",
+    "# for each wel-package list-type file\n",
     "for list_file in list_files:\n",
     "    kper = int(list_file.split(\".\")[1].split('_')[-1]) - 1\n",
     "    # add spatially constant, but temporally correlated parameter\n",
     "    pf.add_parameters(filenames=list_file,par_type=\"constant\",\n",
     "    \t\t\t\t  par_name_base=\"twel_mlt_{0}\".format(kper),\n",
     "                      pargp=\"twel_mlt\".format(kper),index_cols=[0,1,2],\n",
-    "                      use_cols=[3],upper_bound=1.5,lower_bound=0.5, \n",
+    "                      use_cols=[3],upper_bound=1.5,lower_bound=0.5,\n",
     "                      datetime=dts[kper], geostruct=temporal_gs)\n",
     "\n",
-    "    # add temporally indep, but spatially correlated grid-scale \n",
+    "    # add temporally indep, but spatially correlated grid-scale\n",
     "    # parameters, one per well\n",
-    "    pf.add_parameters(filenames=list_file, par_type=\"grid\", \n",
+    "    pf.add_parameters(filenames=list_file, par_type=\"grid\",\n",
     "                      par_name_base=\"wel_grid_{0}\".format(kper),\n",
-    "                      pargp=\"wel_{0}\".format(kper), index_cols=[0, 1, 2], \n",
+    "                      pargp=\"wel_{0}\".format(kper), index_cols=[0, 1, 2],\n",
     "                      use_cols=[3],upper_bound=1.5, lower_bound=0.5)\n",
     "\n",
-    "# add grid-scale parameters for SFR reach conductance.  \n",
-    "# Use layer, row, col and reach number in the \n",
+    "# add grid-scale parameters for SFR reach conductance.\n",
+    "# Use layer, row, col and reach number in the\n",
     "# parameter names\n",
-    "pf.add_parameters(filenames=\"freyberg6.sfr_packagedata.txt\", \n",
+    "pf.add_parameters(filenames=\"freyberg6.sfr_packagedata.txt\",\n",
     "                  par_name_base=\"sfr_rhk\",\n",
-    "                  pargp=\"sfr_rhk\", index_cols=[0,1,2,3], \n",
+    "                  pargp=\"sfr_rhk\", index_cols=[0,1,2,3],\n",
     "                  use_cols=[9], upper_bound=10.,\n",
     "                  lower_bound=0.1,\n",
     "                  par_type=\"grid\")\n",
@@ -1092,18 +1092,11 @@
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
    "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
    "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
    "outputs": [],
-   "source": []
+   "execution_count": null,
+   "source": ""
   }
  ],
  "metadata": {
@@ -1122,7 +1115,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.8"
+   "version": "3.13.5"
   }
  },
  "nbformat": 4,
diff --git a/examples/pstfrom_mf6_ppu.ipynb b/examples/pstfrom_mf6_ppu.ipynb
index 9283543d9..df5d5d4a9 100644
--- a/examples/pstfrom_mf6_ppu.ipynb
+++ b/examples/pstfrom_mf6_ppu.ipynb
@@ -815,7 +815,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.12"
+   "version": "3.13.5"
   }
  },
  "nbformat": 4,
diff --git a/pyemu/utils/os_utils.py b/pyemu/utils/os_utils.py
index 9015f2893..3fada04ee 100644
--- a/pyemu/utils/os_utils.py
+++ b/pyemu/utils/os_utils.py
@@ -140,7 +140,9 @@ def run_ossystem(cmd_str, cwd=".", verbose=False):
                 exe_name = exe_name.replace(".exe", "")
                 raw[0] = exe_name
                 cmd_str = "{0} {1} ".format(*raw)
-            if os.path.exists(exe_name) and not exe_name.startswith("./"):
+            if (os.path.exists(exe_name)
+                    and not exe_name.startswith("./")
+                    and not exe_name.startswith("/")):
                 cmd_str = "./" + cmd_str
 
     except Exception as e:
@@ -192,8 +194,11 @@ def run_sp(cmd_str, cwd=".", verbose=True, logfile=False, **kwargs):
 
     bwd = os.getcwd()
     os.chdir(cwd)
-
-    if platform.system() != "Windows" and not shutil.which(cmd_str.split()[0]):
+    exe_name = cmd_str.split()[0]
+    if (platform.system() != "Windows"
+            and not shutil.which(exe_name)
+            and not exe_name.startswith("./")
+            and not exe_name.startswith("/")):
         cmd_str = "./" + cmd_str
 
     try:

From 1fd8939baeace99ba30ef05a95d9cee0033252a9 Mon Sep 17 00:00:00 2001
From: Brioch <briochh@gmail.com>
Date: Tue, 7 Oct 2025 09:55:07 +0100
Subject: [PATCH 2/3] autotest import not req.

---
 autotest/pst_from_tests.py | 2 +-
 autotest/utils_tests.py    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/autotest/pst_from_tests.py b/autotest/pst_from_tests.py
index 0d6714401..091f9009e 100644
--- a/autotest/pst_from_tests.py
+++ b/autotest/pst_from_tests.py
@@ -10,7 +10,7 @@
 import shutil
 import pytest
 
-from autotest.conftest import full_exe_ref_dict
+from conftest import full_exe_ref_dict
 
 exepath_dict = full_exe_ref_dict()
 ies_exe_path = exepath_dict['pestpp-ies']
diff --git a/autotest/utils_tests.py b/autotest/utils_tests.py
index a5bc8339d..14d4528e4 100644
--- a/autotest/utils_tests.py
+++ b/autotest/utils_tests.py
@@ -11,7 +11,7 @@
 import pyemu
 from pst_from_tests import _get_port
 
-from autotest.conftest import full_exe_ref_dict
+from conftest import full_exe_ref_dict
 
 exepath_dict = full_exe_ref_dict()
 ies_exe_path = exepath_dict['pestpp-ies']

From 21821a5171ba2bd38f7521312069fdd7b3df1a9a Mon Sep 17 00:00:00 2001
From: Brioch <briochh@gmail.com>
Date: Tue, 7 Oct 2025 10:20:09 +0100
Subject: [PATCH 3/3] more cleaning

---
 autotest/emulator_tests.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/autotest/emulator_tests.py b/autotest/emulator_tests.py
index 1aa11817d..36bc4e912 100644
--- a/autotest/emulator_tests.py
+++ b/autotest/emulator_tests.py
@@ -6,11 +6,11 @@
 import pandas as pd
 import platform
 import pyemu
-from pst_from_tests import setup_tmp, bin_path, _get_port
+from pst_from_tests import setup_tmp, _get_port, exepath_dict
 from pyemu.emulators import DSI, LPFA, GPR
 
-ies_exe_path = os.path.join(bin_path, "pestpp-ies")
-mou_exe_path = os.path.join(bin_path, "pestpp-mou")
+ies_exe_path = exepath_dict["pestpp-ies"]
+mou_exe_path = exepath_dict["pestpp-mou"]
 
 def dsi_freyberg(tmp_d,transforms=None,tag=""):