update mf6 version (#154)

* update to use BINARY option for windows builds with ifort
* update zbud6 include files

autotest/ci_setup.py

@@ -1,14 +1,18 @@
 import os
+import pathlib as pl
 import shutil
 
 import pymake
 
-temp_pth = "temp"
-if not os.path.exists(temp_pth):
-    os.makedirs(temp_pth)
-mf6_exdir = os.path.join(temp_pth, "mf6examples")
-if os.path.isdir(mf6_exdir):
+temp_pth = pl.Path("temp")
+if not temp_pth.exists():
+    temp_pth.mkdir()
+mf6_exdir = temp_pth / "mf6examples"
+if mf6_exdir.is_dir():
     shutil.rmtree(mf6_exdir)
+gsflow_exdir = temp_pth / "gsflowexamples"
+if gsflow_exdir.is_dir():
+    shutil.rmtree(gsflow_exdir)
 
 
 def download_mf6_examples(verbose=False):
@@ -84,6 +88,83 @@ def examples_list(verbose=False):
     return
 
 
+def download_gsflow_examples(verbose=False):
+    """Download gsflow examples and return location of folder"""
+
+    examples_dirs = (
+        "sagehen",
+        "acfb_dyn_params",
+        "acfb_water_use",
+    )
+
+    target = "gsflow"
+    pm = pymake.Pymake(verbose=True)
+    pm.target = target
+
+    # download the gsflow release
+    pm.download_target(target, download_path=temp_pth)
+    assert pm.download, f"could not download {target} distribution"
+
+    # get program dictionary
+    prog_dict = pymake.usgs_program_data.get_target(target)
+
+    # set path to example
+    temp_download_dir = temp_pth / prog_dict.dirname
+    temp_dir = temp_download_dir / "data"
+
+    print(f"copying files to...{gsflow_exdir}")
+    shutil.copytree(temp_dir, gsflow_exdir)
+
+    # create list of examples to test and edit files if necessary
+    src_folders = []
+    for ex_dir in examples_dirs:
+        out_path = gsflow_exdir / ex_dir
+
+        if "sagehen" in ex_dir:
+            out_path = out_path / "linux"
+            modify_gsflow_sagehen(out_path)
+        elif "acfb" in ex_dir:
+            shutil.copy(
+                out_path / "control/control", out_path / "gsflow.control"
+            )
+
+        # add final example path to src_folders list
+        src_folders.append(out_path)
+
+    print(f"removing...{temp_download_dir} directory")
+    shutil.rmtree(temp_download_dir)
+
+    # create a  list of gsflow examples
+    fpth = gsflow_exdir / "gsflowexamples.txt"
+    f = open(fpth, "w")
+    for idx, folder in enumerate(src_folders):
+        if verbose:
+            if idx == 0:
+                print(f"\n\nGSFLOW examples:\n{78 * '-'}")
+            print(f"{idx + 1:>3d}: {folder}")
+        f.write(f"{os.path.abspath(folder)}\n")
+    f.close()
+
+    return gsflow_exdir.resolve()
+
+
+def modify_gsflow_sagehen(temp_pth):
+    fpth = temp_pth / "gsflow.control"
+    with open(fpth) as f:
+        lines = f.readlines()
+    with open(fpth, "w") as f:
+        idx = 0
+        while idx < len(lines):
+            line = lines[idx]
+            if "end_time" in line:
+                line += "6\n1\n1981\n"
+                idx += 3
+            f.write(line)
+            idx += 1
+    return
+
+
 if __name__ == "__main__":
     mf6pth = download_mf6_examples(verbose=True)
     examples_list(verbose=True)
+    gsflowpth = download_gsflow_examples(verbose=True)

autotest/test_gsflow.py

@@ -0,0 +1,83 @@
+import os
+from pathlib import Path
+from platform import system
+
+import flopy
+import pytest
+
+import pymake
+
+# set fpth based on current path
+if os.path.basename(os.path.normpath(os.getcwd())) == "autotest":
+    fpth = Path("temp")
+else:
+    fpth = Path("autotest/temp")
+fpth = (fpth / "gsflowexamples/gsflowexamples.txt").resolve()
+if fpth.is_file():
+    with open(fpth) as f:
+        lines = f.read().splitlines()
+    sim_dirs = [line for line in lines if len(line) > 0]
+else:
+    sim_dirs = []
+
+
+@pytest.fixture(scope="module")
+def target(module_tmpdir) -> Path:
+    name = "gsflow"
+    ext = ".exe" if system() == "Windows" else ""
+    return module_tmpdir / f"{name}{ext}"
+
+
+@pytest.fixture(scope="module")
+def prog_data(target) -> dict:
+    return pymake.usgs_program_data.get_target(target.name)
+
+
+@pytest.fixture(scope="module")
+def workspace(module_tmpdir, prog_data) -> Path:
+    return module_tmpdir / prog_data.dirname
+
+
+@pytest.fixture(scope="module")
+def pm(module_tmpdir, target) -> pymake.Pymake:
+    pm = pymake.Pymake(verbose=True)
+    pm.target = str(target)
+    pm.appdir = module_tmpdir
+    pm.makefile = True
+    pm.makeclean = True
+    pm.makefiledir = module_tmpdir
+    pm.inplace = True
+    pm.networkx = True
+    pm.verbose = True
+    yield pm
+    pm.finalize()
+
+
+@pytest.mark.dependency(name="download")
+@pytest.mark.base
+def test_download(pm, module_tmpdir, target):
+    pm.download_target(target, download_path=module_tmpdir)
+    assert pm.download, f"could not download {target} distribution"
+
+
+@pytest.mark.dependency(name="build", depends=["download"])
+@pytest.mark.base
+def test_compile(pm, target):
+    assert pm.build() == 0, f"could not compile {target}"
+
+
+@pytest.mark.dependency(name="test", depends=["build"])
+@pytest.mark.regression
+@pytest.mark.parametrize("ws", sim_dirs)
+def test_gsflow(ws, target):
+    success, _ = flopy.run_model(
+        target,
+        "gsflow.control",
+        model_ws=ws,
+        silent=False,
+        normal_msg=[
+            "normal termination",
+            "Normal completion of GSFLOW",
+        ],
+    )
+    assert success, f"could not run {ws}"

autotest/test_mf6.py

@@ -12,14 +12,11 @@
 
 # set fpth based on current path
 if os.path.basename(os.path.normpath(os.getcwd())) == "autotest":
-    fpth = os.path.abspath(
-        os.path.join("temp", "mf6examples", "mf6examples.txt")
-    )
+    fpth = Path("temp")
 else:
-    fpth = os.path.abspath(
-        os.path.join("autotest", "temp", "mf6examples", "mf6examples.txt")
-    )
-if os.path.isfile(fpth):
+    fpth = Path("autotest/temp")
+fpth = (fpth / "mf6examples/mf6examples.txt").resolve()
+if fpth.is_file():
     with open(fpth) as f:
         lines = f.read().splitlines()
     sim_dirs = [line for line in lines if len(line) > 0]

pymake/config.py

@@ -1,6 +1,6 @@
 __author__ = "Joseph D. Hughes"
-__date__ = "July 5, 2023"
-__version__ = "1.2.9.dev0"
+__date__ = "February 11, 2024"
+__version__ = "1.2.9"
 __maintainer__ = "Joseph D. Hughes"
 __email__ = "[email protected]"
 __status__ = "Production"

pymake/pymake.py

@@ -598,16 +598,20 @@ def _set_extrafiles(self):
                     "../../../src/Utilities/Budget.f90",
                     "../../../src/Utilities/Constants.f90",
                     "../../../src/Utilities/compilerversion.F90",
-                    "../../../src/Utilities/genericutils.f90",
+                    "../../../src/Utilities/ErrorUtil.f90",
+                    "../../../src/Utilities/GeomUtil.f90",
+                    "../../../src/Utilities/MathUtil.f90",
                     "../../../src/Utilities/InputOutput.f90",
                     "../../../src/Utilities/kind.f90",
+                    "../../../src/Utilities/LongLineReader.f90",
                     "../../../src/Utilities/OpenSpec.f90",
                     "../../../src/Utilities/sort.f90",
-                    "../../../src/Utilities/Message.f90",
                     "../../../src/Utilities/defmacro.F90",
                     "../../../src/Utilities/Sim.f90",
                     "../../../src/Utilities/SimVariables.f90",
                     "../../../src/Utilities/version.f90",
+                    "../../../src/Utilities/DevFeature.f90",
+                    "../../../src/Utilities/Message.f90",
                 ]
 
             # evaluate extrafiles type

pymake/pymake_base.py

@@ -271,15 +271,21 @@ def main(
         if not meson:
             if _get_osname() == "win32":
                 if fc is not None:
-                    if fc in ["ifort", "mpiifort"]:
+                    if fc in (
+                        "ifort",
+                        "mpiifort",
+                    ):
                         intelwin = True
                 if cc is not None:
-                    if cc in ["cl", "icl"]:
+                    if cc in (
+                        "cl",
+                        "icl",
+                    ):
                         intelwin = True
 
         # update openspec files based on intelwin
         if not intelwin:
-            _create_openspec(srcfiles, verbose)
+            _create_openspec(intelwin, srcfiles, verbose)
 
         # compile the executable
         if meson:
@@ -666,13 +672,20 @@ def _clean_temp_files(
     return
 
 
-def _create_openspec(srcfiles, verbose):
+def _create_openspec(intelwin, srcfiles, verbose):
     """Create new openspec.inc, FILESPEC.INC, and filespec.inc files that uses
     STREAM ACCESS. This is specific to MODFLOW and MT3D based targets. Source
     directories are scanned and files defining file access are replaced.
 
     Parameters
     ----------
+    intelwin : bool
+        boolean indicating if source files are being built on Windows using
+        intel compilers.
+    srcfiles : list
+        list of source files to be compiled
+    verbose: bool
+        boolean indicating if output will be printed to the terminal
 
     Returns
     -------
@@ -697,17 +710,23 @@ def _create_openspec(srcfiles, verbose):
                 if verbose:
                     print(f'replacing..."{fpth}"')
                 f = open(fpth, "w")
+                if intelwin:
+                    data_access = "SEQUENTIAL"
+                    data_form = "BINARY"
+                else:
+                    data_access = "STREAM"
+                    data_form = "UNFORMATTED"
+
                 line = (
                     "c -- created by pymake_base.py\n"
                     + "      CHARACTER*20 ACCESS,FORM,ACTION(2)\n"
-                    + "      DATA ACCESS/'STREAM'/\n"
-                    + "      DATA FORM/'UNFORMATTED'/\n"
+                    + f"      DATA ACCESS/'{data_access}'/\n"
+                    + f"      DATA FORM/'{data_form}'/\n"
                     + "      DATA (ACTION(I),I=1,2)/'READ','READWRITE'/\n"
                     + "c -- end of include file\n"
                 )
                 f.write(line)
                 f.close()
-    return
 
 
 def _check_out_of_date(srcfile, objfile):

pymake/utils/_usgs_src_update.py

@@ -881,6 +881,7 @@ def _update_mf6_external_dependencies(
         "Utilities/Matrix/PetscMatrix.F90",
         "Solution/PETSc/PetscSolver.F90",
         "Solution/PETSc/PetscConvergence.F90",
+        "Solution/PETSc//PetscImsPreconditioner.F90",
         "Distributed/MpiMessageBuilder.f90",
         "Distributed/MpiRouter.f90",
         "Distributed/MpiRunControl.F90",

pymake/utils/usgsprograms.txt

@@ -1,7 +1,7 @@
 target     ,  version,  current, url                                                                                            , dirname             , srcdir              ,    standard_switch, double_switch, shared_object
-mf6        ,  6.4.2  ,  True   , https://github.com/MODFLOW-USGS/modflow6/releases/download/6.4.2/mf6.4.2_linux.zip             , mf6.4.2_linux       , src                 ,    True           , False        , False
-zbud6      ,  6.4.2  ,  True   , https://github.com/MODFLOW-USGS/modflow6/releases/download/6.4.2/mf6.4.2_linux.zip             , mf6.4.2_linux       , utils/zonebudget/src,    True           , False        , False
-libmf6     ,  6.4.2  ,  True   , https://github.com/MODFLOW-USGS/modflow6/releases/download/6.4.2/mf6.4.2_linux.zip             , mf6.4.2_linux       , srcbmi              ,    True           , False        , True
+mf6        ,  6.4.3  ,  True   , https://github.com/MODFLOW-USGS/modflow6/releases/download/6.4.3/mf6.4.3_linux.zip             , mf6.4.3_linux       , src                 ,    True           , False        , False
+zbud6      ,  6.4.3  ,  True   , https://github.com/MODFLOW-USGS/modflow6/releases/download/6.4.3/mf6.4.3_linux.zip             , mf6.4.3_linux       , utils/zonebudget/src,    True           , False        , False
+libmf6     ,  6.4.3  ,  True   , https://github.com/MODFLOW-USGS/modflow6/releases/download/6.4.3/mf6.4.3_linux.zip             , mf6.4.3_linux       , srcbmi              ,    True           , False        , True
 mp7        ,  7.2.001,  True   , https://water.usgs.gov/water-resources/software/MODPATH/modpath_7_2_001.zip                    , modpath_7_2_001     , source              ,    True           , False        , False
 mt3dms     ,  5.3.0  ,  True   , https://github.com/MODFLOW-USGS/mt3dms/releases/download/2.0/mt3dms-2.0.zip                    , mt3dms-2.0          , true-binary         ,    True           , False        , False
 mt3dusgs   ,  1.1.0  ,  True   , https://water.usgs.gov/water-resources/software/MT3D-USGS/mt3dusgs1.1.0.zip                    , mt3dusgs1.1.0       , src                 ,    True           , False        , False
@@ -21,6 +21,7 @@ zonbud3    ,  3.01   ,  True   , https://water.usgs.gov/water-resources/software
 mfnwt1.1.4 ,  1.1.4  ,  False  , https://water.usgs.gov/water-resources/software/MODFLOW-NWT/MODFLOW-NWT_1.1.4.zip              , MODFLOW-NWT_1.1.4   , src                 ,    True           , False        , False
 mfnwt      ,  1.3.0  ,  True   , https://water.usgs.gov/water-resources/software/MODFLOW-NWT/MODFLOW-NWT_1.3.0.zip              , MODFLOW-NWT         , src                 ,    True           , False        , False
 mfusg_gsi  ,  2.2.2  ,  True   , https://www.gsienv.com/wp-content/uploads/2023/11/USG-Transport_Version-2.2.2.zip              , USGT-v2-2-2-Source  , .                   ,    True           , False        , False
+gsflow     ,  2.2.1  ,  True   , https://water.usgs.gov/water-resources/software/gsflow/gsflow_2.2.1_linux.zip                  , gsflow_2.2.1        , src                 ,    True           , False        , False
 mf6dev     ,  6.5.0.dev0 ,  False  , https://github.com/MODFLOW-USGS/modflow6/archive/refs/heads/develop.zip                    , modflow6-develop    , src                 ,    True           , False        , False
 zbud6dev   ,  6.5.0.dev0 ,  False  , https://github.com/MODFLOW-USGS/modflow6/archive/refs/heads/develop.zip                    , modflow6-develop    , utils/zonebudget/src,    True           , False        , False
 libmf6dev  ,  6.5.0.dev0 ,  False  , https://github.com/MODFLOW-USGS/modflow6/archive/refs/heads/develop.zip                    , modflow6-develop    , srcbmi              ,    True           , False        , True