release(1.2.8): update mf6 version

Also added latest version of gsflow (v 2.3.0) and mfusg_gsi (v2.1.1).

README.md

@@ -2,7 +2,7 @@
 
 Python package for building MODFLOW-based programs from source files.
 
-### Version 1.2.7
+### Version 1.2.8
 
 ![pymake continuous integration](https://github.com/modflowpy/pymake/workflows/pymake%20continuous%20integration/badge.svg)
 [![codecov](https://codecov.io/gh/modflowpy/pymake/branch/master/graph/badge.svg)](https://codecov.io/gh/modflowpy/pymake)

autotest/test_gsflow.py

@@ -0,0 +1,207 @@
+import os
+import shutil
+import sys
+import pathlib as pl
+
+import flopy
+import pytest
+
+import pymake
+
+# use the line below to set fortran compiler using environmental variables
+# os.environ["FC"] = "ifort"
+# if sys.platform.lower() == "win32":
+#     os.environ["CC"] = "icl"
+# else:
+#     os.environ["CC"] = "icc"
+
+
+# define program data
+target = "gsflow"
+if sys.platform.lower() == "win32":
+    target += ".exe"
+
+# get program dictionary
+prog_dict = pymake.usgs_program_data.get_target(target)
+
+# set up paths
+dstpth = os.path.join(f"temp_{os.path.basename(__file__).replace('.py', '')}")
+if not os.path.exists(dstpth):
+    os.makedirs(dstpth, exist_ok=True)
+
+gsflowver = prog_dict.version
+gsflowpth = os.path.join(dstpth, prog_dict.dirname)
+egsflow = os.path.abspath(os.path.join(dstpth, target))
+
+# example path
+expth = os.path.join(gsflowpth, "data")
+examples = (
+    ("sagehen", "prms.control", "Normal completion"),
+    ("sagehen", "gsflow.control", "Normal termination of simulation"),
+    ("sagehen", "modflow.control", "Normal termination of simulation"),
+)
+
+# set up pths and exes
+pths = [gsflowpth]
+exes = [egsflow]
+
+pm = pymake.Pymake(verbose=True)
+pm.target = target
+pm.appdir = dstpth
+pm.makeclean = True
+
+
+def copy_example_dir():
+    if os.path.exists(egsflow):
+        src = os.path.join(expth, "sagehen")
+        dst = os.path.join(dstpth, "sagehen")
+
+        # delete dst if it exists
+        if os.path.isdir(dst):
+            shutil.rmtree(dst)
+
+        # copy the files
+        try:
+            shutil.copytree(src, dst)
+        except:
+            print(f"could not move files from {src} to '{dst}'")
+            return False
+
+        # edit the control file for a shorter run
+        # sagehen
+        tags = {
+            "..\\input\\prms\\": "../input/prms/",
+            ".\\input\\modflow\\": "./input/modflow/",
+            "..\\output\\": "../output/",
+            "..\\output\\prms\\": "../output/prms/",
+            "..\\output\\modflow\\": "../output/modflow/",
+        }
+
+        for _, control_file, _ in examples[1:]:
+            fpth = pl.Path(f"{dst}/windows/{control_file}")
+            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
+
+        # modify available control and name files
+        base_paths = (
+            pl.Path(f"{dst}/windows"),
+            pl.Path(f"{dst}/input/modflow"),
+        )
+        file_paths = []
+        for base_path in base_paths:
+            file_paths += base_path.glob("*.control")
+            file_paths += base_path.glob("*.nam")
+        for file_path in file_paths:
+            with open(file_path) as f:
+                lines = f.readlines()
+            with open(file_path, "w") as f:
+                for line in lines:
+                    for key, value in tags.items():
+                        if key in line:
+                            line = line.replace(key, value)
+                    f.write(line)
+
+    return True
+
+
+def run_gsflow(example, control_file, normal_message):
+    success = False
+    if os.path.exists(egsflow):
+        model_ws = os.path.join(dstpth, example, "windows")
+
+        # run the flow model
+        success, buff = flopy.run_model(
+            egsflow,
+            control_file,
+            model_ws=model_ws,
+            silent=False,
+            normal_msg=normal_message,
+        )
+        if not success:
+            errmsg = f"could not run {control_file}"
+    return success
+
+
+def clean_up():
+    print("Removing test files and directories")
+
+    # finalize pymake object
+    pm.finalize()
+
+    # clean up downloaded directories
+    if os.path.isdir(gsflowpth):
+        print("Removing folder " + gsflowpth)
+        shutil.rmtree(gsflowpth)
+
+    # clean up examples
+    for example, _, _ in examples:
+        pth = os.path.join(dstpth, example)
+        if os.path.isdir(pth):
+            print("Removing example folder " + example)
+            shutil.rmtree(pth)
+
+    # clean up compiled executables
+    if os.path.isfile(egsflow):
+        print("Removing...'" + egsflow + "'")
+        os.remove(egsflow)
+
+    dirs_temp = [dstpth]
+    for d in dirs_temp:
+        if os.path.isdir(d):
+            shutil.rmtree(d)
+
+    return
+
+
+@pytest.mark.base
+@pytest.mark.regression
+def test_download():
+    # Remove the existing target download directory if it exists
+    if os.path.isdir(gsflowpth):
+        shutil.rmtree(gsflowpth)
+
+    # download the target
+    pm.download_target(target, download_path=dstpth)
+    assert pm.download, f"could not download {target} distribution"
+
+
+@pytest.mark.base
+@pytest.mark.regression
+def test_compile():
+    assert pm.build() == 0, f"could not compile {target}"
+
+
+@pytest.mark.regression
+def test_prepare_regression():
+    assert copy_example_dir(), "could not prepare regression files"
+
+
+@pytest.mark.regression
+@pytest.mark.parametrize("ex,cf,msg", examples)
+def test_gsflow(ex, cf, msg):
+    assert run_gsflow(ex, cf, msg), f"could not run {ex}-{cf}"
+
+
+@pytest.mark.base
+@pytest.mark.regression
+def test_clean_up():
+    clean_up()
+    return
+
+
+if __name__ == "__main__":
+    test_download()
+    test_compile()
+    test_prepare_regression()
+    for ex, cf, msg in examples:
+        assert run_gsflow(ex, cf, msg), f"could not run {ex}-{cf}"
+    test_clean_up()

pymake/config.py

@@ -1,6 +1,6 @@
 __author__ = "Joseph D. Hughes"
-__date__ = "December 8, 2022"
-__version__ = "1.2.7"
+__date__ = "June 29, 2023"
+__version__ = "1.2.8"
 __maintainer__ = "Joseph D. Hughes"
 __email__ = "jdhughes@usgs.gov"
 __status__ = "Production"

pymake/utils/_dag.py

@@ -11,6 +11,8 @@
 __status__ = "Production"
 
 import os
+import re
+import re
 
 
 class Node(object):
@@ -149,9 +151,15 @@ def _get_f_nodelist(srcfiles):
             linelist = line.strip().split()
             if len(linelist) == 0:
                 continue
-            if linelist[0].upper() in ["MODULE", "SUBMODULE"]:
+            if linelist[0].upper() in ("MODULE",):
                 modulename = linelist[1].upper()
                 module_dict[modulename] = srcfile
+            if "SUBMODULE" in line.upper():
+                modulename = re.findall(r"\((.+)\)", line)
+                if len(modulename) > 0:
+                    modulename = modulename[0].strip()
+                    if modulename not in modulelist:
+                        modulelist.append(modulename)
             if linelist[0].upper() == "USE":
                 modulename = linelist[1].split(",")[0].upper()
                 if modulename not in modulelist: