Merge pull request #1279 from MODFLOW-USGS/v6.4.2

Release 6.4.2

.build_rtd_docs/conf.py

@@ -17,6 +17,7 @@
 from subprocess import Popen, PIPE
 
 sys.path.insert(0, os.path.abspath(os.path.join("..", "doc")))
+sys.path.insert(0, os.path.abspath(os.path.join("..", "distribution")))
 
 # -- determine if running on readthedocs ------------------------------------
 on_rtd = os.environ.get("READTHEDOCS") == "True"
@@ -35,18 +36,8 @@
 
 # -- Update the modflow 6 version -------------------------------------------
 print("Update the modflow6 version")
-pth = os.path.join("..", "distribution")
-args = (
- "python",
- "update_version.py",
-)
-# run the command
-proc = Popen(args, stdout=PIPE, stderr=PIPE, cwd=pth)
-stdout, stderr = proc.communicate()
-if stdout:
- print(stdout.decode("utf-8"))
-if stderr:
- print("Errors:\n{}".format(stderr.decode("utf-8")))
+from update_version import update_version
+update_version()
 
 # -- import version from doc/version.py -------------------------------------
 from version import __version__
@@ -68,7 +59,7 @@
 # -- build the mf6io markdown files -----------------------------------------
 print("Build the mf6io markdown files")
 pth = os.path.join("..", "doc", "mf6io", "mf6ivar")
-args = ("python", "mf6ivar.py")
+args = (sys.executable, "mf6ivar.py")
 # run the command
 proc = Popen(args, stdout=PIPE, stderr=PIPE, cwd=pth)
 stdout, stderr = proc.communicate()
@@ -92,7 +83,7 @@
 # -- Project information -----------------------------------------------------
 
 project = "MODFLOW 6 Program Documentation"
-copyright = "2020, MODFLOW Development Team"
+copyright = "2023, MODFLOW Development Team"
 author = "MODFLOW Development Team"
 
 # -- Project version ---------------------------------------------------------

.build_rtd_docs/requirements.rtd.txt

@@ -6,9 +6,8 @@ nbsphinx_link
 ipython
 ipykernel
 rtds_action
-myst_parser
+myst-parser
 sphinx_rtd_theme
-
-
-
-
+pytest
+filelock
+modflow-devtools

.doc/conf.py

@@ -49,7 +49,7 @@
 # -- Project information -----------------------------------------------------
 
 project = "MODFLOW 6 Program Documentation"
-copyright = "2020, MODFLOW Development Team"
+copyright = "2023, MODFLOW Development Team"
 author = "MODFLOW Development Team"
 
 # -- General configuration ---------------------------------------------------
@@ -70,7 +70,7 @@
  "sphinx.ext.viewcode",
  "IPython.sphinxext.ipython_console_highlighting", # lowercase didn't work
  "sphinx.ext.autosectionlabel",
- "recommonmark",
+ "myst_parser",
  "sphinx_markdown_tables",
 ]
 

.doc/requirements.txt

@@ -3,4 +3,4 @@ ipython
 ipykernel
 rtds_action
 sphinx_rtd_theme
-recommonmark
+myst-parser

.github/common/fortran_format_check.py

@@ -0,0 +1,125 @@
+import os
+import sys
+import argparse
+import glob
+from pathlib import Path
+from subprocess import run
+
+# MODFLOW 6 repository directories to check (relative to root)
+searchpaths = ["src", "srcbmi", "utils/zonebudget/src"]
+
+# Exclude these directories from checks
+excludedirs = [
+ "src/Utilities/Libraries/blas", # external library blas
+ "src/Utilities/Libraries/daglib", # external library dag
+ "src/Utilities/Libraries/rcm", # external library rcm
+ "src/Utilities/Libraries/sparsekit", # external library sparsekit
+ "src/Utilities/Libraries/sparskit2", # external library sparsekit2
+]
+
+# Exclude these files from checks
+excludefiles = ["src/Utilities/InputOutput.f90"] # excluded until refactored
+
+class FortranFormatCheck:
+ """
+ Verify MODFLOW 6 fortran source code format
+ """
+
+ def __init__(self, root: Path, verbose: bool):
+ self._checkcount = 0
+ self._fprettifyfails = []
+ self._exclude_dirs = []
+ self._exclude_files = []
+ self._root = root.resolve()
+ self._verbose = verbose
+ self._entrypath = Path().cwd()
+
+ os.chdir(self._root)
+
+ def add_search_path(self, path: Path) -> None:
+ p = Path(path)
+
+ for f in p.glob("**/*.[fF]9[05]"):
+ self._check_src_fprettify(f)
+
+ def add_exclude_dirs(self, excl_dirs: list) -> None:
+ self._exclude_dirs += excl_dirs
+
+ def add_exclude_files(self, excl_files: list) -> None:
+ self._exclude_files += excl_files
+
+ def clear_exclude_dirs(self) -> None:
+ self._exclude_dirs = None
+ self._exclude_dirs = []
+
+ def clear_exclude_files(self) -> None:
+ self._exclude_files = None
+ self._exclude_files = []
+
+ def report(self) -> None:
+ print(f"\nFortran source files checked: {self._checkcount}")
+ print(f"Fortran source files failed: {len(self._fprettifyfails)}\n")
+
+ for f in self._fprettifyfails:
+ print(f"fprettify -c .fprettify.yaml {f}")
+
+ print()
+
+ def exit(self) -> int:
+ os.chdir(self._entrypath)
+
+ if len(self._fprettifyfails):
+ return 1
+
+ return 0
+
+ def _check_src_fprettify(self, path: Path) -> None:
+ if self._excluded(path):
+ return
+
+ self._checkcount += 1
+
+ if self._verbose:
+ print(path)
+
+ cmd = f"fprettify -d -c .fprettify.yaml {path}"
+ result = run(cmd, capture_output=True, shell=True)
+
+ if result.stdout or result.stderr:
+ self._fprettifyfails.append(path)
+
+ def _excluded(self, path: Path) -> bool:
+ for f in self._exclude_files:
+ if os.path.exists(f) and os.path.samefile(path, f):
+ return True
+
+ for d in self._exclude_dirs:
+ if os.path.exists(d) and os.path.samefile(path.parents[0], d):
+ return True
+
+ return False
+
+if __name__ == "__main__":
+ parser = argparse.ArgumentParser(
+ "MODFLOW 6 fortran format source code verification"
+ )
+ parser.add_argument(
+ "-r", "--root", help="path to MODFLOW 6 repository root directory"
+ )
+ parser.add_argument(
+ "-v", "--verbose", action="store_true", help="verbose"
+ )
+ args = parser.parse_args()
+
+ # set MODFLOW 6 repository root
+ root = Path(args.root).resolve() if args.root else Path(".").resolve()
+
+ fformat_check = FortranFormatCheck(root=root, verbose=args.verbose)
+ fformat_check.add_exclude_dirs(excl_dirs=excludedirs)
+ fformat_check.add_exclude_files(excl_files=excludefiles)
+
+ for path in searchpaths:
+ fformat_check.add_search_path(path=path)
+
+ fformat_check.report()
+ sys.exit(fformat_check.exit())

.github/dependabot.yml

@@ -0,0 +1,7 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+version: 2
+updates:
+ - package-ecosystem: "github-actions"
+ directory: "/" # Location of package manifests
+ schedule:
+ interval: "daily"