Merge pull request #1594 from MODFLOW-USGS/v6.4.3

Release 6.4.3

.build_rtd_docs/Doxyfile

@@ -37,7 +37,7 @@ PROJECT_NAME = "MODFLOW 6"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER = "version 6.2.2"
+PROJECT_NUMBER = "version 6.5.0.dev0"
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

.build_rtd_docs/conf.py

@@ -56,6 +56,15 @@
 # copy the file
 shutil.copy(src, dst)
 
+# -- copy deprecations markdown ---------------------------------------------
+print("Copy the deprecations table")
+dstdir = "_mf6run"
+fpth = "deprecations.md"
+src = os.path.join("..", "doc", "mf6io", "mf6ivar", "md", fpth)
+dst = os.path.join(dstdir, fpth)
+# copy the file
+shutil.copy(src, dst)
+
 # -- build the mf6io markdown files -----------------------------------------
 print("Build the mf6io markdown files")
 pth = os.path.join("..", "doc", "mf6io", "mf6ivar")
@@ -140,11 +149,9 @@
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ["_static"]
 
-html_context = {
- "css_files": [
- "_static/theme_overrides.css", # override wide tables in RTD theme
- ],
-}
+html_css_files = [
+ "_static/theme_overrides.css", # override wide tables in RTD theme
+]
 
 # html_theme_options = {
 # "github_url": "https://github.com/MODFLOW-USGS/modflow6",

.build_rtd_docs/index.rst

@@ -14,4 +14,5 @@ Contents:
  MODFLOW 6 Source Code Documentation <https://modflow-usgs.github.io/modflow6/>
  mf6io
  _mf6run/run-time-comparison.md
+ _mf6run/deprecations.md
 

.build_rtd_docs/requirements.rtd.txt

@@ -1,13 +1,14 @@
 numpy
 bmipy
+sphinx>=4
 sphinx_markdown_tables
 nbsphinx
 nbsphinx_link
 ipython
 ipykernel
 rtds_action
 myst-parser
-sphinx_rtd_theme
+sphinx_rtd_theme>=1
 pytest
 filelock
 modflow-devtools

.doc/conf.py

@@ -112,14 +112,13 @@
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ["_static"]
-
 html_context = {
  "github_repo": "modflow6",
  "doc_path": ".doc",
- "css_files": [
- "_static/theme_overrides.css", # override wide tables in RTD theme
- ],
 }
+html_css_files = [
+ "_static/theme_overrides.css", # override wide tables in RTD theme
+]
 
 html_theme_options = {}
 

.doc/requirements.txt

@@ -2,5 +2,6 @@ sphinx_markdown_tables
 ipython
 ipykernel
 rtds_action
-sphinx_rtd_theme
+sphinx>=4
+sphinx_rtd_theme>=1
 myst-parser

.fprettify.yaml

@@ -1,6 +1,6 @@
 # MODFLOW 6 configuration for fprettify
 # run from root directory using
-# fprettify -c distribution/.fprettify.yaml SRC
+# fprettify -c .fprettify.yaml SRC
 whitespace-plusminus: 1
 whitespace-multdiv: 1
 line-length: 82

.gitattributes

@@ -13,3 +13,8 @@
 *.png binary
 *.jpg binary
 *.pdf binary
+
+# Configure github-linguist
+*.inc linguist-language=Fortran
+.build_rtd_docs/** linguist-documentation
+.doc/** linguist-documentation

.github/ISSUE_TEMPLATE/bug_report.md

@@ -10,7 +10,7 @@ assignees: ''
 **Describe the bug**
 A clear and concise description of what the bug is.
 
-**To Reproduce**
+**To reproduce**
 Steps to reproduce the behavior:
 1. Go to '...'
 2. Click on '....'
@@ -23,6 +23,7 @@ A clear and concise description of what you expected to happen.
 **Screenshots**
 If applicable, add screenshots to help explain your problem.
 
-**Desktop (please complete the following information):**
- - OS: [e.g. macOS, Linux, Windows]
- - Version [e.g. 22]
+**Environment**
+ - Operating system (e.g. macOS, Linux, Windows) and version
+ - MODFLOW 6 version (if installed via distribution)
+ - Compiler toolchain/version (if built from source)

.github/PULL_REQUEST_TEMPLATE/pull_request_template.md

@@ -0,0 +1,8 @@
+Feel free to remove check-list items that aren't relevant to your change.
+
+- [ ] Closes #xxxx
+- [ ] Passed autotests
+- [ ] Formatted source files with `fprettify`
+- [ ] Updated definition (*.dfn) files with new or modified options
+- [ ] Described new options, features or behavior changes in release notes
+- [ ] Updated meson files, makefiles, and Visual Studio project files if new source files added

.github/common/fortran_format_check.py

@@ -18,7 +18,8 @@
 ]
 
 # Exclude these files from checks
-excludefiles = ["src/Utilities/InputOutput.f90"] # excluded until refactored
+excludefiles = [] # add excluded files here
+
 
 class FortranFormatCheck:
  """
@@ -99,16 +100,15 @@ def _excluded(self, path: Path) -> bool:
 
  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"
- )
+ parser.add_argument("-v", "--verbose", action="store_true", help="verbose")
  args = parser.parse_args()
 
  # set MODFLOW 6 repository root

.github/common/msvs_vfproj_check.py

@@ -0,0 +1,68 @@
+import xml.etree.ElementTree as ET
+from pathlib import Path
+
+
+def get_source_files(src_folder):
+ p = Path(".")
+ src_files = []
+ print(f"Processing {src_folder} folder")
+ ftypes = ("*.[fF]9[05]", "*.inc")
+ src_files = []
+ for ft in ftypes:
+ src_files.extend(p.glob(f"{src_folder}/**/{ft}"))
+ return src_files
+
+
+def get_msvs_files(vfproj_file):
+ print(f"Processing {vfproj_file}")
+ tree = ET.parse(vfproj_file)
+ root = tree.getroot()
+ msvs_files = []
+ for f in root.iter("File"):
+ s = f.attrib["RelativePath"]
+ s = s.replace("\\", "/")
+ s = s.replace("../", "")
+ fpath = Path(s)
+ msvs_files.append(fpath)
+ return msvs_files
+
+
+def check_files(name, src_files, msvs_files):
+ print(
+ f"Verifying {name} files referenced in msvs project files are in src folder..."
+ )
+ s, m = set(src_files), set(msvs_files)
+ diff = s ^ m
+ from pprint import pformat
+
+ assert not any(diff), (
+ f"{name} src files don't match msvs project file\n"
+ f"=> symmetric difference:\n{pformat(diff)}\n"
+ f"=> src - msvs:\n{pformat(s - m)}\n"
+ f"=> msvs - src:\n{pformat(m - s)}\n"
+ "Check to make sure msvs project file is consistent with source files."
+ )
+
+
+def check_mf6():
+ # get list of source files and files referenced in msvs project files
+ src_files = get_source_files("src")
+ msvs_files = []
+ for vfproj in ["./msvs/mf6core.vfproj", "./msvs/mf6.vfproj"]:
+ msvs_files.extend(get_msvs_files(vfproj))
+ check_files("MF6", src_files, msvs_files)
+
+
+def check_bmi():
+ # get list of source files and files referenced in msvs project files
+ src_files = get_source_files("srcbmi")
+ msvs_files = []
+ for vfproj in ["./msvs/mf6bmi.vfproj"]:
+ msvs_files.extend(get_msvs_files(vfproj))
+ check_files("BMI", src_files, msvs_files)
+
+
+if __name__ == "__main__":
+ check_mf6()
+ check_bmi()
+ print("msvs project (vfproj) files appear up-to-date...")

.github/common/update_compat_tables.py

@@ -0,0 +1,35 @@
+"""
+Inserts Markdown compatibility tables
+between tags in target Markdown file.
+"""
+
+import re
+import sys
+from pathlib import Path
+
+name = sys.argv[1] # name of the table, e.g. "compile", "test"
+compat_path = Path(sys.argv[2]) # compatibility table path
+update_path = Path(sys.argv[3]) # path to file to update
+
+assert compat_path.is_file()
+assert update_path.is_file()
+
+with open(compat_path, "r") as compat:
+ table = "".join(compat.readlines())
+ r = re.compile(
+ r"<!\-\- "
+ + name
+ + r" compat starts \-\->.*<!\-\- "
+ + name
+ + r" compat ends \-\->",
+ re.DOTALL,
+ )
+ ct = (
+ "<!-- "
+ + name
+ + " compat starts -->{}<!-- ".format("\n{}\n".format(table))
+ + name
+ + " compat ends -->"
+ )
+ readme = update_path.open().read()
+ update_path.open("w").write(r.sub(ct, readme))

.github/common/wide_compat_reports.py

@@ -0,0 +1,39 @@
+"""
+Converts compatibility reports from long to wide format
+and makes a markdown table from the wide format report.
+"""
+
+from pathlib import Path
+import pandas as pd
+import sys
+
+ip = Path(sys.argv[1]) # input file path
+op = Path(sys.argv[2]) # output file path
+assert ip.is_file()
+assert ip.suffix == ".csv"
+assert op.suffix == ".csv"
+
+# read long CSV
+df = pd.read_csv(ip)
+
+# pivot and sort
+df = pd.pivot(
+ df,
+ index="runner",
+ columns=["compiler", "version"],
+ values="support",
+).sort_values(by=["runner"])
+
+# write wide CSV
+df.to_csv(op)
+
+# write wide markdown table
+with open(op.with_suffix(".md"), "w") as file:
+ file.write(
+ df.to_markdown()
+ .replace("nan", "")
+ .replace("(", "")
+ .replace(")", "")
+ .replace(",", "")
+ .replace("'", "")
+ )

.github/compat/comp.csv

@@ -0,0 +1,9 @@
+compiler,gcc,gcc,gcc,gcc,gcc,gcc,gcc,intel-classic,intel-classic,intel-classic,intel-classic,intel-classic,intel-classic,intel-classic,intel-classic,intel-classic,intel-classic,intel,intel,intel,intel,intel,intel,intel,intel,intel,intel
+version,10,11,12,13,7,8,9,2021.1,2021.10,2021.2,2021.3,2021.4,2021.5,2021.6,2021.7,2021.8,2021.9,2021.1,2021.2,2021.4,2022.0,2022.1,2022.2.1,2022.2,2023.0,2023.1,2023.2
+runner,,,,,,,,,,,,,,,,,,,,,,,,,,,
+macos-11,✓,✓,✓,✓,✓,✓,✓,✓,✓,✓,✓,✓,✓,✓,✓,✓,✓,,,,,,,,,,
+macos-12,✓,✓,✓,✓,✓,✓,✓,✓,✓,✓,✓,✓,✓,✓,✓,✓,✓,,,,,,,,,,
+ubuntu-20.04,✓,✓,,,✓,✓,✓,✓,✓,✓,,✓,✓,✓,✓,✓,✓,,,,,,✓,✓,,,✓
+ubuntu-22.04,✓,✓,✓,✓,,,✓,✓,✓,✓,,✓,✓,✓,✓,✓,✓,,,,,,✓,✓,,,✓
+windows-2019,✓,✓,✓,✓,,,✓,,✓,,,,,✓,✓,✓,✓,,,,,,,✓,,,✓
+windows-2022,✓,✓,✓,✓,,,✓,,✓,,,,,✓,✓,✓,✓,,,,,,,✓,,,✓

.github/compat/test.csv

@@ -0,0 +1,9 @@
+compiler,gcc,gcc,gcc,gcc,gcc,gcc,gcc,intel-classic,intel-classic,intel-classic,intel-classic,intel-classic,intel-classic,intel-classic,intel-classic,intel-classic,intel-classic,intel,intel,intel,intel,intel,intel,intel,intel,intel,intel
+version,10,11,12,13,7,8,9,2021.1,2021.10,2021.2,2021.3,2021.4,2021.5,2021.6,2021.7,2021.8,2021.9,2021.1,2021.2,2021.4,2022.0,2022.1,2022.2.1,2022.2,2023.0,2023.1,2023.2
+runner,,,,,,,,,,,,,,,,,,,,,,,,,,,
+macos-11,✓,✓,✓,✓,✓,✓,✓,✓,,✓,✓,✓,✓,✓,✓,,,,,,,,,,,,
+macos-12,✓,✓,✓,✓,,,,✓,,✓,✓,✓,✓,✓,✓,,,,,,,,,,,,
+ubuntu-20.04,✓,✓,,,✓,✓,✓,✓,,✓,,✓,✓,✓,✓,,,,,,,,,,,,
+ubuntu-22.04,✓,✓,✓,✓,,,✓,✓,,✓,,✓,✓,✓,✓,,,,,,,,,,,,
+windows-2019,,,,✓,,,,,,,,,,✓,✓,,,,,,,,,,,,
+windows-2022,✓,✓,✓,✓,,,✓,,,,,,,✓,✓,,,,,,,,,,,,