Merge pull request MODFLOW-USGS#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,✓,✓,✓,✓,,,✓,,,,,,,✓,✓,,,,,,,,,,,,