Merge pull request #2116 from MODFLOW-USGS/v6.6.0

Release 6.6.0

.build_rtd_docs/Doxyfile

@@ -37,13 +37,13 @@ PROJECT_NAME           = "MODFLOW 6"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = "version 6.5.0"
+PROJECT_NUMBER         = "version 6.6.0"
 
 # 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
 # quick idea about the purpose of the project. Keep the description short.
 
-PROJECT_BRIEF          = "MODFLOW 6 Code Documentation"
+PROJECT_BRIEF          = "USGS Modular Hydrologic Model"
 
 # With the PROJECT_LOGO tag one can specify a logo or an icon that is included
 # in the documentation. The maximum height of the logo should not exceed 55

.build_rtd_docs/MAINPAGE.md

@@ -1,7 +1,7 @@
-# MODFLOW 6 Source Code Documentation
+# Overview
 
 The documentation here is extracted from the source code by [doxygen](https://www.doxygen.nl/index.html).
 
-The source code repository is hosted at https://github.com/MODFLOW-USGS/modflow6 where full details can be found.
+The source code repository is hosted [on GitHub](https://github.com/MODFLOW-USGS/modflow6).
 
-MODFLOW 6 usage documentation can be found at https://modflow6.readthedocs.io/en/latest/
+This documentation is intended for MODFLOW 6 contributors and users of the MODFLOW 6 library/API. MODFLOW 6 usage documentation can be found [on ReadTheDocs](https://modflow6.readthedocs.io/en/latest/).

.build_rtd_docs/conf.py

@@ -1,3 +1,4 @@
+# ruff: noqa: E402
 # Configuration file for the Sphinx documentation builder.
 #
 # This file only contains a selection of the most common options. For a full
@@ -14,7 +15,7 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
 import sys
-from subprocess import Popen, PIPE
+from subprocess import PIPE, Popen
 
 sys.path.insert(0, os.path.abspath(os.path.join("..", "doc")))
 sys.path.insert(0, os.path.abspath(os.path.join("..", "distribution")))
@@ -23,12 +24,12 @@
 on_rtd = os.environ.get("READTHEDOCS") == "True"
 
 # -- print current directory
-print("Current Directory...'{}'".format(os.path.abspath(os.getcwd())))
+print(f"Current Directory...'{os.path.abspath(os.getcwd())}'")
 
 # -- clean up doxygen files -------------------------------------------------
 dox_pths = ("_mf6io",)
 for dox_pth in dox_pths:
-    print("cleaning....{}".format(dox_pth))
+    print(f"cleaning....{dox_pth}")
     for root, dirs, files in os.walk(dox_pth):
         for name in files:
             fpth = os.path.join(root, name)
@@ -37,6 +38,7 @@
 # -- Update the modflow 6 version -------------------------------------------
 print("Update the modflow6 version")
 from update_version import update_version
+
 update_version()
 
 # -- import version from doc/version.py -------------------------------------
@@ -56,6 +58,50 @@
 # copy the file
 shutil.copy(src, dst)
 
+# -- copy developer docs
+dstdir = "_dev"
+fpth = "DEVELOPER.md"
+src = os.path.join("..", fpth)
+dst = os.path.join(dstdir, fpth.lower())
+# clean up an existing _mf6run directory
+if os.path.isdir(dstdir):
+    shutil.rmtree(dstdir)
+# make the directory
+os.makedirs(dstdir)
+# copy the file
+shutil.copy(src, dst)
+
+# -- copy contributor docs
+fpth = "CONTRIBUTING.md"
+src = os.path.join("..", fpth)
+dst = os.path.join(dstdir, fpth.lower())
+shutil.copy(src, dst)
+
+# -- copy style guide
+fpth = "styleguide.md"
+src = os.path.join(fpth)
+dst = os.path.join(dstdir, fpth)
+shutil.copy(src, dst)
+
+# -- copy DFN spec
+fpth = "readme.md"
+src = os.path.join("..", "doc", "mf6io", "mf6ivar", fpth)
+dst = os.path.join(dstdir, "dfn.md")
+shutil.copy(src, dst)
+
+# -- build the deprecations table --------------------------------------------
+print("Build the deprecations markdown table")
+pth = os.path.join("..", "doc", "mf6io", "mf6ivar")
+args = (sys.executable, "deprecations.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:")
+    print(stderr.decode("utf-8"))
+
 # -- copy deprecations markdown ---------------------------------------------
 print("Copy the deprecations table")
 dstdir = "_mf6run"
@@ -75,7 +121,8 @@
 if stdout:
     print(stdout.decode("utf-8"))
 if stderr:
-    print("Errors:\n{}".format(stderr.decode("utf-8")))
+    print("Errors:")
+    print(stderr.decode("utf-8"))
 
 # -- update the doxygen version number ---------------------------------------
 print("Update the Doxyfile with the latest version number")
@@ -86,13 +133,13 @@
 with open("Doxyfile", "w") as fp:
     for line in lines:
         if tag in line:
-            line = '{}         = "version {}"\n'.format(tag, __version__)
+            line = f'{tag}         = "version {__version__}"\n'
         fp.write(line)
 
 # -- Project information -----------------------------------------------------
 
-project = "MODFLOW 6 Program Documentation"
-copyright = "2023, MODFLOW Development Team"
+project = "MODFLOW 6"
+copyright = "2024, MODFLOW Development Team"
 author = "MODFLOW Development Team"
 
 # -- Project version ---------------------------------------------------------
@@ -126,6 +173,8 @@
 # # Tell sphinx what the pygments highlight language should be.
 # highlight_language = 'fortran'
 
+source_suffix = {".rst": "restructuredtext", ".md": "markdown"}
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 

.build_rtd_docs/dev.rst

@@ -0,0 +1,13 @@
+Developer Guide
+---------------
+
+This section includes developer instructions and conventions.
+
+.. toctree::
+   :maxdepth: 1
+   :glob:
+
+   _dev/contributing.md
+   _dev/developer.md
+   _dev/styleguide.md
+   _dev/dfn.md

.build_rtd_docs/index.rst

@@ -11,8 +11,9 @@ Contents:
 .. toctree::
    :maxdepth: 2
 
-   MODFLOW 6 Source Code Documentation <https://modflow-usgs.github.io/modflow6/>
-   mf6io
+   API Reference <https://modflow-usgs.github.io/modflow6/>
    _mf6run/run-time-comparison.md
    _mf6run/deprecations.md
+   mf6io
+   dev
 

.build_rtd_docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

.build_rtd_docs/mf6io.rst

@@ -1,8 +1,9 @@
-MODFLOW 6 Input Guide
----------------------
+Input Guide
+-----------
 
-The latest version of the complete MODFLOW 6 input output guide can be found
+The latest version of the complete MODFLOW 6 input/output guide can be found
 `here <https://github.com/MODFLOW-USGS/modflow6-nightly-build/releases/>`_.
+This section enumerates and describes MODFLOW 6 input files.
 
 Simulation
 ^^^^^^^^^^
@@ -44,6 +45,26 @@ Groundwater Transport
    _mf6io/gwt-*
 
 
+Groundwater Energy Transport
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. toctree::
+   :maxdepth: 1
+   :glob:
+
+   _mf6io/gwe-*
+
+
+Particle Tracking
+^^^^^^^^^^^^^^^^^
+
+.. toctree::
+   :maxdepth: 1
+   :glob:
+
+   _mf6io/prt-*
+
+
 Model Exchanges
 ^^^^^^^^^^^^^^^