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Merge pull request #2116 from MODFLOW-USGS/v6.6.0
Release 6.6.0
2 parents 879f911 + 51f0009 commit 799088c

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‎.build_rtd_docs/Doxyfile‎

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

‎.build_rtd_docs/MAINPAGE.md‎

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@@ -1,7 +1,7 @@
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# MODFLOW 6 Source Code Documentation
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# Overview
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33
The documentation here is extracted from the source code by [doxygen](https://www.doxygen.nl/index.html).
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The source code repository is hosted at https://github.com/MODFLOW-USGS/modflow6 where full details can be found.
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The source code repository is hosted [on GitHub](https://github.com/MODFLOW-USGS/modflow6).
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MODFLOW 6 usage documentation can be found at https://modflow6.readthedocs.io/en/latest/
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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

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@@ -1,3 +1,4 @@
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# ruff: noqa: E402
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# Configuration file for the Sphinx documentation builder.
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#
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# This file only contains a selection of the most common options. For a full
@@ -14,7 +15,7 @@
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# documentation root, use os.path.abspath to make it absolute, like shown here.
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#
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import sys
17-
from subprocess import Popen, PIPE
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from subprocess import PIPE, Popen
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sys.path.insert(0, os.path.abspath(os.path.join("..", "doc")))
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sys.path.insert(0, os.path.abspath(os.path.join("..", "distribution")))
@@ -23,12 +24,12 @@
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on_rtd = os.environ.get("READTHEDOCS") == "True"
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# -- print current directory
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print("Current Directory...'{}'".format(os.path.abspath(os.getcwd())))
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print(f"Current Directory...'{os.path.abspath(os.getcwd())}'")
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# -- clean up doxygen files -------------------------------------------------
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dox_pths = ("_mf6io",)
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for dox_pth in dox_pths:
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print("cleaning....{}".format(dox_pth))
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print(f"cleaning....{dox_pth}")
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for root, dirs, files in os.walk(dox_pth):
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for name in files:
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fpth = os.path.join(root, name)
@@ -37,6 +38,7 @@
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# -- Update the modflow 6 version -------------------------------------------
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print("Update the modflow6 version")
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from update_version import update_version
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update_version()
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# -- import version from doc/version.py -------------------------------------
@@ -56,6 +58,50 @@
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# copy the file
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shutil.copy(src, dst)
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# -- copy developer docs
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dstdir = "_dev"
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fpth = "DEVELOPER.md"
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src = os.path.join("..", fpth)
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dst = os.path.join(dstdir, fpth.lower())
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# clean up an existing _mf6run directory
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if os.path.isdir(dstdir):
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shutil.rmtree(dstdir)
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# make the directory
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os.makedirs(dstdir)
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# copy the file
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shutil.copy(src, dst)
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# -- copy contributor docs
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fpth = "CONTRIBUTING.md"
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src = os.path.join("..", fpth)
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dst = os.path.join(dstdir, fpth.lower())
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shutil.copy(src, dst)
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# -- copy style guide
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fpth = "styleguide.md"
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src = os.path.join(fpth)
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dst = os.path.join(dstdir, fpth)
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shutil.copy(src, dst)
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# -- copy DFN spec
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fpth = "readme.md"
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src = os.path.join("..", "doc", "mf6io", "mf6ivar", fpth)
89+
dst = os.path.join(dstdir, "dfn.md")
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shutil.copy(src, dst)
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92+
# -- build the deprecations table --------------------------------------------
93+
print("Build the deprecations markdown table")
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pth = os.path.join("..", "doc", "mf6io", "mf6ivar")
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args = (sys.executable, "deprecations.py")
96+
# run the command
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proc = Popen(args, stdout=PIPE, stderr=PIPE, cwd=pth)
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stdout, stderr = proc.communicate()
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if stdout:
100+
print(stdout.decode("utf-8"))
101+
if stderr:
102+
print("Errors:")
103+
print(stderr.decode("utf-8"))
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# -- copy deprecations markdown ---------------------------------------------
60106
print("Copy the deprecations table")
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dstdir = "_mf6run"
@@ -75,7 +121,8 @@
75121
if stdout:
76122
print(stdout.decode("utf-8"))
77123
if stderr:
78-
print("Errors:\n{}".format(stderr.decode("utf-8")))
124+
print("Errors:")
125+
print(stderr.decode("utf-8"))
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# -- update the doxygen version number ---------------------------------------
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print("Update the Doxyfile with the latest version number")
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with open("Doxyfile", "w") as fp:
87134
for line in lines:
88135
if tag in line:
89-
line = '{} = "version {}"\n'.format(tag, __version__)
136+
line = f'{tag} = "version {__version__}"\n'
90137
fp.write(line)
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# -- Project information -----------------------------------------------------
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94-
project = "MODFLOW 6 Program Documentation"
95-
copyright = "2023, MODFLOW Development Team"
141+
project = "MODFLOW 6"
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copyright = "2024, MODFLOW Development Team"
96143
author = "MODFLOW Development Team"
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# -- Project version ---------------------------------------------------------
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# # Tell sphinx what the pygments highlight language should be.
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# highlight_language = 'fortran'
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source_suffix = {".rst": "restructuredtext", ".md": "markdown"}
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# Add any paths that contain templates here, relative to this directory.
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templates_path = ["_templates"]
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‎.build_rtd_docs/dev.rst‎

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Developer Guide
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---------------
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4+
This section includes developer instructions and conventions.
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6+
.. toctree::
7+
:maxdepth: 1
8+
:glob:
9+
10+
_dev/contributing.md
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_dev/developer.md
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_dev/styleguide.md
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_dev/dfn.md

‎.build_rtd_docs/index.rst‎

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@@ -11,8 +11,9 @@ Contents:
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.. toctree::
1212
:maxdepth: 2
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14-
MODFLOW 6 Source Code Documentation <https://modflow-usgs.github.io/modflow6/>
15-
mf6io
14+
API Reference <https://modflow-usgs.github.io/modflow6/>
1615
_mf6run/run-time-comparison.md
1716
_mf6run/deprecations.md
17+
mf6io
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dev
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‎.build_rtd_docs/make.bat‎

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1+
@ECHO OFF
2+
3+
pushd %~dp0
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5+
REM Command file for Sphinx documentation
6+
7+
if "%SPHINXBUILD%" == "" (
8+
set SPHINXBUILD=sphinx-build
9+
)
10+
set SOURCEDIR=.
11+
set BUILDDIR=_build
12+
13+
if "%1" == "" goto help
14+
15+
%SPHINXBUILD% >NUL 2>NUL
16+
if errorlevel 9009 (
17+
echo.
18+
echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
19+
echo.installed, then set the SPHINXBUILD environment variable to point
20+
echo.to the full path of the 'sphinx-build' executable. Alternatively you
21+
echo.may add the Sphinx directory to PATH.
22+
echo.
23+
echo.If you don't have Sphinx installed, grab it from
24+
echo.http://sphinx-doc.org/
25+
exit /b 1
26+
)
27+
28+
%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
29+
goto end
30+
31+
:help
32+
%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
33+
34+
:end
35+
popd

‎.build_rtd_docs/mf6io.rst‎

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@@ -1,8 +1,9 @@
1-
MODFLOW 6 Input Guide
2-
---------------------
1+
Input Guide
2+
-----------
33

4-
The latest version of the complete MODFLOW 6 input output guide can be found
4+
The latest version of the complete MODFLOW 6 input/output guide can be found
55
`here <https://github.com/MODFLOW-USGS/modflow6-nightly-build/releases/>`_.
6+
This section enumerates and describes MODFLOW 6 input files.
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78
Simulation
89
^^^^^^^^^^
@@ -44,6 +45,26 @@ Groundwater Transport
4445
_mf6io/gwt-*
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4647

48+
Groundwater Energy Transport
49+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
50+
51+
.. toctree::
52+
:maxdepth: 1
53+
:glob:
54+
55+
_mf6io/gwe-*
56+
57+
58+
Particle Tracking
59+
^^^^^^^^^^^^^^^^^
60+
61+
.. toctree::
62+
:maxdepth: 1
63+
:glob:
64+
65+
_mf6io/prt-*
66+
67+
4768
Model Exchanges
4869
^^^^^^^^^^^^^^^
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