mf6rtm 0.1.0__tar.gz

mf6rtm-0.1.0/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2024, Pablo Ortega
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

mf6rtm-0.1.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: mf6rtm
+Version: 0.1.0
+Summary: Reactive transport model through MODFLOW 6 and PHREEQCRM
+Author: Pablo Ortega
+Author-email: portega@intera.com
+License: BSD 3-Clause
+Platform: unix
+Platform: linux
+Platform: osx
+Platform: cygwin
+Platform: win32
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.6
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.6
+License-File: LICENSE
+Requires-Dist: phreeqcrm
+Requires-Dist: modflowapi
+Requires-Dist: flopy
+Provides-Extra: testing
+Requires-Dist: pytest>=7.0; extra == "testing"
+Requires-Dist: pytest-cov>=2.0; extra == "testing"
+Requires-Dist: mypy>=1.10; extra == "testing"
+Requires-Dist: flake8>=3.9; extra == "testing"
+Requires-Dist: tox>=3.24; extra == "testing"
+Requires-Dist: flaky>=3.8; extra == "testing"
+Requires-Dist: jupytext>=1.16.0; extra == "testing"
+Requires-Dist: nbconvert>=7.16; extra == "testing"
+Requires-Dist: ipykernel>=6.29; extra == "testing"

mf6rtm-0.1.0/README.md

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+# MF6RTM: Reactive Transport Model via the MODFLOW 6 and PHREEQCRM APIs
+![Tests](https://github.com/p-ortega/mf6rtm/actions/workflows/tests_main.yml/badge.svg)
+![Tests](https://github.com/p-ortega/mf6rtm/actions/workflows/tests_macos.yml/badge.svg)
+
+## Benchmarks
+Benchmark comparing model results against PHT3D are in `benchmark/`. Each folder contains a Jupyter notebook to write and execute an MF6RTM model via the MUP3D class. Additionally, PHT3D files are provided in the corresponding `pht3d` directory for each example.
+
+## Considerations
+The current version is intended to work with structured grids (dis object in MF6) and one MF6 simulation that includes the flow and transport solutions. No support is currently provided for a 'flow then transport scheme,' meaning that advanced packages cannot be incorporated yet.
+
+On the PHREEQC side, the following have been included:
+
+- Solution
+- Equilibrium phases
+- Cation Exchange
+- Surface Complexation
+- Kinetic Phases
+
+Most options for each phreeqc block can be passed by adding list with options. However, not all options had been tested, so please create an issue if any option is not working or crashing the model.
+
+## Software requirements
+All dependencies and executables are included in this repo. This package extensively uses [modflowapi](https://github.com/MODFLOW-USGS/modflowapi) and [phreeqcrm](https://github.com/usgs-coupled/phreeqcrm)
+
+## Installation
+The package is still not published in PyPi but it can be installed through pip by cloning the repository. 
+
+Once the repository is already cloned in your local machine, please just type the following in your conda prompt:
+
+```commandline
+conda env create -f env.yml
+```
+
+Otherwise, the package can be installed through pip as:
+
+```commandline
+pip install git+https://github.com/p-ortega/mf6rtm.git#egg=mf6rtm
+```
+
+## Funding
+The developing of mf6rtm was kindly funded and supported by [Intera, Inc](https://www.intera.com).
+
+## Authors
+Pablo Ortega (Portega)

mf6rtm-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=42.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tool.pytest.ini_options]
+# addopts = [
+#     "--cov=mf6rtm",
+#     "-rs",
+#     "-vvv "
+#     ]
+testpaths = [
+    "autotest",
+]
+
+[tool.mypy]
+mypy_path = "src"
+check_untyped_defs = true
+disallow_any_generics = true
+ignore_missing_imports = true
+no_implicit_optional = true
+show_error_codes = true
+strict_equality = true
+warn_redundant_casts = true
+warn_return_any = true
+warn_unreachable = true
+warn_unused_configs = true
+no_implicit_reexport = true
+
+[tool.scripts]
+mf6rtm = "mf6rtm:run_cmd"

mf6rtm-0.1.0/setup.cfg

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+[metadata]
+name = mf6rtm
+description = Reactive transport model through MODFLOW 6 and PHREEQCRM
+author = Pablo Ortega
+author-email = portega@intera.com
+license = BSD 3-Clause
+license_file = LICENSE
+platforms = unix, linux, osx, cygwin, win32
+classifiers = 
+	Programming Language :: Python :: 3
+	Programming Language :: Python :: 3 :: Only
+	Programming Language :: Python :: 3.6
+	Programming Language :: Python :: 3.7
+	Programming Language :: Python :: 3.8
+	Programming Language :: Python :: 3.9
+	Programming Language :: Python :: 3.10
+	Programming Language :: Python :: 3.11
+	Programming Language :: Python :: 3.12
+version = 0.1.0
+
+[options]
+packages = 
+	mf6rtm
+py_modules = 
+	mf6rtm
+	utils
+install_requires = 
+	phreeqcrm
+	modflowapi
+	flopy
+python_requires = >=3.6
+package_dir = 
+	=src
+zip_safe = no
+
+[options.extras_require]
+testing = 
+	pytest>=7.0
+	pytest-cov>=2.0
+	mypy>=1.10
+	flake8>=3.9
+	tox>=3.24
+	flaky>=3.8
+	jupytext>=1.16.0
+	nbconvert>=7.16
+	ipykernel>=6.29
+
+[options.package_data]
+mf6rtm = py.typed
+
+[flake8]
+max-line-length = 160
+extend-ignore = E, F
+
+[options.entry_points]
+console_scripts = 
+	mf6rtm = mf6rtm:run_cmd
+
+[egg_info]
+tag_build = 
+tag_date = 0
+

mf6rtm-0.1.0/setup.py

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+from setuptools import setup
+
+if __name__ == "__main__":
+    setup(
+        entry_points={
+            'console_scripts': [
+                'mf6rtm = mf6rtm:run_cmd',
+            ],
+        },
+    )

mf6rtm-0.1.0/src/mf6rtm/__init__.py

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+from mf6rtm import mf6rtm
+import os
+
+__author__ = "Pablo Ortega"
+
+def run_cmd():
+    # get the current directory
+    cwd = os.getcwd()
+    # run the solve function
+    mf6rtm.solve(cwd)

mf6rtm-0.1.0/src/mf6rtm/__main__.py

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+from . import run_cmd
+
+if __name__ == '__main__':
+    run_cmd()