mf6rtm 0.0.0__tar.gz

mf6rtm-0.0.0/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-0.0.0/MANIFEST.in

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+include src/mf6rtm/mrbeaker.png

mf6rtm-0.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: mf6rtm
+Version: 0.0.0
+Summary: Reactive transport model through MODFLOW 6 and PHREEQCRM
+Author: Pablo Ortega
+Author-email: portega@intera.com
+License: BSD 3-Clause
+Keywords: MODFLOW,PHREEQCRM,reactive transport,groundwater,hydrology
+Platform: unix
+Platform: linux
+Platform: osx
+Platform: cygwin
+Platform: win32
+Classifier: Development Status :: 3 - Alpha
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Topic :: Scientific/Engineering :: Hydrology
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+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"
+Dynamic: license-file
+
+# 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)
+
+<!-- [![GitHub tag](https://img.shields.io/github/tag/mf6rtm/mf6rtm.svg)](https://github.com/p-ortega/mf6rtm/releases/tag/latest) -->
+[![PyPI License](https://img.shields.io/pypi/l/mf6rtm)](https://pypi.python.org/pypi/mf6rtm)
+<!-- [![PyPI Status](https://img.shields.io/pypi/status/mf6rtm.png)](https://pypi.python.org/pypi/mf6rtm) -->
+<!-- [![PyPI Format](https://img.shields.io/pypi/format/mf6rtm)](https://pypi.python.org/pypi/mf6rtm) -->
+[![PyPI Version](https://img.shields.io/pypi/v/mf6rtm.png)](https://pypi.python.org/pypi/mf6rtm)
+[![PyPI Versions](https://img.shields.io/pypi/pyversions/mf6rtm.png)](https://pypi.python.org/pypi/mf6rtm)
+
+## 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 can be installed through pip as:
+
+```commandline
+pip install mf6rtm
+```
+## Developing
+We recommend forking and cloning a local version of this repo. A development Conda environment is provided in the `env.yml` file, which should install all required dependencies to run tests and modify the package on the fly. To install the environment, use the following command:
+
+```commandline
+conda env create -f env.yml
+```
+
+## Funding
+The developing of mf6rtm was kindly funded and supported by [Intera, Inc](https://www.intera.com).
+
+## Authors
+Pablo Ortega (Portega)

mf6rtm-0.0.0/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)
+
+<!-- [![GitHub tag](https://img.shields.io/github/tag/mf6rtm/mf6rtm.svg)](https://github.com/p-ortega/mf6rtm/releases/tag/latest) -->
+[![PyPI License](https://img.shields.io/pypi/l/mf6rtm)](https://pypi.python.org/pypi/mf6rtm)
+<!-- [![PyPI Status](https://img.shields.io/pypi/status/mf6rtm.png)](https://pypi.python.org/pypi/mf6rtm) -->
+<!-- [![PyPI Format](https://img.shields.io/pypi/format/mf6rtm)](https://pypi.python.org/pypi/mf6rtm) -->
+[![PyPI Version](https://img.shields.io/pypi/v/mf6rtm.png)](https://pypi.python.org/pypi/mf6rtm)
+[![PyPI Versions](https://img.shields.io/pypi/pyversions/mf6rtm.png)](https://pypi.python.org/pypi/mf6rtm)
+
+## 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 can be installed through pip as:
+
+```commandline
+pip install mf6rtm
+```
+## Developing
+We recommend forking and cloning a local version of this repo. A development Conda environment is provided in the `env.yml` file, which should install all required dependencies to run tests and modify the package on the fly. To install the environment, use the following command:
+
+```commandline
+conda env create -f env.yml
+```
+
+## Funding
+The developing of mf6rtm was kindly funded and supported by [Intera, Inc](https://www.intera.com).
+
+## Authors
+Pablo Ortega (Portega)

mf6rtm-0.0.0/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-0.0.0/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
+keywords = MODFLOW, PHREEQCRM, reactive transport, groundwater, hydrology
+classifiers = 
+	Development Status :: 3 - Alpha
+	Programming Language :: Python :: 3
+	Programming Language :: Python :: 3 :: Only
+	Programming Language :: Python :: 3.9
+	Programming Language :: Python :: 3.10
+	Programming Language :: Python :: 3.11
+	Programming Language :: Python :: 3.12
+	License :: OSI Approved :: BSD License
+	Topic :: Scientific/Engineering :: Hydrology
+version = 
+long_description = file: README.md
+long_description_content_type = text/markdown
+
+[options]
+packages = 
+	mf6rtm
+include_package_data = True
+py_modules = 
+	mf6rtm
+	utils
+install_requires = 
+	phreeqcrm
+	modflowapi
+	flopy
+python_requires = >=3.9
+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-0.0.0/setup.py

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

mf6rtm-0.0.0/src/mf6rtm/__init__.py

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+"""
+The MF6RTM (Modflow 6 Reactive Transport Model) package is a python package
+for reactive transport modeling via the MODFLOW 6 and PhreeqcRM APIs.
+"""
+
+# populate package namespace
+from mf6rtm import (
+    mf6rtm,
+    mup3d,
+    utils,
+)
+
+from mf6rtm.mf6rtm import run_cmd
+
+__author__ = "Pablo Ortega"

mf6rtm-0.0.0/src/mf6rtm/__main__.py

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