aqequil 1.0.0__tar.gz

aqequil-1.0.0/CITATION.cff

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+# YAML 1.2
+---
+authors: 
+  -
+    affiliation: "Arizona State University, School of Earth and Space Exploration"
+    family-names: Boyer
+    given-names: Grayson
+    orcid: "https://orcid.org/0000-0002-7670-9273"
+  -
+    affiliation: "University of Washington, Department of Genome Sciences"
+    family-names: Robare
+    given-names: Jordyn
+    orcid: "https://orcid.org/0000-0001-9133-8485"
+  -
+    affiliation: "Arizona State University, School of Earth and Space Exploration"
+    family-names: Park
+    given-names: Nuri
+  -
+    affiliation: "University of Minnesota, Department of Soil, Water, and Climate"
+    family-names: Ely
+    given-names: Tucker
+    orcid: "https://orcid.org/0000-0002-2955-4184"
+  -
+    affiliation: "Arizona State University, School of Earth and Space Exploration"
+    family-names: Shock
+    given-names: Everett
+    orcid: "https://orcid.org/0000-0002-4283-0163"
+cff-version: "0.20.0"
+license: MIT
+message: "If you use this software, please cite it using these metadata."
+repository-code: "https://github.com/worm-portal/AqEquil"
+title: "AqEquil: Python package for aqueous geochemical speciation"
+version: "0.20.0"
+date-released: 2025-06-18
+...

aqequil-1.0.0/LICENSE.txt

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+MIT License
+
+Copyright (c) 2026 Grayson Boyer, Jordyn Robare, Nuri Park, Tucker Ely, and Everett Shock
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
+================================================================================
+
+This package includes third-party software. See THIRD_PARTY_LICENSES.txt for
+additional license information.

aqequil-1.0.0/MANIFEST.in

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+# Include important documentation files
+include README.md
+include LICENSE.txt
+include THIRD_PARTY_LICENSES.txt
+include CITATION.cff
+include pyproject.toml
+
+# Include EQ3/6 compilation script (needed for building wheels)
+include compile_eq3_6.py
+
+# Include integration test script (needed for wheel testing)
+include test_integration.py
+
+# Include HTML documentation
+recursive-include html *.html *.css *.js
+
+# Include data files
+recursive-include aqequil *.r *.min *.csv *.txt
+
+# Include test data
+recursive-include aqequil/test_data *.csv
+
+# Include bin package (needed for wheel building)
+include aqequil/bin/__init__.py
+
+# Include EQ3/6 source files (will be compiled during wheel build)
+recursive-include aqequil/eq3_6_src *.f *.f90 *.for
+include aqequil/eq3_6_src/Makefile
+recursive-include aqequil/eq3_6_src/include *.inc *.h
+
+# NOTE: EQ3/6 executables (eq3nr, eq6, etc.) are NOT included in the source distribution
+# They are compiled during the wheel build process via compile_eq3_6.py
+# The aqequil.bin package and its contents will be included in wheels via package-data in pyproject.toml
+
+# Exclude test files and development artifacts
+prune test
+global-exclude *.pyc
+global-exclude *.pyo
+global-exclude *.pyd
+global-exclude __pycache__
+global-exclude .pytest_cache
+global-exclude .ipynb_checkpoints
+global-exclude *~
+global-exclude *.swp
+global-exclude .DS_Store

aqequil-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: aqequil
+Version: 1.0.0
+Summary: Python tools for aqueous chemical speciation.
+Author-email: Grayson Boyer <gmboyer@asu.edu>
+License: MIT
+Project-URL: Homepage, https://github.com/worm-portal/aqequil
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: pandas
+Requires-Dist: numpy
+Requires-Dist: matplotlib
+Requires-Dist: plotly
+Requires-Dist: ipython
+Requires-Dist: chemparse
+Requires-Dist: dill
+Requires-Dist: periodictable
+Requires-Dist: natsort
+Requires-Dist: roman
+Requires-Dist: ipywidgets
+Requires-Dist: wormutils
+Requires-Dist: pychnosz
+Dynamic: license-file
+
+# AqEquil
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5534831.svg)](https://doi.org/10.5281/zenodo.5534831)
+
+Boyer, G., Robare, J., Park, N., Ely, T., Shock, E.L.
+
+## About
+
+AqEquil is a Python 3 package that enables users to rapidly perform aqueous speciation calculations of water chemistry data for multiple samples by interfacing with [geochemical speciation software EQ3/6](https://github.com/LLNL/EQ3_6) (Wolery 2013, [Wolery 1979](https://inis.iaea.org/collection/NCLCollectionStore/_Public/10/474/10474294.pdf)). AqEquil uses [a modified version of EQ3/6](https://github.com/39alpha/eq3_6/tree/main) created by the 39Alpha research team for easy local installation.
+
+Water sample data in CSV format is automatically converted to a format readable by EQ3 and then speciated. Distributions of aqueous species, mineral saturation indices, oxidation reduction potentials, and more are data-mined and returned as Pandas tables and interactive Plotly visualizations.
+
+Speciated fluids can be further reacted with minerals or other fluids in mass transfer calculations to produce tables and interactive diagrams of reaction paths and composition changes as a function of reaction progress.
+
+Development of AqEquil was made possible by National Science Foundation (NSF) grants EAR-1949030 and EAR-2149016.
+
+## Requirements
+
+AqEquil works on Linux, macOS, and Windows.
+
+**Python Requirements:**
+- Python >= 3.10
+- pandas, numpy, matplotlib, plotly, and other dependencies (automatically installed)
+
+**Note:** As of version 1.0.0, EQ3/6 executables are bundled with aqequil and no longer need to be installed separately. The package includes pre-compiled binaries for Linux, macOS, and Windows.
+
+## Installation
+
+Install AqEquil using pip:
+
+```bash
+pip install aqequil
+```
+
+The bundled EQ3/6 executables will be automatically installed with the package. No additional configuration or environment variables are needed.
+
+## Usage
+
+See this [demo notebook](https://nbviewer.jupyter.org/github/worm-portal/WORM-Library/blob/master/3-Aqueous-Speciation/1-Introduction-to-Aq-Speciation/2-Intro-to-Multi-Aq-Speciation.ipynb) for usage examples.
+
+## Bundled Software
+
+This package includes pre-compiled binaries from [EQ3/6 v8.0a](https://github.com/39alpha/eq3_6), a software package for geochemical modeling developed by Thomas Wolery at Lawrence Livermore National Laboratory and updated by [39 Alpha](https://github.com/39alpha/eq3_6).
+
+**EQ3/6 License:** BSD 3-Clause License
+**Copyright:** (c) 1987, 1990-1993, 1995, 1997, 2002, 2013 The Regents of the University of California, Lawrence Livermore National Laboratory.
+
+See `THIRD_PARTY_LICENSES.txt` for the full EQ3/6 license text.
+
+**References:**
+- Wolery, T. J., and USDOE. EQ3/6 A Software Package for Geochemical Modeling. Computer software. December 13, 2010. https://www.osti.gov//servlets/purl/1231666. doi:https://doi.org/10.11578/dc.20210416.44.
+- Wolery, T. J. and R. L. Jarek. Software User's Manual EQ36, Version 8.0. U.S. Tech. Rep. 2003. Department of Energy, Office of Civilian Radioactive Waste Management, Office of Repository Development. 10813-UM-8.0-00.

aqequil-1.0.0/README.md

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+# AqEquil
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5534831.svg)](https://doi.org/10.5281/zenodo.5534831)
+
+Boyer, G., Robare, J., Park, N., Ely, T., Shock, E.L.
+
+## About
+
+AqEquil is a Python 3 package that enables users to rapidly perform aqueous speciation calculations of water chemistry data for multiple samples by interfacing with [geochemical speciation software EQ3/6](https://github.com/LLNL/EQ3_6) (Wolery 2013, [Wolery 1979](https://inis.iaea.org/collection/NCLCollectionStore/_Public/10/474/10474294.pdf)). AqEquil uses [a modified version of EQ3/6](https://github.com/39alpha/eq3_6/tree/main) created by the 39Alpha research team for easy local installation.
+
+Water sample data in CSV format is automatically converted to a format readable by EQ3 and then speciated. Distributions of aqueous species, mineral saturation indices, oxidation reduction potentials, and more are data-mined and returned as Pandas tables and interactive Plotly visualizations.
+
+Speciated fluids can be further reacted with minerals or other fluids in mass transfer calculations to produce tables and interactive diagrams of reaction paths and composition changes as a function of reaction progress.
+
+Development of AqEquil was made possible by National Science Foundation (NSF) grants EAR-1949030 and EAR-2149016.
+
+## Requirements
+
+AqEquil works on Linux, macOS, and Windows.
+
+**Python Requirements:**
+- Python >= 3.10
+- pandas, numpy, matplotlib, plotly, and other dependencies (automatically installed)
+
+**Note:** As of version 1.0.0, EQ3/6 executables are bundled with aqequil and no longer need to be installed separately. The package includes pre-compiled binaries for Linux, macOS, and Windows.
+
+## Installation
+
+Install AqEquil using pip:
+
+```bash
+pip install aqequil
+```
+
+The bundled EQ3/6 executables will be automatically installed with the package. No additional configuration or environment variables are needed.
+
+## Usage
+
+See this [demo notebook](https://nbviewer.jupyter.org/github/worm-portal/WORM-Library/blob/master/3-Aqueous-Speciation/1-Introduction-to-Aq-Speciation/2-Intro-to-Multi-Aq-Speciation.ipynb) for usage examples.
+
+## Bundled Software
+
+This package includes pre-compiled binaries from [EQ3/6 v8.0a](https://github.com/39alpha/eq3_6), a software package for geochemical modeling developed by Thomas Wolery at Lawrence Livermore National Laboratory and updated by [39 Alpha](https://github.com/39alpha/eq3_6).
+
+**EQ3/6 License:** BSD 3-Clause License
+**Copyright:** (c) 1987, 1990-1993, 1995, 1997, 2002, 2013 The Regents of the University of California, Lawrence Livermore National Laboratory.
+
+See `THIRD_PARTY_LICENSES.txt` for the full EQ3/6 license text.
+
+**References:**
+- Wolery, T. J., and USDOE. EQ3/6 A Software Package for Geochemical Modeling. Computer software. December 13, 2010. https://www.osti.gov//servlets/purl/1231666. doi:https://doi.org/10.11578/dc.20210416.44.
+- Wolery, T. J. and R. L. Jarek. Software User's Manual EQ36, Version 8.0. U.S. Tech. Rep. 2003. Department of Energy, Office of Civilian Radioactive Waste Management, Office of Repository Development. 10813-UM-8.0-00.

aqequil-1.0.0/THIRD_PARTY_LICENSES.txt

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+Third-Party Software Licenses
+================================================================================
+
+This package includes pre-compiled binaries from the following third-party
+software:
+
+================================================================================
+EQ3/6 Software Package
+================================================================================
+
+BSD 3-Clause License
+
+Copyright (c) 1987, 1990-1993, 1995, 1997, 2002, 2013 The Regents of the
+University of California, Lawrence Livermore National Laboratory.
+
+All rights reserved.
+
+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.
+
+References:
+- Wolery, T. J., and USDOE. EQ3/6 A Software Package for Geochemical Modeling.
+  Computer software. December 13, 2010.
+  https://www.osti.gov//servlets/purl/1231666.
+  doi:https://doi.org/10.11578/dc.20210416.44.
+- Wolery, T. J. and R. L. Jarek. Software User's Manual EQ36, Version 8.0.
+  U.S. Tech. Rep. 2003. Department of Energy, Office of Civilian Radioactive
+  Waste Management, Office of Repository Development. 10813-UM-8.0-00.