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diff --git a/python-aqequil.spec b/python-aqequil.spec new file mode 100644 index 0000000..0b60c70 --- /dev/null +++ b/python-aqequil.spec @@ -0,0 +1,234 @@ +%global _empty_manifest_terminate_build 0 +Name: python-AqEquil +Version: 0.16.7 +Release: 1 +Summary: Python tools for aqueous chemical speciation. +License: MIT License +URL: https://pypi.org/project/AqEquil/ +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/5a/24/f56ea2c7128d6ae990547de69f0103efa190b3b55f797a4d7d914cbab4ae/AqEquil-0.16.7.tar.gz +BuildArch: noarch + +Requires: python3-rpy2 +Requires: python3-pandas +Requires: python3-numpy +Requires: python3-matplotlib +Requires: python3-plotly +Requires: python3-ipython +Requires: python3-chemparse +Requires: python3-dill +Requires: python3-periodictable + +%description +# AqEquil + +[](https://doi.org/10.5281/zenodo.7601102) + +Boyer, G., Robare, J., 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)). + +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 in mass transfer calculations to produce tables and interactive diagrams of reaction paths and composition changes as a function of reaction progress. + +## Requirements + +AqEquil has only been tested with Ubuntu LTS 20.04. + +This installation requires the Linux version of EQ3/6 v8.0a, which can downloaded [here](https://github.com/LLNL/EQ3_6). Installation instructions are provided there. + +AqEquil must be installed into an environment with an R installation. See [these instructions](https://docs.anaconda.com/anaconda/user-guide/tasks/using-r-language/) for installing R with Anaconda. + +Additionally, the CHNOSZ package must be installed in R (see instructions below). + +## Installation + +### Installing EQ3/6 for Linux + +Installation instructions are packaged along with the Linux distribution of [EQ3/6 v8.0a](https://www-gs.llnl.gov/energy-homeland-security/geochemistry). + +Set the environment variable EQ36DA to the EQ3/6 database directory containing data1 files (the 'db' folder by default). Likewise, set EQ36CO to the directory with the eq3 executable (the 'bin' folder by default). + +### Installing CHNOSZ + +Open an R session. Install the CHNOSZ package with: + +```install.packages("CHNOSZ")``` + +Once CHNOSZ is installed you can quit the R session. + +### Installing AqEquil + +Install AqEquil using pip: + +```pip install AqEquil``` + +### 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. + + + + +%package -n python3-AqEquil +Summary: Python tools for aqueous chemical speciation. +Provides: python-AqEquil +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-AqEquil +# AqEquil + +[](https://doi.org/10.5281/zenodo.7601102) + +Boyer, G., Robare, J., 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)). + +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 in mass transfer calculations to produce tables and interactive diagrams of reaction paths and composition changes as a function of reaction progress. + +## Requirements + +AqEquil has only been tested with Ubuntu LTS 20.04. + +This installation requires the Linux version of EQ3/6 v8.0a, which can downloaded [here](https://github.com/LLNL/EQ3_6). Installation instructions are provided there. + +AqEquil must be installed into an environment with an R installation. See [these instructions](https://docs.anaconda.com/anaconda/user-guide/tasks/using-r-language/) for installing R with Anaconda. + +Additionally, the CHNOSZ package must be installed in R (see instructions below). + +## Installation + +### Installing EQ3/6 for Linux + +Installation instructions are packaged along with the Linux distribution of [EQ3/6 v8.0a](https://www-gs.llnl.gov/energy-homeland-security/geochemistry). + +Set the environment variable EQ36DA to the EQ3/6 database directory containing data1 files (the 'db' folder by default). Likewise, set EQ36CO to the directory with the eq3 executable (the 'bin' folder by default). + +### Installing CHNOSZ + +Open an R session. Install the CHNOSZ package with: + +```install.packages("CHNOSZ")``` + +Once CHNOSZ is installed you can quit the R session. + +### Installing AqEquil + +Install AqEquil using pip: + +```pip install AqEquil``` + +### 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. + + + + +%package help +Summary: Development documents and examples for AqEquil +Provides: python3-AqEquil-doc +%description help +# AqEquil + +[](https://doi.org/10.5281/zenodo.7601102) + +Boyer, G., Robare, J., 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)). + +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 in mass transfer calculations to produce tables and interactive diagrams of reaction paths and composition changes as a function of reaction progress. + +## Requirements + +AqEquil has only been tested with Ubuntu LTS 20.04. + +This installation requires the Linux version of EQ3/6 v8.0a, which can downloaded [here](https://github.com/LLNL/EQ3_6). Installation instructions are provided there. + +AqEquil must be installed into an environment with an R installation. See [these instructions](https://docs.anaconda.com/anaconda/user-guide/tasks/using-r-language/) for installing R with Anaconda. + +Additionally, the CHNOSZ package must be installed in R (see instructions below). + +## Installation + +### Installing EQ3/6 for Linux + +Installation instructions are packaged along with the Linux distribution of [EQ3/6 v8.0a](https://www-gs.llnl.gov/energy-homeland-security/geochemistry). + +Set the environment variable EQ36DA to the EQ3/6 database directory containing data1 files (the 'db' folder by default). Likewise, set EQ36CO to the directory with the eq3 executable (the 'bin' folder by default). + +### Installing CHNOSZ + +Open an R session. Install the CHNOSZ package with: + +```install.packages("CHNOSZ")``` + +Once CHNOSZ is installed you can quit the R session. + +### Installing AqEquil + +Install AqEquil using pip: + +```pip install AqEquil``` + +### 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. + + + + +%prep +%autosetup -n AqEquil-0.16.7 + +%build +%py3_build + +%install +%py3_install +install -d -m755 %{buildroot}/%{_pkgdocdir} +if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi +if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi +if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi +if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi +pushd %{buildroot} +if [ -d usr/lib ]; then + find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/lib64 ]; then + find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/bin ]; then + find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/sbin ]; then + find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst +fi +touch doclist.lst +if [ -d usr/share/man ]; then + find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst +fi +popd +mv %{buildroot}/filelist.lst . +mv %{buildroot}/doclist.lst . + +%files -n python3-AqEquil -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Tue Apr 11 2023 Python_Bot <Python_Bot@openeuler.org> - 0.16.7-1 +- Package Spec generated |