%global _empty_manifest_terminate_build 0 Name: python-pyCHNOSZ Version: 0.8.12 Release: 1 Summary: Python wrapper for the R package CHNOSZ. License: MIT License URL: https://pypi.org/project/pyCHNOSZ/ Source0: https://mirrors.nju.edu.cn/pypi/web/packages/9f/6c/adb44cf05fb9c3069c4779bcf8386d2684c088d532b6369439274d39d091/pyCHNOSZ-0.8.12.tar.gz BuildArch: noarch Requires: python3-rpy2 Requires: python3-pandas Requires: python3-ipython Requires: python3-plotly Requires: python3-simplegeneric Requires: python3-chemparse %description # pyCHNOSZ Author: Dr. Grayson Boyer, GEOPIG Lab, Arizona State University [CHNOSZ](https://www.chnosz.net/) is a package written by [Dr. Jeff Dick](https://chnosz.net/jeff/) for performing thermodynamic calculations in aqueous geochemistry and biogeochemistry. pyCHNOSZ is a wrapper for CHNOSZ that allows these calculations to be carried out in Python 3 Jupyter notebooks. ## Features The following CHNOSZ functions are supported in pyCHNOSZ: - [info](https://chnosz.net/manual/info.html) - Search for chemical species by name or formula and retrieve their thermodynamic parameters. - [add_OBIGT](https://chnosz.net/manual/add.OBIGT.html) - Add or overwrite species in the OBIGT thermodynamic database by supplying a comma separated value (csv) file with custom data. - [mod_OBIGT](https://chnosz.net/manual/add.OBIGT.html) - Modify species in the OBIGT thermodynamic database. Optionally, supply a Pandas dataframe containing custom data. - [reset](https://chnosz.net/manual/thermo.html) - reset data to default values. - [subcrt](https://chnosz.net/manual/subcrt.html) - Calculate standard state partial molal thermodynamic properties of reactions at elevated temperatures and pressures. - [basis](https://chnosz.net/manual/basis.html) - Define basis species of a chemical system. - [species](https://chnosz.net/manual/species.html) - Define the species of interest in a system. - [equilibrate](https://chnosz.net/manual/equilibrate.html) - Calculate equilibrium chemical activities of species from the affinities of formation of the species at unit activity. - [affinity](https://chnosz.net/manual/affinity.html) - Calculate the chemical affinities of formation reactions of species. - [diagram](https://chnosz.net/manual/diagram.html) - Plot equilibrium chemical activity (1-D speciation) or equal-activity (2-D predominance) diagrams as a function of chemical activities of basis species, temperature and/or pressure. ## Requirements This package must be installed into an environment with an [R](https://www.r-project.org/) installation. See [these instructions](https://docs.anaconda.com/anaconda/user-guide/tasks/using-r-language/) for installing R with Anaconda. Additionally, the CHNOSZ package for R must be installed (see instructions below). ## Installation ### Installing CHNOSZ Open an R session. Install the CHNOSZ package with: ```r install.packages("CHNOSZ") ``` Once CHNOSZ is installed you may quit the R session. ### Installing pyCHNOSZ Install pyCHNOSZ using pip: ``` $ pip install pyCHNOSZ ``` ## Usage Import pyCHNOSZ in your python code with: ```python import pyCHNOSZ ``` In the following examples, pyCHNOSZ functions are imported with: ```python from pyCHNOSZ import info, add_OBIGT, mod_OBIGT, reset, subcrt ``` ### Search for chemical species The `info()` function can be used to look up chemical species by name or formula. If names or formulas are provided, database index integers are returned. A list of integers will look up chemical species by index and return a table of thermodynamic properties. See the `info()` function's [original documentation](https://chnosz.net/manual/info.html) to learn more about what this function can do. A few examples are shown below. Look up the database index value of Fe+2: ```python info("Fe+2") ``` Look up multiple chemical species: ```python info(["HCO3-", "CH4"]) ``` Define chemical states: ```python info(["HCO3-", "CH4"], state=["aq", "gas"]) ``` Search species by index values to look up their thermodynamic parameters. ```python info([13, 872]) ``` Nest `info` functions to look up thermodynamic properties directly from names or formulas: ```python info(info("Fe+2")) ``` Look up and add a protein to the database: ```python info("LYSC_CHICK") ``` ### Add or replace thermodynamic data in the database See the original R documentation for `add_OBIGT()` and `reset()` for basic useage. A few examples are given below. Load the SUPCRT92 database. ```python a = add_OBIGT("SUPCRT92") ``` The variable `a` is assigned a list of integers corresponding to the indices of chemical species that are added or replaced in the OBIGT thermodynamic database used by pyCHNOSZ. It is possible to add a custom table of thermodynamic parameters. ```python a = add_OBIGT("my_custom_entries.csv") info(a) # confirm new entries have been added ``` The entries of `my_custom_entries.csv` would then be available for thermodynamic calculations with `subcrt()`, for example. Reset thermodynamic database to its original configuration. ```python reset() ``` Modify values in the thermodynamic database with `mod_OBIGT()`: ```python mod_OBIGT("HCO3-", G = -140283.7, Cp = -9) info(info("HCO3-")) ``` ### Calculate thermodynamic properties of reactions See the [original documentation](https://chnosz.net/manual/subcrt.html) for `subcrt()`. Useage in pyCHNOSZ is the same, except python lists are used in place of R's vectors. The function produces a dictionary of results stored in pandas dataframes. An example is shown below for the reaction H2 (aq) + 0.5 O2 (gas) = H2O(liq) at 30 and 50 degrees C and 100 bars pressure: ```python subcrt(species=["H2", "O2", "H2O"], coeff=[-1.0, -0.5, 1.0], state=["aq", "gas", "liq"], T=[30, 50], P=100) ``` Output is a python dictionary of dataframes: ``` subcrt: 3 species at 2 values of T (ºC) and P (bar) (wet) [energy units: cal] {'reaction': coeff name formula state ispecies 62 -1.0 H2 H2 aq 62.0 2612 -0.5 oxygen O2 gas 2612.0 1 1.0 water H2O liq 1.0, 'out': T P rho logK G H S \ 1 30.0 100 1.000017 43.855086 -60832.380282 -67420.887872 -21.89070 2 50.0 100 0.992305 40.834419 -60379.262657 -67882.530994 -23.36663 V Cp 1 -7.494052 -24.126268 2 -8.259704 -20.941879 } ``` ### More examples: For more examples, like plotting activity and predominance diagrams, check out the [pyCHNOSZ demo notebook](https://nbviewer.org/github/worm-portal/pyCHNOSZ/blob/master/test/pyCHNOSZ-demo.ipynb). %package -n python3-pyCHNOSZ Summary: Python wrapper for the R package CHNOSZ. Provides: python-pyCHNOSZ BuildRequires: python3-devel BuildRequires: python3-setuptools BuildRequires: python3-pip %description -n python3-pyCHNOSZ # pyCHNOSZ Author: Dr. Grayson Boyer, GEOPIG Lab, Arizona State University [CHNOSZ](https://www.chnosz.net/) is a package written by [Dr. Jeff Dick](https://chnosz.net/jeff/) for performing thermodynamic calculations in aqueous geochemistry and biogeochemistry. pyCHNOSZ is a wrapper for CHNOSZ that allows these calculations to be carried out in Python 3 Jupyter notebooks. ## Features The following CHNOSZ functions are supported in pyCHNOSZ: - [info](https://chnosz.net/manual/info.html) - Search for chemical species by name or formula and retrieve their thermodynamic parameters. - [add_OBIGT](https://chnosz.net/manual/add.OBIGT.html) - Add or overwrite species in the OBIGT thermodynamic database by supplying a comma separated value (csv) file with custom data. - [mod_OBIGT](https://chnosz.net/manual/add.OBIGT.html) - Modify species in the OBIGT thermodynamic database. Optionally, supply a Pandas dataframe containing custom data. - [reset](https://chnosz.net/manual/thermo.html) - reset data to default values. - [subcrt](https://chnosz.net/manual/subcrt.html) - Calculate standard state partial molal thermodynamic properties of reactions at elevated temperatures and pressures. - [basis](https://chnosz.net/manual/basis.html) - Define basis species of a chemical system. - [species](https://chnosz.net/manual/species.html) - Define the species of interest in a system. - [equilibrate](https://chnosz.net/manual/equilibrate.html) - Calculate equilibrium chemical activities of species from the affinities of formation of the species at unit activity. - [affinity](https://chnosz.net/manual/affinity.html) - Calculate the chemical affinities of formation reactions of species. - [diagram](https://chnosz.net/manual/diagram.html) - Plot equilibrium chemical activity (1-D speciation) or equal-activity (2-D predominance) diagrams as a function of chemical activities of basis species, temperature and/or pressure. ## Requirements This package must be installed into an environment with an [R](https://www.r-project.org/) installation. See [these instructions](https://docs.anaconda.com/anaconda/user-guide/tasks/using-r-language/) for installing R with Anaconda. Additionally, the CHNOSZ package for R must be installed (see instructions below). ## Installation ### Installing CHNOSZ Open an R session. Install the CHNOSZ package with: ```r install.packages("CHNOSZ") ``` Once CHNOSZ is installed you may quit the R session. ### Installing pyCHNOSZ Install pyCHNOSZ using pip: ``` $ pip install pyCHNOSZ ``` ## Usage Import pyCHNOSZ in your python code with: ```python import pyCHNOSZ ``` In the following examples, pyCHNOSZ functions are imported with: ```python from pyCHNOSZ import info, add_OBIGT, mod_OBIGT, reset, subcrt ``` ### Search for chemical species The `info()` function can be used to look up chemical species by name or formula. If names or formulas are provided, database index integers are returned. A list of integers will look up chemical species by index and return a table of thermodynamic properties. See the `info()` function's [original documentation](https://chnosz.net/manual/info.html) to learn more about what this function can do. A few examples are shown below. Look up the database index value of Fe+2: ```python info("Fe+2") ``` Look up multiple chemical species: ```python info(["HCO3-", "CH4"]) ``` Define chemical states: ```python info(["HCO3-", "CH4"], state=["aq", "gas"]) ``` Search species by index values to look up their thermodynamic parameters. ```python info([13, 872]) ``` Nest `info` functions to look up thermodynamic properties directly from names or formulas: ```python info(info("Fe+2")) ``` Look up and add a protein to the database: ```python info("LYSC_CHICK") ``` ### Add or replace thermodynamic data in the database See the original R documentation for `add_OBIGT()` and `reset()` for basic useage. A few examples are given below. Load the SUPCRT92 database. ```python a = add_OBIGT("SUPCRT92") ``` The variable `a` is assigned a list of integers corresponding to the indices of chemical species that are added or replaced in the OBIGT thermodynamic database used by pyCHNOSZ. It is possible to add a custom table of thermodynamic parameters. ```python a = add_OBIGT("my_custom_entries.csv") info(a) # confirm new entries have been added ``` The entries of `my_custom_entries.csv` would then be available for thermodynamic calculations with `subcrt()`, for example. Reset thermodynamic database to its original configuration. ```python reset() ``` Modify values in the thermodynamic database with `mod_OBIGT()`: ```python mod_OBIGT("HCO3-", G = -140283.7, Cp = -9) info(info("HCO3-")) ``` ### Calculate thermodynamic properties of reactions See the [original documentation](https://chnosz.net/manual/subcrt.html) for `subcrt()`. Useage in pyCHNOSZ is the same, except python lists are used in place of R's vectors. The function produces a dictionary of results stored in pandas dataframes. An example is shown below for the reaction H2 (aq) + 0.5 O2 (gas) = H2O(liq) at 30 and 50 degrees C and 100 bars pressure: ```python subcrt(species=["H2", "O2", "H2O"], coeff=[-1.0, -0.5, 1.0], state=["aq", "gas", "liq"], T=[30, 50], P=100) ``` Output is a python dictionary of dataframes: ``` subcrt: 3 species at 2 values of T (ºC) and P (bar) (wet) [energy units: cal] {'reaction': coeff name formula state ispecies 62 -1.0 H2 H2 aq 62.0 2612 -0.5 oxygen O2 gas 2612.0 1 1.0 water H2O liq 1.0, 'out': T P rho logK G H S \ 1 30.0 100 1.000017 43.855086 -60832.380282 -67420.887872 -21.89070 2 50.0 100 0.992305 40.834419 -60379.262657 -67882.530994 -23.36663 V Cp 1 -7.494052 -24.126268 2 -8.259704 -20.941879 } ``` ### More examples: For more examples, like plotting activity and predominance diagrams, check out the [pyCHNOSZ demo notebook](https://nbviewer.org/github/worm-portal/pyCHNOSZ/blob/master/test/pyCHNOSZ-demo.ipynb). %package help Summary: Development documents and examples for pyCHNOSZ Provides: python3-pyCHNOSZ-doc %description help # pyCHNOSZ Author: Dr. Grayson Boyer, GEOPIG Lab, Arizona State University [CHNOSZ](https://www.chnosz.net/) is a package written by [Dr. Jeff Dick](https://chnosz.net/jeff/) for performing thermodynamic calculations in aqueous geochemistry and biogeochemistry. pyCHNOSZ is a wrapper for CHNOSZ that allows these calculations to be carried out in Python 3 Jupyter notebooks. ## Features The following CHNOSZ functions are supported in pyCHNOSZ: - [info](https://chnosz.net/manual/info.html) - Search for chemical species by name or formula and retrieve their thermodynamic parameters. - [add_OBIGT](https://chnosz.net/manual/add.OBIGT.html) - Add or overwrite species in the OBIGT thermodynamic database by supplying a comma separated value (csv) file with custom data. - [mod_OBIGT](https://chnosz.net/manual/add.OBIGT.html) - Modify species in the OBIGT thermodynamic database. Optionally, supply a Pandas dataframe containing custom data. - [reset](https://chnosz.net/manual/thermo.html) - reset data to default values. - [subcrt](https://chnosz.net/manual/subcrt.html) - Calculate standard state partial molal thermodynamic properties of reactions at elevated temperatures and pressures. - [basis](https://chnosz.net/manual/basis.html) - Define basis species of a chemical system. - [species](https://chnosz.net/manual/species.html) - Define the species of interest in a system. - [equilibrate](https://chnosz.net/manual/equilibrate.html) - Calculate equilibrium chemical activities of species from the affinities of formation of the species at unit activity. - [affinity](https://chnosz.net/manual/affinity.html) - Calculate the chemical affinities of formation reactions of species. - [diagram](https://chnosz.net/manual/diagram.html) - Plot equilibrium chemical activity (1-D speciation) or equal-activity (2-D predominance) diagrams as a function of chemical activities of basis species, temperature and/or pressure. ## Requirements This package must be installed into an environment with an [R](https://www.r-project.org/) installation. See [these instructions](https://docs.anaconda.com/anaconda/user-guide/tasks/using-r-language/) for installing R with Anaconda. Additionally, the CHNOSZ package for R must be installed (see instructions below). ## Installation ### Installing CHNOSZ Open an R session. Install the CHNOSZ package with: ```r install.packages("CHNOSZ") ``` Once CHNOSZ is installed you may quit the R session. ### Installing pyCHNOSZ Install pyCHNOSZ using pip: ``` $ pip install pyCHNOSZ ``` ## Usage Import pyCHNOSZ in your python code with: ```python import pyCHNOSZ ``` In the following examples, pyCHNOSZ functions are imported with: ```python from pyCHNOSZ import info, add_OBIGT, mod_OBIGT, reset, subcrt ``` ### Search for chemical species The `info()` function can be used to look up chemical species by name or formula. If names or formulas are provided, database index integers are returned. A list of integers will look up chemical species by index and return a table of thermodynamic properties. See the `info()` function's [original documentation](https://chnosz.net/manual/info.html) to learn more about what this function can do. A few examples are shown below. Look up the database index value of Fe+2: ```python info("Fe+2") ``` Look up multiple chemical species: ```python info(["HCO3-", "CH4"]) ``` Define chemical states: ```python info(["HCO3-", "CH4"], state=["aq", "gas"]) ``` Search species by index values to look up their thermodynamic parameters. ```python info([13, 872]) ``` Nest `info` functions to look up thermodynamic properties directly from names or formulas: ```python info(info("Fe+2")) ``` Look up and add a protein to the database: ```python info("LYSC_CHICK") ``` ### Add or replace thermodynamic data in the database See the original R documentation for `add_OBIGT()` and `reset()` for basic useage. A few examples are given below. Load the SUPCRT92 database. ```python a = add_OBIGT("SUPCRT92") ``` The variable `a` is assigned a list of integers corresponding to the indices of chemical species that are added or replaced in the OBIGT thermodynamic database used by pyCHNOSZ. It is possible to add a custom table of thermodynamic parameters. ```python a = add_OBIGT("my_custom_entries.csv") info(a) # confirm new entries have been added ``` The entries of `my_custom_entries.csv` would then be available for thermodynamic calculations with `subcrt()`, for example. Reset thermodynamic database to its original configuration. ```python reset() ``` Modify values in the thermodynamic database with `mod_OBIGT()`: ```python mod_OBIGT("HCO3-", G = -140283.7, Cp = -9) info(info("HCO3-")) ``` ### Calculate thermodynamic properties of reactions See the [original documentation](https://chnosz.net/manual/subcrt.html) for `subcrt()`. Useage in pyCHNOSZ is the same, except python lists are used in place of R's vectors. The function produces a dictionary of results stored in pandas dataframes. An example is shown below for the reaction H2 (aq) + 0.5 O2 (gas) = H2O(liq) at 30 and 50 degrees C and 100 bars pressure: ```python subcrt(species=["H2", "O2", "H2O"], coeff=[-1.0, -0.5, 1.0], state=["aq", "gas", "liq"], T=[30, 50], P=100) ``` Output is a python dictionary of dataframes: ``` subcrt: 3 species at 2 values of T (ºC) and P (bar) (wet) [energy units: cal] {'reaction': coeff name formula state ispecies 62 -1.0 H2 H2 aq 62.0 2612 -0.5 oxygen O2 gas 2612.0 1 1.0 water H2O liq 1.0, 'out': T P rho logK G H S \ 1 30.0 100 1.000017 43.855086 -60832.380282 -67420.887872 -21.89070 2 50.0 100 0.992305 40.834419 -60379.262657 -67882.530994 -23.36663 V Cp 1 -7.494052 -24.126268 2 -8.259704 -20.941879 } ``` ### More examples: For more examples, like plotting activity and predominance diagrams, check out the [pyCHNOSZ demo notebook](https://nbviewer.org/github/worm-portal/pyCHNOSZ/blob/master/test/pyCHNOSZ-demo.ipynb). %prep %autosetup -n pyCHNOSZ-0.8.12 %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-pyCHNOSZ -f filelist.lst %dir %{python3_sitelib}/* %files help -f doclist.lst %{_docdir}/* %changelog * Mon May 29 2023 Python_Bot - 0.8.12-1 - Package Spec generated