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diff --git a/python-pychnosz.spec b/python-pychnosz.spec new file mode 100644 index 0000000..131370c --- /dev/null +++ b/python-pychnosz.spec @@ -0,0 +1,567 @@ +%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 H<sub>2 (aq)</sub> + 0.5 O<sub>2 (gas)</sub> = H<sub>2</sub>O<sub>(liq)</sub> 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 H<sub>2 (aq)</sub> + 0.5 O<sub>2 (gas)</sub> = H<sub>2</sub>O<sub>(liq)</sub> 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 H<sub>2 (aq)</sub> + 0.5 O<sub>2 (gas)</sub> = H<sub>2</sub>O<sub>(liq)</sub> 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 <Python_Bot@openeuler.org> - 0.8.12-1 +- Package Spec generated |