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@@ -0,0 +1 @@ +/equilibrator-api-0.4.7.tar.gz diff --git a/python-equilibrator-api.spec b/python-equilibrator-api.spec new file mode 100644 index 0000000..25d97d6 --- /dev/null +++ b/python-equilibrator-api.spec @@ -0,0 +1,262 @@ +%global _empty_manifest_terminate_build 0 +Name: python-equilibrator-api +Version: 0.4.7 +Release: 1 +Summary: Calculation of standard thermodynamic potentials of biochemical reactions. +License: MIT +URL: https://gitlab.com/equilibrator/equilibrator-api/ +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/15/fc/4024b4ba267b0ca33fc065f080e15530bb55c6e029f26c3f63478b27b983/equilibrator-api-0.4.7.tar.gz +BuildArch: noarch + +Requires: python3-pyparsing +Requires: python3-slugify +Requires: python3-equilibrator-cache +Requires: python3-component-contribution +Requires: python3-click +Requires: python3-click-log +Requires: python3-dateutil +Requires: python3-requests +Requires: python3-black +Requires: python3-isort +Requires: python3-safety +Requires: python3-tox +Requires: python3-twine +Requires: python3-cobra +Requires: python3-pytest +Requires: python3-pytest-cov +Requires: python3-pytest-raises +Requires: python3-pytest-allclose +Requires: python3-sbtab + +%description +# eQuilibrator - a thermodynamics calculator for biochemical reactions + +[](https://badge.fury.io/py/equilibrator-api) +[](https://anaconda.org/conda-forge/equilibrator-api) +[](https://gitlab.com/elad.noor/equilibrator-api/commits/master) +[](https://gitlab.com/elad.noor/equilibrator-api/commits/master) +[](https://gitter.im/equilibrator-devs/equilibrator-api?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) +[](https://equilibrator.readthedocs.io/en/latest/?badge=latest) + +## What is `equilibrator-api`? + +`equilibrator-api` is a Python package for obtaining estimates of reactions Gibbs energies. +It is mainly meant for biologists/bioengineers with basic programming skills that +work on metabolism and want to easily add thermodynamic data to their models. + +The documentation is browseable online at +[readthedocs](https://equilibrator.readthedocs.io/en/latest/index.html). + +If your list of reactions is very short, we recommend trying our +website called [eQuilibrator](http://equilibrator.weizmann.ac.il/) before spending +the time necessary for learning how to use `equilibrator-api`. + +The main advantages of `equilibrator-api` are: + +* Batch mode: can be used for large reaction datasets (even more than 1000 reactions) +* Does not require a network connection (except during installation and initialization) +* Works with standard compound identifiers (such as ChEBI, KEGG, BiGG and MetaNetX) for more than 500,000 compounds + +To access more advanced features, such as adding new compounds that are not +among the 500,000 currently in the MetaNetX database, try using our +[equilibrator-assets](https://gitlab.com/equilibrator/equilibrator-assets) +package. + +## Cite us + +If you plan to use results from `equilibrator-api` in a scientific publication, +please cite our paper: + +Noor E, Haraldsdóttir HS, Milo R, Fleming RMT (2013) +[Consistent Estimation of Gibbs Energy Using Component Contributions](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003098), +PLoS Comput Biol 9:e1003098, DOI: 10.1371/journal.pcbi.1003098 + +## A very simple example + +Note that creating a `ComponentContribution` object for the first time after +installation, starts an initialization step which downloads ~1.5 GBytes of data +to your computer. It can take more than an hour (depending on the connection speed). +Note that the initialization might not work inside a Jupyter notebook environment - +in that case you should try running it in a standard python shell first and then +run the Jupyter notebook. + +```python +from equilibrator_api import ComponentContribution +cc = ComponentContribution() +rxn = cc.parse_reaction_formula("kegg:C00002 + kegg:C00001 = kegg:C00008 + kegg:C00009") +print(f"ΔG'0 = {cc.standard_dg_prime(rxn)}") +``` + + +%package -n python3-equilibrator-api +Summary: Calculation of standard thermodynamic potentials of biochemical reactions. +Provides: python-equilibrator-api +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-equilibrator-api +# eQuilibrator - a thermodynamics calculator for biochemical reactions + +[](https://badge.fury.io/py/equilibrator-api) +[](https://anaconda.org/conda-forge/equilibrator-api) +[](https://gitlab.com/elad.noor/equilibrator-api/commits/master) +[](https://gitlab.com/elad.noor/equilibrator-api/commits/master) +[](https://gitter.im/equilibrator-devs/equilibrator-api?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) +[](https://equilibrator.readthedocs.io/en/latest/?badge=latest) + +## What is `equilibrator-api`? + +`equilibrator-api` is a Python package for obtaining estimates of reactions Gibbs energies. +It is mainly meant for biologists/bioengineers with basic programming skills that +work on metabolism and want to easily add thermodynamic data to their models. + +The documentation is browseable online at +[readthedocs](https://equilibrator.readthedocs.io/en/latest/index.html). + +If your list of reactions is very short, we recommend trying our +website called [eQuilibrator](http://equilibrator.weizmann.ac.il/) before spending +the time necessary for learning how to use `equilibrator-api`. + +The main advantages of `equilibrator-api` are: + +* Batch mode: can be used for large reaction datasets (even more than 1000 reactions) +* Does not require a network connection (except during installation and initialization) +* Works with standard compound identifiers (such as ChEBI, KEGG, BiGG and MetaNetX) for more than 500,000 compounds + +To access more advanced features, such as adding new compounds that are not +among the 500,000 currently in the MetaNetX database, try using our +[equilibrator-assets](https://gitlab.com/equilibrator/equilibrator-assets) +package. + +## Cite us + +If you plan to use results from `equilibrator-api` in a scientific publication, +please cite our paper: + +Noor E, Haraldsdóttir HS, Milo R, Fleming RMT (2013) +[Consistent Estimation of Gibbs Energy Using Component Contributions](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003098), +PLoS Comput Biol 9:e1003098, DOI: 10.1371/journal.pcbi.1003098 + +## A very simple example + +Note that creating a `ComponentContribution` object for the first time after +installation, starts an initialization step which downloads ~1.5 GBytes of data +to your computer. It can take more than an hour (depending on the connection speed). +Note that the initialization might not work inside a Jupyter notebook environment - +in that case you should try running it in a standard python shell first and then +run the Jupyter notebook. + +```python +from equilibrator_api import ComponentContribution +cc = ComponentContribution() +rxn = cc.parse_reaction_formula("kegg:C00002 + kegg:C00001 = kegg:C00008 + kegg:C00009") +print(f"ΔG'0 = {cc.standard_dg_prime(rxn)}") +``` + + +%package help +Summary: Development documents and examples for equilibrator-api +Provides: python3-equilibrator-api-doc +%description help +# eQuilibrator - a thermodynamics calculator for biochemical reactions + +[](https://badge.fury.io/py/equilibrator-api) +[](https://anaconda.org/conda-forge/equilibrator-api) +[](https://gitlab.com/elad.noor/equilibrator-api/commits/master) +[](https://gitlab.com/elad.noor/equilibrator-api/commits/master) +[](https://gitter.im/equilibrator-devs/equilibrator-api?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) +[](https://equilibrator.readthedocs.io/en/latest/?badge=latest) + +## What is `equilibrator-api`? + +`equilibrator-api` is a Python package for obtaining estimates of reactions Gibbs energies. +It is mainly meant for biologists/bioengineers with basic programming skills that +work on metabolism and want to easily add thermodynamic data to their models. + +The documentation is browseable online at +[readthedocs](https://equilibrator.readthedocs.io/en/latest/index.html). + +If your list of reactions is very short, we recommend trying our +website called [eQuilibrator](http://equilibrator.weizmann.ac.il/) before spending +the time necessary for learning how to use `equilibrator-api`. + +The main advantages of `equilibrator-api` are: + +* Batch mode: can be used for large reaction datasets (even more than 1000 reactions) +* Does not require a network connection (except during installation and initialization) +* Works with standard compound identifiers (such as ChEBI, KEGG, BiGG and MetaNetX) for more than 500,000 compounds + +To access more advanced features, such as adding new compounds that are not +among the 500,000 currently in the MetaNetX database, try using our +[equilibrator-assets](https://gitlab.com/equilibrator/equilibrator-assets) +package. + +## Cite us + +If you plan to use results from `equilibrator-api` in a scientific publication, +please cite our paper: + +Noor E, Haraldsdóttir HS, Milo R, Fleming RMT (2013) +[Consistent Estimation of Gibbs Energy Using Component Contributions](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003098), +PLoS Comput Biol 9:e1003098, DOI: 10.1371/journal.pcbi.1003098 + +## A very simple example + +Note that creating a `ComponentContribution` object for the first time after +installation, starts an initialization step which downloads ~1.5 GBytes of data +to your computer. It can take more than an hour (depending on the connection speed). +Note that the initialization might not work inside a Jupyter notebook environment - +in that case you should try running it in a standard python shell first and then +run the Jupyter notebook. + +```python +from equilibrator_api import ComponentContribution +cc = ComponentContribution() +rxn = cc.parse_reaction_formula("kegg:C00002 + kegg:C00001 = kegg:C00008 + kegg:C00009") +print(f"ΔG'0 = {cc.standard_dg_prime(rxn)}") +``` + + +%prep +%autosetup -n equilibrator-api-0.4.7 + +%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-equilibrator-api -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Thu May 18 2023 Python_Bot <Python_Bot@openeuler.org> - 0.4.7-1 +- Package Spec generated @@ -0,0 +1 @@ +124d077f177eef0ec8200a65690656fb equilibrator-api-0.4.7.tar.gz |