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diff --git a/python-grenadine.spec b/python-grenadine.spec new file mode 100644 index 0000000..eb77d53 --- /dev/null +++ b/python-grenadine.spec @@ -0,0 +1,251 @@ +%global _empty_manifest_terminate_build 0 +Name: python-GReNaDIne +Version: 0.0.21 +Release: 1 +Summary: Data-Driven Gene Regulatory Network Inference +License: GNU General Public License (GPL) +URL: https://pypi.org/project/GReNaDIne/ +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/5c/9f/e4bfe40b8db8ff5cae684ada99cfd81b2ec299cfebc4719cecd8a555a633/GReNaDIne-0.0.21.tar.gz +BuildArch: noarch + +Requires: python3-pandas +Requires: python3-numpy +Requires: python3-scikit-learn +Requires: python3-tqdm +Requires: python3-scipy + +%description +# GReNaDIne: Gene Regulatory Network Data-driven Inference + +<div style="display: flex; justify-content: center;"> + <img src="logo.png" height="250"> +</div> + +This Python 3.7 package allows to infer Gene Regulatory Networks through several +Data-driven methods. Pre-processing and evaluation methods are also included. + +### Dependencies + ++ `pip install numpy` version 1.16.2 ++ `pip install pandas` version 0.24.2 ++ `pip install matplotlib` version 3.0.3 ++ `pip install joblib` version 0.13.2 ++ `pip install Cython` version 0.29.6 ++ `pip install scikit-learn` version 0.20.3 ++ `pip install networkx` ++ `pip install seaborn` ++ `pip install pot` version 0.5.1 +POT is not included in the automatic dependencies install +You have to install it if you want to use columns_matrix_OT_norm() normalization function. +The other functions of the package do not need POT. ++ `pip install rpy2` version 3.0.2 +rpy2 is not included in the automatic dependencies install +You have to install it if you want to use DEseq2() normalization function. +The other functions of the package do not need rpy2. + +### Installation: + +`pip install GReNaDIne` + +### Docker Image + +`docker run speignier/grenadine` + +### Documentation: + +[grenadine.readthedocs.io](https://grenadine.readthedocs.io/en/latest/) + +### Tutorials: + +Check the jupyter notebook tutorials located in the __tutorial__ folder ++ `Infer_dream5_E_coli_GRN_using_GENIE3.ipynb` to infer GRNs using the GENIE3 method (random forest regression) ++ `Infer_dream5_E_coli_GRN_using_SVMs.ipynb` to infer GRNs using the SVM method (SVM classification) + +### Authors: + +For bug reports and feedback do not hesitate to contact the authors + ++ Sergio Peignier: sergio.peignier AT insa-lyon.fr ++ Pauline Schmitt: pauline.schmitt AT insa-lyon.fr + +### Maintainer: + ++ Sergio Peignier: sergio.peignier AT insa-lyon.fr + + + + +%package -n python3-GReNaDIne +Summary: Data-Driven Gene Regulatory Network Inference +Provides: python-GReNaDIne +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-GReNaDIne +# GReNaDIne: Gene Regulatory Network Data-driven Inference + +<div style="display: flex; justify-content: center;"> + <img src="logo.png" height="250"> +</div> + +This Python 3.7 package allows to infer Gene Regulatory Networks through several +Data-driven methods. Pre-processing and evaluation methods are also included. + +### Dependencies + ++ `pip install numpy` version 1.16.2 ++ `pip install pandas` version 0.24.2 ++ `pip install matplotlib` version 3.0.3 ++ `pip install joblib` version 0.13.2 ++ `pip install Cython` version 0.29.6 ++ `pip install scikit-learn` version 0.20.3 ++ `pip install networkx` ++ `pip install seaborn` ++ `pip install pot` version 0.5.1 +POT is not included in the automatic dependencies install +You have to install it if you want to use columns_matrix_OT_norm() normalization function. +The other functions of the package do not need POT. ++ `pip install rpy2` version 3.0.2 +rpy2 is not included in the automatic dependencies install +You have to install it if you want to use DEseq2() normalization function. +The other functions of the package do not need rpy2. + +### Installation: + +`pip install GReNaDIne` + +### Docker Image + +`docker run speignier/grenadine` + +### Documentation: + +[grenadine.readthedocs.io](https://grenadine.readthedocs.io/en/latest/) + +### Tutorials: + +Check the jupyter notebook tutorials located in the __tutorial__ folder ++ `Infer_dream5_E_coli_GRN_using_GENIE3.ipynb` to infer GRNs using the GENIE3 method (random forest regression) ++ `Infer_dream5_E_coli_GRN_using_SVMs.ipynb` to infer GRNs using the SVM method (SVM classification) + +### Authors: + +For bug reports and feedback do not hesitate to contact the authors + ++ Sergio Peignier: sergio.peignier AT insa-lyon.fr ++ Pauline Schmitt: pauline.schmitt AT insa-lyon.fr + +### Maintainer: + ++ Sergio Peignier: sergio.peignier AT insa-lyon.fr + + + + +%package help +Summary: Development documents and examples for GReNaDIne +Provides: python3-GReNaDIne-doc +%description help +# GReNaDIne: Gene Regulatory Network Data-driven Inference + +<div style="display: flex; justify-content: center;"> + <img src="logo.png" height="250"> +</div> + +This Python 3.7 package allows to infer Gene Regulatory Networks through several +Data-driven methods. Pre-processing and evaluation methods are also included. + +### Dependencies + ++ `pip install numpy` version 1.16.2 ++ `pip install pandas` version 0.24.2 ++ `pip install matplotlib` version 3.0.3 ++ `pip install joblib` version 0.13.2 ++ `pip install Cython` version 0.29.6 ++ `pip install scikit-learn` version 0.20.3 ++ `pip install networkx` ++ `pip install seaborn` ++ `pip install pot` version 0.5.1 +POT is not included in the automatic dependencies install +You have to install it if you want to use columns_matrix_OT_norm() normalization function. +The other functions of the package do not need POT. ++ `pip install rpy2` version 3.0.2 +rpy2 is not included in the automatic dependencies install +You have to install it if you want to use DEseq2() normalization function. +The other functions of the package do not need rpy2. + +### Installation: + +`pip install GReNaDIne` + +### Docker Image + +`docker run speignier/grenadine` + +### Documentation: + +[grenadine.readthedocs.io](https://grenadine.readthedocs.io/en/latest/) + +### Tutorials: + +Check the jupyter notebook tutorials located in the __tutorial__ folder ++ `Infer_dream5_E_coli_GRN_using_GENIE3.ipynb` to infer GRNs using the GENIE3 method (random forest regression) ++ `Infer_dream5_E_coli_GRN_using_SVMs.ipynb` to infer GRNs using the SVM method (SVM classification) + +### Authors: + +For bug reports and feedback do not hesitate to contact the authors + ++ Sergio Peignier: sergio.peignier AT insa-lyon.fr ++ Pauline Schmitt: pauline.schmitt AT insa-lyon.fr + +### Maintainer: + ++ Sergio Peignier: sergio.peignier AT insa-lyon.fr + + + + +%prep +%autosetup -n GReNaDIne-0.0.21 + +%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-GReNaDIne -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Mon May 29 2023 Python_Bot <Python_Bot@openeuler.org> - 0.0.21-1 +- Package Spec generated |