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author | CoprDistGit <infra@openeuler.org> | 2023-06-20 05:55:51 +0000 |
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committer | CoprDistGit <infra@openeuler.org> | 2023-06-20 05:55:51 +0000 |
commit | 7a88d2e44e6730e5197fc0c0a857f09783616ccd (patch) | |
tree | a9b2ee8b3784ead446b34054554e23f1e01b06a9 | |
parent | ac7918a4a44193eeb1da7c57b34e59be7fba8cc8 (diff) |
automatic import of python-KEGGutilsopeneuler20.03
-rw-r--r-- | .gitignore | 1 | ||||
-rw-r--r-- | python-keggutils.spec | 333 | ||||
-rw-r--r-- | sources | 1 |
3 files changed, 335 insertions, 0 deletions
@@ -0,0 +1 @@ +/KEGGutils-0.4.0.tar.gz diff --git a/python-keggutils.spec b/python-keggutils.spec new file mode 100644 index 0000000..97405dc --- /dev/null +++ b/python-keggutils.spec @@ -0,0 +1,333 @@ +%global _empty_manifest_terminate_build 0 +Name: python-KEGGutils +Version: 0.4.0 +Release: 1 +Summary: Simple utils to work with KEGG data on NetworkX +License: Unlicense +URL: https://github.com/filippocastelli/KEGGutils +Source0: https://mirrors.aliyun.com/pypi/web/packages/fa/d9/44c080def3e22242287be0f4a9f97b8ac986eeb6fabf5ea1fbfa70cf50e8/KEGGutils-0.4.0.tar.gz +BuildArch: noarch + +Requires: python3-networkx +Requires: python3-matplotlib +Requires: python3-awesome-slugify +Requires: python3-requests +Requires: python3-Pillow +Requires: python3-scipy +Requires: python3-pytest +Requires: python3-pytest-cov +Requires: python3-jupyter + +%description +# KEGGutils: +Working with **KEGG** in **Python** and **NetworkX** +# <img src="/img/logo_cut.png" alt="Drawing" width = "630"></img> + + + +**KEGGutils** is a toolkit designed for working with the *Kyoto Encyclopedia of Genes and Genome* database in *Python* with a quick and easy to use interface: in a single line you can download data from KEGG's REST API, organize in a graph-like format provided by *NetworkX* and immediately start exploring. + +*KEGGutils* is much more than just an API interface: other than a series of tools to better interface yourself with the service, it provides expanded *NetworkX* classes and methods ( totally nx-compatible ) to handle different types of data and help you better exploit underlying structures. +KEGGutils is easily expandable and can be immediately integrated anywhere you use *NetworkX* to process data. + +## Current build status: + +*master branch* : [](https://circleci.com/gh/filippocastelli/KEGGutils) + +*devel branch* : [](https://circleci.com/gh/filippocastelli/KEGGutils/tree/dev) + +## Installing KEGGutils +# <a href="https://pypi.org/"><img alt = PyPi src="https://pypi.org/static/images/logo-large.72ad8bf1.svg" height="100"></img></a> + +You can just clone this repo and use it's content as any other python package, but if you just need a super easy drop-in solution *KEGGutils* is available as a *PyPi* package: + +to install it you just need to run + +`pip install KEGGutils` + + and that should be it! + +## Dependencies +KEGGutils is tested and working against python `3.8`, `3.9`, `3.10` and `3.11`. + +`3.6` and `3.7` are untested but should work. + +To make sure KEGGutils works as it should, a few dependencies must be satisfied: +- `networkx` +- `matplotlib` +- `awesome-slugify` +- `requests` +- `Pillow` +- `scipy` + +note: if you use pip to install KEGGutils, it should automatically get the needed dependencies for you! + +note: you can create an environment with all the required dependencies using the incldued anaconda environment configurator, you just need to run + +`conda env create -f keggutils_env.yml` + +to create a `keggutils_env` anaconda environment with all the required dependencies. + +## Getting started + +In this repo can find four dense yet easy to follow tutorials covering most of *KEGGutils*'s functionalities and more are coming in the next future. +To start just follow the links below: +- [**Tutorial 0 - Basics and KEGG API**](https://github.com/filippocastelli/KEGGutils/blob/dev/tutorials/Tutorial%200%20-%20Basics%20and%20KEGG%20API.ipynb) +- [**Tutorial 1 - Enzymatic Graphs**](https://github.com/filippocastelli/KEGGutils/blob/dev/tutorials/Tutorial%201%20-%20EnzymeGraphs.ipynb) +- [**Tutorial 2 - KEGGgraphs, KGGlinkgraphs and KEGGchains**](https://github.com/filippocastelli/KEGGutils/blob/dev/tutorials/Tutorial%202%20-%20KEGGgraphs%2C%20KGGlinkgraphs%20and%20KEGGchains.ipynb) +- [**Tutorial 3 - KEGGpathways**](https://github.com/filippocastelli/KEGGutils/blob/dev/tutorials/Tutorial%203%20-%20KEGGpathways.ipynb) + + +## Contributing + +The project is open to contributions and suggestions, just open an issue on the repo or contact me directly (contacts below). + +## External links + +Here are a few useful links +- [KEGG: Kyoto Encyclopedia of Genes and Genomes](https://www.kegg.jp/) +- [KEGG REST API reference page](https://www.kegg.jp/kegg/rest/keggapi.html) +- [KEGG KGML (KEGG Markup Language) reference page](https://www.kegg.jp/kegg/xml/) +- [Networkx Github IO](https://networkx.github.io/) + + + +## Contacts + +**Author:** + +Filippo Maria Castelli +castelli@lens.unifi.it +LENS, European Laboratory for Non-linear Spectroscopy +Via Nello Carrara 1 +50019 Sesto Fiorentino (FI), Italy + + + + +%package -n python3-KEGGutils +Summary: Simple utils to work with KEGG data on NetworkX +Provides: python-KEGGutils +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-KEGGutils +# KEGGutils: +Working with **KEGG** in **Python** and **NetworkX** +# <img src="/img/logo_cut.png" alt="Drawing" width = "630"></img> + + + +**KEGGutils** is a toolkit designed for working with the *Kyoto Encyclopedia of Genes and Genome* database in *Python* with a quick and easy to use interface: in a single line you can download data from KEGG's REST API, organize in a graph-like format provided by *NetworkX* and immediately start exploring. + +*KEGGutils* is much more than just an API interface: other than a series of tools to better interface yourself with the service, it provides expanded *NetworkX* classes and methods ( totally nx-compatible ) to handle different types of data and help you better exploit underlying structures. +KEGGutils is easily expandable and can be immediately integrated anywhere you use *NetworkX* to process data. + +## Current build status: + +*master branch* : [](https://circleci.com/gh/filippocastelli/KEGGutils) + +*devel branch* : [](https://circleci.com/gh/filippocastelli/KEGGutils/tree/dev) + +## Installing KEGGutils +# <a href="https://pypi.org/"><img alt = PyPi src="https://pypi.org/static/images/logo-large.72ad8bf1.svg" height="100"></img></a> + +You can just clone this repo and use it's content as any other python package, but if you just need a super easy drop-in solution *KEGGutils* is available as a *PyPi* package: + +to install it you just need to run + +`pip install KEGGutils` + + and that should be it! + +## Dependencies +KEGGutils is tested and working against python `3.8`, `3.9`, `3.10` and `3.11`. + +`3.6` and `3.7` are untested but should work. + +To make sure KEGGutils works as it should, a few dependencies must be satisfied: +- `networkx` +- `matplotlib` +- `awesome-slugify` +- `requests` +- `Pillow` +- `scipy` + +note: if you use pip to install KEGGutils, it should automatically get the needed dependencies for you! + +note: you can create an environment with all the required dependencies using the incldued anaconda environment configurator, you just need to run + +`conda env create -f keggutils_env.yml` + +to create a `keggutils_env` anaconda environment with all the required dependencies. + +## Getting started + +In this repo can find four dense yet easy to follow tutorials covering most of *KEGGutils*'s functionalities and more are coming in the next future. +To start just follow the links below: +- [**Tutorial 0 - Basics and KEGG API**](https://github.com/filippocastelli/KEGGutils/blob/dev/tutorials/Tutorial%200%20-%20Basics%20and%20KEGG%20API.ipynb) +- [**Tutorial 1 - Enzymatic Graphs**](https://github.com/filippocastelli/KEGGutils/blob/dev/tutorials/Tutorial%201%20-%20EnzymeGraphs.ipynb) +- [**Tutorial 2 - KEGGgraphs, KGGlinkgraphs and KEGGchains**](https://github.com/filippocastelli/KEGGutils/blob/dev/tutorials/Tutorial%202%20-%20KEGGgraphs%2C%20KGGlinkgraphs%20and%20KEGGchains.ipynb) +- [**Tutorial 3 - KEGGpathways**](https://github.com/filippocastelli/KEGGutils/blob/dev/tutorials/Tutorial%203%20-%20KEGGpathways.ipynb) + + +## Contributing + +The project is open to contributions and suggestions, just open an issue on the repo or contact me directly (contacts below). + +## External links + +Here are a few useful links +- [KEGG: Kyoto Encyclopedia of Genes and Genomes](https://www.kegg.jp/) +- [KEGG REST API reference page](https://www.kegg.jp/kegg/rest/keggapi.html) +- [KEGG KGML (KEGG Markup Language) reference page](https://www.kegg.jp/kegg/xml/) +- [Networkx Github IO](https://networkx.github.io/) + + + +## Contacts + +**Author:** + +Filippo Maria Castelli +castelli@lens.unifi.it +LENS, European Laboratory for Non-linear Spectroscopy +Via Nello Carrara 1 +50019 Sesto Fiorentino (FI), Italy + + + + +%package help +Summary: Development documents and examples for KEGGutils +Provides: python3-KEGGutils-doc +%description help +# KEGGutils: +Working with **KEGG** in **Python** and **NetworkX** +# <img src="/img/logo_cut.png" alt="Drawing" width = "630"></img> + + + +**KEGGutils** is a toolkit designed for working with the *Kyoto Encyclopedia of Genes and Genome* database in *Python* with a quick and easy to use interface: in a single line you can download data from KEGG's REST API, organize in a graph-like format provided by *NetworkX* and immediately start exploring. + +*KEGGutils* is much more than just an API interface: other than a series of tools to better interface yourself with the service, it provides expanded *NetworkX* classes and methods ( totally nx-compatible ) to handle different types of data and help you better exploit underlying structures. +KEGGutils is easily expandable and can be immediately integrated anywhere you use *NetworkX* to process data. + +## Current build status: + +*master branch* : [](https://circleci.com/gh/filippocastelli/KEGGutils) + +*devel branch* : [](https://circleci.com/gh/filippocastelli/KEGGutils/tree/dev) + +## Installing KEGGutils +# <a href="https://pypi.org/"><img alt = PyPi src="https://pypi.org/static/images/logo-large.72ad8bf1.svg" height="100"></img></a> + +You can just clone this repo and use it's content as any other python package, but if you just need a super easy drop-in solution *KEGGutils* is available as a *PyPi* package: + +to install it you just need to run + +`pip install KEGGutils` + + and that should be it! + +## Dependencies +KEGGutils is tested and working against python `3.8`, `3.9`, `3.10` and `3.11`. + +`3.6` and `3.7` are untested but should work. + +To make sure KEGGutils works as it should, a few dependencies must be satisfied: +- `networkx` +- `matplotlib` +- `awesome-slugify` +- `requests` +- `Pillow` +- `scipy` + +note: if you use pip to install KEGGutils, it should automatically get the needed dependencies for you! + +note: you can create an environment with all the required dependencies using the incldued anaconda environment configurator, you just need to run + +`conda env create -f keggutils_env.yml` + +to create a `keggutils_env` anaconda environment with all the required dependencies. + +## Getting started + +In this repo can find four dense yet easy to follow tutorials covering most of *KEGGutils*'s functionalities and more are coming in the next future. +To start just follow the links below: +- [**Tutorial 0 - Basics and KEGG API**](https://github.com/filippocastelli/KEGGutils/blob/dev/tutorials/Tutorial%200%20-%20Basics%20and%20KEGG%20API.ipynb) +- [**Tutorial 1 - Enzymatic Graphs**](https://github.com/filippocastelli/KEGGutils/blob/dev/tutorials/Tutorial%201%20-%20EnzymeGraphs.ipynb) +- [**Tutorial 2 - KEGGgraphs, KGGlinkgraphs and KEGGchains**](https://github.com/filippocastelli/KEGGutils/blob/dev/tutorials/Tutorial%202%20-%20KEGGgraphs%2C%20KGGlinkgraphs%20and%20KEGGchains.ipynb) +- [**Tutorial 3 - KEGGpathways**](https://github.com/filippocastelli/KEGGutils/blob/dev/tutorials/Tutorial%203%20-%20KEGGpathways.ipynb) + + +## Contributing + +The project is open to contributions and suggestions, just open an issue on the repo or contact me directly (contacts below). + +## External links + +Here are a few useful links +- [KEGG: Kyoto Encyclopedia of Genes and Genomes](https://www.kegg.jp/) +- [KEGG REST API reference page](https://www.kegg.jp/kegg/rest/keggapi.html) +- [KEGG KGML (KEGG Markup Language) reference page](https://www.kegg.jp/kegg/xml/) +- [Networkx Github IO](https://networkx.github.io/) + + + +## Contacts + +**Author:** + +Filippo Maria Castelli +castelli@lens.unifi.it +LENS, European Laboratory for Non-linear Spectroscopy +Via Nello Carrara 1 +50019 Sesto Fiorentino (FI), Italy + + + + +%prep +%autosetup -n KEGGutils-0.4.0 + +%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-KEGGutils -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Tue Jun 20 2023 Python_Bot <Python_Bot@openeuler.org> - 0.4.0-1 +- Package Spec generated @@ -0,0 +1 @@ +84ff07b186adf22087459c5f025886ec KEGGutils-0.4.0.tar.gz |