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|
%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
|
