From 3abff0add08551e7ce85b037ef6ff2cca5ab0609 Mon Sep 17 00:00:00 2001 From: CoprDistGit Date: Tue, 11 Apr 2023 20:22:07 +0000 Subject: automatic import of python-fastobo --- .gitignore | 1 + python-fastobo.spec | 332 ++++++++++++++++++++++++++++++++++++++++++++++++++++ sources | 1 + 3 files changed, 334 insertions(+) create mode 100644 python-fastobo.spec create mode 100644 sources diff --git a/.gitignore b/.gitignore index e69de29..c32b775 100644 --- a/.gitignore +++ b/.gitignore @@ -0,0 +1 @@ +/fastobo-0.12.2.tar.gz diff --git a/python-fastobo.spec b/python-fastobo.spec new file mode 100644 index 0000000..a0c5601 --- /dev/null +++ b/python-fastobo.spec @@ -0,0 +1,332 @@ +%global _empty_manifest_terminate_build 0 +Name: python-fastobo +Version: 0.12.2 +Release: 1 +Summary: Faultless AST for Open Biomedical Ontologies in Python. +License: MIT +URL: https://github.com/fastobo/fastobo-py +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/a7/45/807969ee86218115b54aae7ced45d1439ddc60a05a89f3812db179f168a0/fastobo-0.12.2.tar.gz + + +%description +# `fastobo-py` [![Star me](https://img.shields.io/github/stars/fastobo/fastobo-py.svg?style=social&label=Star&maxAge=3600)](https://github.com/fastobo/fastobo-py/stargazers) + +*Faultless AST for Open Biomedical Ontologies in Python.* + +[![Actions](https://img.shields.io/github/workflow/status/fastobo/fastobo-py/Test?style=flat-square&maxAge=600)](https://github.com/fastobo/fastobo-py/actions) +[![AppVeyor](https://img.shields.io/appveyor/ci/althonos/fastobo-py/master?logo=appveyor&style=flat-square&maxAge=600)](https://ci.appveyor.com/project/althonos/fastobo-py) +[![Codecov](https://img.shields.io/codecov/c/gh/fastobo/fastobo-py/master.svg?style=flat-square&maxAge=600)](https://codecov.io/gh/fastobo/fastobo-py) +[![License](https://img.shields.io/badge/license-MIT-blue.svg?style=flat-square&maxAge=2678400)](https://choosealicense.com/licenses/mit/) +[![Source](https://img.shields.io/badge/source-GitHub-303030.svg?maxAge=2678400&style=flat-square)](https://github.com/fastobo/fastobo-py/) +[![PyPI](https://img.shields.io/pypi/v/fastobo.svg?style=flat-square&maxAge=600)](https://pypi.org/project/fastobo) +[![Wheel](https://img.shields.io/pypi/wheel/fastobo.svg?style=flat-square&maxAge=2678400)](https://pypi.org/project/fastobo/#files) +[![Bioconda](https://img.shields.io/conda/vn/bioconda/fastobo?style=flat-square&maxAge=3600)](https://anaconda.org/bioconda/fastobo) +[![Python Versions](https://img.shields.io/pypi/pyversions/fastobo.svg?style=flat-square&maxAge=600)](https://pypi.org/project/fastobo/#files) +[![PyPI - Implementation](https://img.shields.io/pypi/implementation/fastobo.svg?style=flat-square&maxAge=600)](https://pypi.org/project/fastobo/#files) +[![Changelog](https://img.shields.io/badge/keep%20a-changelog-8A0707.svg?maxAge=2678400&style=flat-square)](https://github.com/fastobo/fastobo-py/blob/master/CHANGELOG.md) +[![Documentation](https://img.shields.io/readthedocs/fastobo.svg?maxAge=3600&style=flat-square)](https://fastobo.readthedocs.io/) +[![GitHub issues](https://img.shields.io/github/issues/fastobo/fastobo-py.svg?style=flat-square&maxAge=600)](https://github.com/fastobo/fastobo-py/issues) +[![DOI](https://img.shields.io/badge/doi-10.7490%2Ff1000research.1117405.1-brightgreen?style=flat-square&maxAge=31536000)](https://f1000research.com/posters/8-1500) +[![Downloads](https://img.shields.io/badge/dynamic/json?style=flat-square&color=303f9f&maxAge=86400&label=downloads&query=%24.total_downloads&url=https%3A%2F%2Fapi.pepy.tech%2Fapi%2Fprojects%2Ffastobo)](https://pepy.tech/project/fastobo) + + +## Overview + +[`fastobo`](https://crates.io/crates/fastobo) is a Rust library implementing a +reliable parser for the OBO file format 1.4. This extension module exports +idiomatic Python bindings that can be used to load, edit and serialize ontologies +in the OBO format. + + +## Installation + +If your platform has no pre-built binaries available, you will need to have the Rust +compiler installed. See the [documentation on `rust-lang.org`](https://forge.rust-lang.org/other-installation-methods.html) +to learn how to install Rust on your machine. + +Installation is then supported through `pip`: +```console +$ pip install fastobo --user +``` + + +## Usage + +An `OboDoc` instance can be instantiated from a path or from a binary file handle +using the `fastobo.load` function, or from a string using the `fastobo.loads` function. + +```python +import fastobo +obodoc = fastobo.load("../data/ms.obo") +``` + +Loading from a `gzip` file is supported: +```python +import fastobo +import gzip +gzdoc = fastobo.load(gzip.open("../data/cl.obo.gz")) +``` + +*Comments can be parsed but neither edited nor serialized, because of a limitation +with `pyo3` (the library used to generate the Python bindings). They are supported +in the Rust version of `fastobo`.* + +## Feedback + +Found a bug ? Have an enhancement request ? Head over to the +[GitHub issue tracker](https://github.com/fastobo/fastobo-py/issues) of the project if +you need to report or ask something. If you are filling in on a bug, please include as much +information as you can about the issue, and try to recreate the same bug in a simple, easily +reproducible situation. + +The following people have contributed to this project: + +- Alex Henrie ([@alexhenrie](https://github.com/alexhenrie)) +- Patrick Kalita ([@pkalita-lbl](https://github.com/pkalita-lbl)) + + +## About + +This project was developed by [Martin Larralde](https://github.com/althonos) +as part of a Master's Degree internship in the [BBOP team](http://berkeleybop.org/) of the +[Lawrence Berkeley National Laboratory](https://www.lbl.gov/), under the supervision of +[Chris Mungall](http://biosciences.lbl.gov/profiles/chris-mungall/). Cite this project as: + +*Larralde M.* **Developing Python and Rust libraries to improve the ontology ecosystem** +*\[version 1; not peer reviewed\].* F1000Research 2019, 8(ISCB Comm J):1500 (poster) +([https://doi.org/10.7490/f1000research.1117405.1](https://doi.org/10.7490/f1000research.1117405.1)) + + +%package -n python3-fastobo +Summary: Faultless AST for Open Biomedical Ontologies in Python. +Provides: python-fastobo +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +BuildRequires: python3-cffi +BuildRequires: gcc +BuildRequires: gdb +%description -n python3-fastobo +# `fastobo-py` [![Star me](https://img.shields.io/github/stars/fastobo/fastobo-py.svg?style=social&label=Star&maxAge=3600)](https://github.com/fastobo/fastobo-py/stargazers) + +*Faultless AST for Open Biomedical Ontologies in Python.* + +[![Actions](https://img.shields.io/github/workflow/status/fastobo/fastobo-py/Test?style=flat-square&maxAge=600)](https://github.com/fastobo/fastobo-py/actions) +[![AppVeyor](https://img.shields.io/appveyor/ci/althonos/fastobo-py/master?logo=appveyor&style=flat-square&maxAge=600)](https://ci.appveyor.com/project/althonos/fastobo-py) +[![Codecov](https://img.shields.io/codecov/c/gh/fastobo/fastobo-py/master.svg?style=flat-square&maxAge=600)](https://codecov.io/gh/fastobo/fastobo-py) +[![License](https://img.shields.io/badge/license-MIT-blue.svg?style=flat-square&maxAge=2678400)](https://choosealicense.com/licenses/mit/) +[![Source](https://img.shields.io/badge/source-GitHub-303030.svg?maxAge=2678400&style=flat-square)](https://github.com/fastobo/fastobo-py/) +[![PyPI](https://img.shields.io/pypi/v/fastobo.svg?style=flat-square&maxAge=600)](https://pypi.org/project/fastobo) +[![Wheel](https://img.shields.io/pypi/wheel/fastobo.svg?style=flat-square&maxAge=2678400)](https://pypi.org/project/fastobo/#files) +[![Bioconda](https://img.shields.io/conda/vn/bioconda/fastobo?style=flat-square&maxAge=3600)](https://anaconda.org/bioconda/fastobo) +[![Python Versions](https://img.shields.io/pypi/pyversions/fastobo.svg?style=flat-square&maxAge=600)](https://pypi.org/project/fastobo/#files) +[![PyPI - Implementation](https://img.shields.io/pypi/implementation/fastobo.svg?style=flat-square&maxAge=600)](https://pypi.org/project/fastobo/#files) +[![Changelog](https://img.shields.io/badge/keep%20a-changelog-8A0707.svg?maxAge=2678400&style=flat-square)](https://github.com/fastobo/fastobo-py/blob/master/CHANGELOG.md) +[![Documentation](https://img.shields.io/readthedocs/fastobo.svg?maxAge=3600&style=flat-square)](https://fastobo.readthedocs.io/) +[![GitHub issues](https://img.shields.io/github/issues/fastobo/fastobo-py.svg?style=flat-square&maxAge=600)](https://github.com/fastobo/fastobo-py/issues) +[![DOI](https://img.shields.io/badge/doi-10.7490%2Ff1000research.1117405.1-brightgreen?style=flat-square&maxAge=31536000)](https://f1000research.com/posters/8-1500) +[![Downloads](https://img.shields.io/badge/dynamic/json?style=flat-square&color=303f9f&maxAge=86400&label=downloads&query=%24.total_downloads&url=https%3A%2F%2Fapi.pepy.tech%2Fapi%2Fprojects%2Ffastobo)](https://pepy.tech/project/fastobo) + + +## Overview + +[`fastobo`](https://crates.io/crates/fastobo) is a Rust library implementing a +reliable parser for the OBO file format 1.4. This extension module exports +idiomatic Python bindings that can be used to load, edit and serialize ontologies +in the OBO format. + + +## Installation + +If your platform has no pre-built binaries available, you will need to have the Rust +compiler installed. See the [documentation on `rust-lang.org`](https://forge.rust-lang.org/other-installation-methods.html) +to learn how to install Rust on your machine. + +Installation is then supported through `pip`: +```console +$ pip install fastobo --user +``` + + +## Usage + +An `OboDoc` instance can be instantiated from a path or from a binary file handle +using the `fastobo.load` function, or from a string using the `fastobo.loads` function. + +```python +import fastobo +obodoc = fastobo.load("../data/ms.obo") +``` + +Loading from a `gzip` file is supported: +```python +import fastobo +import gzip +gzdoc = fastobo.load(gzip.open("../data/cl.obo.gz")) +``` + +*Comments can be parsed but neither edited nor serialized, because of a limitation +with `pyo3` (the library used to generate the Python bindings). They are supported +in the Rust version of `fastobo`.* + +## Feedback + +Found a bug ? Have an enhancement request ? Head over to the +[GitHub issue tracker](https://github.com/fastobo/fastobo-py/issues) of the project if +you need to report or ask something. If you are filling in on a bug, please include as much +information as you can about the issue, and try to recreate the same bug in a simple, easily +reproducible situation. + +The following people have contributed to this project: + +- Alex Henrie ([@alexhenrie](https://github.com/alexhenrie)) +- Patrick Kalita ([@pkalita-lbl](https://github.com/pkalita-lbl)) + + +## About + +This project was developed by [Martin Larralde](https://github.com/althonos) +as part of a Master's Degree internship in the [BBOP team](http://berkeleybop.org/) of the +[Lawrence Berkeley National Laboratory](https://www.lbl.gov/), under the supervision of +[Chris Mungall](http://biosciences.lbl.gov/profiles/chris-mungall/). Cite this project as: + +*Larralde M.* **Developing Python and Rust libraries to improve the ontology ecosystem** +*\[version 1; not peer reviewed\].* F1000Research 2019, 8(ISCB Comm J):1500 (poster) +([https://doi.org/10.7490/f1000research.1117405.1](https://doi.org/10.7490/f1000research.1117405.1)) + + +%package help +Summary: Development documents and examples for fastobo +Provides: python3-fastobo-doc +%description help +# `fastobo-py` [![Star me](https://img.shields.io/github/stars/fastobo/fastobo-py.svg?style=social&label=Star&maxAge=3600)](https://github.com/fastobo/fastobo-py/stargazers) + +*Faultless AST for Open Biomedical Ontologies in Python.* + +[![Actions](https://img.shields.io/github/workflow/status/fastobo/fastobo-py/Test?style=flat-square&maxAge=600)](https://github.com/fastobo/fastobo-py/actions) +[![AppVeyor](https://img.shields.io/appveyor/ci/althonos/fastobo-py/master?logo=appveyor&style=flat-square&maxAge=600)](https://ci.appveyor.com/project/althonos/fastobo-py) +[![Codecov](https://img.shields.io/codecov/c/gh/fastobo/fastobo-py/master.svg?style=flat-square&maxAge=600)](https://codecov.io/gh/fastobo/fastobo-py) +[![License](https://img.shields.io/badge/license-MIT-blue.svg?style=flat-square&maxAge=2678400)](https://choosealicense.com/licenses/mit/) +[![Source](https://img.shields.io/badge/source-GitHub-303030.svg?maxAge=2678400&style=flat-square)](https://github.com/fastobo/fastobo-py/) +[![PyPI](https://img.shields.io/pypi/v/fastobo.svg?style=flat-square&maxAge=600)](https://pypi.org/project/fastobo) +[![Wheel](https://img.shields.io/pypi/wheel/fastobo.svg?style=flat-square&maxAge=2678400)](https://pypi.org/project/fastobo/#files) +[![Bioconda](https://img.shields.io/conda/vn/bioconda/fastobo?style=flat-square&maxAge=3600)](https://anaconda.org/bioconda/fastobo) +[![Python Versions](https://img.shields.io/pypi/pyversions/fastobo.svg?style=flat-square&maxAge=600)](https://pypi.org/project/fastobo/#files) +[![PyPI - Implementation](https://img.shields.io/pypi/implementation/fastobo.svg?style=flat-square&maxAge=600)](https://pypi.org/project/fastobo/#files) +[![Changelog](https://img.shields.io/badge/keep%20a-changelog-8A0707.svg?maxAge=2678400&style=flat-square)](https://github.com/fastobo/fastobo-py/blob/master/CHANGELOG.md) +[![Documentation](https://img.shields.io/readthedocs/fastobo.svg?maxAge=3600&style=flat-square)](https://fastobo.readthedocs.io/) +[![GitHub issues](https://img.shields.io/github/issues/fastobo/fastobo-py.svg?style=flat-square&maxAge=600)](https://github.com/fastobo/fastobo-py/issues) +[![DOI](https://img.shields.io/badge/doi-10.7490%2Ff1000research.1117405.1-brightgreen?style=flat-square&maxAge=31536000)](https://f1000research.com/posters/8-1500) +[![Downloads](https://img.shields.io/badge/dynamic/json?style=flat-square&color=303f9f&maxAge=86400&label=downloads&query=%24.total_downloads&url=https%3A%2F%2Fapi.pepy.tech%2Fapi%2Fprojects%2Ffastobo)](https://pepy.tech/project/fastobo) + + +## Overview + +[`fastobo`](https://crates.io/crates/fastobo) is a Rust library implementing a +reliable parser for the OBO file format 1.4. This extension module exports +idiomatic Python bindings that can be used to load, edit and serialize ontologies +in the OBO format. + + +## Installation + +If your platform has no pre-built binaries available, you will need to have the Rust +compiler installed. See the [documentation on `rust-lang.org`](https://forge.rust-lang.org/other-installation-methods.html) +to learn how to install Rust on your machine. + +Installation is then supported through `pip`: +```console +$ pip install fastobo --user +``` + + +## Usage + +An `OboDoc` instance can be instantiated from a path or from a binary file handle +using the `fastobo.load` function, or from a string using the `fastobo.loads` function. + +```python +import fastobo +obodoc = fastobo.load("../data/ms.obo") +``` + +Loading from a `gzip` file is supported: +```python +import fastobo +import gzip +gzdoc = fastobo.load(gzip.open("../data/cl.obo.gz")) +``` + +*Comments can be parsed but neither edited nor serialized, because of a limitation +with `pyo3` (the library used to generate the Python bindings). They are supported +in the Rust version of `fastobo`.* + +## Feedback + +Found a bug ? Have an enhancement request ? Head over to the +[GitHub issue tracker](https://github.com/fastobo/fastobo-py/issues) of the project if +you need to report or ask something. If you are filling in on a bug, please include as much +information as you can about the issue, and try to recreate the same bug in a simple, easily +reproducible situation. + +The following people have contributed to this project: + +- Alex Henrie ([@alexhenrie](https://github.com/alexhenrie)) +- Patrick Kalita ([@pkalita-lbl](https://github.com/pkalita-lbl)) + + +## About + +This project was developed by [Martin Larralde](https://github.com/althonos) +as part of a Master's Degree internship in the [BBOP team](http://berkeleybop.org/) of the +[Lawrence Berkeley National Laboratory](https://www.lbl.gov/), under the supervision of +[Chris Mungall](http://biosciences.lbl.gov/profiles/chris-mungall/). Cite this project as: + +*Larralde M.* **Developing Python and Rust libraries to improve the ontology ecosystem** +*\[version 1; not peer reviewed\].* F1000Research 2019, 8(ISCB Comm J):1500 (poster) +([https://doi.org/10.7490/f1000research.1117405.1](https://doi.org/10.7490/f1000research.1117405.1)) + + +%prep +%autosetup -n fastobo-0.12.2 + +%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-fastobo -f filelist.lst +%dir %{python3_sitearch}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Tue Apr 11 2023 Python_Bot - 0.12.2-1 +- Package Spec generated diff --git a/sources b/sources new file mode 100644 index 0000000..f0aa144 --- /dev/null +++ b/sources @@ -0,0 +1 @@ +b2f4e0221ace007045828b6052be1d3a fastobo-0.12.2.tar.gz -- cgit v1.2.3