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|
%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` [](https://github.com/fastobo/fastobo-py/stargazers)
*Faultless AST for Open Biomedical Ontologies in Python.*
[](https://github.com/fastobo/fastobo-py/actions)
[](https://ci.appveyor.com/project/althonos/fastobo-py)
[](https://codecov.io/gh/fastobo/fastobo-py)
[](https://choosealicense.com/licenses/mit/)
[](https://github.com/fastobo/fastobo-py/)
[](https://pypi.org/project/fastobo)
[](https://pypi.org/project/fastobo/#files)
[](https://anaconda.org/bioconda/fastobo)
[](https://pypi.org/project/fastobo/#files)
[](https://pypi.org/project/fastobo/#files)
[](https://github.com/fastobo/fastobo-py/blob/master/CHANGELOG.md)
[](https://fastobo.readthedocs.io/)
[](https://github.com/fastobo/fastobo-py/issues)
[](https://f1000research.com/posters/8-1500)
[](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` [](https://github.com/fastobo/fastobo-py/stargazers)
*Faultless AST for Open Biomedical Ontologies in Python.*
[](https://github.com/fastobo/fastobo-py/actions)
[](https://ci.appveyor.com/project/althonos/fastobo-py)
[](https://codecov.io/gh/fastobo/fastobo-py)
[](https://choosealicense.com/licenses/mit/)
[](https://github.com/fastobo/fastobo-py/)
[](https://pypi.org/project/fastobo)
[](https://pypi.org/project/fastobo/#files)
[](https://anaconda.org/bioconda/fastobo)
[](https://pypi.org/project/fastobo/#files)
[](https://pypi.org/project/fastobo/#files)
[](https://github.com/fastobo/fastobo-py/blob/master/CHANGELOG.md)
[](https://fastobo.readthedocs.io/)
[](https://github.com/fastobo/fastobo-py/issues)
[](https://f1000research.com/posters/8-1500)
[](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` [](https://github.com/fastobo/fastobo-py/stargazers)
*Faultless AST for Open Biomedical Ontologies in Python.*
[](https://github.com/fastobo/fastobo-py/actions)
[](https://ci.appveyor.com/project/althonos/fastobo-py)
[](https://codecov.io/gh/fastobo/fastobo-py)
[](https://choosealicense.com/licenses/mit/)
[](https://github.com/fastobo/fastobo-py/)
[](https://pypi.org/project/fastobo)
[](https://pypi.org/project/fastobo/#files)
[](https://anaconda.org/bioconda/fastobo)
[](https://pypi.org/project/fastobo/#files)
[](https://pypi.org/project/fastobo/#files)
[](https://github.com/fastobo/fastobo-py/blob/master/CHANGELOG.md)
[](https://fastobo.readthedocs.io/)
[](https://github.com/fastobo/fastobo-py/issues)
[](https://f1000research.com/posters/8-1500)
[](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 <Python_Bot@openeuler.org> - 0.12.2-1
- Package Spec generated
|
