Metadata-Version: 2.1
Name: fastobo
Version: 0.9.0
Summary: Faultless AST for Open Biomedical Ontologies in Python.
Home-page: https://github.com/fastobo/fastobo-py
Author: Martin Larralde
Author-email: martin.larralde@ens-paris-saclay.fr
License: MIT
Project-URL: Bug Tracker, https://github.com/fastobo/fastobo-py/issues
Project-URL: Changelog, https://fastobo.readthedocs.io/en/latest/changes.html
Project-URL: Documentation, https://fastobo.readthedocs.io/en/latest/
Project-URL: Conda Recipe, https://anaconda.org/bioconda/fastobo
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.*
        
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        ## 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.
        
        
        ## 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))
        
Keywords: ontologies,ontology,obo,obofoundry,parser,syntax,ast
Platform: any
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Healthcare Industry
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Rust
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Programming Language :: Python :: Implementation :: PyPy
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Python: >=3.5.*
Description-Content-Type: text/markdown
