diff --git a/README.md b/README.md deleted file mode 100644 index f104324..0000000 --- a/README.md +++ /dev/null @@ -1,25 +0,0 @@ -[![PyPI](https://img.shields.io/pypi/v/ontobio.svg)](https://pypi.python.org/pypi/ontobio) - -# ontobio - a python API for working with ontologies and associations - -This module provides objects and utility methods for working with -ontologies and associations of entities (genes, variants, etc) to -ontology classes. - -The ontologies and associations can either be local files or provided -by remote services (currently the OntoBee SPARQL service for -ontologies and a Monarch or GO Golr service for associations). - -# Documentation - -Documentation is on [readthedocs](https://ontobio.readthedocs.io) - -# Notebooks - -See the [Jupyter Notebooks](http://nbviewer.jupyter.org/github/biolink/ontobio/tree/master/notebooks/) for code examples - -# Mailing list - - * [biolink-api google group](https://groups.google.com/forum/#!forum/biolink-api) - - diff --git a/README.rst b/README.rst new file mode 100644 index 0000000..f81c4d9 --- /dev/null +++ b/README.rst @@ -0,0 +1,33 @@ +|PyPI| + +ontobio - a python API for working with ontologies and associations +=================================================================== + +This module provides objects and utility methods for working with +ontologies and associations of entities (genes, variants, etc) to +ontology classes. + +The ontologies and associations can either be local files or provided by +remote services (currently the OntoBee SPARQL service for ontologies and +a Monarch or GO Golr service for associations). + +Documentation +============= + +Documentation is on `readthedocs `__ + +Notebooks +========= + +See the `Jupyter +Notebooks `__ +for code examples + +Mailing list +============ + +- `biolink-api google + group `__ + +.. |PyPI| image:: https://img.shields.io/pypi/v/ontobio.svg + :target: https://pypi.python.org/pypi/ontobio diff --git a/setup.cfg b/setup.cfg index b88034e..5aef279 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,2 +1,2 @@ [metadata] -description-file = README.md +description-file = README.rst diff --git a/setup.py b/setup.py index 1984e97..379010e 100644 --- a/setup.py +++ b/setup.py @@ -13,20 +13,6 @@ pattern = re.compile(r"^__version__ = ['\"]([^'\"]*)['\"]", re.MULTILINE) version = pattern.search(text).group(1) -# long_description -readme_path = os.path.join(directory, 'README.md') -try: - # copied from dhimmel/obonet: - # Try to create an reStructuredText long_description from README.md - args = 'pandoc', '--from', 'markdown', '--to', 'rst', readme_path - long_description = subprocess.check_output(args) - long_description = long_description.decode() -except Exception as error: - # Fallback to markdown (unformatted on PyPI) long_description - print('README.md conversion to reStructuredText failed. Error:') - print(error) - with open(readme_path) as read_file: - long_description = read_file.read() setuptools.setup( name='ontobio', @@ -35,7 +21,7 @@ author_email='cmungall@gmail.com', url='https://github.com/biolink/ontobio', description='Library for working with OBO Library Ontologies and associations', - long_description=long_description, + long_description=open("README.rst").read(), license='BSD', #packages=['ontobio'], packages=setuptools.find_packages(),