From 5914d9830fdb801cc17f824a684ca81f39406057 Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Mon, 3 Jul 2017 13:59:03 -0700 Subject: [PATCH 1/4] mv --- README.md => README.rst | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename README.md => README.rst (100%) diff --git a/README.md b/README.rst similarity index 100% rename from README.md rename to README.rst From 07bcfd4ea128007de94c339e0947e47314c352d5 Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Mon, 3 Jul 2017 13:59:22 -0700 Subject: [PATCH 2/4] format as rst --- README.rst | 32 ++++++++++++++++++++------------ 1 file changed, 20 insertions(+), 12 deletions(-) diff --git a/README.rst b/README.rst index f104324..f81c4d9 100644 --- a/README.rst +++ b/README.rst @@ -1,25 +1,33 @@ -[![PyPI](https://img.shields.io/pypi/v/ontobio.svg)](https://pypi.python.org/pypi/ontobio) +|PyPI| -# ontobio - a python API for working with ontologies and associations +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). +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 +============= -Documentation is on [readthedocs](https://ontobio.readthedocs.io) +Documentation is on `readthedocs `__ -# Notebooks +Notebooks +========= -See the [Jupyter Notebooks](http://nbviewer.jupyter.org/github/biolink/ontobio/tree/master/notebooks/) for code examples +See the `Jupyter +Notebooks `__ +for code examples -# Mailing list - - * [biolink-api google group](https://groups.google.com/forum/#!forum/biolink-api) +Mailing list +============ +- `biolink-api google + group `__ +.. |PyPI| image:: https://img.shields.io/pypi/v/ontobio.svg + :target: https://pypi.python.org/pypi/ontobio From d44d69d1585292858c4b9b6a850dc32e691df01e Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Mon, 3 Jul 2017 14:01:46 -0700 Subject: [PATCH 3/4] tweaking setup, no need to convert --- setup.cfg | 2 +- setup.py | 14 +------------- 2 files changed, 2 insertions(+), 14 deletions(-) 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..da7c11d 100644 --- a/setup.py +++ b/setup.py @@ -14,19 +14,7 @@ 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() +readme_path = os.path.join(directory, 'README.rst') setuptools.setup( name='ontobio', From a868bc1ef5a5be147189a309d1cd04215354ea5e Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Mon, 3 Jul 2017 14:05:20 -0700 Subject: [PATCH 4/4] get desc from readme.rst --- setup.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/setup.py b/setup.py index da7c11d..379010e 100644 --- a/setup.py +++ b/setup.py @@ -13,8 +13,6 @@ pattern = re.compile(r"^__version__ = ['\"]([^'\"]*)['\"]", re.MULTILINE) version = pattern.search(text).group(1) -# long_description -readme_path = os.path.join(directory, 'README.rst') setuptools.setup( name='ontobio', @@ -23,7 +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(),