Merge pull request #8 from NatalieThurlby/dev

Major refactoring for release as ontolopy

.gitignore

@@ -1,9 +1,9 @@
 *.DS_Store
+_build/
 build/
 _build/
 dist/
 tests/data/
 __pycache__/
-data/
 *.egg-info/
 .idea/

CONTRIBUTING.md

@@ -0,0 +1,3 @@
+# Contributing
+
+[//]: # (TODO: Link to contributing in docs)

LICENSE.md

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021 Natalie Thurlby
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -1,28 +1,26 @@
-# `uberon_py`: a python package for the Uberon ontology
-:construction: :construction: This package is under development :construction: :construction: 
-
-## Summary
-I created this package to be able to easily interrogate relationships between Uberon terms in Python. 
+# Ontolo**py** a python package for working with .obo files
+:construction: This package is in development :construction:
 
 ## Installation
-`uberon_py` is available on pip, and can be installed using:
+Ontolopy is available on pip, and can be installed using:
+
 ```bash
-pip3 install uberon_py
+pip install ontolopy
 ```
 
 ## Usage
 Example usage:
 
 ```python
-import uberon_py
+import ontolopy
 
 # read an ontology in obo format
-obo = uberon_py.Obo('path_to_file/uberon_ext.obo')
+obo = ontolopy.Obo('path_to_file/uberon_ext.obo')
 
 # find relationships between terms of interest:
 # (in this case, are any of the source_terms, is_a or part_of the brain?)
 source_terms = ['UBERON:0003290','UBERON:0003369','UBERON:0003703'] 
 target_terms = ['UBERON:0000955'] #  brain term
-relations_of_interest  = 'is_a','part_of']
-relations = uberon_py.Relations(source_terms,target_terms,relations_of_interest[,obo.ont).relations
+relations_of_interest  = ['is_a','part_of']
+relations = ontolopy.Relations(source_terms,target_terms,relations_of_interest,obo.ont).relations
 ```

conftest.py

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+# Adds tests marked with download won't run without pytest --download
+def pytest_addoption(parser):
+    parser.addoption('--download', action='store_true', dest="download",
+                     default=False, help="enable download-decorated tests")
+
+
+def pytest_configure(config):
+    if not config.option.download:
+        setattr(config.option, 'markexpr', 'not download')