Merge pull request #62 from biolink/tox

add tox, add biolink-2.2.3 support

.github/workflows/run_tox.yml

@@ -0,0 +1,32 @@
+name: Run Tox
+
+on:
+  # Triggers the workflow on push or pull request events but only for the master branch
+  push:
+    branches: [ master ]
+  pull_request:
+    types: [opened, synchronize, reopened]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+    types: trigger-run-tox
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python: [3.7, 3.8, 3.9]
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python }}
+      - name: Install Tox and any other packages
+        run: pip install tox
+      - name: Run Tox
+        # Run tox using the version of Python in `PATH`
+        run: tox -e py

MANIFEST.in

@@ -0,0 +1 @@
+include requirements.txt

Makefile

@@ -4,7 +4,7 @@ dev-install:
 install:
 	python setup.py install
 
-tests:
+test:
 	pytest tests/*
 
 cleandist:

bmt/toolkit.py

@@ -10,7 +10,7 @@
 Url = str
 Path = str
 
-REMOTE_PATH = 'https://raw.githubusercontent.com/biolink/biolink-model/2.2.0/biolink-model.yaml'
+REMOTE_PATH = 'https://raw.githubusercontent.com/biolink/biolink-model/2.2.3/biolink-model.yaml'
 RELATED_TO = 'related to'
 CACHE_SIZE = 1024
 

requirements.txt

@@ -8,3 +8,6 @@ sphinx-rtd-theme
 sphinxcontrib-napoleon
 numpydoc
 recommonmark
+tox
+flake8
+black

setup.py

@@ -4,7 +4,7 @@
     REQUIREMENTS = FH.readlines()
 
 NAME = 'bmt'
-VERSION = '0.7.3'
+VERSION = '0.7.4'
 DESCRIPTION = 'Biolink Model Toolkit: A Python API for working with the Biolink Model'
 URL = 'https://github.com/biolink/biolink-model-toolkit'
 AUTHOR = 'Deepak Unni', 'Sierra Moxon'

tests/unit/test_toolkit.py

@@ -31,7 +31,12 @@ def toolkit():
 
 def test_get_model_version(toolkit):
     version = toolkit.get_model_version()
-    assert version == '2.2.0'
+    assert version == '2.2.3'
+
+
+def test_get_element_by_mapping(toolkit):
+    element_name = toolkit.get_element_by_mapping('RO:0002410')
+    assert element_name == 'causes'
 
 
 def test_get_all_elements(toolkit):
@@ -254,16 +259,14 @@ def test_get_slot_domain(toolkit):
     assert BIOLINK_BIOLOGICAL_ENTITY in toolkit.get_slot_domain(ENABLED_BY, include_ancestors=True, formatted=True)
     assert 'entity' in toolkit.get_slot_domain('name')
     assert 'entity' in toolkit.get_slot_domain('category')
-    assert ASSOCIATION in toolkit.get_slot_domain('relation')
+    assert ASSOCIATION in toolkit.get_slot_domain('predicate')
 
 
 def test_get_slot_range(toolkit):
     assert 'disease or phenotypic feature' in toolkit.get_slot_range('treats')
     assert BIOLOGICAL_ENTITY in toolkit.get_slot_range('treats', include_ancestors=True)
     assert BIOLINK_BIOLOGICAL_ENTITY in toolkit.get_slot_range('treats', include_ancestors=True, formatted=True)
     assert 'label type' in toolkit.get_slot_range('name')
-    assert 'uriorcurie' in toolkit.get_slot_range('relation')
-    assert 'metatype:Uriorcurie' in toolkit.get_slot_range('relation', formatted=True)
 
 
 def test_get_all_slots_with_class_domain(toolkit):

tox.ini

@@ -0,0 +1,50 @@
+# TODO explain tox and testenv reserved words
+[tox]
+envlist = py37
+          py38
+          py39
+          black-diff
+          flake8
+          example
+
+[testenv]
+extras =
+    jupyter
+allowlist_externals =
+    /usr/bin/make
+    /bin/cat
+    /bin/cp
+    /bin/mkdir
+    /usr/bin/git
+deps =
+    -rrequirements.txt
+commands = pytest
+
+#  TODO document how these inherit from testenv
+[testenv:black-diff]
+line_length = 120
+commands =
+    black --check --diff bmt tests
+
+[testenv:black]
+line_length = 120
+commands =
+    black bmt tests
+
+[testenv:flake8]
+commands =
+    flake8 bmt tests
+
+[flake8]
+ignore = E501
+max_line_length = 70
+max-complexity = 10
+per-file-ignores = __init__.py:F401
+
+[testenv:example]
+deps =
+    -rrequirements.txt
+setenv =
+  PYTHONPATH=.
+commands =
+    python examples/edgelabel.py