Merge pull request #157 from biolink/biolink_model_4.0

Biolink model 3.6.0 update, and extra dependency resolution action

.github/workflows/check-dependencies.yaml

@@ -0,0 +1,44 @@
+---
+name: Check Dependencies in Pyproject.toml
+
+# Controls when the action will run.
+on:
+  pull_request:
+    types: [opened, synchronize, reopened]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+    types: trigger-run-check-dependencies
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "build"
+  build:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python: [ "3.9", "3.10" ]
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v2
+
+      - uses: actions/setup-python@v2
+        name: setup python environment
+        with:
+          python-version: ${{ matrix.python }}
+
+      # this step we remove and rebuild the poetry.lock file to ensure that the tests that follow can be run
+      # with the latest dependencies
+      - name: Install dependencies
+        run: |
+          pip install --upgrade pip
+          pip install poetry
+          rm -rf poetry.lock
+          poetry install 
+
+      - name: Run tests
+        run: |
+          make test

.github/workflows/initialize-toolkit-daily.yaml

@@ -0,0 +1,42 @@
+---
+name: Check BMT initialization daily
+
+on:
+  pull_request:
+  schedule:
+    - cron: '0 5 * * *'  # once per day at midnight ET
+  workflow_dispatch:
+  # Allows you to run this workflow manually from the Actions tab
+    types: trigger-run-check-toolkit-initialization
+
+jobs:
+  # This workflow contains a single job called "build"
+  build:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python: [ "3.9", "3.10" ]
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v2
+
+      - uses: actions/setup-python@v2
+        name: setup python environment
+        with:
+          python-version: ${{ matrix.python }}
+
+      # this step we remove and rebuild the poetry.lock file to ensure that the tests that follow can be run
+      # with the latest dependencies
+      - name: Install dependencies
+        run: |
+          pip install --upgrade pip
+          pip install poetry
+          rm -rf poetry.lock
+          poetry install 
+
+      - name: Run tests
+        run: |
+          make test

bmt/toolkit.py

@@ -19,7 +19,7 @@
 Url = str
 Path = str
 
-LATEST_BIOLINK_RELEASE = "3.5.4"
+LATEST_BIOLINK_RELEASE = "3.6.0"
 
 REMOTE_PATH = f"https://raw.githubusercontent.com/biolink/biolink-model/v{LATEST_BIOLINK_RELEASE}/biolink-model.yaml"
 PREDICATE_MAP = f"https://raw.githubusercontent.com/biolink/biolink-model/v{LATEST_BIOLINK_RELEASE}/predicate_mapping.yaml"

tests/unit/test_toolkit.py

@@ -86,6 +86,12 @@ def test_get_model_version(toolkit):
     assert version == LATEST_BIOLINK_RELEASE
 
 
+def test_sv(toolkit):
+    v = toolkit.view
+    ancs = v.slot_ancestors('broad match')
+    print(ancs)
+    assert 'related to' in ancs
+
 def test_get_denormalized_association_slots(toolkit):
     annotations = toolkit.get_denormalized_association_slots(formatted=True)
     print(annotations)
@@ -896,11 +902,11 @@ def test_descendants(toolkit):
 def test_children(toolkit):
     assert CAUSES in toolkit.get_children("contributes to")
     assert "physically interacts with" in toolkit.get_children(INTERACTS_WITH)
-    assert "transcript" in toolkit.get_children(NUCLEIC_ACID_ENTITY)
+    assert "transcript" in toolkit.get_children(BIOLOGICAL_ENTITY)
     assert GENE in toolkit.get_children(GENE_OR_GENE_PRODUCT)
     assert GENE not in toolkit.get_children(GENE_OR_GENE_PRODUCT, mixin=False)
     assert "biolink:Transcript" in toolkit.get_children(
-        NUCLEIC_ACID_ENTITY, formatted=True
+        BIOLOGICAL_ENTITY, formatted=True
     )