gha

.github/workflows/main.yaml

@@ -0,0 +1,77 @@
+# Built from:
+# https://docs.github.com/en/actions/guides/building-and-testing-python
+# https://github.com/snok/install-poetry#workflows-and-tips
+
+name: Build and test linkml-datalog
+
+on: [pull_request]
+
+jobs:
+  test:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.8, 3.9]
+
+    steps:
+
+      #----------------------------------------------
+      #       check-out repo and set-up python     
+      #----------------------------------------------
+      - name: Check out repository
+        uses: actions/checkout@v2
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      #----------------------------------------------
+      #          install & configure poetry         
+      #----------------------------------------------
+      - name: Install Poetry
+        uses: snok/install-poetry@v1.1.1
+        with:
+          virtualenvs-create: true
+          virtualenvs-in-project: true      
+
+      #----------------------------------------------
+      #       load cached venv if cache exists      
+      #----------------------------------------------
+      - name: Load cached venv
+        id: cached-poetry-dependencies
+        uses: actions/cache@v2
+        with:
+          path: .venv
+          key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
+
+      #----------------------------------------------
+      # install dependencies if cache does not exist 
+      #----------------------------------------------
+      - name: Install dependencies
+        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run: poetry install --no-interaction --no-root
+
+      #----------------------------------------------
+      #    install your root project, if required 
+      #----------------------------------------------      
+      - name: Install library
+        run: poetry install --no-interaction
+
+      #----------------------------------------------
+      #              run test suite   
+      #----------------------------------------------
+      - name: Run tests
+        run: poetry run python -m unittest discover -p 'test_*.py'
+
+      #----------------------------------------------
+      #           upload coverage results
+      #----------------------------------------------
+      - name: Upload pytest test results
+        uses: actions/upload-artifact@v2
+        with:
+          name: pytest-results
+          path: htmlcov
+        # Use always() to always run this step to publish test results when there are test failures
+        if: ${{ always() }}

.github/workflows/pypi-publish.yaml

@@ -0,0 +1,53 @@
+name: Publish Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI
+    runs-on: ubuntu-latest
+
+    #----------------------------------------------
+    #       check-out repo and set-up python     
+    #----------------------------------------------
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v2.2.2
+      with:
+        python-version: 3.9
+
+    #----------------------------------------------
+    #          install & configure poetry         
+    #----------------------------------------------
+    - name: Install Poetry
+      uses: snok/install-poetry@v1.1.6
+      with:
+        virtualenvs-create: true
+        virtualenvs-in-project: true
+
+    #----------------------------------------------
+    #            install dependencies
+    #----------------------------------------------
+    - name: Install dependencies
+      run: poetry install --no-interaction
+
+    #----------------------------------------------
+    #                 build dist
+    #----------------------------------------------
+    - name: Build source and wheel archives
+      run: |
+        poetry version $(git describe --tags --abbrev=0)
+        poetry build
+
+    #----------------------------------------------
+    #          publish package to PyPI     
+    #----------------------------------------------
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@v1.2.2
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_PASSWORD }}

README.md

@@ -21,7 +21,7 @@ Docker containers will be provided in future
 Pass in a schema and a data file
 
 ```bash
-poetry run python -m linkml_datalog.engines.datalog_engine -d tmp -s personinfo.yaml example_personinfo_data.yaml
+poetry run linkml-dl -d tmp -s personinfo.yaml example_personinfo_data.yaml
 ```
 
 The output will be a ValidationReport object, in yaml

linkml_datalog/generators/dataloggen.py

@@ -399,6 +399,8 @@ def domains(self, slot: SlotDefinition) -> List[ClassDefinitionName]:
         for cn in sv.all_classes().keys():
             if slot.name in sv.class_slots(cn, direct=True):
                 domains.append(cn)
+        if slot.domain:
+            domains.append(slot.domain)
         return domains
 
     def get_slot_range(self, sn: SlotDefinitionName):

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
+version = "0.0.0"
 name = "linkml_datalog"
-version = "0.1.0"
 description = ""
 authors = ["cmungall <cjm@berkeleybop.org>"]
 
@@ -14,3 +14,6 @@ pytest = "^5.2"
 [build-system]
 requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"
+
+[tool.poetry.scripts]
+linkml-dl = "linkml_datalog.engines.datalog_engine:cli"

tests/inputs/biolink-model.yaml

@@ -4881,6 +4881,8 @@ slots:
 
   part of:
     is_a: overlaps
+    annotations:
+      transitive: true
     description: >-
       holds between parts and wholes (material entities or processes)
     in_subset: