Merge pull request #292 from linkml/issue-1749-gh-actions

Issue 1749 gh actions - add once a week dependency check

Author: sierra-moxon

.github/workflows/check-dependencies.yaml

@@ -0,0 +1,65 @@
+name: Build and test linkml-runtime with latest dependency versions
+
+on:
+  schedule:
+    - cron: '0 5 * * 1'  # once per week on Monday at 05:00 UTC
+  workflow_dispatch:
+  # Allows you to run this workflow manually from the Actions tab
+    types: trigger-run-check-dependencies
+
+jobs:
+  test:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest]
+        python-version: ["3.8", "3.9", "3.10"]
+        exclude:
+        - os: windows-latest
+          python-version: "3.8"
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+
+      #----------------------------------------------
+      #          install poetry
+      #----------------------------------------------
+      - name: Install Poetry
+        # Pin to 1.3.2 to workaround https://github.com/python-poetry/poetry/issues/7611
+        run: pipx install poetry==1.3.2
+
+      #----------------------------------------------
+      #       check-out repo and set-up python
+      #----------------------------------------------
+      - name: Check out repository
+        uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'poetry'
+
+      #----------------------------------------------
+      #    install your root project, if required
+      #----------------------------------------------
+      - name: Install library
+        run: poetry install --no-interaction
+
+      # this step we remove and rebuild the poetry.lock file to ensure that the tests that follow can be run
+      # with the latest dependencies
+
+      #----------------------------------------------
+      # Remove and Rebuild the poetry.lock File
+      #----------------------------------------------
+      - name: Remove poetry.lock (Unix)
+        if: runner.os != 'Windows'
+        run: rm -rf poetry.lock
+
+      - name: Remove poetry.lock (Windows)
+        if: runner.os == 'Windows'
+        run: Remove-Item poetry.lock -Force
+
+      - name: Run tests
+        run: poetry run python -m unittest discover

.github/workflows/main.yaml

@@ -12,10 +12,8 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest]
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.8", "3.9", "3.10"]
         exclude:
-        - os: windows-latest
-          python-version: "3.7"
         - os: windows-latest
           python-version: "3.8"
 

linkml_runtime/loaders/yaml_loader.py

@@ -9,6 +9,7 @@
 from linkml_runtime.utils.yamlutils import YAMLRoot, DupCheckYamlLoader
 from pydantic import BaseModel
 
+
 class YAMLLoader(Loader):
     """
     A Loader that is capable of instantiating LinkML data objects from a YAML file
@@ -34,7 +35,7 @@ def load_as_dict(self,
 
     def load_any(self,
                  source: Union[str, dict, TextIO],
-                 target_class: Union[Type[YAMLRoot],Type[BaseModel]],
+                 target_class: Union[Type[YAMLRoot], Type[BaseModel]],
                  *, base_dir: Optional[str] = None,
                  metadata: Optional[FileInfo] = None, **_) -> Union[YAMLRoot, List[YAMLRoot]]:
         data_as_dict = self.load_as_dict(source, base_dir=base_dir, metadata=metadata)