Use GitHub CI

.github/workflows/build-test.yml

@@ -0,0 +1,50 @@
+name: Build and Test
+
+on: push
+
+concurrency:
+  group: "${{ github.ref }}"
+  cancel-in-progress: true
+
+env:
+  NDIP_DOCKER_REPOSITORY: "${{ secrets.NDIP_DOCKER_REPOSITORY }}"
+  READTHEDOCS_WEBHOOK_URL: "${{ secrets.READTHEDOCS_WEBHOOK_URL }}"
+  READTHEDOCS_WEBHOOK_SECRET: "${{ secrets.READTHEDOCS_WEBHOOK_SECRET }}"
+  GALAXY_URL: "${{ secrets.GALAXY_URL }}"
+  GALAXY_KEY: "${{ secrets.GALAXY_KEY }}"
+
+jobs:
+  build-and-test:
+    runs-on: ubuntu-latest
+    timeout-minutes: 60
+    env:
+      GIT_STRATEGY: clone
+      IMAGE_NAME: "${NDIP_DOCKER_REPOSITORY}/${{ github.repository }}"
+    steps:
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      - name: Checkout repo
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 20
+          lfs: true
+      - name: Build
+        uses: docker/build-push-action@v6
+        id: build
+        with:
+          file: dockerfiles/Dockerfile
+          load: true
+      - name: Run ruff check
+        run: docker run --rm ${{ steps.build.outputs.imageid }} poetry run ruff check
+      - name: Run format check
+        run: docker run --rm ${{ steps.build.outputs.imageid }} poetry run ruff format --check
+      - name: Run mypy
+        run: docker run --rm ${{ steps.build.outputs.imageid }} poetry run mypy .
+      - name: Unit tests
+        run: docker run -e NOVA_GALAXY_TEST_GALAXY_KEY=${{ env.GALAXY_KEY }} -e NOVA_GALAXY_TEST_GALAXY_URL=${{ env.GALAXY_URL }} --rm ${{ steps.build.outputs.imageid }} poetry run pytest
+      - name: Run coverage
+        run: docker run -e NOVA_GALAXY_TEST_GALAXY_KEY=${{ env.GALAXY_KEY }} -e NOVA_GALAXY_TEST_GALAXY_URL=${{ env.GALAXY_URL }} --rm ${{ steps.build.outputs.imageid }} sh -c "poetry run coverage run && poetry run coverage report"
+      - name: Docs test
+        run: docker run --rm ${{ steps.build.outputs.imageid }} bash build_docs.sh

.github/workflows/nova-galaxy.yml

@@ -0,0 +1,61 @@
+name: Publish Package
+
+on: workflow_dispatch
+
+concurrency:
+  group: "${{ github.ref }}"
+  cancel-in-progress: true
+
+env:
+  PYPI_API_TOKEN: "${{ secrets.PYPI_API_TOKEN }}"
+
+jobs:
+  tag-release:
+    runs-on: ubuntu-latest
+    timeout-minutes: 60
+    permissions: write-all
+    env:
+      GIT_STRATEGY: clone
+      IMAGE_NAME: "${NDIP_DOCKER_REPOSITORY}/${{ github.repository }}"
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 20
+          lfs: true
+      - name: Parse version
+        run: echo "VERSION=$(cat pyproject.toml | grep "version =" | head -n 1 | awk '{ print $3 }' | tr -d '"')" >> $GITHUB_ENV
+      - name: Create release
+        uses: actions/create-release@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tag_name: ${{ env.VERSION }}
+          release_name: ${{ env.VERSION }}
+
+  publish-package:
+    needs: tag-release
+    runs-on: ubuntu-latest
+    if: github.event_name == 'workflow_dispatch'
+    timeout-minutes: 60
+    env:
+      GIT_STRATEGY: clone
+      IMAGE_NAME: "${NDIP_DOCKER_REPOSITORY}/${{ github.repository }}"
+    steps:
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      - name: Checkout repo
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 20
+          lfs: true
+      - name: Build
+        uses: docker/build-push-action@v6
+        id: build
+        with:
+          file: dockerfiles/Dockerfile
+          load: true
+      - name: Publish
+        run: docker run --rm ${{ steps.build.outputs.imageid }} poetry publish -u __token__ -p ${PYPI_API_TOKEN}

dockerfiles/Dockerfile

@@ -1,8 +1,6 @@
-FROM --platform=amd64 regproxy.ornl.gov/hub_proxy/python:3.10-slim AS source
+FROM --platform=amd64 python:3.10-slim AS source
 
 # make sure image can run as non-root user
-
-
 ENV POETRY_CACHE_DIR=/poetry/.cache
 ENV POETRY_CONFIG_DIR=/poetry/.config
 ENV POETRY_HOME=/poetry
@@ -14,16 +12,5 @@
 RUN poetry install
 RUN poetry build --format=wheel
 
-RUN chmod og+rwX /poetry
+RUN chmod og+rwX -R /poetry
 RUN chmod og+rwX -R /src
-
-
-
-FROM --platform=amd64 regproxy.ornl.gov/hub_proxy/ubuntu:22.04 AS run
-
-RUN DEBIAN_FRONTEND="noninteractive" apt-get update && apt-get -y install tzdata
-RUN apt-get install -y python3.10 curl
-RUN curl -ksS https://bootstrap.pypa.io/get-pip.py | python3.10
-
-COPY --from=source /src/dist /dist
-RUN pip install /dist/*.whl

tests/test_workflow.py

@@ -11,7 +11,6 @@
 GALAXY_API_KEY = os.environ.get("NOVA_GALAXY_TEST_GALAXY_KEY", "")
 
 
-WORKFLOW_NAME = "Simple_test_workflow"
 TEST_HISTORY_NAME_WF = "nova_galaxy_workflow_test_history"
 
 
@@ -23,13 +22,9 @@ def test_workflow_lifecycle_with_placeholder_id(nova_instance: Connection) -> No
     """
     with nova_instance.connect() as connection:
         ds = connection.get_data_store(name=TEST_HISTORY_NAME_WF)
-        workflows = connection.galaxy_instance.workflows.get_workflows(name=WORKFLOW_NAME, published=True)
-        workflow_id = workflows[0]["id"]
-        params = WorkflowParameters()
-
-        workflow = Workflow(id=workflow_id)
+        workflow = Workflow(id="placeholder_id")
 
-        outputs = workflow.run(data_store=ds, params=params, wait=True)
+        outputs = workflow.run(data_store=ds, wait=False)
         assert outputs is None
 
         status = workflow.get_status()
@@ -40,9 +35,10 @@ def test_workflow_lifecycle_with_placeholder_id(nova_instance: Connection) -> No
         print(f"Invocation ID after run(wait=True): {invocation_id}")
         print(f"Full status details: {full_status.details if full_status else 'N/A'}")
 
-        assert status in [WorkState.ERROR, WorkState.QUEUED], (
-            f"Expected ERROR or QUEUED state after run(wait=False), got {status}"
-        )
+        assert status in [
+            WorkState.ERROR,
+            WorkState.QUEUED,
+        ], f"Expected ERROR or QUEUED state after run(wait=False), got {status}"
 
         if status == WorkState.ERROR:
             assert full_status is not None
@@ -64,9 +60,11 @@ def test_workflow_lifecycle_with_placeholder_id(nova_instance: Connection) -> No
         assert len(step_jobs) == 0, "Expected no step jobs for a placeholder/failed workflow"
 
         final_status = workflow.get_status()
-        assert final_status in [WorkState.ERROR, WorkState.CANCELED, WorkState.QUEUED], (
-            f"Unexpected final state: {final_status}"
-        )
+        assert final_status in [
+            WorkState.ERROR,
+            WorkState.CANCELED,
+            WorkState.QUEUED,
+        ], f"Unexpected final state: {final_status}"
 
 
 def test_simple_test_workflow_with_dataset(nova_instance: Connection) -> None: