feat: support virtool-workflow^6.0.0-alpha10

* Use `virtool-workflow==6.0.0alpha10`.
* Add `subtraction_read_ids.txt` to gitignore.
* Overhaul tests and test data.
* Improve Docker-based CI testing.

Author: igboyes

.dockerignore

@@ -1 +1,3 @@
+.github
+subtracted_read_ids.txt
 target

.github/workflows/ci.yml

@@ -13,38 +13,42 @@ jobs:
     runs-on: ubuntu-22.04
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - name: commitlint
         uses: wagoid/commitlint-github-action@v5
-  build:
-    runs-on: ubuntu-22.04
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v3
-      - name: Build
-        run: docker build --target=base .
   test:
     runs-on: ubuntu-22.04
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
+      - name: Setup Docker
+        uses: docker/setup-buildx-action@v3
+      - name: Build
+        id: build
+        uses: docker/build-push-action@v5
+        with:
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+          context: .
+          load: true
+          target: test
       - name: Test
-        run: docker build --target=test .
+        run: docker run --rm -t ${{ steps.build.outputs.imageid }} pytest
   release:
     runs-on: ubuntu-22.04
-    needs: test
+    needs: [commitlint, test]
     if: github.event_name == 'push'
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Setup Node
-        uses: actions/setup-node@v3
+        uses: actions/setup-node@v4
         with:
-          node-version: 18
+          node-version: 20
       - name: Install semantic-release
-        run: npm i semantic-release@v18.0.0 conventional-changelog-conventionalcommits@4.6.1
+        run: npm i semantic-release@v23.0.0 conventional-changelog-conventionalcommits@7.0.2
       - name: Release
         env:
           GITHUB_USERNAME: ${{ secrets.GH_USERNAME }}

.gitignore

@@ -2,6 +2,7 @@
 .idea
 .pytest_cache
 .vscode
-__pycache__
 *.pyc
+__pycache__
+subtracted_read_ids.txt
 target

.pre-commit-config.yaml

@@ -30,16 +30,15 @@ ENV PATH="/root/.cargo/bin:/root/.local/bin:${PATH}"
 RUN pip install --upgrade pip
 RUN pip install maturin==0.14.5
 COPY src src
-COPY Cargo.toml Cargo.lock fixtures.py pathoscope.py  poetry.lock pyproject.toml workflow.py ./
+COPY Cargo.toml Cargo.lock fixtures.py utils.py  poetry.lock pyproject.toml workflow.py ./
 RUN maturin build --release
 RUN poetry export > requirements.txt
 RUN pip install -r requirements.txt
 RUN pip install /app/target/wheels/rust_utils*.whl
 
-
 FROM base as test
 WORKDIR /app
-RUN poetry export  --with dev > requirements.txt
+RUN poetry export --with dev > requirements.txt
 RUN pip install -r requirements.txt
+COPY example ./example
 COPY tests ./tests
-RUN pytest