fix: improve redis connection reliability

- Use mise and uv.
- Update CI. Use mise and Docker build caching.
- Overhaul Dockerfile.
- Migrate `virtool-workflow` -> `virtool`.

Author: igboyes

.deepsource.toml

@@ -31,6 +31,8 @@ jobs:
         uses: actions/checkout@v4
       - name: Setup Docker
         uses: docker/setup-buildx-action@v3
+      - name: Setup mise
+        uses: jdx/mise-action@v2
       - name: Build
         id: build
         uses: docker/build-push-action@v5
@@ -41,7 +43,7 @@ jobs:
           load: true
           target: test
       - name: Test
-        run: docker run --rm -t ${{ steps.build.outputs.imageid }} poetry run pytest
+        run: docker run --rm -t ${{ steps.build.outputs.imageid }} uv run pytest
   release:
     name: Release
     runs-on: ubuntu-24.04
@@ -76,12 +78,10 @@ jobs:
       uses: actions/checkout@v4
       with:
         ref: ${{ needs.release.outputs.git-tag }}
-    - name: Install Poetry
-      uses: snok/install-poetry@v1
+    - name: Setup mise
+      uses: jdx/mise-action@v2
     - name: Write VERSION file
       run: echo ${{ needs.release.outputs.git-tag }} > VERSION
-    - name: Update Version
-      run: poetry version ${{ needs.release.outputs.git-tag }}
     - name: Login
       uses: docker/login-action@v3
       with:

.github/workflows/ci.yml renamed to .github/workflows/ci.yaml

@@ -1,48 +1,28 @@
-FROM debian:bookworm as pigz
-WORKDIR /build
-RUN apt-get update && apt-get install -y gcc make wget zlib1g-dev
-RUN wget https://zlib.net/pigz/pigz-2.8.tar.gz && \
-    tar -xzvf pigz-2.8.tar.gz && \
-    cd pigz-2.8 && \
-    make
-
-FROM debian:bookworm as bowtie2
-WORKDIR /build
-RUN apt-get update && apt-get install -y unzip wget
-RUN wget https://github.com/BenLangmead/bowtie2/releases/download/v2.3.2/bowtie2-2.3.2-legacy-linux-x86_64.zip && \
-    unzip bowtie2-2.3.2-legacy-linux-x86_64.zip && \
-    mkdir bowtie2 && \
-    cp bowtie2-2.3.2-legacy/bowtie2* bowtie2
-
-FROM python:3.12.3-bookworm as build
-WORKDIR /workflow
-RUN curl -sSL https://install.python-poetry.org | python -
+FROM python:3.13-bookworm AS uv
+WORKDIR /app
+RUN apt-get update && apt-get install -y git && rm -rf /var/lib/apt/lists/*
+RUN curl -LsSf https://astral.sh/uv/install.sh | sh
 ENV PATH="/root/.local/bin:${PATH}" \
-    POETRY_CACHE_DIR='/tmp/poetry_cache' \
-    POETRY_NO_INTERACTION=1 \
-    POETRY_VIRTUALENVS_IN_PROJECT=1 \
-    POETRY_VIRTUALENVS_CREATE=1
-COPY pyproject.toml poetry.lock ./
-RUN poetry install --without dev --no-root
+    UV_CACHE_DIR='/tmp/uv_cache'
+COPY uv.lock pyproject.toml README.md ./
+RUN uv sync
+
+FROM python:3.13-bookworm AS deps
+COPY --from=ghcr.io/virtool/tools:1.1.0 /tools/bowtie2/2.5.4/bowtie* /usr/local/bin/
+COPY --from=ghcr.io/virtool/tools:1.1.0 /tools/pigz/2.8/pigz /usr/local/bin/
 
-FROM python:3.12.3-bookworm as base
-WORKDIR /workflow
-ENV VIRTUAL_ENV=/app/.venv \
-    PATH="/workflow/.venv/bin:/opt/fastqc:${PATH}"
-COPY --from=bowtie2 /build/bowtie2/* /usr/local/bin/
-COPY --from=pigz /build/pigz-2.8/pigz /usr/local/bin/pigz
-COPY --from=build /workflow/.venv /workflow/.venv
+FROM deps AS base 
+WORKDIR /app
+ENV PATH="/app/.venv/bin:${PATH}"
+COPY --from=uv /app/.venv /app/.venv
 COPY fixtures.py utils.py workflow.py VERSION* ./
 
-FROM build as test
-COPY --from=bowtie2 /build/bowtie2/* /usr/local/bin/
-COPY --from=pigz /build/pigz-2.8/pigz /usr/local/bin/pigz
-RUN curl -sSL https://install.python-poetry.org | python -
+FROM deps AS test
+WORKDIR /app
+RUN apt-get update && apt-get install -y git && rm -rf /var/lib/apt/lists/*
+RUN curl -LsSf https://astral.sh/uv/install.sh | sh
 ENV PATH="/root/.local/bin:${PATH}" \
-    POETRY_CACHE_DIR='/tmp/poetry_cache' \
-    POETRY_NO_INTERACTION=1 \
-    POETRY_VIRTUALENVS_IN_PROJECT=1 \
-    POETRY_VIRTUALENVS_CREATE=1
-RUN poetry install
+    UV_CACHE_DIR='/tmp/uv_cache'
+COPY uv.lock pyproject.toml README.md ./
 COPY tests ./tests
 COPY fixtures.py utils.py workflow.py ./

Dockerfile

@@ -0,0 +1,14 @@
+[tools]
+uv = "latest"
+
+[tasks.test]
+description = "Run tests using uv"
+run = "uv run pytest"
+
+[tasks.lint]
+description = "Run ruff linter"
+run = "uv run ruff check"
+
+[tasks.format]
+description = "Format code with ruff"
+run = "uv run ruff format"

mise.toml

@@ -1,34 +1,37 @@
 [project]
 name = "workflow-build-index"
-version = "0.0.0"
+version = "0.1.0"
+readme = "README.md"
 description = "A workflow for building Virtool reference indexes"
 authors = [
     { name = "Ian Boyes"},
     { name = "Blake Smith" },
-    { name = "Tiensheng Sui" }
+    { name = "Tiensheng Sui" },
+    { name = "Christine Wong Chong" },
+    { name = "Markus Swoveland" },
+    { name = "Matt Curtis" }
 ]
-license = "MIT"
-requires-python = ">=3.12.3,<3.13"
+license="MIT"
+requires-python = ">=3.13.7,<3.14.0"
 
-[tool.poetry]
-package-mode = false
-
-[tool.poetry.dependencies]
-virtool-workflow = "7.2.3"
+dependencies = [
+    "virtool",
+]
 
-[tool.poetry.group.dev.dependencies]
-pytest = ">=7.4.2"
-pytest-asyncio = ">=0.23.3"
-pytest-mock = ">=3.6.1"
-syrupy = ">=4.6.0"
-ruff = ">=0.4.5"
+[dependency-groups]
+dev = [
+    "pytest>=8.4.1",
+    "pytest-asyncio>=1.1.0",
+    "pytest-mock>=3.14.1",
+    "ruff>=0.12.11",
+    "syrupy>=4.9.1",
+]
 
 [tool.pytest.ini_options]
 asyncio_mode = "auto"
 
 [tool.ruff.lint]
 select = ["ALL"]
 
-[build-system]
-requires = ["poetry-core>=1.0.0"]
-build-backend = "poetry.core.masonry.api"
+[tool.uv.sources]
+virtool = { git = "https://github.com/virtool/virtool", tag = "31.11.3" }