chore: use uv

.github/CODEOWNERS

@@ -1 +1 @@
-*       @igboyes
+*       @igboyes @reecehoffmann

.github/workflows/ci.yml → .github/workflows/ci.yaml

@@ -1,26 +1,59 @@
-name: ci
+name: CI
+
+permissions:
+  contents: read
 
 on:
   push:
     branches:
       - "main"
+  pull_request:
+    branches:
+      - "main"
 
   workflow_dispatch:
 
 env:
   REGISTRY: ghcr.io
+  RUNS_ON: ubuntu-24.04
 
 jobs:
+  ruff-format:
+    name: Ruff / Format
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+      - name: Install dependencies
+        run: uv sync --dev
+      - name: Check formatting
+        run: uv run ruff format --check .
+
+  ruff-lint:
+    name: Ruff / Lint
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+      - name: Install dependencies
+        run: uv sync --dev
+      - name: Run linting
+        run: uv run ruff check .
+
   build:
-    name: build
-    runs-on: ubuntu-24.04
+    name: Build
+    runs-on: ubuntu-latest
     steps:
       - name: Checkout
         uses: actions/checkout@v4
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3
       - name: Build Docker image
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
           context: .
           push: false
@@ -29,10 +62,11 @@ jobs:
           cache-to: type=gha,mode=max
   release:
     needs: [build]
-    name: release
+    name: Publish / Release
+    if: github.event_name == 'push' && github.ref == 'refs/heads/main'
     outputs:
       git-tag: ${{ steps.semantic.outputs.git-tag }}
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-latest
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -48,22 +82,25 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: npx semantic-release
   ghcr:
-    runs-on: ubuntu-24.04
+    name: Publish / GHCR
+    runs-on: ubuntu-latest
     if: |
       github.repository_owner == 'Virtool' &&
-      (github.event_name == 'push' || github.event_name == 'workflow_dispatch') &&
+      github.event_name == 'push' &&
+      github.ref == 'refs/heads/main' &&
       needs.release.outputs.git-tag != ''
     needs: [release]
     steps:
     - name: Checkout
       uses: actions/checkout@v4
       with:
         ref: ${{ needs.release.outputs.git-tag }}
-    - uses: snok/install-poetry@v1
+    - name: Install uv
+      uses: astral-sh/setup-uv@v4
     - name: Write VERSION file
       run: echo ${{ needs.release.outputs.git-tag }} > VERSION
     - name: Update Version
-      run: poetry version ${{ needs.release.outputs.git-tag }}
+      run: uv version ${{ needs.release.outputs.git-tag }}
     - uses: docker/login-action@v3
       with:
         registry: ${{ env.REGISTRY }}

Dockerfile

@@ -1,21 +1,19 @@
-FROM python:3.12.3-bookworm AS build
+FROM python:3.13-bookworm AS build
 WORKDIR /app
-RUN curl -sSL https://install.python-poetry.org | python -
-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
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/
+ENV UV_COMPILE_BYTECODE=1 \
+    UV_LINK_MODE=copy
+COPY pyproject.toml uv.lock ./
+RUN --mount=type=cache,target=/root/.cache/uv \
+    uv sync --locked --no-install-project --no-dev
 
-FROM python:3.12.3-bookworm AS base
+FROM python:3.13-bookworm AS base
 WORKDIR /app
 RUN apt-get update && \
     apt-get install -y --no-install-recommends default-jre && \
     rm -rf /var/lib/apt/lists/* && \
     apt-get clean
-COPY --from=ghcr.io/virtool/workflow-tools:2.0.1 /opt/fastqc /opt/fastqc
+COPY --from=ghcr.io/virtool/tools:1.1.0 /tools/fastqc/0.11.9/ /opt/fastqc
 ENV VIRTUAL_ENV=/app/.venv \
     PATH="/app/.venv/bin/:/opt/fastqc:${PATH}"
 RUN chmod ugo+x /opt/fastqc/fastqc

pyproject.toml

@@ -1,25 +1,24 @@
 [project]
 name = "workflow-create-sample"
-version = "0.0.0"
+version = "0.1.0"
 description = "A workflow for creating new samples in Virtool."
+readme = "README.md"
+requires-python = ">=3.13.7,<3.14"
 authors = [
     {name = "Ian Boyes"},
     {name = "Jake Alexander"},
     {name = "Blake Smith"},
 ]
 license = "MIT"
-readme = "README.md"
-requires-python = ">=3.12.3,<3.13"
-
-[tool.poetry]
-package-mode = false
 
-[tool.poetry.dependencies]
-pyfixtures = "^1.1.0"
-virtool-workflow = "7.2.3"
+dependencies = [
+    "virtool",
+]
 
-[tool.poetry.group.dev.dependencies]
-ruff = "^0.12.10"
+[dependency-groups]
+dev = [
+    "ruff>=0.12.11",
+]
 
-[build-system]
-requires = ["poetry-core>=1.0.0"]
+[tool.uv.sources]
+virtool = { git = "https://github.com/virtool/virtool", tag = "31.11.1" }