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fix: improve redis connection reliability
* Use uv and mise. * Use virtool over virtool-workflow.
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‎.deepsource.toml‎

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‎.github/CODEOWNERS‎

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

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name: ci
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name: CI
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on:
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pull_request:
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workflow_dispatch:
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permissions:
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contents: read
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env:
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NODE_VERION: 22
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REGISTRY: ghcr.io
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TEST_TAG: user/create-subtraction:test
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jobs:
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commitlint:
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runs-on: ubuntu-24.04
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name: "Commitlint"
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runs-on: ubuntu-latest
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if: github.event_name == 'pull_request'
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steps:
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- name: Checkout
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- name: Commitlint
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uses: wagoid/commitlint-github-action@v6
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build:
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runs-on: ubuntu-24.04
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name: "Build"
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Build
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run: docker build --target base .
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test:
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runs-on: ubuntu-24.04
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v3
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- name: Build Docker Image
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uses: docker/build-push-action@v5
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with:
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context: .
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target: base
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push: false
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cache-from: type=gha
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cache-to: type=gha,mode=max
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tags: workflow-create-subtraction:base
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ruff-format:
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name: Ruff / Format
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Build
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id: build-push
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uses: docker/build-push-action@v5
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- name: Install mise
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uses: jdx/mise-action@v2
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- name: Install uv
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uses: astral-sh/setup-uv@v4
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with:
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context: .
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load: true
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tags: ${{ env.TEST_TAG }}
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target: test
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version: "latest"
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- name: Set up Python
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run: uv python install
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- name: Install dependencies
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run: uv sync
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- name: Check formatting
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run: uv run ruff format --check .
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ruff-lint:
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name: Ruff / Lint
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Install mise
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uses: jdx/mise-action@v2
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- name: Install uv
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uses: astral-sh/setup-uv@v4
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with:
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version: "latest"
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- name: Set up Python
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run: uv python install
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- name: Install dependencies
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run: uv sync
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- name: Check linting
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run: uv run ruff check .
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test:
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name: "Test"
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runs-on: ubuntu-latest
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needs: [build]
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v3
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- name: Install Mise
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uses: jdx/mise-action@v2
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- name: Test
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run: docker run ${{ env.TEST_TAG }}
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run: mise run test
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release:
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runs-on: ubuntu-24.04
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name: "Publish / Release"
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runs-on: ubuntu-latest
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if: github.event_name == 'push'
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needs: [build, test]
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needs: [test, commitlint]
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permissions:
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contents: write
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outputs:
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git-tag: ${{ steps.semantic.outputs.git-tag }}
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Setup NodeJS
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uses: actions/setup-node@v4
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with:
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node-version: 22
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- name: Install semantic-release
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run: npm i semantic-release@v24.2.5 @semantic-release/exec@v7.1.0 conventional-changelog-conventionalcommits@9.0.0
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- name: Run semantic-release
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run: npx semantic-release
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ghcr:
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runs-on: ubuntu-24.04
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needs: [build, release, test]
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name: "Publish / GHCR"
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runs-on: ubuntu-latest
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needs: [release]
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if: github.repository_owner == 'Virtool'
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permissions:
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packages: write
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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labels: ${{ steps.meta.outputs.labels }}
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push: true
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tags: ${{ steps.meta.outputs.tags }}
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target: "base"
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target: "base"

‎Dockerfile‎

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

‎README.md‎

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3. Compress the FASTA file for upload and long term retention.
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4. Upload the index files to the Virtool server and add sequence count and nucleotide distribution data to
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the subtraction record.
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## Contributing
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### Commits
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All commits must follow the [Conventional Commits](https://www.conventionalcommits.org/en/v1.0.0) specification.
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These standardized commit messages are used to automatically publish releases using [`semantic-release`](https://semantic-release.gitbook.io/semantic-release)
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after commits are merged to `main` from successful PRs.
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**Example**
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```text
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feat: add API support for assigning labels to existing samples
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```
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Descriptive bodies and footers are required where necessary to describe the impact of the commit. Use bullets where appropriate.
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Additional Requirements
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1. **Write in the imperative**. For example, _"fix bug"_, not _"fixed bug"_ or _"fixes bug"_.
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2. **Don't refer to issues or code reviews**. For example, don't write something like this: _"make style changes requested in review"_.
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Instead, _"update styles to improve accessibility"_.
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3. **Commits are not your personal journal**. For example, don't write something like this: _"got server running again"_
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or _"oops. fixed my code smell"_.
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From Tim Pope: [A Note About Git Commit Messages](https://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html)

‎docker-compose.yaml‎

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services:
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test:
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build:
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context: .
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target: test
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volumes:
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# Mount entire project directory
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- .:/workflow
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# Persistent volumes for build artifacts
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- venv-data:/workflow/.venv
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- uv-cache:/tmp/uv_cache
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working_dir: /workflow
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command: sleep infinity
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volumes:
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venv-data:
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uv-cache:

‎mise.toml‎

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[tools]
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uv = "latest"
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[vars]
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test_exec = "docker compose exec test"
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[tasks."test"]
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description = "Run Python tests in container"
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depends = ["test:start"]
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run = [
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"{{vars.test_exec}} bash -c 'uv sync'",
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'{{vars.test_exec}} uv run pytest {{arg(name="pytest_args", var=true, default="")}}'
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]
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[tasks."test:bash"]
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description = "Open interactive shell in test container"
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run = "{{vars.test_exec}} bash"
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[tasks."test:rebuild"]
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description = "Force rebuild the test container"
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run = [
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"docker compose down -v --remove-orphans",
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"docker compose build test",
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"docker compose up -d"
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]
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[tasks."test:start"]
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description = "Start the test container"
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run = "docker compose up -d test"
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[tasks."test:stop"]
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description = "Stop the test container"
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run = "docker compose down --remove-orphans"

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