fix(deps): use python-3.12

* Move fixtures to dedicated module
* Make Docker strategy consistent with other workflows.
* Use Python 3.12.
* Use ruff.

Author: igboyes

.github/workflows/ci.yml

@@ -32,7 +32,7 @@ jobs:
           load: true
           target: test
       - name: Test
-        run: docker run --rm -t ${{ steps.build.outputs.imageid }} pytest
+        run: docker run --rm -t ${{ steps.build.outputs.imageid }} poetry run pytest
   release:
     runs-on: ubuntu-22.04
     needs: [commitlint, test]

.pre-commit-config.yaml

@@ -1,26 +1,48 @@
-FROM debian:buster as prep
+FROM debian:bookworm as pigz
 WORKDIR /build
-RUN apt-get update && apt-get install -y make gcc zlib1g-dev wget unzip
+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:3.10-buster as base
+FROM python:3.12-bookworm as build
 WORKDIR /workflow
-COPY --from=prep /build/bowtie2/* /usr/local/bin/
-COPY --from=prep /build/pigz-2.8/pigz /usr/local/bin/pigz
 RUN curl -sSL https://install.python-poetry.org | python -
-ENV PATH="/root/.local/bin:${PATH}"
-COPY pyproject.toml poetry.lock utils.py workflow.py VERSION* ./
-RUN poetry export > requirements.txt
-RUN pip install -r requirements.txt
+ENV PATH="/root/.local/bin:${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
 
-FROM base as test
-RUN poetry export  --with dev > requirements.txt
-RUN pip install -r requirements.txt
+FROM python:3.12-bookworm as base
+WORKDIR /workflow
+ENV VIRTUAL_ENV=/app/.venv \
+    PATH="/workflow/.venv/bin:/opt/fastqc:${PATH}"
+COPY --from=bowtie2 /build/bowtie2/* /usr/local/bin/
+COPY --from=pigz /build/pigz-2.8/pigz /usr/local/bin/pigz
+COPY --from=build /workflow/.venv /workflow/.venv
+COPY fixtures.py utils.py workflow.py VERSION* ./
+
+FROM build as test
+COPY --from=bowtie2 /build/bowtie2/* /usr/local/bin/
+COPY --from=pigz /build/pigz-2.8/pigz /usr/local/bin/pigz
+RUN curl -sSL https://install.python-poetry.org | python -
+ENV PATH="/root/.local/bin:${PATH}" \
+    POETRY_CACHE_DIR='/tmp/poetry_cache' \
+    POETRY_NO_INTERACTION=1 \
+    POETRY_VIRTUALENVS_IN_PROJECT=1 \
+    POETRY_VIRTUALENVS_CREATE=1
+RUN poetry install
 COPY tests ./tests
+COPY fixtures.py utils.py workflow.py ./

Dockerfile

@@ -19,33 +19,3 @@ A workflow for building Virtool reference indexes.
 poetry install
 poetry run pytest
 ```
-
-#### Docker Container With External Dependencies Installed
-
-```shell script
-cd tests && docker-compose up
-```
-
-### Commits
-
-All commits must follow the [Conventional Commits](https://www.conventionalcommits.org/en/v1.0.0) specification.
-
-These standardized commit messages are used to automatically publish releases using [`semantic-release`](https://semantic-release.gitbook.io/semantic-release)
-after commits are merged to `main` from successful PRs.
-
-**Example**
-
-```text
-feat: add API support for assigning labels to existing samples
-```
-
-Descriptive bodies and footers are required where necessary to describe the impact of the commit. Use bullets where appropriate.
-
-Additional Requirements
-1. **Write in the imperative**. For example, _"fix bug"_, not _"fixed bug"_ or _"fixes bug"_.
-2. **Don't refer to issues or code reviews**. For example, don't write something like this: _"make style changes requested in review"_.
-Instead, _"update styles to improve accessibility"_.
-3. **Commits are not your personal journal**. For example, don't write something like this: _"got server running again"_
-or _"oops. fixed my code smell"_.
-
-From Tim Pope: [A Note About Git Commit Messages](https://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html)

README.md

@@ -0,0 +1,25 @@
+import asyncio
+from pathlib import Path
+
+from pyfixtures import fixture
+
+
+@fixture
+async def bowtie_path(work_path: Path) -> Path:
+    """The path to the generated Bowtie2 index files."""
+    path = work_path / "bowtie"
+    await asyncio.to_thread(path.mkdir)
+
+    return path / "reference"
+
+
+@fixture
+async def export_json_path(work_path: Path) -> Path:
+    """The path to the generated JSON index export file."""
+    return work_path / "reference.json.gz"
+
+
+@fixture
+async def fasta_path(work_path: Path) -> Path:
+    """The path to the generated index file."""
+    return work_path / "reference.fa"