From e68d32c90f3947da7e1f276222b74eaa0718ecc8 Mon Sep 17 00:00:00 2001 From: Ian Date: Mon, 27 May 2024 13:59:30 -0700 Subject: [PATCH 1/3] fix(deps): use python-3.12 --- .pre-commit-config.yaml | 5 - Dockerfile | 46 ++++++-- README.md | 30 ----- poetry.lock | 252 ++++++---------------------------------- pyproject.toml | 10 +- 5 files changed, 76 insertions(+), 267 deletions(-) delete mode 100644 .pre-commit-config.yaml diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml deleted file mode 100644 index 6627e59..0000000 --- a/.pre-commit-config.yaml +++ /dev/null @@ -1,5 +0,0 @@ -repos: -- repo: https://github.com/psf/black - rev: 23.1.0 - hooks: - - id: black \ No newline at end of file diff --git a/Dockerfile b/Dockerfile index 6d8fc95..243a3ee 100644 --- a/Dockerfile +++ b/Dockerfile @@ -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:${PATH}" +COPY --from=bowtie2 /build/bowtie2/* /usr/local/bin/ +COPY --from=pigz /build/pigz-2.8/pigz /usr/local/bin/pigz +COPY --from=build /workflow/.venv /workflow/.venv +COPY utils.py workflow.py VERSION* ./ + +FROM build as test +COPY --from=bowtie2 /build/bowtie2/* /usr/local/bin/ +COPY --from=pigz /build/pigz-2.8/pigz /usr/local/bin/pigz +RUN curl -sSL https://install.python-poetry.org | python - +ENV PATH="/root/.local/bin:${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 utils.py workflow.py ./ diff --git a/README.md b/README.md index b4da053..460b1e9 100644 --- a/README.md +++ b/README.md @@ -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) diff --git a/poetry.lock b/poetry.lock index e0bc1cd..46b0037 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. 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{file = "virtualenv-20.25.0-py3-none-any.whl", hash = "sha256:4238949c5ffe6876362d9c0180fc6c3a824a7b12b80604eeb8085f2ed7460de3"}, - {file = "virtualenv-20.25.0.tar.gz", hash = "sha256:bf51c0d9c7dd63ea8e44086fa1e4fb1093a31e963b86959257378aef020e1f1b"}, -] - -[package.dependencies] -distlib = ">=0.3.7,<1" -filelock = ">=3.12.2,<4" -platformdirs = ">=3.9.1,<5" - -[package.extras] -docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] -test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"] - [[package]] name = "yarl" version = "1.9.4" @@ -1583,5 +1407,5 @@ multidict = ">=4.0" [metadata] lock-version = "2.0" -python-versions = "~3.10" -content-hash = "e7b3736ade80072c871d8e8415abcefb7ab14d566482d6340a9daa8b3fdf021a" +python-versions = "~3.12" +content-hash = "de508988e3d089eb27b9f2f1690299043c1b0b5592b6ebf1739103323aa8307f" diff --git a/pyproject.toml b/pyproject.toml index 15901c4..e59b74c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,20 +4,18 @@ version = "0.0.0" description = "A workflow for building Virtool reference indexes" authors = ["Ian Boyes", "Blake Smith", "Tiensheng Sui"] license = "MIT" -classifiers=[ - "Programming Language:: Python:: 3.10", -] [tool.poetry.dependencies] -python = "~3.10" -virtool-workflow = {version="^6.0.0a10", allow-prereleases=true} +python = "~3.12" +virtool-workflow = "^6.0.0" +setuptools = "^70.0.0" [tool.poetry.group.dev.dependencies] -pre-commit = "^3.4.0" pytest = "^7.4.2" pytest-asyncio = "^0.23.3" pytest-mock = "^3.6.1" syrupy = "^4.6.0" +ruff = "^0.4.5" [tool.pytest.ini_options] asyncio_mode = "auto" From fb19fe1e088e5e784dd92afb9edf801835e63f8b Mon Sep 17 00:00:00 2001 From: Ian Date: Mon, 27 May 2024 14:02:54 -0700 Subject: [PATCH 2/3] refactor: move fixtures to dedicated module --- Dockerfile | 4 ++-- fixtures.py | 25 +++++++++++++++++++++++++ workflow.py | 22 ---------------------- 3 files changed, 27 insertions(+), 24 deletions(-) create mode 100644 fixtures.py diff --git a/Dockerfile b/Dockerfile index 243a3ee..e2804df 100644 --- a/Dockerfile +++ b/Dockerfile @@ -32,7 +32,7 @@ ENV VIRTUAL_ENV=/app/.venv \ 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 utils.py workflow.py VERSION* ./ +COPY fixtures.py utils.py workflow.py VERSION* ./ FROM build as test COPY --from=bowtie2 /build/bowtie2/* /usr/local/bin/ @@ -45,4 +45,4 @@ ENV PATH="/root/.local/bin:${PATH}" \ POETRY_VIRTUALENVS_CREATE=1 RUN poetry install COPY tests ./tests -COPY utils.py workflow.py ./ +COPY fixtures.py utils.py workflow.py ./ diff --git a/fixtures.py b/fixtures.py new file mode 100644 index 0000000..a724977 --- /dev/null +++ b/fixtures.py @@ -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" diff --git a/workflow.py b/workflow.py index effce92..43bad28 100644 --- a/workflow.py +++ b/workflow.py @@ -2,7 +2,6 @@ import os from pathlib import Path -from pyfixtures import fixture from virtool_core.utils import compress_file from virtool_workflow import RunSubprocess, hooks, step from virtool_workflow.data.indexes import WFNewIndex @@ -15,27 +14,6 @@ async def delete_index(new_index: WFNewIndex): await new_index.delete() -@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" - - @step(name="Process OTUs") async def process_otus( export_json_path: Path, From 0d99b007ba1c4a0d55ca3f46d839b9caf059710d Mon Sep 17 00:00:00 2001 From: Ian Date: Mon, 27 May 2024 14:05:54 -0700 Subject: [PATCH 3/3] ci: fix test command --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 8a4f171..7f498b7 100644 --- a/.github/workflows/ci.yml +++ b/.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]