From 713b333a8dbc54e7b19d15292b8bbe44ca5c9fee Mon Sep 17 00:00:00 2001 From: Ian Date: Mon, 27 May 2024 12:20:52 -0700 Subject: [PATCH] fix(deps): use python-3.12 --- .dockerignore | 1 - .github/workflows/ci.yml | 18 +- .pre-commit-config.yaml | 5 - Cargo.lock | 263 ------- Cargo.toml | 13 - Dockerfile | 67 +- poetry.lock | 1611 ++++++++++++++++++-------------------- pyproject.toml | 8 +- src/lib.rs | 56 -- tests/test_workflow.py | 18 +- workflow.py | 29 +- 11 files changed, 856 insertions(+), 1233 deletions(-) delete mode 100644 .dockerignore delete mode 100644 .pre-commit-config.yaml delete mode 100644 Cargo.lock delete mode 100644 Cargo.toml delete mode 100644 src/lib.rs diff --git a/.dockerignore b/.dockerignore deleted file mode 100644 index eb5a316..0000000 --- a/.dockerignore +++ /dev/null @@ -1 +0,0 @@ -target diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index a9c1261..9b5d34e 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -17,39 +17,43 @@ jobs: if: github.event_name == 'pull_request' steps: - name: Checkout - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: fetch-depth: 0 - - uses: wagoid/commitlint-github-action@v5 + - name: Commitlint + uses: wagoid/commitlint-github-action@v5 build: runs-on: ubuntu-22.04 steps: - name: Checkout uses: actions/checkout@v3 - name: Build - run: docker build . + run: docker build --target base . test: runs-on: ubuntu-22.04 steps: - name: Checkout - uses: actions/checkout@v3 - - name: Build and Test + uses: actions/checkout@v4 + - name: Build + id: build-push uses: docker/build-push-action@v4 with: context: . load: true tags: ${{ env.TEST_TAG }} target: test + - name: Test + run: docker run ${{ env.TEST_TAG }} release: runs-on: ubuntu-22.04 if: github.event_name == 'push' steps: - name: Checkout - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Setup NodeJS uses: actions/setup-node@v3 with: - node-version: 16 + node-version: 20 - name: Install semantic-release run: npm i semantic-release@v18.0.0 conventional-changelog-conventionalcommits@4.6.1 - 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tar -xzvf pigz-2.8.tar.gz && \ - cd pigz-2.8 && \ - make +RUN apt-get update && apt-get install -y unzip wget RUN wget https://github.com/BenLangmead/bowtie2/releases/download/v2.3.2/bowtie2-2.3.2-legacy-linux-x86_64.zip && \ unzip bowtie2-2.3.2-legacy-linux-x86_64.zip && \ mkdir bowtie2 && \ cp bowtie2-2.3.2-legacy/bowtie2* bowtie2 -FROM python:3.10-buster as rust +FROM debian:bookworm as pigz WORKDIR /build -RUN apt-get update && apt-get install -y curl build-essential -RUN curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y -ENV PATH="/root/.cargo/bin:${PATH}" -RUN pip install maturin==0.14.7 -COPY src src -COPY Cargo.toml Cargo.lock ./ -RUN maturin build --release +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 python:3.10-buster as base +FROM python:3.12-bookworm as build WORKDIR /workflow RUN curl -sSL https://install.python-poetry.org | python - -ENV PATH="/root/.local/bin:${PATH}" -COPY --from=prep /build/bowtie2/* /usr/local/bin/ -COPY --from=prep /build/pigz-2.8/pigz /usr/local/bin/pigz -COPY --from=rust /build/target/wheels/count_nucleotides_and_seqs*.whl ./ -COPY workflow.py pyproject.toml poetry.lock VERSION* ./ -RUN poetry export > requirements.txt -RUN pip install --upgrade pip -RUN pip install -r requirements.txt -RUN pip install ./count_nucleotides_and_seqs*.whl +ENV PATH="/root/.local/bin:${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 +FROM python:3.12-bookworm as base WORKDIR /workflow -RUN poetry export --with dev > requirements.txt -RUN pip install -r requirements.txt -COPY tests ./tests -RUN pytest \ No newline at end of file +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 workflow.py VERSION* ./ + +FROM build as test +WORKDIR /workflow +RUN curl -sSL https://install.python-poetry.org | python - 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b/pyproject.toml @@ -11,18 +11,18 @@ authors = [ ] [tool.poetry.dependencies] -python = "~3.10" -virtool-workflow = "6.0.0a7" +python = "~3.12" +virtool-workflow = "^6.0.0" +setuptools = "^70.0.0" [tool.poetry.group.dev.dependencies] pytest = "^7.4.2" -pytest-aiohttp = "^1.0.5" pytest-asyncio = "^0.21.1" pytest-datafiles = "^2.0.1" pytest-mock = "^3.12.0" +ruff = "^0.4.5" [tool.pytest.ini_options] -markers = ["asyncio_mode: auto"] asyncio_mode = "auto" [build-system] diff --git a/src/lib.rs b/src/lib.rs deleted file mode 100644 index 6cbcb8e..0000000 --- a/src/lib.rs +++ /dev/null @@ -1,56 +0,0 @@ -use std::fs::File; -use std::io::{self, BufRead}; -use std::path::Path; -use pyo3::prelude::*; - -#[pymodule] -fn count_nucleotides_and_seqs(_py: Python, m: &PyModule) -> Result<(), PyErr> -{ - m.add_function(wrap_pyfunction!(run, m)?)?; - return Ok(()); -} - -#[pyfunction] -fn run(filename: String) -> (u64, u64, u64, u64, u64, u32) -{ - - let mut a: u64 = 0; - let mut t: u64 = 0; - let mut g: u64 = 0; - let mut c: u64 = 0; - let mut n: u64 = 0; - - let mut count: u32 = 0; - - if let Ok(lines) = read_lines(filename) { - for line in lines { - if let Ok(fasta_line) = line { - if fasta_line.starts_with('>') { - count = count + 1; - continue; - } - - for letter in fasta_line.chars() { - match letter { - 'a' | 'A' => a = a + 1, - 't' | 'T' => t = t + 1, - 'g' | 'G' => g = g + 1, - 'c' | 'C' => c = c + 1, - 'n' | 'N' => n = n + 1, - _ => continue, - } - } - } - } - } - - return (a, t, g, c, n, count); -} - -fn read_lines

(filename: P) -> io::Result>> -where - P: AsRef, -{ - let file = File::open(filename)?; - Ok(io::BufReader::new(file).lines()) -} diff --git a/tests/test_workflow.py b/tests/test_workflow.py index ac3befc..50c3282 100644 --- a/tests/test_workflow.py +++ b/tests/test_workflow.py @@ -9,13 +9,19 @@ ARABIDOPSIS_PATH = Path(__file__).parent / "files/subtraction.fa.gz" - - @pytest.mark.datafiles(ARABIDOPSIS_PATH) -async def test_decompress_and_compute_gc(datafiles, tmpdir, mocker): - fasta_path = Path(tmpdir) / "decompress.fa" - - new_subtraction = WFNewSubtraction(id="foo", delete=mocker.Mock(), finalize=mocker.Mock(), name="bar", nickname="baz", path=Path(tmpdir), upload=mocker.Mock()) +async def test_decompress_and_compute_gc(datafiles, mocker, tmp_path: Path): + fasta_path = tmp_path / "decompress.fa" + + new_subtraction = WFNewSubtraction( + id="foo", + delete=mocker.Mock(), + finalize=mocker.Mock(), + name="bar", + nickname="baz", + path=tmp_path, + upload=mocker.Mock(), + ) await decompress(fasta_path, new_subtraction, 1) diff --git a/workflow.py b/workflow.py index 992e60b..4fb37a4 100644 --- a/workflow.py +++ b/workflow.py @@ -3,7 +3,6 @@ from pathlib import Path from types import SimpleNamespace -import count_nucleotides_and_seqs from pyfixtures import fixture from virtool_core.utils import compress_file, decompress_file, is_gzipped from virtool_workflow import hooks, step @@ -63,20 +62,28 @@ async def compute_gc_and_count( decompressed_fasta_path: Path, intermediate: SimpleNamespace ): """Compute the GC and count.""" - a, t, g, c, n, count = count_nucleotides_and_seqs.run(str(decompressed_fasta_path)) - - nucleotides = { - "a": int(a), - "t": int(t), - "g": int(g), - "c": int(c), - "n": int(n), - } - intermediate.count = int(count) + def func(path: Path): + _count = 0 + _nucleotides = {"a": 0, "t": 0, "g": 0, "c": 0, "n": 0} + + with open(path, "r") as f: + for line in f: + if line[0] == ">": + _count += 1 + + elif line: + for i in ["a", "t", "g", "c", "n"]: + # Find lowercase and uppercase nucleotide characters + _nucleotides[i] += line.lower().count(i) + + return _count, _nucleotides + + count, nucleotides = await asyncio.to_thread(func, decompressed_fasta_path) nucleotides_sum = sum(nucleotides.values()) + intermediate.count = count intermediate.gc = { key: round(nucleotides[key] / nucleotides_sum, 3) for key in nucleotides }