fix: support int | str group ids

* Update `virtool-workflow` to support `int | str` ids.
* Remove deepsource coverage analyzer.

Author: igboyes

.deepsource.toml

@@ -2,10 +2,6 @@ version = 1
 
 test_patterns = ["tests/**"]
 
-[[analyzers]]
-name = "test-coverage"
-enabled = true
-
 [[analyzers]]
 name = "python"
 enabled = true

.github/workflows/publish.yml

@@ -34,6 +34,7 @@ jobs:
         uses: docker/build-push-action@v4
         with:
           context: .
+          labels: ${{ steps.meta.outputs.labels }}
           push: true
           tags: ${{ steps.meta.outputs.tags }}
-          labels: ${{ steps.meta.outputs.labels }}
+          target: "base"

Dockerfile

@@ -1,32 +1,42 @@
-FROM python:3.10-buster as rustPyo3
+FROM debian:buster as prep
+WORKDIR /build
+RUN apt-get update && apt-get install -y make gcc zlib1g-dev wget unzip
+RUN wget https://zlib.net/pigz/pigz-2.8.tar.gz && \
+    tar -xzvf pigz-2.8.tar.gz && \
+    cd pigz-2.8 && \
+    make
+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
 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==0.14.5
+RUN pip install maturin==0.14.7
 COPY src src
 COPY Cargo.toml Cargo.lock ./
 RUN maturin build --release
 
-FROM virtool/workflow:5.3.0 as test
-WORKDIR /test
-COPY poetry.lock pyproject.toml /test/
+FROM python:3.10-buster as base
+WORKDIR /workflow
 RUN curl -sSL https://install.python-poetry.org | python -
-RUN poetry install
-COPY tests / test/
-COPY fixtures.py workflow.py pytest.ini /test/
-COPY --from=rustPyo3 /build/target/wheels/count_nucleotides_and_seqs*.whl ./
-RUN ls
-RUN pip3.10 install count_nucleotides_and_seqs*.whl
-RUN poetry install
-RUN poetry add ./count_nucleotides_and_seqs*.whl
-RUN poetry run pytest
+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 fixtures.py workflow.py pyproject.toml poetry.lock ./
+RUN poetry export > requirements.txt
+RUN pip install --upgrade pip
+RUN pip install -r requirements.txt
+RUN pip install ./count_nucleotides_and_seqs*.whl
 
-FROM virtool/workflow:5.3.0 as build
+FROM base as test
 WORKDIR /workflow
-COPY fixtures.py workflow.py /workflow/
-COPY --from=rustPyo3 /build/target/wheels/count_nucleotides_and_seqs*.whl ./
-RUN ls
-RUN pip3.10 install count_nucleotides_and_seqs*.whl
-RUN poetry install
-RUN poetry add ./count_nucleotides_and_seqs*.whl
+RUN poetry export --with dev > requirements.txt
+RUN pip install -r requirements.txt
+COPY pytest.ini ./
+COPY tests ./tests
+RUN pytest

fixtures.py

@@ -1,20 +1,14 @@
 from pathlib import Path
 from types import SimpleNamespace
-from typing import List
 
 from pyfixtures import fixture
 from virtool_workflow.api.subtractions import SubtractionProvider
 
 
 @fixture
-def subtraction_provider(subtraction_providers: List[SubtractionProvider]):
-    return subtraction_providers[0]
-
-
-@fixture
-def intermediate():
-    """A namespace for intermediate variables."""
-    return SimpleNamespace()
+def fasta_path(work_path: Path) -> Path:
+    """The path to the decompressed FASTA file."""
+    return work_path / "subtraction.fa"
 
 
 @fixture
@@ -24,6 +18,13 @@ def input_path(input_files: dict) -> Path:
 
 
 @fixture
-def fasta_path(work_path: Path) -> Path:
-    """The path to the decompressed FASTA file."""
-    return work_path / "subtraction.fa"
+def intermediate() -> SimpleNamespace:
+    """A namespace for intermediate variables."""
+    return SimpleNamespace()
+
+
+@fixture
+def subtraction_provider(
+    subtraction_providers: list[SubtractionProvider],
+) -> SubtractionProvider:
+    return subtraction_providers[0]

poetry.lock

@@ -1,21 +1,24 @@
 [tool.poetry]
 name = "workflow-create-subtraction"
 version = "0.0.0"
-description = ""
-authors = ["Ian Boyes <igboyes@gmail.com>"]
+description = "A workflow for creating Virtool subtractions"
+authors = [
+    "Ian Boyes",
+    "Blake Smith",
+    "Tiansheng Sui",
+    "Markus Swoveland",
+    "Christine Wong Chong"
+]
 
 [tool.poetry.dependencies]
-python = "^3.10"
-pyfixtures = "^1.1.0"
-virtool-workflow = "^5.0.0"
-pre-commit = "^3.0.4"
-black = "^23.1.0"
+python = "~3.10"
+virtool-workflow = "^5.4.2"
 
 [tool.poetry.group.dev.dependencies]
-pytest = "^7.1.2"
-pytest-aiohttp = "^1.0.4"
+pytest = "^7.4.2"
+pytest-aiohttp = "^1.0.5"
+pytest-asyncio = "^0.21.1"
 pytest-datafiles = "^2.0.1"
-pytest-asyncio = "^0.17.0"
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]

pyproject.toml

@@ -21,7 +21,5 @@ async def test_decompress_and_compute_gc(datafiles, tmpdir):
 
     await compute_gc_and_count(fasta_path, intermediate)
 
-    print(intermediate.gc)
-
     assert intermediate.gc == {"a": 0.319, "t": 0.319, "g": 0.18, "c": 0.18, "n": 0.002}
     assert intermediate.count == 7

tests/test_workflow.py

@@ -4,7 +4,6 @@
 from types import SimpleNamespace
 
 import count_nucleotides_and_seqs
-
 from virtool_core.utils import compress_file, decompress_file, is_gzipped
 from virtool_workflow import hooks, step
 from virtool_workflow.api.subtractions import SubtractionProvider
@@ -60,11 +59,11 @@ async def compute_gc_and_count(fasta_path: Path, intermediate: SimpleNamespace):
 
 @step
 async def build_index(
-    proc: int,
     fasta_path: Path,
     intermediate: SimpleNamespace,
-    work_path: Path,
+    proc: int,
     run_subprocess: RunSubprocess,
+    work_path: Path,
 ):
     """Build a Bowtie2 index."""
     bowtie_path = work_path / "index-build"
@@ -88,8 +87,8 @@ async def build_index(
 async def finalize(
     fasta_path: Path,
     intermediate: SimpleNamespace,
-    subtraction_provider: SubtractionProvider,
     proc: int,
+    subtraction_provider: SubtractionProvider,
 ):
     """Compress and subtraction data."""
     compressed_path = fasta_path.parent / "subtraction.fa.gz"