refactor: move fixtures to dedicated module

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 ./

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"

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,