ci: fix poetry error during ci image build

Author: igboyes

.github/workflows/publish.yml

@@ -19,8 +19,6 @@ jobs:
         uses: actions/checkout@v3
       - name: Write VERSION file
         run: echo ${{ github.event.release.tag_name }} > VERSION
-      - name: Update pyproject.toml
-        run: sed -i 's/0\.0\.0/${{ github.event.release.tag_name }}/' pyproject.toml
       - name: Login to Registry
         uses: docker/login-action@v2
         with:

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 workflow.py VERSION* ./
+COPY fixtures.py workflow.py VERSION* ./
 
 FROM build as test
 WORKDIR /workflow
@@ -45,6 +45,5 @@ ENV PATH="/root/.local/bin:${PATH}" \
 COPY --from=build /workflow/.venv /workflow/.venv
 COPY pyproject.toml poetry.lock ./
 RUN poetry install
-COPY workflow.py ./
+COPY fixtures.py workflow.py ./
 COPY tests/ ./tests/
-RUN poetry run pytest

fixtures.py

@@ -0,0 +1,26 @@
+import asyncio
+from pathlib import Path
+from types import SimpleNamespace
+
+from pyfixtures import fixture
+
+
+@fixture
+async def bowtie_index_path(work_path: Path) -> Path:
+    """The output directory for the subtraction's Bowtie2 index."""
+    path = work_path / "bowtie"
+    await asyncio.to_thread(path.mkdir)
+
+    return path
+
+
+@fixture
+async def decompressed_fasta_path(work_path: Path) -> Path:
+    """The path to the input FASTA file for the subtraction."""
+    return work_path / "subtraction.fa"
+
+
+@fixture
+def intermediate() -> SimpleNamespace:
+    """A namespace for intermediate variables."""
+    return SimpleNamespace()

tests/test_workflow.py

@@ -11,7 +11,7 @@
 
 @pytest.mark.datafiles(ARABIDOPSIS_PATH)
 async def test_decompress_and_compute_gc(datafiles, mocker, tmp_path: Path):
-    fasta_path = tmp_path / "decompress.fa"
+    decompressed_fasta_path = tmp_path / "decompressed.fa"
 
     new_subtraction = WFNewSubtraction(
         id="foo",
@@ -23,13 +23,13 @@ async def test_decompress_and_compute_gc(datafiles, mocker, tmp_path: Path):
         upload=mocker.Mock(),
     )
 
-    await decompress(fasta_path, new_subtraction, 1)
+    await decompress(decompressed_fasta_path, new_subtraction, 1)
 
-    assert fasta_path.is_file()
+    assert decompressed_fasta_path.is_file()
 
     intermediate = SimpleNamespace()
 
-    await compute_gc_and_count(fasta_path, intermediate)
+    await compute_gc_and_count(decompressed_fasta_path, intermediate)
 
     assert intermediate.gc == {"a": 0.319, "t": 0.319, "g": 0.18, "c": 0.18, "n": 0.002}
     assert intermediate.count == 7

workflow.py

@@ -3,7 +3,6 @@
 from pathlib import Path
 from types import SimpleNamespace
 
-from pyfixtures import fixture
 from virtool_core.utils import compress_file, decompress_file, is_gzipped
 from virtool_workflow import hooks, step
 from virtool_workflow.data.subtractions import WFNewSubtraction
@@ -16,27 +15,6 @@ async def delete_subtraction(new_subtraction: WFNewSubtraction):
     await new_subtraction.delete()
 
 
-@fixture
-async def bowtie_index_path(work_path: Path) -> Path:
-    """The output directory for the subtraction's Bowtie2 index."""
-    path = work_path / "bowtie"
-    await asyncio.to_thread(path.mkdir)
-
-    return path
-
-
-@fixture
-async def decompressed_fasta_path(work_path: Path) -> Path:
-    """The path to the input FASTA file for the subtraction."""
-    return work_path / "subtraction.fa"
-
-
-@fixture
-def intermediate() -> SimpleNamespace:
-    """A namespace for intermediate variables."""
-    return SimpleNamespace()
-
-
 @step(name="Decompress FASTA")
 async def decompress(
     decompressed_fasta_path: Path,
@@ -64,6 +42,9 @@ async def compute_gc_and_count(
     """Compute the GC and count."""
 
     def func(path: Path):
+        if not path.suffix != "fa":
+            raise ValueError("Input file is not a FASTA file.")
+
         _count = 0
         _nucleotides = {"a": 0, "t": 0, "g": 0, "c": 0, "n": 0}