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Merged
MatthiasZepper merged 5 commits into from
Nov 18, 2025
Merged

Enable CI tests for pipelines/download #3898

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d52b8b3
Enable CI tests for pipelines/download
rrahn Nov 13, 2025
b9f76e0
Fix docker test
rrahn Nov 13, 2025
734a5e7
Ensure container out dir exists
rrahn Nov 13, 2025
bae5110
Fix singularity error
rrahn Nov 13, 2025
01acabf
Swich to Apptainer in pytest
rrahn Nov 18, 2025
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8 changes: 4 additions & 4 deletions .github/workflows/pytest.yml
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@MatthiasZepper MatthiasZepper Nov 17, 2025 •
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Excellent catch! It totally escaped me, that we are running Singularity tests in that action as well.

In the pipeline template, we have upgraded the download test nf_core/pipeline-template/.github/workflows/download_pipeline.yml to Apptainer 1.34 instead of Singularity 3.8.3, which is about 3 years more recent. I think, this would be a good opportunity to piggy-back this change to the #tools test as well.

@mirpedrol @mashehu, @JulianFlesch any opinions against which Apptainer version we should test the pipelines and thus also tools?

Original file line number Diff line number Diff line change
Expand Up @@ -79,11 +79,11 @@ jobs:
python -m pip install --upgrade pip -r requirements-dev.txt
pip install -e .

- name: Set up Singularity
if: ${{ matrix.test == 'test_download.py'}}
uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
- name: Set up Apptainer
if: ${{ startsWith(matrix.test, 'pipelines/download/') }}
uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0
with:
singularity-version: 3.8.3
apptainer-version: 1.3.4

- name: Get current date
id: date
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8 changes: 8 additions & 0 deletions nf_core/pipelines/download/singularity.py
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Original file line number Diff line number Diff line change
Expand Up @@ -595,6 +595,7 @@ def pull_image(self, container: str, output_path: Path, library: str) -> bool:
progress_type="singularity_pull",
current_log="",
) as task:
self._ensure_output_dir_exists()
with intermediate_file_no_creation(output_path) as output_path_tmp:
singularity_command = self.construct_pull_command(output_path_tmp, address)
log.debug(f"Building singularity image: {address}")
Expand Down Expand Up @@ -629,6 +630,12 @@ def pull_image(self, container: str, output_path: Path, library: str) -> bool:
self.symlink_registries(output_path)
return True

def _ensure_output_dir_exists(self) -> None:
"""Ensure that the container output directory exists."""
if not self.get_container_output_dir().is_dir():
log.debug(f"Container output directory not found, creating: {self.get_container_output_dir()}")
self.get_container_output_dir().mkdir(parents=True, exist_ok=True)


# Distinct errors for the Singularity container download, required for acting on the exceptions
class SingularityError(Exception):
Expand Down Expand Up @@ -671,6 +678,7 @@ def __init__(
r"manifest\sunknown": self.InvalidTagError,
# The container image is no native Singularity Image Format.
r"ORAS\sSIF\simage\sshould\shave\sa\ssingle\slayer": self.NoSingularityContainerError,
r"received\smediaType:\sapplication/vnd\.docker\.distribution\.manifest": self.NoSingularityContainerError,
}
# Loop through the error messages and patterns. Since we want to have the option of
# no matches at all, we use itertools.product to allow for the use of the for ... else construct.
Expand Down
1 change: 1 addition & 0 deletions tests/pipelines/download/test_docker.py
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Original file line number Diff line number Diff line change
Expand Up @@ -200,6 +200,7 @@ def test_fetch_containers_docker(self, tmp_path, mock_fetch_wf_config):
docker_fetcher.fetch_containers(
download_obj.containers,
download_obj.containers_remote,
workflow_directory=Path("pipeline-dummy"),
)

#
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1 change: 1 addition & 0 deletions tests/pipelines/download/test_singularity.py
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Original file line number Diff line number Diff line change
Expand Up @@ -434,6 +434,7 @@ def test_singularity_pull_image_successfully(self, tmp_dir, mock_cachedir_prompt
container_cache_utilisation="none",
container_cache_index=None,
)
singularity_fetcher.registry_set = set()
singularity_fetcher.check_and_set_implementation()
singularity_fetcher.progress = mock_progress()
singularity_fetcher.pull_image("hello-world", tmp_dir / "yet-another-hello-world.sif", "docker.io")
Expand Down