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Move gather_registries function to ContainerFetcher subclasses (#3634 follow-up) #3696

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JulianFlesch merged 13 commits into from
Aug 29, 2025
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Move gather_registries function to ContainerFetcher subclasses (#3634 follow-up) #3696

JulianFlesch merged 13 commits into from
Aug 29, 2025

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@ErikDanielsson ErikDanielsson commented Jul 31, 2025 •
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This is a follow up PR on the large nf-core pipelines download refactor PR #3634 and the test PR #3712, and should be merged AFTER it.

This PR moves the gather_registries function from nf-core/pipelines/download/download.py to ContainerFetcher and subclasses.

  • The gather_registries function in SingularityFetcher mirrors the previous one.
  • The function in the DockerFetcher class only uses the docker.registry and podman.registry in the config and the Seqera Docker container registry (community.wave.seqera.io/library).

A diff with the refactor-download-tests base branch can be found in the dummy PR ErikDanielsson#1

PR checklist

  • This comment contains a description of changes (with reason)
  • CHANGELOG.md is updated
  • If you've fixed a bug or added code that should be tested, add tests!
  • Documentation in docs is updated

@ErikDanielsson ErikDanielsson added the download nf-core download label Jul 31, 2025
@ErikDanielsson ErikDanielsson mentioned this pull request Jul 31, 2025
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codecov bot commented Jul 31, 2025 •
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Codecov Report

❌ Patch coverage is 89.09091% with 6 lines in your changes missing coverage. Please review.
✅ Project coverage is 77.76%. Comparing base (7420367) to head (f6c7836).
⚠️ Report is 14 commits behind head on dev.

Files with missing lines Patch % Lines
nf_core/pipelines/download/docker.py 58.33% 5 Missing ⚠️
nf_core/pipelines/download/container_fetcher.py 95.23% 1 Missing ⚠️

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@ErikDanielsson ErikDanielsson force-pushed the move-gather-registries branch from 1ddc474 to 957190e Compare August 1, 2025 12:03
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ErikDanielsson commented Aug 14, 2025 •
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I've looked into this a bit more and since it seems that nextflow inspect always produces an absolute URI, so with the current code we will never try different registries rendering the information provided via the -l flag unused. I am not sure how to best proceed here -- to either try to strip the container strings of the registry and then try all libraries provided with -l and default libraries, or to blindly pull from the output of nextflow inspect.

Of course, this is true for the other PRs too (this PR only changes where the gather_registries function is located) so the refactor might be actually be breaking the download API but somewhat silently.

@ErikDanielsson ErikDanielsson mentioned this pull request Aug 15, 2025
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ErikDanielsson commented Aug 15, 2025

Docs updated in nf-core/website#3463. Note that I have not addressed the issue in the comment above

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Important: Check and create issue for potential bug, when docker daemon is not running. We don't have to solve this here.

@JulianFlesch JulianFlesch merged commit 6c759f2 into nf-core:dev Aug 29, 2025
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