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Dev -> Master for 2.13.1 #2811

Merged
merged 59 commits into from
Feb 29, 2024
Merged

Dev -> Master for 2.13.1 #2811

merged 59 commits into from
Feb 29, 2024

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mashehu
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@mashehu mashehu commented Feb 29, 2024

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mirpedrol and others added 30 commits February 20, 2024 16:50
@mirpedrol
bump version to 3.0dev
7642616
@maxulysse
update badges
d36a503
@maxulysse
add nf-test badge
f48caff
@maxulysse
fix typo
5602f95
@maxulysse
unit-tests
aeab913
@maxulysse
use jinja
e5d78f0
@mashehu
Merge pull request #2783 from mirpedrol/bump-3.0dev
df699d1 
bump version to 3.0dev
@mashehu
Merge branch 'dev' into template_update
984b120
@mashehu
Merge pull request #2785 from maxulysse/template_update
ec13bfd 
Templates: update Nextflow Tower -> Seqera Platform badge and keep some newlines in local subworkflow
@renovate
chore(deps): update seqeralabs/action-tower-launch digest to aa88624
15195a2
@nf-core-bot @renovate
[automated] Update CHANGELOG.md
ef0b87b
@renovate
chore(deps): update codecov/codecov-action digest to 0cfda1d
daa28ea
@nf-core-bot @renovate
[automated] Update CHANGELOG.md
b0a268b
@kenibrewer
fix(devcontainer): remove deprecated linters
a059e16 
With the migration of linting functionality out of the core vscode python extension to individual extensions (https://github.com/microsoft/vscode-python/wiki/Migration-to-Python-Tools-Extensions), these linter paths are no longer needed. In addition, with the adoption of ruff for python formatting & linting, these linters may also be no longer correct in some settings.
@mashehu
copy changes over to template, update extensions in gitpod.yml
4052a02
@mashehu
update changelog
622601e
@kenibrewer
Merge pull request #2795 from kenibrewer/fix/remove-deprecated-linters
f64d486 
Fix/remove deprecated linters
@MatthiasZepper
Write a new helper function: gather_registries() to read the config.
a0381de
@MatthiasZepper
nf-core download: Write function to symlink containers to different l…
6f83b61 
…ibraries (registries).
@MatthiasZepper
Refactor: Always trim registry from output name. Naming collisions ar…
80f2d34 
…e presumably unlikely, names including the registry are now consistently always symlinks.
@MatthiasZepper
Modify the pytest.yml action such that Singularity is used for the nf…
7954bcb 
…-core download tests.
@MatthiasZepper
Extend ContainerError to match ghcr.io error message.
5cfccd3
@MatthiasZepper
Add test_gather_registries() to test_download.py
0817024
@MatthiasZepper
Finally a comprehensive test for symlink_singularity_images()
d1fb738
@MatthiasZepper
Changelog.
5a3fa12
@MatthiasZepper @Aratz
Apply @Aratz 's suggestions from code review
d1179a4 
Co-authored-by: Adrien Coulier <adrien.coulier@medsci.uu.se>
@MatthiasZepper
Improved the documentation of the singularity_image_filenames() funct…
e3c7f5b 
…ion.
@MatthiasZepper
Added a test for the so far untested singularity_image_filenames() fu…
dceb7b3 
…nction.
@nvnieuwk
Fixed a typo in the template
27e6f7e
@nvnieuwk
Merge branch 'dev' into nvnieuwk-patch-1
9eb5d6e
@codecov Codecov
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codecov bot commented Feb 29, 2024 •
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Codecov Report

Attention: Patch coverage is 90.47619% with 6 lines in your changes are missing coverage. Please review.

Project coverage is 74.79%. Comparing base (b51c7d8) to head (412a43c).

❗ Current head 412a43c differs from pull request most recent head d6b459c. Consider uploading reports for the commit d6b459c to get more accurate results

Files Patch % Lines
nf_core/download.py 90.47% 6 Missing ⚠️
Additional details and impacted files

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

drpatelh
drpatelh approved these changes Feb 29, 2024
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LGTM!

ewels
ewels approved these changes Feb 29, 2024
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LGTM!

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mashehu
mashehu commented Feb 29, 2024
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mashehu
mashehu commented Feb 29, 2024
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JoseEspinosa
JoseEspinosa approved these changes Feb 29, 2024
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LGTM! 🚀

@mashehu mashehu merged commit 9eac5e9 into master Feb 29, 2024
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@drpatelh drpatelh drpatelh approved these changes

@JoseEspinosa JoseEspinosa JoseEspinosa approved these changes

@ewels ewels ewels approved these changes

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