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dev -> main for 3.1.1 #3369

Merged
merged 89 commits into from
Dec 20, 2024
Merged

dev -> main for 3.1.1 #3369

merged 89 commits into from
Dec 20, 2024
+142 −71

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mirpedrol
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mashehu and others added 30 commits December 10, 2024 12:17
@mashehu
set default_branch to master for now
e9cde59
@mashehu
update changelog
7110fff
@mashehu
Merge branch 'dev' into set-default-branch-to-master
47054ad
@mashehu
Merge pull request #3335 from mashehu/set-default-branch-to-master
a791707 
set default_branch to master for now
@mashehu
set git defaultBranch to master in sync action
de00162
@mashehu
update changelog
60ae1af
@mashehu
use nextflow.config to set defaultBranch
5ee2d52
@mashehu
Merge pull request #3337 from mashehu/fix-init-branch-in-sync-action
0e7c870 
set git defaultBranch to master in sync action
@mashehu
fix path for nextflow.config grep
666fc9f
@mashehu
Merge branch 'dev' of github.com:nf-core/tools into fix-sync-grep
7a69b8c
@mashehu
change working dir when setting defaultBranch
15b044d
@mashehu
fix Changelog
1a22106
@mashehu
Be more verbose in approval check action
0b7fe50
@mashehu
fix if clause
f7ced6b
@mashehu
update changelog
1748613
@mashehu
add verbose mode to sync action
fa4e074
@mashehu
update changelog
5c8937e
@mirpedrol
Apply suggestions from code review
bb3a252
@mirpedrol
add input debug for workflow_dispatch sync action
379bad0
@mirpedrol
Merge pull request #3339 from mashehu/add-verbose-mode-to-sync
06db03f 
Add verbose mode to sync action
@mirpedrol
go back to original directory after configuring git defaultBranch
6148983
@mirpedrol
Merge pull request #3342 from mirpedrol/sync-default-branch
a4965f3 
go back to original directory after configuring git defaultBranch [no changelog]
@mirpedrol
add more debugging on sync GHA
df5b323
@mirpedrol
Merge pull request #3345 from mirpedrol/sync-default-branch
e8b6a9f 
add more debugging on sync GHA [no changelog]
@mirpedrol
echo message to sync GHA
1de1034
@mirpedrol
try exiting pipeline directory before saving defaultBranch
3858e38
@mirpedrol
cleanup debugging echo
380be6c
@mashehu
use same ref in checkout as triggered the workflow
be38c15
@mashehu
Merge pull request #3347 from mashehu/specify-ref-in-sync-yml
1af4c61
@mirpedrol
don't set up loggin level to error
e92f327
mirpedrol and others added 25 commits December 16, 2024 11:34
@mirpedrol
prettify template and printing .nf-core.yml
2b2b435
@mirpedrol
Merge branch 'dev' into fix-pre-commit-template
0c4b0c0
@mirpedrol
Remove Dumpler from ruamel yaml
709e67f
@mirpedrol
don't create rocrate file when we skip the feature
ac703bf
@mirpedrol
fix more prettier modifications form the template
13e553f
@mirpedrol
don't try running pre-commit if code-linters or github are not used i…
d19e3e0 
…n the template
@mirpedrol
more template prittier fixing
2c78c5e
@mirpedrol
more prettier fixes
d44bcdf
@mirpedrol
Merge pull request #3358 from mirpedrol/fix-pre-commit-template
769f8dd 
Fix pre commit template
@mirpedrol
use manifest.contributors names if available, otherwise default to ma…
745df4d 
…nifest.author
@nf-core-bot
[automated] Update CHANGELOG.md
ac7fd48
@mirpedrol
Merge pull request #3362 from mirpedrol/fix-3359-lint-repo
728a91c 
Use `manifest.contributors` names if available, otherwise default to `manifest.author`
@mirpedrol
properly parse the names form manifest.contributors
767618c
@mirpedrol
update changelog
5ecf583
@mirpedrol
LICENSE copyright to nf-core community, lint LICENSE file is a warnin…
dc369ac 
…g instead of a failure
@nf-core-bot
[automated] Update CHANGELOG.md
05b1f84
@mirpedrol
update changelog
e00679f
@mirpedrol @SPPearce
Apply suggestions from code review
136418f 
Co-authored-by: Simon Pearce <[email protected]>
@mirpedrol
use pipeline team in license for non-nf-core pipelines
304728c
@mirpedrol
Merge pull request #3364 from mirpedrol/fix-3361-rocrate-contributors
fe5c5ac 
Properly parse the names form `manifest.contributors`
@mirpedrol
Merge pull request #3366 from mirpedrol/update-license-linting
a0cdd41 
Template: set LICENSE copyright to nf-core community
@mirpedrol
bump to 3.1.1 for release
a8578f0
@mirpedrol
small modification of license, adding pipeline team
8aeb629
@mirpedrol
Merge pull request #3368 from mirpedrol/license-modification
0c89959 
small modification of license, adding pipeline team [no changelog]
@mirpedrol
Merge pull request #3367 from mirpedrol/bump-3.1.1
b9b92d0 
bump to 3.1.1 for release
@codecov Codecov
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codecov bot commented Dec 20, 2024 •
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Codecov Report

Attention: Patch coverage is 85.71429% with 3 lines in your changes missing coverage. Please review.

Project coverage is 75.92%. Comparing base (8232947) to head (82eccbe).
Report is 90 commits behind head on main.

Files with missing lines Patch % Lines
nf_core/pipelines/lint/files_unchanged.py 60.00% 2 Missing ⚠️
nf_core/pipelines/rocrate.py 80.00% 1 Missing ⚠️
Additional details and impacted files

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

@mirpedrol mirpedrol merged commit 45c7879 into main Dec 20, 2024
177 checks passed
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@mashehu mashehu mashehu approved these changes

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6 participants
@mirpedrol @mashehu @MatthiasZepper @nf-core-bot @jfy133 @sateeshperi