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dev -> main for 3.1.2 #3406

Merged
merged 68 commits into from
Jan 20, 2025
Merged

dev -> main for 3.1.2 #3406

merged 68 commits into from
Jan 20, 2025

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mirpedrol
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mirpedrol and others added 30 commits December 20, 2024 14:23
@mirpedrol
bump to 3.2.0dev
390c03a
@nf-core-bot
[automated] Update CHANGELOG.md
40fa26e
@mirpedrol
fix trailing spaces in conf/test.config
20de879
@mirpedrol
run pre-comit when rendering template for pipelines sync
3cb8775
@mirpedrol
add newline
6b43881
@mirpedrol
bump to 3.1.2dev
4bd4d23
@muffato
Allow downloading a specific commit ID
bf3224c
@fellen31 @muffato
Added tests
9dcb4a0
@muffato
Added more tests
7b931f1
@muffato
Updated the changelog
c356337
@muffato
Added some documentation
b0b9559
@renovate
Update pre-commit hook pre-commit/mirrors-mypy to v1.14.1
132d09c
@renovate
Update pre-commit hook astral-sh/ruff-pre-commit to v0.8.6
6fe8f28
@mirpedrol
Merge pull request #3370 from mirpedrol/bump-3.2.0dev
340523c 
bump to 3.2.0dev
@mirpedrol
Merge branch 'dev' into download_commits
12f6e36
@mirpedrol
only append module name if it is a dir and contains main.nf
a335212
@mirpedrol
update changelog
983dced
@mashehu
Merge branch 'dev' into renovate/pre-commit-mirrors-mypy-1.x
e0d8732
@mirpedrol
add tests for get_installed_modules() utils function
069fce2
@mashehu
remove type hint to make mypy pass
19070e5
@mashehu
Merge branch 'dev' into renovate/astral-sh-ruff-pre-commit-0.x
72f2ed1
@mirpedrol
Merge pull request #3384 from mirpedrol/modules-bump-versions
53703f4 
Modules: fix bump-versions: only append module name if it is a dir and contains main.nf
@mashehu
Merge pull request #3376 from nf-core/renovate/astral-sh-ruff-pre-com…
21222f4 
…mit-0.x

Update pre-commit hook astral-sh/ruff-pre-commit to v0.8.6
@mashehu
Merge pull request #3379 from nf-core/renovate/pre-commit-mirrors-myp…
73ee4a1 
…y-1.x

Update pre-commit hook pre-commit/mirrors-mypy to v1.14.1
@renovate
Update python:3.12-slim Docker digest to 10f3aaa (#3381)
011d15a 
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
@mirpedrol
remove required from oneOf, allOf and anyOf instances in a schema
4a74d5b
@mirpedrol
print complete error message from schema validation on debug
5782edf
@nf-core-bot
[automated] Update CHANGELOG.md
958f58e
@mirpedrol
reduce code
51fba5a
@mirpedrol
handle anyOf, allOf, oneOf in top level
2f2950f
MatthiasZepper and others added 19 commits January 13, 2025 18:09
@MatthiasZepper
Add explicit container cache inspection to action.
2184cab
@MatthiasZepper
Changelog.
737b515
@MatthiasZepper
Merge pull request #3389 from MatthiasZepper/no_env_in_download_action
65969d9 
Pipeline template: Fix the faulty Download test / GitHub action
@mirpedrol
fix sync GHA by removing quotes from parsed branch name
df41fc0
@nf-core-bot
[automated] Update CHANGELOG.md
ed1cbde
@mirpedrol
make rocrate no git info message a debug message to avoid seeing it e…
4bdf77e 
…very time we run nf-core pipelines lint
@mirpedrol
manifest.authors is not mandatory anymore
225b0b7
@nf-core-bot
[automated] Update CHANGELOG.md
7641e5f
@mirpedrol
Merge pull request #3397 from mirpedrol/make-author-not-required
6680f41 
General: manifest.author is not required anymore
@mirpedrol
Merge branch 'dev' into fix-sync-gha
24e6c80
@mirpedrol
Merge pull request #3394 from mirpedrol/fix-sync-gha
7fa5d5b 
General: Fix sync GHA by removing quotes from parsed branch name
@nvnieuwk
update nf-schema version
cd72f97
@nvnieuwk
update changelog
e62a94b
@nvnieuwk
Merge pull request #3401 from nvnieuwk/update-nf-schema
e6402db 
update nf-schema version
@mirpedrol
bump version to 3.1.2
bd5c641
@mirpedrol
remove jinja formatting which was deleting line breaks
373ad61
@mirpedrol
Merge pull request #3405 from mirpedrol/fix-jinja
4746cfd 
Template: remove jinja formatting which was deleting line breaks
@mirpedrol
Merge branch 'dev' into bump-3.1.2
ce69545
@mirpedrol
Merge pull request #3404 from mirpedrol/bump-3.1.2
c1ab12f 
bump version to 3.1.2
mashehu
mashehu approved these changes Jan 20, 2025
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codecov bot commented Jan 20, 2025 •
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Codecov Report

Attention: Patch coverage is 91.66667% with 5 lines in your changes missing coverage. Please review.

Project coverage is 76.09%. Comparing base (45c7879) to head (112bf2b).

Files with missing lines Patch % Lines
nf_core/pipelines/lint_utils.py 80.00% 4 Missing ⚠️
nf_core/modules/modules_utils.py 85.71% 1 Missing ⚠️
Additional details and impacted files

☔ View full report in Codecov by Sentry.
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@mirpedrol
Merge pull request #3407 from mirpedrol/changelog
112bf2b 
changelog updates [no changelog]
mashehu
mashehu previously requested changes Jan 20, 2025
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@mashehu mashehu left a comment •
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maybe merge this first? #3399

@mashehu mashehu dismissed their stale review January 20, 2025 12:53

will be part of 3.2

@mirpedrol mirpedrol enabled auto-merge January 20, 2025 14:08
@mirpedrol mirpedrol merged commit 34bc338 into main Jan 20, 2025
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9 participants
@mirpedrol @mashehu @nf-core-bot @muffato @fellen31 @sateeshperi @maxulysse @MatthiasZepper @nvnieuwk