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dev -> main for 3.2.0 release #3428

Merged
merged 47 commits into from
Jan 27, 2025
Merged

dev -> main for 3.2.0 release #3428

merged 47 commits into from
Jan 27, 2025

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mirpedrol
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mirpedrol and others added 30 commits January 20, 2025 15:32
@mirpedrol
bump version to 3.2.0dev
fd0016c
@mirpedrol
Merge pull request #3409 from mirpedrol/bump-to-3.2.0
0716d91 
bump version to 3.2.0dev
@awgymer
fix(1929): more type-gating
c1692f5
@nf-core-bot @awgymer
fix CHANGELOG.md
90978ea
@awgymer
fix(1929): update subworkflow tests and add lint test markdown
a5bb0f0
@awgymer @mirpedrol
Apply suggestions from code review
732c786 
Co-authored-by: Júlia Mir Pedrol <[email protected]>
@awgymer
feat(1929): allow missing files when linting local modules
7ba6f79
@awgymer
feat(1929): local linting option now *only* lints local modules. Add …
8a1d44a 
…tests
@awgymer
feat(1929): don't ask for a module/subworkflow name to lint if lintin…
6c9c1b1 
…g local
@awgymer
feat(1929): add test for new pipeline lint check of local component dirs
19df044
@awgymer
feat(1929): run todo linting on local subworkflows
5d1d44b
@awgymer
fix: Update to latest CHANGELOG
5689ff6
@awgymer
fix: Clean up CHANGELOG.md
3f76e99
@renovate
Update pre-commit hook editorconfig-checker/editorconfig-checker.pyth…
660c8a7 
…on to v3.1.2
@nf-core-bot
[automated] Update CHANGELOG.md
8d33662
@ewels
Fix 'process.shell' in nextflow.config
d1f6dc7
@mashehu
Merge branch 'dev' into fix-process-shell
ca8b93d
@nf-core-bot
[automated] Update CHANGELOG.md
702e00c
@ewels
Merge pull request #3416 from ewels/fix-process-shell
0b6b151 
Template: Fix `process.shell` in `nextflow.config`
@ewels
Remove automated release tweets
bee0520
@nf-core-bot
[automated] Update CHANGELOG.md
078e4ee
@nf-core-bot
[automated] Update CHANGELOG.md
48ee89c
@ewels
Merge pull request #3419 from ewels/remove-twitter-release-notifications
ed1667f
@awgymer
Merge branch 'dev' into 1929-local-modules-use-remote-format
391ae2c
@awgymer
fix: broken test. Need to assign component_dir to the parent dir if a…
3dd2e00 
… local module is an nf file only
@awgymer
fix: Add new lint test to lint config pydantic model
262dea3
@renovate @nf-core-bot
Update python:3.12-slim Docker digest to 123be56 (#3421)
583809c 
* Update python:3.12-slim Docker digest to 123be56

* [automated] Update CHANGELOG.md

---------

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Co-authored-by: nf-core-bot <[email protected]>
@renovate
Update pre-commit hook astral-sh/ruff-pre-commit to v0.9.3
1283406
@nf-core-bot
[automated] Fix code linting
52e8d4b
@awgymer
Merge pull request #3256 from awgymer/1929-local-modules-use-remote-f…
bc3417a 
…ormat

1929: local modules use remote format from template
mashehu and others added 15 commits January 27, 2025 08:24
@mashehu
Merge branch 'dev' into renovate/astral-sh-ruff-pre-commit-0.x
3048627
@renovate
chore(deps): update dawidd6/action-download-artifact action to v8 (#3424
3be4b60 
)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
@mashehu
fix mypy error
61d9710
@mashehu
Merge pull request #3413 from nf-core/renovate/astral-sh-ruff-pre-com…
2f71183 
…mit-0.x

Update pre-commit hook astral-sh/ruff-pre-commit to v0.9.3
@mashehu
Merge branch 'dev' into renovate/editorconfig-checker-editorconfig-ch…
dcf27d9 
…ecker.python-3.x
@ewels
Separate -o pipefail into separate list elements
f8b099c
@nf-core-bot
[automated] Update CHANGELOG.md
2d7e1a6
@mashehu
Merge pull request #3414 from nf-core/renovate/editorconfig-checker-e…
df9d892 
…ditorconfig-checker.python-3.x

Update pre-commit hook editorconfig-checker/editorconfig-checker.python to v3.1.2
@ewels
Merge pull request #3425 from ewels/o-pipefail-newline
2e01c36 
`-o pipefail` newline
@mirpedrol
update template components
008dabb
@nf-core-bot
[automated] Update CHANGELOG.md
ae92258
@mirpedrol
Merge pull request #3426 from mirpedrol/update-template-modules
5236c85 
Template: Update template components
@mirpedrol
bump to v3.2.0
92408c3
@mirpedrol
template line break fixes
0d9a4f1
@mirpedrol
Merge pull request #3427 from mirpedrol/bump-to-3.2.0
a7d86d8 
bump to v3.2.0
@mirpedrol mirpedrol requested a review from mashehu January 27, 2025 11:51
mashehu
mashehu approved these changes Jan 27, 2025
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codecov bot commented Jan 27, 2025 •
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Codecov Report

Attention: Patch coverage is 77.86885% with 27 lines in your changes missing coverage. Please review.

Project coverage is 76.26%. Comparing base (112bf2b) to head (0355435).
Report is 51 commits behind head on main.

Files with missing lines Patch % Lines
nf_core/modules/lint/module_tests.py 33.33% 8 Missing ⚠️
nf_core/subworkflows/lint/subworkflow_tests.py 33.33% 8 Missing ⚠️
nf_core/components/create.py 81.25% 3 Missing ⚠️
nf_core/modules/lint/meta_yml.py 62.50% 3 Missing ⚠️
nf_core/pipelines/download.py 0.00% 2 Missing ⚠️
nf_core/subworkflows/lint/meta_yml.py 84.61% 2 Missing ⚠️
nf_core/modules/lint/__init__.py 92.85% 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 52e8109 into main Jan 27, 2025
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5 participants
@mirpedrol @mashehu @awgymer @nf-core-bot @ewels