Skip to content

dev -> main for 3.2.0 release #3428

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
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

Conversation

@mirpedrol
Copy link
Member

No description provided.

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
View reviewed changes
@codecov
Copy link

codecov bot commented Jan 27, 2025 •
edited
Loading

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
95 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@mashehu mashehu mashehu approved these changes

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

6 participants

@mirpedrol @mashehu @awgymer @nf-core-bot @ewels