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feat: Add Claude Code hooks for automated testing and linting#3774

Draft

edmundmiller wants to merge 136 commits intomainfrom

capture-versions

Commits on Jun 5, 2025

feat: nf-core modules bump-version supports specifying the toolkit
nh13
committed

Commits on Jun 7, 2025

chore: add unit test
nh13
committed

Commits on Jun 8, 2025

Commits on Jun 20, 2025

Commits on Jul 1, 2025

fix variable names and make dry_run a valid paramter
mashehu
committed
switch logic: no need for trailing backslash
mashehu
committed
Merge branch 'dev' of github.com:nf-core/tools into feat/bump-versions-for-sub-modules
mashehu
committed
fix argument syntax
mashehu
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fix ruff linting
mashehu
committed
test(#3590): Copy tests over from env sorter
edmundmiller
committed
test(#3590): Refactor tests for environment.yml sorting and error handling
edmundmiller
committed
fint(#3590): Enhance environment.yml handling and sorting
edmundmiller
committed
refactor(#3590): Replace ruamel.yaml with PyYAML for environment.yml processing
edmundmiller
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test(#3590): Move integration tests to new lint test file
edmundmiller
committed
test(#3590): Update dependency order on a test
edmundmiller
committed
Revert "refactor(#3590): Replace ruamel.yaml with PyYAML for environment.yml processing"

edmundmiller
and
mashehu
committed
fix(#3590): Having first pip and then immediately followed by pip dependencies

edmundmiller
and
mashehu
committed
refactor(#3590): Simplify environment.yml handling by removing channel sorting

edmundmiller
and
mashehu
committed
style: Clean up parameterized tests
edmundmiller
committed
test(#3590): Refactor environment.yml tests with factory fixtures
edmundmiller
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style: Fix code linting
edmundmiller
committed
chore: Add integration marker to pytest configuration
edmundmiller
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fix(test): Update assertion in environment.yml sorting test to use lint_test attribute
edmundmiller
committed
fix(modules): Check if they are not the exact same lines
edmundmiller
committed

Commits on Jul 7, 2025

Add module install autocompletion
LouisLeNezet
committed
Add completion for all modules subcommand
LouisLeNezet
committed

Commits on Jul 8, 2025

Commits on Jul 9, 2025

Merge pull request #3670 from mashehu/bump-to-3_4_0dev
mirpedrol
authored
Change location pipeline autocompletion and use gitlab dummy
LouisLeNezet
committed
Fix import
LouisLeNezet
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Update pipelines completion test
LouisLeNezet
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Update test
LouisLeNezet
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Update test
LouisLeNezet
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Fix test
LouisLeNezet
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Merge branch 'dev' into autocomplete
LouisLeNezet
authored

Commits on Jul 10, 2025

Commits on Jul 16, 2025

Merge branch 'dev' into module_exec
muffato
committed

Commits on Jul 21, 2025

Commits on Jul 22, 2025

Update .nftignore
jonasscheid
authored

Commits on Jul 23, 2025

update multiQC to 1.30
jonasscheid
committed

Commits on Jul 24, 2025

Commits on Jul 29, 2025

Commits on Jul 30, 2025

Update nf_core/pipelines/schema.py

shenkers
and
mirpedrol
authored

Commits on Aug 1, 2025

Commits on Aug 12, 2025

Commits on Aug 13, 2025

Commits on Aug 14, 2025

refactor: Consolidate module installation in test setUp methods

edmundmiller
and
claude
committed

Commits on Aug 19, 2025

Commits on Aug 25, 2025

Commits on Aug 26, 2025

Commits on Sep 27, 2025

fix: Address PR review feedback
edmundmiller
committed

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