Container load scripts #2
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Did my best, and wanted to keep the code verbatim before things really start shifting.
… version handling - Introduced separate test files for module changes, deprecations, todos, and version functionalities. - Implemented basic structure and placeholder tests for each new test file to ensure future functionality can be added. - Removed the old test_lint.py file to streamline the test organization.
…ssed tests - Updated the assertion to verify the presence of "test_snap_md5sum" in the passed tests. - Improved handling to accommodate both LintResult objects and tuple formats for better robustness.
BREAKING CHANGE: The `arm` profile has been renamed to `arm64` and now provides native ARM64 support using Wave containers instead of x86 emulation. - Replace `arm` profile with `arm64` profile for native ARM64 execution - Add `emulate_amd64` profile for users who need x86 emulation on ARM hardware - The `arm64` profile works universally on Apple Silicon, AWS Graviton, and other ARM64 platforms - Users must update: `-profile arm` → `-profile arm64` (for native) or `-profile emulate_amd64` (for emulation) Fixes nf-core#3536 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>
- Replace skeleton tests with actual implementations for module_changes, module_deprecations, module_version, and module_todos - Remove duplicate MockModuleLint class definitions and consolidate imports to test_lint_utils - Rename TestMainNf to TestMainNfLinting with improved documentation - Add comprehensive test coverage for lint functionality including edge cases and error conditions - Add CLAUDE.md to .gitignore 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>
Instead of raising a UserWarning when a cached JSON config file is corrupted, now logs a warning and attempts to delete the corrupted cache file, allowing the config to be regenerated. This prevents test failures in CI when cache files become corrupted. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>
ErikDanielsson
changed the base branch from
download-refactor-again
to
refactor-download-tests
4 tasks
- Move samtools/sort installation from individual test methods to setUp methods - Rename test_modules_lint_registry to test_main_nf_lint_with_alternative_registry to clarify scope - Eliminate redundant module installations across TestModuleChanges, TestModuleTodos, TestModuleDeprecations, TestModuleVersion, and TestMainNfLinting - Improve test performance by installing modules once per test class instead of per test method Addresses PR review comments about test setup optimization and method naming clarity. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>
Replace arm profile with arm64 and emulate_amd64 profiles
…compatibility with nextflow
Remove workflow.trace from nf-test snapshot
ignore files in gitignore also for pipeline_if_empty_null lint test
Add GHA to update template nf-test snapshots
- Replace assertions in setUp methods with skipTest() for proper error handling - Remove unnecessary setUp methods where only one test needs module installation - Eliminate manual test cleanup code relying on test framework isolation - Consolidate module installation in setUp where all tests in class need it - Update registry test to properly expect failures with mismatched registries Addresses code review feedback on test best practices and structure. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>
Refactor module lint tests
…asy-copy Ftr/test datasets easy copy
…-again Refactor pipeline downloads command to use `nextflow inspect` for container detection
…/nf-core-tools into issues/3732-upd-download-wf
…nload-wf fix: Remove dependency on dev branch of tools
…talled and assume python instead.
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Dummy PR to show changes between the major download refactor PR nf-core#3634 and the container load script PR nf-core#3706
PR checklist
CHANGELOG.mdis updateddocsis updated