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Dev -> main for 3.1.0#3324

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mashehu merged 227 commits intomainnf-core/tools:mainfrom devnf-core/tools:devCopy head branch name to clipboardDec 10, 2024

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Commits on Dec 20, 2023

• set gitpod.yml docker image to latest

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Commits on Mar 18, 2024

• added patch command for subworkflows

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• Merge branch 'dev' into master

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• forgot to import patch in init

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• Merge branch 'master' of https://github.com/ctuni/tools

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• added files for the tests

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• created draft for test file

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• ruff format

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• cleaning up

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• added tests

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• ruff

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• ruff format

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• removed split

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• mypy

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• setup_patch

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• called function correctly

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• wraping up for the day

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Commits on Aug 27, 2024

• change pipeline template and tooling to allow main as default branch

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• handle missing self.default_branch

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• fix order of initialization

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• fix schema check

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• set default value for default branch

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• fix order in lint

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• fix quotes

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• revert to format

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• use format instead of f-string

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Commits on Oct 17, 2024

• allow mixed list and dict in lint config

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• nested too deeply

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• [automated] Update CHANGELOG.md

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Commits on Oct 21, 2024

• handle new nf-core.yml structure

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• update documentation for multiqc_config linting

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• parse yaml correctly

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• found a better way to handle the ignore file being None

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• handle new lint config structure

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• add tests with different valid yaml structures

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• Merge branch 'fix-yml-config-type' of github.com:mashehu/tools into fix-yml-config-type

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• remove last traces of LintConfigType

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• fix incorrect type

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• more type fixes

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Commits on Oct 22, 2024

• add all lint tests to config

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• switch all defaults to None and drop them on dump

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• drop None values when checking for test names

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• fix test_lint tests

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Commits on Oct 23, 2024

• Merge branch 'dev' of github.com:nf-core/tools into fix-yml-config-type

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• Merge branch 'fix-yml-config-type' of github.com:mashehu/tools into fix-yml-config-type

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• move test in correct directory

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• fix tests

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Commits on Oct 24, 2024

• Merge branch 'dev' of github.com:nf-core/tools into add-rocreate

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• run tests without commiting ro-crate

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• add ro-crate creation to pipelines create command

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• fix command import

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• remove schema loading, because it is not needed anymore

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• update snapshots

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• try to fix coverage report generation

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• Merge branch 'add-rocreate' of github.com:mashehu/tools into add-rocreate

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Commits on Nov 15, 2024

• Merge branch 'dev' of https://github.com/nf-core/tools

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• update and fix swf patch tests

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Commits on Nov 21, 2024

• Merge branch 'dev' into master

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• build: Setup VS Code tests

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Commits on Nov 22, 2024

• apply patch reverse when linting a patched subworkflow

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• update get_patch_fn to work with subworkflows

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• move modules_differ.py to components_differ.py

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Commits on Nov 25, 2024

• add subworkflows patch missing tests

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• fix subworkflows update test

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• add help text for --remove flag

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• apply code review suggestions to patch tests

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• Update tests/modules/test_patch.py

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• apply suggestions by @mashehu

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• Merge pull request #2861 from ctuni/master

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• remove def from nextflow.config and add trace_report_suffix param

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• fix(#3297): Update warning message for pytest-workflow

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Commits on Nov 26, 2024

• Add Python terminal env settings

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• Update pre-commit hook astral-sh/ruff-pre-commit to v0.8.0

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• add validation.monochromeLogs to config

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• ignore trace_report_suffix default check

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Commits on Nov 27, 2024

• Merge branch 'dev' of github.com:nf-core/tools into add-rocreate

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• update snapshots

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• add more tests

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• enable zip output

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Commits on Nov 28, 2024

• Move modules config import after base.config

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• Fix linting

  

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Commits on Nov 29, 2024

• Download: Need to deduplicate Seqera Container matches as well, otherwise a race condition emerges.

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• Add new function to handle Seqera Container Oras URIs.

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• Ensure, that oras:// containers are correctly handled.

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• Download: Add test data for oras:// modules.

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• Changelog.

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Commits on Nov 30, 2024

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• Update dependency textual-dev to v1.7.0

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• Update gitpod/workspace-base Docker digest to 12853f7 (#3309)

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• fix: linting error in meta_yml where module.process_name is always ""

  

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Commits on Dec 4, 2024

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• fix: add explicit str type to self.process_name

  

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• fix: module section linter regex

  

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