diff --git a/CHANGELOG.md b/CHANGELOG.md index 518fa1bdd6..b3fc48382c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,16 @@ # nf-core/tools: Changelog +## [v2.3.2 - Mercury Vulture Fixed Formatting](https://github.com/nf-core/tools/releases/tag/2.3.2) - [2022-03-24] + +Very minor patch release to fix the full size AWS tests and re-run the template sync, which partially failed due to GitHub pull-requests being down at the time of release. + +### Template + +- Updated the AWS GitHub actions to let nf-core/tower-action use it's defaults for pipeline and git sha ([#1488](https://github.com/nf-core/tools/pull/1488)) +- Add prettier editor extension to `gitpod.yml` in template ([#1485](https://github.com/nf-core/tools/pull/1485)) +- Remove traces of markdownlint in the template ([#1486](https://github.com/nf-core/tools/pull/1486) +- Remove accidentally added line in `CHANGELOG.md` in the template ([#1487](https://github.com/nf-core/tools/pull/1487)) + ## [v2.3.1 - Mercury Vulture Formatting](https://github.com/nf-core/tools/releases/tag/2.3.1) - [2022-03-23] This patch release is primarily to address problems that we had in the v2.3 release with code linting. @@ -44,8 +55,6 @@ Please note that there are many excellent integrations for Prettier available, f - New pipeline lint test `multiqc_config` that checks YAML structure instead of basic file contents ([#1461](https://github.com/nf-core/tools/pull/1461)) - Updates to the GitPod docker image to install the latest version of nf-core/tools -### Modules - ## [v2.3 - Mercury Vulture](https://github.com/nf-core/tools/releases/tag/2.3) - [2022-03-15] ### Template diff --git a/nf_core/lint/files_exist.py b/nf_core/lint/files_exist.py index f1c372672d..74693d03e3 100644 --- a/nf_core/lint/files_exist.py +++ b/nf_core/lint/files_exist.py @@ -82,6 +82,7 @@ def files_exist(self): .github/ISSUE_TEMPLATE/feature_request.md docs/images/nf-core-PIPELINE_logo.png .markdownlint.yml + .yamllint.yml Files that *should not* be present: @@ -164,6 +165,7 @@ def files_exist(self): os.path.join(".github", "ISSUE_TEMPLATE", "feature_request.md"), os.path.join("docs", "images", f"nf-core-{short_name}_logo.png"), ".markdownlint.yml", + ".yamllint.yml", ] files_warn_ifexists = [".travis.yml"] diff --git a/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md b/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md index 3047cba874..7759916864 100644 --- a/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md +++ b/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md @@ -10,7 +10,6 @@ Remember that PRs should be made against the dev branch, unless you're preparing Learn more about contributing: [CONTRIBUTING.md](https://github.com/{{ name }}/tree/master/.github/CONTRIBUTING.md) --> - ## PR checklist diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml index 4851b2875c..6b8c3ce077 100644 --- a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml +++ b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml @@ -22,8 +22,6 @@ jobs: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - pipeline: ${{ github.repository }} - revision: ${{ github.sha }} workdir: s3://${{ secrets.AWS_S3_BUCKET }}{% endraw %}/work/{{ short_name }}/{% raw %}work-${{ github.sha }}{% endraw %} parameters: | { diff --git a/nf_core/pipeline-template/.github/workflows/awstest.yml b/nf_core/pipeline-template/.github/workflows/awstest.yml index 6a58539b80..0715c6b9dd 100644 --- a/nf_core/pipeline-template/.github/workflows/awstest.yml +++ b/nf_core/pipeline-template/.github/workflows/awstest.yml @@ -17,8 +17,6 @@ jobs: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - pipeline: ${{ github.repository }} - revision: ${{ github.sha }} workdir: s3://${{ secrets.AWS_S3_BUCKET }}{% endraw %}/work/{{ short_name }}/{% raw %}work-${{ github.sha }}{% endraw %} parameters: | { diff --git a/nf_core/pipeline-template/.gitpod.yml b/nf_core/pipeline-template/.gitpod.yml index c452ee93e5..85d95ecc8e 100644 --- a/nf_core/pipeline-template/.gitpod.yml +++ b/nf_core/pipeline-template/.gitpod.yml @@ -4,7 +4,7 @@ vscode: extensions: # based on nf-core.nf-core-extensionpack - codezombiech.gitignore # Language support for .gitignore files # - cssho.vscode-svgviewer # SVG viewer - - davidanson.vscode-markdownlint # Markdown/CommonMark linting and style checking for Visual Studio Code + - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar diff --git a/nf_core/pipeline-template/CHANGELOG.md b/nf_core/pipeline-template/CHANGELOG.md index 75c4211992..c9bd47f145 100644 --- a/nf_core/pipeline-template/CHANGELOG.md +++ b/nf_core/pipeline-template/CHANGELOG.md @@ -11,8 +11,6 @@ Initial release of {{ name }}, created with the [nf-core](https://nf-co.re/) tem ### `Fixed` -- Clarified conda usage and added an installation tutorial for Singularity since the one on Syllabs' website uses an outdate version of GO Compiler - ### `Dependencies` ### `Deprecated` diff --git a/setup.py b/setup.py index 9e407d082f..90949a1dd7 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ from setuptools import setup, find_packages -version = "2.3.1" +version = "2.3.2" with open("README.md") as f: readme = f.read()