From a5890a399acee79814d3236061e2d8f6ced0f8e5 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 30 Aug 2024 10:53:24 +0200 Subject: [PATCH 1/3] run lint --release on PRs to master --- .github/workflows/linting.yml | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 1fcafe8..bfcf804 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -46,12 +46,21 @@ jobs: python -m pip install --upgrade pip pip install nf-core - - name: Run nf-core lint + - name: Run nf-core pipelines lint env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} - run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md + run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md + if: ${{ github.event_name == 'pull_request' || github.event_name == 'push' }} + + - name: Run nf-core pipelines lint --release + env: + GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} + run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md + if: ${{ github.event_name == 'release' }} - name: Save PR number if: ${{ always() }} From 7d5d5a3ad933ac9a03a00820736c7f904326a26c Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 30 Aug 2024 11:21:18 +0200 Subject: [PATCH 2/3] remove 'pipelines' from command --- .github/workflows/linting.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index bfcf804..7249427 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -46,20 +46,20 @@ jobs: python -m pip install --upgrade pip pip install nf-core - - name: Run nf-core pipelines lint + - name: Run nf-core lint env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} - run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md + run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md if: ${{ github.event_name == 'pull_request' || github.event_name == 'push' }} - - name: Run nf-core pipelines lint --release + - name: Run nf-core lint --release env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} - run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md + run: nf-core -l lint_log.txt lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md if: ${{ github.event_name == 'release' }} - name: Save PR number From 7b2d08a0d2e32839c566e7493203525fd44fecd7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Fri, 30 Aug 2024 09:27:36 +0000 Subject: [PATCH 3/3] fix linting --- .github/workflows/linting.yml | 9 --------- 1 file changed, 9 deletions(-) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 7249427..1fcafe8 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -52,15 +52,6 @@ jobs: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - if: ${{ github.event_name == 'pull_request' || github.event_name == 'push' }} - - - name: Run nf-core lint --release - env: - GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} - run: nf-core -l lint_log.txt lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - if: ${{ github.event_name == 'release' }} - name: Save PR number if: ${{ always() }}