From beb6acb205ab3718ffbba5cbbea37f01427f1258 Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Thu, 20 Jan 2022 08:55:43 +0100 Subject: [PATCH 1/7] CI: print out pytest logs on failure --- .github/workflows/pytest-workflow.yml | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml index cc7c9313f31..272e1f1d5aa 100644 --- a/.github/workflows/pytest-workflow.yml +++ b/.github/workflows/pytest-workflow.yml @@ -93,6 +93,16 @@ jobs: # only use one thread for pytest-workflow to avoid race condition on conda cache. run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof + - name: Output log on failure + if: failure() + run: | + echo "======> log.out <=======" + cat /home/runner/pytest_workflow_*/*/log.out + echo + echo + echo "======> log.err <=======" + cat /home/runner/pytest_workflow_*/*/log.err + - name: Upload logs on failure if: failure() uses: actions/upload-artifact@v2 From 37961f7320e302dd198baf3df8937e6b5068d1e1 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 20 Jan 2022 21:34:08 -0600 Subject: [PATCH 2/7] ci(pytest-workflow): cat => bat --- .github/workflows/pytest-workflow.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml index 272e1f1d5aa..44feaf48372 100644 --- a/.github/workflows/pytest-workflow.yml +++ b/.github/workflows/pytest-workflow.yml @@ -96,12 +96,13 @@ jobs: - name: Output log on failure if: failure() run: | + sudo apt install bat echo "======> log.out <=======" - cat /home/runner/pytest_workflow_*/*/log.out + bat /home/runner/pytest_workflow_*/*/log.out echo echo echo "======> log.err <=======" - cat /home/runner/pytest_workflow_*/*/log.err + bat /home/runner/pytest_workflow_*/*/log.err - name: Upload logs on failure if: failure() From bc78e5e8d144a823e70f6c57265ac80db687e5fe Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Fri, 21 Jan 2022 08:34:43 +0100 Subject: [PATCH 3/7] Introduce bug --- modules/fastqc/main.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/fastqc/main.nf b/modules/fastqc/main.nf index d250eca0758..9c728e24e7a 100644 --- a/modules/fastqc/main.nf +++ b/modules/fastqc/main.nf @@ -6,6 +6,7 @@ process FASTQC { container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : 'quay.io/biocontainers/fastqc:0.11.9--0' }" + cpus 42 input: tuple val(meta), path(reads) From 5ebfe7d27249095c6c34cb1d0b7631781796bc74 Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Fri, 21 Jan 2022 08:41:48 +0100 Subject: [PATCH 4/7] Use batcat --- .github/workflows/pytest-workflow.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml index 7d33b89d117..34af24fe03d 100644 --- a/.github/workflows/pytest-workflow.yml +++ b/.github/workflows/pytest-workflow.yml @@ -91,8 +91,8 @@ jobs: - name: Output log on failure if: failure() run: | - sudo apt install -qq bat - bat /home/runner/pytest_workflow_*/*/log.{out,err} + sudo apt install bat > /dev/null + batcat /home/runner/pytest_workflow_*/*/log.{out,err} - name: Upload logs on failure if: failure() From 6d622bfe549c35032ec2967ca42dc7d5170767e9 Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Fri, 21 Jan 2022 08:44:21 +0100 Subject: [PATCH 5/7] Force fancification --- .github/workflows/pytest-workflow.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml index 34af24fe03d..da8ce54f61e 100644 --- a/.github/workflows/pytest-workflow.yml +++ b/.github/workflows/pytest-workflow.yml @@ -92,7 +92,7 @@ jobs: if: failure() run: | sudo apt install bat > /dev/null - batcat /home/runner/pytest_workflow_*/*/log.{out,err} + batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err} - name: Upload logs on failure if: failure() From 799c6af79547046fa1772bdc0472466cde3b61b0 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Tue, 25 Jan 2022 13:40:00 -0600 Subject: [PATCH 6/7] ci: Use colored output for pytest --- .github/workflows/pytest-workflow.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml index da8ce54f61e..56959666148 100644 --- a/.github/workflows/pytest-workflow.yml +++ b/.github/workflows/pytest-workflow.yml @@ -86,7 +86,7 @@ jobs: # Test the module - name: Run pytest-workflow # only use one thread for pytest-workflow to avoid race condition on conda cache. - run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof + run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --color=yes - name: Output log on failure if: failure() From adb33424e7443da70fc9ab28759bcba13906f29f Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Mon, 7 Feb 2022 17:36:35 +0100 Subject: [PATCH 7/7] Revert "Introduce bug" This reverts commit bc78e5e8d144a823e70f6c57265ac80db687e5fe. --- modules/fastqc/main.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/modules/fastqc/main.nf b/modules/fastqc/main.nf index c116020eb57..ed6b8c50b1f 100644 --- a/modules/fastqc/main.nf +++ b/modules/fastqc/main.nf @@ -6,7 +6,6 @@ process FASTQC { container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : 'quay.io/biocontainers/fastqc:0.11.9--0' }" - cpus 42 input: tuple val(meta), path(reads)