From e54d268c9c5eae4e48903e240876e98921e5bf10 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 8 Jan 2024 08:48:56 +0100 Subject: [PATCH 1/3] use pdiff also on gitpod for nf-test See https://github.com/nf-core/modules/pull/4682 --- .gitpod.yml | 6 ++++++ nf_core/pipeline-template/.gitpod.yml | 4 ++++ 2 files changed, 10 insertions(+) diff --git a/.gitpod.yml b/.gitpod.yml index 91c04d7f94..cadccac4ba 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -9,6 +9,12 @@ tasks: - name: unset JAVA_TOOL_OPTIONS command: | unset JAVA_TOOL_OPTIONS + + - name: Use pdiff for nf-test diff viewing + command: | + export NFT_DIFF="pdiff" + export NFT_DIFF_ARGS="--line-numbers --expand-tabs=2" + vscode: extensions: # based on nf-core.nf-core-extensionpack - codezombiech.gitignore # Language support for .gitignore files diff --git a/nf_core/pipeline-template/.gitpod.yml b/nf_core/pipeline-template/.gitpod.yml index acf7269536..78d68ffcb0 100644 --- a/nf_core/pipeline-template/.gitpod.yml +++ b/nf_core/pipeline-template/.gitpod.yml @@ -7,6 +7,10 @@ tasks: - name: unset JAVA_TOOL_OPTIONS command: | unset JAVA_TOOL_OPTIONS + - name: Use pdiff for nf-test diff viewing + command: | + export NFT_DIFF="pdiff" + export NFT_DIFF_ARGS="--line-numbers --expand-tabs=2" vscode: extensions: # based on nf-core.nf-core-extensionpack - codezombiech.gitignore # Language support for .gitignore files From 012153976e474699cb4354026e22166cc9dad0dc Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 8 Jan 2024 07:49:58 +0000 Subject: [PATCH 2/3] [automated] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2f18b559b4..4317b6fa65 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,10 +17,10 @@ ### General - Run CI-pytests for nf-core tools on self-hosted runners ([#2550](https://github.com/nf-core/tools/pull/2550)) - - Add Ruff linter and formatter replacing Black, isort and pyupgrade ([#2620](https://github.com/nf-core/tools/pull/2620)) - Update pre-commit hook pre-commit/mirrors-mypy to v1.8.0 ([#2630](https://github.com/nf-core/tools/pull/2630)) - Update mshick/add-pr-comment action to v2 ([#2632](https://github.com/nf-core/tools/pull/2632)) +- use pdiff also on gitpod for nf-test ([#2640](https://github.com/nf-core/tools/pull/2640)) # [v2.11.1 - Magnesium Dragon Patch](https://github.com/nf-core/tools/releases/tag/2.11) - [2023-12-20] From 9b45d585ed75d867dc1120dfaf28bdefb0c7e785 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 8 Jan 2024 11:07:04 +0100 Subject: [PATCH 3/3] put changelog comment in correct section --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4317b6fa65..a4a033fa4c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,7 @@ ### Template - Use `pre-commit` to lint files in GitHub CI ([#2635](https://github.com/nf-core/tools/pull/2635)) +- Use pdiff also on gitpod for nf-test ([#2640](https://github.com/nf-core/tools/pull/2640)) ### Download @@ -20,7 +21,6 @@ - Add Ruff linter and formatter replacing Black, isort and pyupgrade ([#2620](https://github.com/nf-core/tools/pull/2620)) - Update pre-commit hook pre-commit/mirrors-mypy to v1.8.0 ([#2630](https://github.com/nf-core/tools/pull/2630)) - Update mshick/add-pr-comment action to v2 ([#2632](https://github.com/nf-core/tools/pull/2632)) -- use pdiff also on gitpod for nf-test ([#2640](https://github.com/nf-core/tools/pull/2640)) # [v2.11.1 - Magnesium Dragon Patch](https://github.com/nf-core/tools/releases/tag/2.11) - [2023-12-20]