From dd2944a366fe4289cc974e6deff8b5053cc1e809 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Wed, 21 Feb 2024 13:24:13 -0500 Subject: [PATCH 1/4] add contributing section about CI nested in PRs --- CONTRIBUTING.md | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 5bf0bde2..a363ef00 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -20,6 +20,19 @@ To allow for efficient review, please include in any pull request a concise and When the changes in `development` merit a new release, a pull request will be filed to merge the current version of the `development` branch into `main`, followed by tagging a release on the `main` branch. +### Continuous integration in pull requests + +There are several automatic checks performed by GitHub Actions in all pull requests filed to `main` or `development`. + +These checks are required to pass before pull requests can be merged: + +- [Spell check R Markdown and Markdown files](.github/workflows/spell-check.yml): This workflow ensures there are no spelling errors in R Markdown and Markdown files. +- [Check Nextflow stub](.github/workflows/nextflow-stub-check.yaml): This workflow ensures that the [stub workflow](#stub-workflows) runs without errors. +- [Check Nextflow config](.github/workflows/nextflow-config-check.yaml): This workflow ensures that there are no syntax errors in the Nextflow configuration files + +There is also one additional `pre-commit ci` workflow which runs all [pre-commit hooks as described in this section](#pre-commit-hooks), except for the spell check pre-commit hook. +Although highly recommended, it is not required that this workflow passes before pull requests can be merged. + ## Stub workflows All Nextflow processes should include a [`stub` block](https://www.nextflow.io/docs/latest/process.html#stub) with a minimal script that can be run quickly to produce files in the expected output locations. From 551753aa4b424ef042053e785ea3cbf8b9db6f87 Mon Sep 17 00:00:00 2001 From: Stephanie Spielman Date: Wed, 21 Feb 2024 14:02:51 -0500 Subject: [PATCH 2/4] Update CONTRIBUTING.md Co-authored-by: Joshua Shapiro --- CONTRIBUTING.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index a363ef00..2b79d4f1 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -26,9 +26,9 @@ There are several automatic checks performed by GitHub Actions in all pull reque These checks are required to pass before pull requests can be merged: -- [Spell check R Markdown and Markdown files](.github/workflows/spell-check.yml): This workflow ensures there are no spelling errors in R Markdown and Markdown files. -- [Check Nextflow stub](.github/workflows/nextflow-stub-check.yaml): This workflow ensures that the [stub workflow](#stub-workflows) runs without errors. - [Check Nextflow config](.github/workflows/nextflow-config-check.yaml): This workflow ensures that there are no syntax errors in the Nextflow configuration files +- [Check Nextflow stub](.github/workflows/nextflow-stub-check.yaml): This workflow ensures that the [stub workflow](#stub-workflows) runs without errors. +- [Spell check R Markdown and Markdown files](.github/workflows/spell-check.yml): This workflow ensures there are no spelling errors in R Markdown and Markdown files. There is also one additional `pre-commit ci` workflow which runs all [pre-commit hooks as described in this section](#pre-commit-hooks), except for the spell check pre-commit hook. Although highly recommended, it is not required that this workflow passes before pull requests can be merged. From e35d45540e681a0098e626a60ae0c2735f94eb6b Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Wed, 21 Feb 2024 14:05:07 -0500 Subject: [PATCH 3/4] update language about required checks, and precommit ci only runs on development --- CONTRIBUTING.md | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 2b79d4f1..d499f22b 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -22,15 +22,13 @@ When the changes in `development` merit a new release, a pull request will be fi ### Continuous integration in pull requests -There are several automatic checks performed by GitHub Actions in all pull requests filed to `main` or `development`. +There are several automatic checks performed by GitHub Actions in all pull requests filed to `main` or `development`: -These checks are required to pass before pull requests can be merged: +- [Check Nextflow config](.github/workflows/nextflow-config-check.yaml): This workflow ensures that there are no syntax errors in the Nextflow configuration files. This check is required to pass before pull requests can be merged. +- [Check Nextflow stub](.github/workflows/nextflow-stub-check.yaml): This workflow ensures that the [stub workflow](#stub-workflows) runs without errors. This check is required to pass before pull requests can be merged. +- [Spell check R Markdown and Markdown files](.github/workflows/spell-check.yml): This workflow ensures there are no spelling errors in R Markdown and Markdown files. This check is not required to pass before pull requests can be merged. -- [Check Nextflow config](.github/workflows/nextflow-config-check.yaml): This workflow ensures that there are no syntax errors in the Nextflow configuration files -- [Check Nextflow stub](.github/workflows/nextflow-stub-check.yaml): This workflow ensures that the [stub workflow](#stub-workflows) runs without errors. -- [Spell check R Markdown and Markdown files](.github/workflows/spell-check.yml): This workflow ensures there are no spelling errors in R Markdown and Markdown files. - -There is also one additional `pre-commit ci` workflow which runs all [pre-commit hooks as described in this section](#pre-commit-hooks), except for the spell check pre-commit hook. +There is also one additional `pre-commit ci` workflow which runs all [pre-commit hooks as described in this section](#pre-commit-hooks), except for the spell check pre-commit hook, on pull requests filed to the `development` branch. Although highly recommended, it is not required that this workflow passes before pull requests can be merged. ## Stub workflows From 53f9f4bfce091a5bc3db5fed07cd7cbf015108ce Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Wed, 21 Feb 2024 14:20:54 -0500 Subject: [PATCH 4/4] not just on development --- CONTRIBUTING.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index d499f22b..6f5ce9f6 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -28,7 +28,7 @@ There are several automatic checks performed by GitHub Actions in all pull reque - [Check Nextflow stub](.github/workflows/nextflow-stub-check.yaml): This workflow ensures that the [stub workflow](#stub-workflows) runs without errors. This check is required to pass before pull requests can be merged. - [Spell check R Markdown and Markdown files](.github/workflows/spell-check.yml): This workflow ensures there are no spelling errors in R Markdown and Markdown files. This check is not required to pass before pull requests can be merged. -There is also one additional `pre-commit ci` workflow which runs all [pre-commit hooks as described in this section](#pre-commit-hooks), except for the spell check pre-commit hook, on pull requests filed to the `development` branch. +There is also one additional `pre-commit ci` workflow which runs all [pre-commit hooks as described in this section](#pre-commit-hooks), except for the spell check pre-commit hook. Although highly recommended, it is not required that this workflow passes before pull requests can be merged. ## Stub workflows