From 584955459fca5231b8916ad69b5c9c3446f61a1d Mon Sep 17 00:00:00 2001 From: walkowif <59475134+walkowif@users.noreply.github.com> Date: Mon, 16 Sep 2024 10:46:06 +0200 Subject: [PATCH 1/2] Workflow propagations (#391) --- .github/workflows/check.yaml | 3 +++ .github/workflows/scheduled.yaml | 34 +++++++++++++++++++++++++++++++- README.md | 6 +++--- 3 files changed, 39 insertions(+), 4 deletions(-) diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index 974abfc6..70417e4f 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -45,6 +45,9 @@ jobs: uses: insightsengineering/r.pkg.template/.github/workflows/test-coverage.yaml@main secrets: REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }} + with: + additional-env-vars: | + NOT_CRAN=true linter: if: github.event_name != 'push' name: SuperLinter ๐Ÿฆธโ€โ™€๏ธ diff --git a/.github/workflows/scheduled.yaml b/.github/workflows/scheduled.yaml index d0cc5045..32599115 100644 --- a/.github/workflows/scheduled.yaml +++ b/.github/workflows/scheduled.yaml @@ -1,13 +1,30 @@ --- -name: On-demand ๐Ÿง‘โ€๐Ÿ”ฌ +name: Scheduled ๐Ÿ•ฐ๏ธ on: schedule: - cron: '45 3 * * 0' workflow_dispatch: + inputs: + chosen-workflow: + description: | + Select which workflow you'd like to run + required: true + type: choice + default: rhub + options: + - rhub + - dependency-test + - branch-cleanup + - revdepcheck jobs: dependency-test: + if: > + github.event_name == 'schedule' || ( + github.event_name == 'workflow_dispatch' && + inputs.chosen-workflow == 'dependency-test' + ) strategy: fail-fast: false matrix: @@ -22,13 +39,28 @@ jobs: additional-env-vars: | PKG_SYSREQS_DRY_RUN=true branch-cleanup: + if: > + github.event_name == 'schedule' || ( + github.event_name == 'workflow_dispatch' && + inputs.chosen-workflow == 'branch-cleanup' + ) name: Branch Cleanup ๐Ÿงน uses: insightsengineering/r.pkg.template/.github/workflows/branch-cleanup.yaml@main secrets: REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }} revdepcheck: + if: > + github.event_name == 'schedule' || ( + github.event_name == 'workflow_dispatch' && + inputs.chosen-workflow == 'revdepcheck' + ) name: revdepcheck โ†ฉ๏ธ uses: insightsengineering/r.pkg.template/.github/workflows/revdepcheck.yaml@main rhub: + if: > + github.event_name == 'schedule' || ( + github.event_name == 'workflow_dispatch' && + inputs.chosen-workflow == 'rhub' + ) name: R-hub ๐ŸŒ uses: insightsengineering/r.pkg.template/.github/workflows/rhub.yaml@main diff --git a/README.md b/README.md index 366c96c1..1a7094f8 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ [![Check ๐Ÿ› ](https://github.com/insightsengineering/teal.modules.hermes/actions/workflows/check.yaml/badge.svg)](https://github.com/insightsengineering/teal.modules.hermes/actions/workflows/check.yaml) -[![Docs ๐Ÿ“š](https://github.com/insightsengineering/teal.modules.hermes/actions/workflows/docs.yaml/badge.svg)](https://insightsengineering.github.io/teal.modules.hermes/) +[![Docs ๐Ÿ“š](https://github.com/insightsengineering/teal.modules.hermes/actions/workflows/docs.yaml/badge.svg)](https://insightsengineering.github.io/teal.modules.hermes/latest-tag/) [![Code Coverage ๐Ÿ“”](https://raw.githubusercontent.com/insightsengineering/teal.modules.hermes/_xml_coverage_reports/data/main/badge.svg)](https://raw.githubusercontent.com/insightsengineering/teal.modules.hermes/_xml_coverage_reports/data/main/coverage.xml) ![GitHub forks](https://img.shields.io/github/forks/insightsengineering/teal.modules.hermes?style=social) @@ -24,7 +24,7 @@ ### What is `teal`? `teal` is a shiny-based interactive exploration framework for analyzing clinical trials data. `teal` currently provides a dynamic filtering facility and diverse data viewers. `teal` shiny applications are built using standard [shiny modules](https://shiny.rstudio.com/articles/modules.html). -See [`teal` page](https://insightsengineering.github.io/teal) for more details. +See [`teal` page](https://insightsengineering.github.io/teal/) for more details. ### What is `hermes`? @@ -38,7 +38,7 @@ See the [vignette](https://insightsengineering.github.io/hermes/articles/hermes. ## Installation -From July 2023 `insightsengineering` packages are available on [r-universe](https://r-universe.dev/). +From July 2023 `insightsengineering` packages are available on [r-universe](https://r-universe.dev/search). ```r # stable versions From 9d6f82fe375be675e184aa8510ef6410457a7b02 Mon Sep 17 00:00:00 2001 From: walkowif Date: Mon, 16 Sep 2024 08:47:01 +0000 Subject: [PATCH 2/2] [skip actions] Bump version to 0.1.6.9021 --- .pre-commit-config.yaml | 2 +- DESCRIPTION | 4 ++-- NEWS.md | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 13e16302..15509fa7 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -6,7 +6,7 @@ default_language_version: python: python3 repos: - repo: https://github.com/lorenzwalthert/precommit - rev: v0.4.3 + rev: v0.4.3.9001 hooks: - id: style-files name: Style code with `styler` diff --git a/DESCRIPTION b/DESCRIPTION index 149c4cc0..7a3ccd85 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Type: Package Package: teal.modules.hermes Title: RNA-Seq Analysis Modules to Add to a Teal Application -Version: 0.1.6.9020 -Date: 2024-08-29 +Version: 0.1.6.9021 +Date: 2024-09-16 Authors@R: c( person("Daniel", "Sabanรฉs Bovรฉ", , "daniel.sabanes_bove@roche.com", role = c("aut", "cre")), person("Nikolas", "Burkoff", role = "aut"), diff --git a/NEWS.md b/NEWS.md index 31e7c9a4..f21bef2d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# teal.modules.hermes 0.1.6.9020 +# teal.modules.hermes 0.1.6.9021 ### Miscellaneous * Added placeholders for `assaySpec`, `adtteSpec` and `geneSpec` inputs when no option is selected.