From ae1976f79cd2fa9237194aa307dc863d6130ecf0 Mon Sep 17 00:00:00 2001 From: vedhav Date: Tue, 10 Dec 2024 17:02:50 +0530 Subject: [PATCH 1/4] add setup-r-dependencies --- .github/workflows/check.yaml | 56 ++++++++++++++++++++++++++++++++ .github/workflows/docs.yaml | 14 ++++++++ .github/workflows/release.yaml | 43 ++++++++++++++++++++++++ .github/workflows/scheduled.yaml | 30 ++++++++++++++++- 4 files changed, 142 insertions(+), 1 deletion(-) diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index 70417e4f..b7f5c1ae 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -29,6 +29,20 @@ jobs: _R_CHECK_CRAN_INCOMING_REMOTE_=false _R_CHECK_EXAMPLE_TIMING_THRESHOLD_=10 additional-r-cmd-check-params: --as-cran + deps-installation-method: setup-r-dependencies + lookup-refs: | + insightsengineering/formatters + insightsengineering/rtables + insightsengineering/rtables.officer + insightsengineering/hermes + insightsengineering/teal + insightsengineering/teal.transform + insightsengineering/teal.code + insightsengineering/teal.data + insightsengineering/teal.logger + insightsengineering/teal.reporter + insightsengineering/teal.widgets + insightsengineering/teal.slice r-cmd-non-cran: name: R CMD Check (non-CRAN) 🧬 uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@main @@ -40,6 +54,20 @@ jobs: enforce-note-blocklist: true concurrency-group: non-cran unit-test-report-directory: unit-test-report-non-cran + deps-installation-method: setup-r-dependencies + lookup-refs: | + insightsengineering/formatters + insightsengineering/rtables + insightsengineering/rtables.officer + insightsengineering/hermes + insightsengineering/teal + insightsengineering/teal.transform + insightsengineering/teal.code + insightsengineering/teal.data + insightsengineering/teal.logger + insightsengineering/teal.reporter + insightsengineering/teal.widgets + insightsengineering/teal.slice coverage: name: Coverage πŸ“” uses: insightsengineering/r.pkg.template/.github/workflows/test-coverage.yaml@main @@ -48,6 +76,20 @@ jobs: with: additional-env-vars: | NOT_CRAN=true + deps-installation-method: setup-r-dependencies + lookup-refs: | + insightsengineering/formatters + insightsengineering/rtables + insightsengineering/rtables.officer + insightsengineering/hermes + insightsengineering/teal + insightsengineering/teal.transform + insightsengineering/teal.code + insightsengineering/teal.data + insightsengineering/teal.logger + insightsengineering/teal.reporter + insightsengineering/teal.widgets + insightsengineering/teal.slice linter: if: github.event_name != 'push' name: SuperLinter πŸ¦Έβ€β™€οΈ @@ -59,6 +101,20 @@ jobs: REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }} with: auto-update: true + deps-installation-method: setup-r-dependencies + lookup-refs: | + insightsengineering/formatters + insightsengineering/rtables + insightsengineering/rtables.officer + insightsengineering/hermes + insightsengineering/teal + insightsengineering/teal.transform + insightsengineering/teal.code + insightsengineering/teal.data + insightsengineering/teal.logger + insightsengineering/teal.reporter + insightsengineering/teal.widgets + insightsengineering/teal.slice gitleaks: name: gitleaks πŸ’§ uses: insightsengineering/r.pkg.template/.github/workflows/gitleaks.yaml@main diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml index 57ae8004..49588685 100644 --- a/.github/workflows/docs.yaml +++ b/.github/workflows/docs.yaml @@ -42,3 +42,17 @@ jobs: with: default-landing-page: latest-tag additional-unit-test-report-directories: unit-test-report-non-cran + deps-installation-method: setup-r-dependencies + lookup-refs: | + insightsengineering/formatters + insightsengineering/rtables + insightsengineering/rtables.officer + insightsengineering/hermes + insightsengineering/teal + insightsengineering/teal.transform + insightsengineering/teal.code + insightsengineering/teal.data + insightsengineering/teal.logger + insightsengineering/teal.reporter + insightsengineering/teal.widgets + insightsengineering/teal.slice diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml index cf7732ab..b3ed87fb 100644 --- a/.github/workflows/release.yaml +++ b/.github/workflows/release.yaml @@ -17,6 +17,20 @@ jobs: with: skip-r-cmd-check: true skip-r-cmd-install: true + deps-installation-method: setup-r-dependencies + lookup-refs: | + insightsengineering/formatters + insightsengineering/rtables + insightsengineering/rtables.officer + insightsengineering/hermes + insightsengineering/teal + insightsengineering/teal.transform + insightsengineering/teal.code + insightsengineering/teal.data + insightsengineering/teal.logger + insightsengineering/teal.reporter + insightsengineering/teal.widgets + insightsengineering/teal.slice docs: name: Pkgdown Docs πŸ“š needs: release @@ -25,12 +39,41 @@ jobs: REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }} with: default-landing-page: latest-tag + deps-installation-method: setup-r-dependencies + lookup-refs: | + insightsengineering/formatters + insightsengineering/rtables + insightsengineering/rtables.officer + insightsengineering/hermes + insightsengineering/teal + insightsengineering/teal.transform + insightsengineering/teal.code + insightsengineering/teal.data + insightsengineering/teal.logger + insightsengineering/teal.reporter + insightsengineering/teal.widgets + insightsengineering/teal.slice validation: name: R Package Validation report πŸ“ƒ needs: release uses: insightsengineering/r.pkg.template/.github/workflows/validation.yaml@main secrets: REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }} + with: + deps-installation-method: setup-r-dependencies + lookup-refs: | + insightsengineering/formatters + insightsengineering/rtables + insightsengineering/rtables.officer + insightsengineering/hermes + insightsengineering/teal + insightsengineering/teal.transform + insightsengineering/teal.code + insightsengineering/teal.data + insightsengineering/teal.logger + insightsengineering/teal.reporter + insightsengineering/teal.widgets + insightsengineering/teal.slice release: name: Create release πŸŽ‰ uses: insightsengineering/r.pkg.template/.github/workflows/release.yaml@main diff --git a/.github/workflows/scheduled.yaml b/.github/workflows/scheduled.yaml index 32599115..a1198468 100644 --- a/.github/workflows/scheduled.yaml +++ b/.github/workflows/scheduled.yaml @@ -3,7 +3,7 @@ name: Scheduled πŸ•°οΈ on: schedule: - - cron: '45 3 * * 0' + - cron: "45 3 * * 0" workflow_dispatch: inputs: chosen-workflow: @@ -56,6 +56,20 @@ jobs: ) name: revdepcheck ↩️ uses: insightsengineering/r.pkg.template/.github/workflows/revdepcheck.yaml@main + with: + lookup-refs: | + insightsengineering/formatters + insightsengineering/rtables + insightsengineering/rtables.officer + insightsengineering/hermes + insightsengineering/teal + insightsengineering/teal.transform + insightsengineering/teal.code + insightsengineering/teal.data + insightsengineering/teal.logger + insightsengineering/teal.reporter + insightsengineering/teal.widgets + insightsengineering/teal.slice rhub: if: > github.event_name == 'schedule' || ( @@ -64,3 +78,17 @@ jobs: ) name: R-hub 🌐 uses: insightsengineering/r.pkg.template/.github/workflows/rhub.yaml@main + with: + lookup-refs: | + insightsengineering/formatters + insightsengineering/rtables + insightsengineering/rtables.officer + insightsengineering/hermes + insightsengineering/teal + insightsengineering/teal.transform + insightsengineering/teal.code + insightsengineering/teal.data + insightsengineering/teal.logger + insightsengineering/teal.reporter + insightsengineering/teal.widgets + insightsengineering/teal.slice From a3fb50971d55f64696bc6dc83cfa16919f8d2745 Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Tue, 10 Dec 2024 11:51:12 +0000 Subject: [PATCH 2/4] [skip roxygen] [skip vbump] Roxygen Man Pages Auto Update --- man/sampleVarSpecServer.Rd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/man/sampleVarSpecServer.Rd b/man/sampleVarSpecServer.Rd index e218e58c..a5bbe24a 100644 --- a/man/sampleVarSpecServer.Rd +++ b/man/sampleVarSpecServer.Rd @@ -44,7 +44,7 @@ from.} \item{label_modal_title}{(\code{string})\cr title for the dialog that asks for the text input.} } \value{ -Reactive \code{\link[SummarizedExperiment:RangedSummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}} which can be used as +Reactive \code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}} which can be used as input for the relevant \code{hermes} functions. } \description{ From 305df4dfa85a347caf298b3f58d9708503622dee Mon Sep 17 00:00:00 2001 From: vedhav Date: Tue, 10 Dec 2024 17:33:05 +0530 Subject: [PATCH 3/4] rip `staged_dependencies.yaml` --- staged_dependencies.yaml | 30 ------------------------------ 1 file changed, 30 deletions(-) delete mode 100644 staged_dependencies.yaml diff --git a/staged_dependencies.yaml b/staged_dependencies.yaml deleted file mode 100644 index e97283d4..00000000 --- a/staged_dependencies.yaml +++ /dev/null @@ -1,30 +0,0 @@ ---- -current_repo: - repo: insightsengineering/teal.modules.hermes - host: https://github.com -upstream_repos: - insightsengineering/rtables: - repo: insightsengineering/rtables - host: https://github.com - insightsengineering/hermes: - repo: insightsengineering/hermes - host: https://github.com - insightsengineering/teal.logger: - repo: insightsengineering/teal.logger - host: https://github.com - insightsengineering/teal.data: - repo: insightsengineering/teal.data - host: https://github.com - insightsengineering/teal.reporter: - repo: insightsengineering/teal.reporter - host: https://github.com - insightsengineering/teal.widgets: - repo: insightsengineering/teal.widgets - host: https://github.com - insightsengineering/teal: - repo: insightsengineering/teal - host: https://github.com - insightsengineering/tern: - repo: insightsengineering/tern - host: https://github.com -downstream_repos: From 160cd5ce7e258cc43feca3702cb22c5fb2c55419 Mon Sep 17 00:00:00 2001 From: vedhav Date: Wed, 11 Dec 2024 18:40:08 +0530 Subject: [PATCH 4/4] revert sd --- staged_dependencies.yaml | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 staged_dependencies.yaml diff --git a/staged_dependencies.yaml b/staged_dependencies.yaml new file mode 100644 index 00000000..e97283d4 --- /dev/null +++ b/staged_dependencies.yaml @@ -0,0 +1,30 @@ +--- +current_repo: + repo: insightsengineering/teal.modules.hermes + host: https://github.com +upstream_repos: + insightsengineering/rtables: + repo: insightsengineering/rtables + host: https://github.com + insightsengineering/hermes: + repo: insightsengineering/hermes + host: https://github.com + insightsengineering/teal.logger: + repo: insightsengineering/teal.logger + host: https://github.com + insightsengineering/teal.data: + repo: insightsengineering/teal.data + host: https://github.com + insightsengineering/teal.reporter: + repo: insightsengineering/teal.reporter + host: https://github.com + insightsengineering/teal.widgets: + repo: insightsengineering/teal.widgets + host: https://github.com + insightsengineering/teal: + repo: insightsengineering/teal + host: https://github.com + insightsengineering/tern: + repo: insightsengineering/tern + host: https://github.com +downstream_repos: