From 0c93d64a02a289b3a6d8e468813b667a09ac7aab Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Wed, 26 Jul 2023 00:35:08 +0200 Subject: [PATCH 1/7] docs: add minimal version of deps --- .github/workflows/scheduled.yaml | 10 +++++-- DESCRIPTION | 45 ++++++++++++++++++++++++-------- NEWS.md | 4 +++ 3 files changed, 46 insertions(+), 13 deletions(-) diff --git a/.github/workflows/scheduled.yaml b/.github/workflows/scheduled.yaml index b752a49b1..e5174e1bd 100644 --- a/.github/workflows/scheduled.yaml +++ b/.github/workflows/scheduled.yaml @@ -5,14 +5,20 @@ on: schedule: - cron: '45 3 * * 0' workflow_dispatch: + # Section to be removed before action is merged + # note: branch below needs to point to main instead of new-verdepcheck-strategy + push: + branches: + - verdepcheck_action + # end of section to be removed jobs: dependency-test: strategy: fail-fast: false matrix: - test-strategy: ["min", "release", "max"] - uses: insightsengineering/r.pkg.template/.github/workflows/verdepcheck.yaml@main + test-strategy: ["min_cohort", "min_isolated", "release", "max"] + uses: insightsengineering/r.pkg.template/.github/workflows/verdepcheck.yaml@new-verdepcheck-strategy name: Dependency Test - ${{ matrix.test-strategy }} 🔢 secrets: REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }} diff --git a/DESCRIPTION b/DESCRIPTION index 152cc40f0..d551ed677 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -29,37 +29,60 @@ URL: https://insightsengineering.github.io/teal.slice/, BugReports: https://github.com/insightsengineering/teal.slice/issues Depends: R (>= 4.0), - shiny + shiny (>= 1.6.0) Imports: bslib (>= 0.4.0), - checkmate, - dplyr, + checkmate (>= 2.1.0), + dplyr (>= 1.0.5), grDevices, - htmltools, + htmltools (>= 0.5.4), jsonlite, - lifecycle, + lifecycle (>= 0.2.0), logger (>= 0.2.0), methods, - plotly, - R6, - shinycssloaders, + plotly (>= 4.9.2.2), + R6 (>= 2.2.0), + shinycssloaders (>= 1.0.0), shinyjs, shinyWidgets (>= 0.6.2), teal.data (>= 0.3.0), teal.logger (>= 0.1.1), teal.widgets (>= 0.4.0) Suggests: - knitr, + knitr (>= 1.34), MultiAssayExperiment, - rmarkdown, + rmarkdown (>= 2.19), SummarizedExperiment, testthat (>= 3.1.5), utils, - withr + withr (>= 2.1.0) VignetteBuilder: knitr RdMacros: lifecycle +Config/Needs/verdepcheck: + rstudio/shiny, + rstudio/bslib, + mllg/checkmate, + tidyverse/dplyr, + rstudio/htmltools, + jeroen/jsonlite, + r-lib/lifecycle, + daroczig/logger, + plotly/plotly, + r-lib/R6, + daattali/shinycssloaders, + daattali/shinyjs, + dreamRs/shinyWidgets, + insightsengineering/teal.data, + insightsengineering/teal.logger, + insightsengineering/teal.widgets, + yihui/knitr, + bioc::MultiAssayExperiment, + rstudio/rmarkdown, + bioc::SummarizedExperiment, + r-lib/testthat, + r-lib/withr Config/Needs/website: insightsengineering/nesttemplate Encoding: UTF-8 Language: en-US diff --git a/NEWS.md b/NEWS.md index c2e9c2ea8..bef5246d7 100644 --- a/NEWS.md +++ b/NEWS.md @@ -22,6 +22,10 @@ * Removed `CDISCFilteredData` and `CDISCFilteredDataset` and implementing `JoinKeys` handling in their parent classes (`FilteredData` and `DefaultFilteredDataset`). * Specifying set of filterable columns is done through `include_varnames` and `exclude_varnames` in `teal_slices`. Specifying `attr(, "filterable")` is hard deprecated. +### Miscellaneous + +* Specify minimal version of dependent packages. + # teal.slice 0.3.0 * Examples now use `scda.2022` instead of `scda.2021`. From b9235da1da7778bb0eb050d37c0e24fb62d82d79 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Wed, 26 Jul 2023 13:54:31 +0200 Subject: [PATCH 2/7] fix: bioc-related packages --- DESCRIPTION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index d551ed677..742056bdf 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -78,9 +78,9 @@ Config/Needs/verdepcheck: insightsengineering/teal.logger, insightsengineering/teal.widgets, yihui/knitr, - bioc::MultiAssayExperiment, + MultiAssayExperiment=bioc::MultiAssayExperiment, rstudio/rmarkdown, - bioc::SummarizedExperiment, + SummarizedExperiment=bioc::SummarizedExperiment, r-lib/testthat, r-lib/withr Config/Needs/website: insightsengineering/nesttemplate From 1ad97b15e56b89a3f98dbb5e9cede240204e0338 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Fri, 1 Sep 2023 15:16:29 +0200 Subject: [PATCH 3/7] doc: corrects NEWS after rebase --- NEWS.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/NEWS.md b/NEWS.md index bef5246d7..893f2aa97 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,9 @@ # teal.slice 0.4.0.9013 +### Miscellaneous + +* Specify minimal version of dependent packages. + # teal.slice 0.4.0 ### New features @@ -22,10 +26,6 @@ * Removed `CDISCFilteredData` and `CDISCFilteredDataset` and implementing `JoinKeys` handling in their parent classes (`FilteredData` and `DefaultFilteredDataset`). * Specifying set of filterable columns is done through `include_varnames` and `exclude_varnames` in `teal_slices`. Specifying `attr(, "filterable")` is hard deprecated. -### Miscellaneous - -* Specify minimal version of dependent packages. - # teal.slice 0.3.0 * Examples now use `scda.2022` instead of `scda.2021`. From dc685db38e48f3628469671b6025e74e797775a7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Fri, 1 Sep 2023 15:25:42 +0200 Subject: [PATCH 4/7] docs: remove old working branch --- .github/workflows/scheduled.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/scheduled.yaml b/.github/workflows/scheduled.yaml index e5174e1bd..e3a6a44b6 100644 --- a/.github/workflows/scheduled.yaml +++ b/.github/workflows/scheduled.yaml @@ -18,7 +18,7 @@ jobs: fail-fast: false matrix: test-strategy: ["min_cohort", "min_isolated", "release", "max"] - uses: insightsengineering/r.pkg.template/.github/workflows/verdepcheck.yaml@new-verdepcheck-strategy + uses: insightsengineering/r.pkg.template/.github/workflows/verdepcheck.yaml@main name: Dependency Test - ${{ matrix.test-strategy }} 🔢 secrets: REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }} From 7f0ad75ac63b195a5ae5e2f306ec062231ca303f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Fri, 1 Sep 2023 17:41:32 +0200 Subject: [PATCH 5/7] docs: remove rmarkdown --- DESCRIPTION | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 742056bdf..2a69df786 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -49,9 +49,8 @@ Imports: teal.logger (>= 0.1.1), teal.widgets (>= 0.4.0) Suggests: - knitr (>= 1.34), + knitr (>= 1.42), MultiAssayExperiment, - rmarkdown (>= 2.19), SummarizedExperiment, testthat (>= 3.1.5), utils, @@ -79,7 +78,6 @@ Config/Needs/verdepcheck: insightsengineering/teal.widgets, yihui/knitr, MultiAssayExperiment=bioc::MultiAssayExperiment, - rstudio/rmarkdown, SummarizedExperiment=bioc::SummarizedExperiment, r-lib/testthat, r-lib/withr From a5ab9a3dab0731ad6c5260cc70d4ce16f9cd6751 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Tue, 5 Sep 2023 13:32:43 +0200 Subject: [PATCH 6/7] docs: typo on NEWS.md --- NEWS.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index 893f2aa97..6439fa1c7 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,7 +2,7 @@ ### Miscellaneous -* Specify minimal version of dependent packages. +* Specified minimal version of package dependencies. # teal.slice 0.4.0 From eda0ac52e27fc79243e8f26696df2d3d1fc0340a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Wed, 20 Sep 2023 13:31:01 +0200 Subject: [PATCH 7/7] ci: revert action on push --- .github/workflows/scheduled.yaml | 6 ------ 1 file changed, 6 deletions(-) diff --git a/.github/workflows/scheduled.yaml b/.github/workflows/scheduled.yaml index e3a6a44b6..f2ddf6862 100644 --- a/.github/workflows/scheduled.yaml +++ b/.github/workflows/scheduled.yaml @@ -5,12 +5,6 @@ on: schedule: - cron: '45 3 * * 0' workflow_dispatch: - # Section to be removed before action is merged - # note: branch below needs to point to main instead of new-verdepcheck-strategy - push: - branches: - - verdepcheck_action - # end of section to be removed jobs: dependency-test: