From 236817aa2df622b7a3ab1bb920f6f1b8cd5e1570 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 00:26:25 +0200 Subject: [PATCH 1/5] docs: add minimal version of deps --- .github/workflows/scheduled.yaml | 10 +++++-- DESCRIPTION | 46 +++++++++++++++++++++++--------- NEWS.md | 3 +++ 3 files changed, 45 insertions(+), 14 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 }} đŸ”¢ secrets: REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }} diff --git a/DESCRIPTION b/DESCRIPTION index 9cd25a65b..031b674da 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -17,36 +17,58 @@ Description: Data Model for `teal` Applications. License: Apache License 2.0 | file LICENSE Depends: R (>= 4.0), - shiny + shiny (>= 1.6.0) Imports: - checkmate, + checkmate (>= 2.1.0), digest, - lifecycle, + lifecycle (>= 0.2.0), logger (>= 0.2.0), methods, - R6, - rlang, + R6 (>= 2.2.0), + rlang (>= 1.1.0), shinyjs, stats, teal.logger (>= 0.1.1), utils, - yaml + yaml (>= 1.1.0) Suggests: bslib, - dplyr, - knitr, - magrittr, + dplyr (>= 1.1.0), + knitr (>= 1.34), + magrittr (>= 1.5), MultiAssayExperiment, readr, reticulate (>= 1.22), - rmarkdown, + rmarkdown (>= 2.19), SummarizedExperiment, - testthat (>= 2.0), - withr + testthat (>= 3.0.4), + withr (>= 2.1.0) VignetteBuilder: knitr RdMacros: lifecycle +Config/Needs/verdepcheck: + rstudio/shiny, + mllg/checkmate, + eddelbuettel/digest, + r-lib/lifecycle, + daroczig/logger, + r-lib/R6, + r-lib/rlang, + daattali/shinyjs, + insightsengineering/teal.logger, + yaml=vubiostat/r-yaml, + rstudio/bslib, + tidyverse/dplyr, + yihui/knitr, + tidyverse/magrittr, + bioc::MultiAssayExperiment, + tidyverse/readr, + rstudio/reticulate, + 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 1bb02ea9c..976de7400 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,6 +2,9 @@ # teal.data 0.3.0 +### Miscellaneous +* Specify minimal version of dependent packages. + ### Enhancements * Removed `scda` package dependency from examples. * Added `col_labels` function and removed `formatters` dependency. From 9493c2d125f7c6434ba1cee5f14f2607f1f97848 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 17:58:37 +0200 Subject: [PATCH 2/5] fix: removes bioc:: prefix in verdepcheck section --- DESCRIPTION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 031b674da..c5473737c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -62,11 +62,11 @@ Config/Needs/verdepcheck: tidyverse/dplyr, yihui/knitr, tidyverse/magrittr, - bioc::MultiAssayExperiment, + MultiAssayExperiment, tidyverse/readr, rstudio/reticulate, rstudio/rmarkdown, - bioc::SummarizedExperiment, + SummarizedExperiment, r-lib/testthat, r-lib/withr Config/Needs/website: insightsengineering/nesttemplate From aca6f41c62b7716721bf454e5e2a9b3ec2070b58 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 17:48:07 +0200 Subject: [PATCH 3/5] docs: updated branch on CI, correct NEWS after rebase, remove rmarkdown --- .github/workflows/scheduled.yaml | 2 +- DESCRIPTION | 4 +--- NEWS.md | 4 ++-- 3 files changed, 4 insertions(+), 6 deletions(-) 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 }} đŸ”¢ secrets: REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }} diff --git a/DESCRIPTION b/DESCRIPTION index c5473737c..de63ce0ff 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -34,12 +34,11 @@ Imports: Suggests: bslib, dplyr (>= 1.1.0), - knitr (>= 1.34), + knitr (>= 1.42), magrittr (>= 1.5), MultiAssayExperiment, readr, reticulate (>= 1.22), - rmarkdown (>= 2.19), SummarizedExperiment, testthat (>= 3.0.4), withr (>= 2.1.0) @@ -65,7 +64,6 @@ Config/Needs/verdepcheck: MultiAssayExperiment, tidyverse/readr, rstudio/reticulate, - rstudio/rmarkdown, SummarizedExperiment, r-lib/testthat, r-lib/withr diff --git a/NEWS.md b/NEWS.md index 976de7400..20993b703 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,10 +1,10 @@ # teal.data 0.3.0.9002 -# teal.data 0.3.0 - ### Miscellaneous * Specify minimal version of dependent packages. +# teal.data 0.3.0 + ### Enhancements * Removed `scda` package dependency from examples. * Added `col_labels` function and removed `formatters` dependency. From a249394a5246931bf0c9a993c8d59b886607f179 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Mon, 4 Sep 2023 16:43:38 +0200 Subject: [PATCH 4/5] ci: remove push on branch to prepare merge --- .github/workflows/scheduled.yaml | 6 ------ DESCRIPTION | 2 ++ 2 files changed, 2 insertions(+), 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: diff --git a/DESCRIPTION b/DESCRIPTION index de63ce0ff..802ffc3de 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -39,6 +39,7 @@ Suggests: MultiAssayExperiment, readr, reticulate (>= 1.22), + rmarkdown (>= 2.19), SummarizedExperiment, testthat (>= 3.0.4), withr (>= 2.1.0) @@ -64,6 +65,7 @@ Config/Needs/verdepcheck: MultiAssayExperiment, tidyverse/readr, rstudio/reticulate, + rstudio/rmarkdown, SummarizedExperiment, r-lib/testthat, r-lib/withr From a226722d9936d64196031e3603f8cf6b99b59b4c 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 10:02:21 +0200 Subject: [PATCH 5/5] Update NEWS.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Aleksander Chlebowski <114988527+chlebowa@users.noreply.github.com> Signed-off-by: AndrĂ© VerĂ­ssimo <211358+averissimo@users.noreply.github.com> --- NEWS.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index 20993b703..2341c76a4 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,7 +1,7 @@ # teal.data 0.3.0.9002 ### Miscellaneous -* Specify minimal version of dependent packages. +* Specified minimal version of package dependencies. # teal.data 0.3.0