From b1ce971bb273977e50a719736410d5e8ec77f420 Mon Sep 17 00:00:00 2001 From: kartikeya kirar Date: Thu, 17 Aug 2023 14:30:48 +0530 Subject: [PATCH 1/9] Application header goes below horizontal line upon resizing (#896) this fixes https://github.com/insightsengineering/teal/issues/893 Demo https://github.com/insightsengineering/teal/assets/6700955/8def3b74-b747-4df0-8434-4dde85f484cf --------- Co-authored-by: kartikeya --- NEWS.md | 1 + inst/css/custom.css | 4 ++++ 2 files changed, 5 insertions(+) diff --git a/NEWS.md b/NEWS.md index 3da4a7a08a..57f0d2b28e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -17,6 +17,7 @@ ### Miscellaneous * Removed `scda` package dependency from examples. +* Updated the header tag style to enhance element containment. # teal 0.13.0 diff --git a/inst/css/custom.css b/inst/css/custom.css index b70c0c7bc2..c22169b932 100644 --- a/inst/css/custom.css +++ b/inst/css/custom.css @@ -54,6 +54,10 @@ flex-wrap: wrap; } +header { + display: flow-root; +} + footer { text-align: left; padding: 5px; From 7136e30ad14b1e6d609e21622ea58c5143a53502 Mon Sep 17 00:00:00 2001 From: kartikeyakirar Date: Thu, 17 Aug 2023 09:01:56 +0000 Subject: [PATCH 2/9] [skip actions] Bump version to 0.14.0.9001 --- DESCRIPTION | 4 ++-- NEWS.md | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 8a287e4700..0bbeb43d42 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Type: Package Package: teal Title: Exploratory Web Apps for Analyzing Clinical Trials Data -Version: 0.14.0.9000 -Date: 2023-08-14 +Version: 0.14.0.9001 +Date: 2023-08-17 Authors@R: c( person("Dawid", "Kaledkowski", , "dawid.kaledkowski@roche.com", role = c("aut", "cre")), person("Pawel", "Rucki", , "pawel.rucki@roche.com", role = "aut"), diff --git a/NEWS.md b/NEWS.md index 57f0d2b28e..7ea1387ca9 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# teal 0.14.0.9000 +# teal 0.14.0.9001 # teal 0.14.0 From 513a211b0d00ccacab83a0fa100aeca50912fa66 Mon Sep 17 00:00:00 2001 From: walkowif <59475134+walkowif@users.noreply.github.com> Date: Mon, 21 Aug 2023 17:51:14 +0200 Subject: [PATCH 3/9] Workflow propagation (#902) --- .github/ISSUE_TEMPLATE/release.yaml | 107 ++++++++++++++++++++++++++++ .github/workflows/check.yaml | 13 ++-- 2 files changed, 112 insertions(+), 8 deletions(-) create mode 100644 .github/ISSUE_TEMPLATE/release.yaml diff --git a/.github/ISSUE_TEMPLATE/release.yaml b/.github/ISSUE_TEMPLATE/release.yaml new file mode 100644 index 0000000000..1d97dff5a3 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/release.yaml @@ -0,0 +1,107 @@ +--- +name: 🚀 Release +description: Template for package release +title: "[Release]: " +labels: ["release"] +assignees: + - KlaudiaBB + - cicdguy +body: + - type: markdown + attributes: + value: | + ⚠️ Please do not link or mention any internal references in this issue. This includes internal URLs, intellectual property and references. + - type: textarea + id: blocked-by + attributes: + label: Blocked by + description: Any PRs or issues that this release is blocked by. + placeholder: Add a list of blocking PRs or issues here. + value: | + ### PRs + + - [ ] PR 1 + + ### Issues + + - [ ] Issue 1 + validations: + required: true + - type: textarea + id: pre-requisites + attributes: + label: Pre-requisites + description: Pre-requisites that must be fulfilled before initiating the release process. + placeholder: Add your list of pre-requisites here. + value: | + - [ ] Make sure that high priority bugs (label "priority" + "bug") have been resolved before going into the release. + - [ ] Review old/hanging PRs before going into the release. + - [ ] Revisit R-package's lifecycle badges (Optional). + - [ ] Discuss package dependencies before going into release activities. + - [ ] Create a plan to sequentially close release activities and submit groups of packages for internal validation (Applicable only for regulatory release). + - [ ] Make sure all relevant integration tests are green 2-3 days before the release. Look carefully through logs (check for warnings and notes). + - [ ] Check if a package is installable on our supported internal systems (Optional). + - [ ] Inform about the soft code freeze, decide what gets merged in before starting release activities. + - type: textarea + id: release-checklist + attributes: + label: Release Checklist + description: The steps to be taken in order to create a release. + placeholder: Steps to create a release. + value: | + - [ ] Recurring tasks: Execute the manual tests on Shiny apps that are deployed on various hosting providers (Posit connect and shinyapps.io) - track the results in GitHub issue (Applicable only for frameworks that use Shiny). + - [ ] Recurring tasks: Monitor integration tests, if integration fails, create priority issues on the board. + - [ ] Sanity checks for Shiny applications e.g. checking if Shiny apps are deployable and making sure there are no errors/warnings. + - [ ] Update NEWS.md file: make sure it reflects a holistic summary of what has changed in the package, check README. + - [ ] Remove the additional fields (`Remotes` and `Config/Needs/*`) from the DESCRIPTION file where applicable. + - [ ] Make sure that the minimum dependency versions are updated in the DESCRIPTION file for the package. + - [ ] Increase versioned dependency on {package name} to >=X.X.X. + - [ ] Create a pull request to make necessary bug fixes/changes (add "[skip vbump]" in the PR title), and after merging the PR, tag the update(s) as a release candidate v < intended release version > -rc < release candidate iteration > on the main branch. Note that tags are created in GitHub and synchronized with GitLab automatically. + - [ ] The package is submitted for internal validation by Release Coordinator (Applicable only for regulatory release). + - [ ] Address any feedback (internal validation/user testing), retag the package as a release candidate vX.X.X-rc(n+1). Repeat the submission for internal validation if necessary. + - [ ] Get the package validated (Applicable only for regulatory release). + - [ ] If the additional fields were removed, add them back in a separate PR, and then merge the PR back to main (add "[skip vbump]" in the PR title). + - [ ] Create a git tag with the final version set to X.X.X on the main branch. + - [ ] Update downstream package dependencies to (>=X.X.X) in {package name}. + - type: textarea + id: testing + attributes: + label: Testing + description: Summary of testing activities - integration tests, UAT, other. + placeholder: Tests results + value: | + - [ ] Integration tests results - accepted. + - [ ] UAT results - accepted. + - [ ] Shiny apps test results - accepted (Applicable only for Shiny apps). + - [ ] Necessary testing on target environment - performed (up to ETL). + - type: textarea + id: feedback + attributes: + label: Release Feedback + description: Feedback received from internal validation/UAT testers. + placeholder: Feedback to be implemented after submission for internal validation/testing. + value: | + - [ ] Fix 1 + - [ ] Enhancement 1 + - [ ] Defect 1 + - type: textarea + id: post-release + attributes: + label: Post-release Checklist + description: The list of activities to be completed after the release. + placeholder: The steps that must be taken after the release. + value: | + - [ ] Make sure that the package is published to internal repositories (Validated and/or Non-Validated repository). + - [ ] Review and update installation instructions for the package if needed. + - [ ] Verify if a new dev version (.9XXX) has been added to the NEWS.md file and DESCRIPTION file as a placeholder for release notes by automation. + - [ ] Make sure internal documentation/documentation catalogs are up to date. + - [ ] Notify the IDR team to start post-release/clean-up activities. + - [ ] Announce the release on ________. + - type: textarea + id: decision-tree + attributes: + label: Decision tree + description: Any decision tree(s) that would aid release management + placeholder: Any decision tree(s) that would aid release management. + value: | + Click [here](https://github.com/insightsengineering/.github/blob/main/.github/ISSUE_TEMPLATE/RELEASE_DECISION_TREE.md) to see the release decision tree. diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index c656083bee..e401c44ae5 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -15,13 +15,6 @@ on: - main workflow_dispatch: - # Rerun workflows once pkgdown has finished running, to add coverage - # and unit test report to gh-pages branch. - workflow_run: - workflows: ["Docs 📚"] - types: - - completed - jobs: audit: name: Audit Dependencies 🕵️‍♂️ @@ -41,6 +34,9 @@ jobs: checking R code for possible problems .* NOTE checking examples .* NOTE checking Rd line widths .* NOTE + checking S3 generic/method consistency .* NOTE + checking Rd .usage sections .* NOTE + checking for unstated dependencies in vignettes .* NOTE unit-test-report-brand: >- https://raw.githubusercontent.com/insightsengineering/hex-stickers/main/thumbs/teal.png coverage: @@ -63,9 +59,10 @@ jobs: name: gitleaks 💧 uses: insightsengineering/r.pkg.template/.github/workflows/gitleaks.yaml@main spelling: - if: github.event_name != 'push' name: Spell Check 🆎 uses: insightsengineering/r.pkg.template/.github/workflows/spelling.yaml@main + secrets: + REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }} links: if: github.event_name != 'push' name: Check URLs 🌐 From 246443a9e446b29f655ddaedb0d09591087eec87 Mon Sep 17 00:00:00 2001 From: walkowif Date: Mon, 21 Aug 2023 15:52:24 +0000 Subject: [PATCH 4/9] [skip actions] Bump version to 0.14.0.9002 --- DESCRIPTION | 4 ++-- NEWS.md | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0bbeb43d42..1319db487e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Type: Package Package: teal Title: Exploratory Web Apps for Analyzing Clinical Trials Data -Version: 0.14.0.9001 -Date: 2023-08-17 +Version: 0.14.0.9002 +Date: 2023-08-21 Authors@R: c( person("Dawid", "Kaledkowski", , "dawid.kaledkowski@roche.com", role = c("aut", "cre")), person("Pawel", "Rucki", , "pawel.rucki@roche.com", role = "aut"), diff --git a/NEWS.md b/NEWS.md index 7ea1387ca9..c3c002b874 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# teal 0.14.0.9001 +# teal 0.14.0.9002 # teal 0.14.0 From 195e1884fd424373e6f5c939c7966b0418be837f Mon Sep 17 00:00:00 2001 From: walkowif Date: Mon, 21 Aug 2023 15:53:30 +0000 Subject: [PATCH 5/9] [skip actions] Update WORDLIST --- inst/WORDLIST | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/inst/WORDLIST b/inst/WORDLIST index 24b9e8af9d..fc9934a03d 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -4,8 +4,10 @@ TLG UI UIs UX +cloneable funder omics +pharmaverse preselected programmatically repo @@ -14,5 +16,3 @@ tabsetted themer theming uncheck -cloneable -pharmaverse From ecc880ee2036aa491efc8c311a5c0e5ebd2d4244 Mon Sep 17 00:00:00 2001 From: Pawel Rucki <12943682+pawelru@users.noreply.github.com> Date: Wed, 23 Aug 2023 06:52:51 +0200 Subject: [PATCH 6/9] only hard deps in pre-commit - roxygenize - additional deps (#891) --- .pre-commit-config.yaml | 19 +++++++------------ 1 file changed, 7 insertions(+), 12 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index c32d981d16..1fc1101055 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -16,25 +16,20 @@ repos: name: Regenerate package documentation additional_dependencies: - checkmate - - digest - - dplyr - - ggplot2 - - glue - - grDevices - lifecycle - logger - magrittr - - methods - - bioc::MultiAssayExperiment - - R6 - rlang - - rtables + - shiny - shinyjs - - shinyWidgets - stats - - bioc::SummarizedExperiment + - insightsengineering/teal.data + - insightsengineering/teal.logger + - insightsengineering/teal.reporter + - insightsengineering/teal.slice + - insightsengineering/teal.transform + - insightsengineering/teal.widgets - utils - - yaml - id: spell-check name: Check spelling with `spelling` exclude: > From eed93d796ab2e97957c592e6f202950811130924 Mon Sep 17 00:00:00 2001 From: pawelru Date: Wed, 23 Aug 2023 04:53:48 +0000 Subject: [PATCH 7/9] [skip actions] Bump version to 0.14.0.9003 --- DESCRIPTION | 4 ++-- NEWS.md | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 1319db487e..534c0e15ec 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Type: Package Package: teal Title: Exploratory Web Apps for Analyzing Clinical Trials Data -Version: 0.14.0.9002 -Date: 2023-08-21 +Version: 0.14.0.9003 +Date: 2023-08-23 Authors@R: c( person("Dawid", "Kaledkowski", , "dawid.kaledkowski@roche.com", role = c("aut", "cre")), person("Pawel", "Rucki", , "pawel.rucki@roche.com", role = "aut"), diff --git a/NEWS.md b/NEWS.md index c3c002b874..c908a92df3 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# teal 0.14.0.9002 +# teal 0.14.0.9003 # teal 0.14.0 From 17fb575a6e4316f0a3294aa07bb51e1a598ea502 Mon Sep 17 00:00:00 2001 From: Pawel Rucki <12943682+pawelru@users.noreply.github.com> Date: Thu, 24 Aug 2023 11:37:38 +0200 Subject: [PATCH 8/9] don't throw validation messages unnecessarily (#901) During rendering TLG-Catalog I noticed that each shiny app throws a message about `data` argument in the reporter previewer module. This fix aim to silent unnecessary messages https://github.com/insightsengineering/tlg-catalog/actions/runs/5888144351/job/15968763355 --- NEWS.md | 4 ++++ R/modules.R | 2 +- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index c908a92df3..dbb288fa72 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,9 @@ # teal 0.14.0.9003 +### Miscellaneous + +* Enhance a `module` validation checks so that it won't throw messages about `data` argument unnecessarily. + # teal 0.14.0 ### New features diff --git a/R/modules.R b/R/modules.R index a80ac984c8..d5d7ce016b 100644 --- a/R/modules.R +++ b/R/modules.R @@ -232,7 +232,7 @@ module <- function(label = "module", ) } - if (!is.element("data", server_formals)) { + if (!is.element("data", server_formals) && !is.null(datanames)) { message(sprintf("module \"%s\" server function takes no data so \"datanames\" will be ignored", label)) datanames <- NULL } From 54c683b92f845075a787e2aeef582640769ccf61 Mon Sep 17 00:00:00 2001 From: pawelru Date: Thu, 24 Aug 2023 09:38:51 +0000 Subject: [PATCH 9/9] [skip actions] Bump version to 0.14.0.9004 --- DESCRIPTION | 4 ++-- NEWS.md | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 534c0e15ec..c747092a9a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Type: Package Package: teal Title: Exploratory Web Apps for Analyzing Clinical Trials Data -Version: 0.14.0.9003 -Date: 2023-08-23 +Version: 0.14.0.9004 +Date: 2023-08-24 Authors@R: c( person("Dawid", "Kaledkowski", , "dawid.kaledkowski@roche.com", role = c("aut", "cre")), person("Pawel", "Rucki", , "pawel.rucki@roche.com", role = "aut"), diff --git a/NEWS.md b/NEWS.md index dbb288fa72..e1e7ee24c7 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# teal 0.14.0.9003 +# teal 0.14.0.9004 ### Miscellaneous