From e963bd39a6620cbc57724516645e489f47b53ed5 Mon Sep 17 00:00:00 2001 From: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com> Date: Fri, 31 May 2024 09:52:40 +0100 Subject: [PATCH 01/16] #71 make this easier for new pkg ext teams to directly use i feel like we forgot the purpose of admiraltemplate here - people dont need to track the changes of this template as they always only care about the latest version. we should set it up so that each pkg ext team has the minimum amount of updates and clarity on how they should update. --- NEWS.md | 66 ++++++--------------------------------------------------- 1 file changed, 6 insertions(+), 60 deletions(-) diff --git a/NEWS.md b/NEWS.md index 23bb9e6..ad1cce1 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,62 +1,8 @@ -# admiraltemplate 0.0.3 +# admiraltemplate 0.1.0 -- Removed renv and related files (#70) - -## Updates to site - - - Package Extension guidance on the front page was updated and moved to [this location](https://pharmaverse.github.io/admiraldev/articles/package_extensions.html) in `{admiraldev}`, and a link was added to point to the new location (#61). - -## CI workflows - -- [`admiralci` workflows](https://github.com/pharmaverse/admiralci) has been updated. Indeed, workflows are not anymore based on `renv` framework to manage dependencies (`devtools` is used instead). Moreover, we now use latest version of `R` for all workflows, and run `R CMD CHECKS` for following R release version (R latest stable version), R devel version (in development version), and R previous release. More details are available in [admiralci doc](https://pharmaverse.github.io/admiralci/index.html). -As a result, `.github/workflows/common.yml` file has been updated, and all `renv` configurations has been removed. - -## admiral.test removed - -- `admiral.test` package has been replaced by [`pharmaversesdtm`](https://github.com/pharmaverse/pharmaversesdtm) - -# admiraltemplate 0.0.2 - -## New Features - - - New `renv` lock files were setup (#48) - -## Updates of Existing Functions - -## Breaking Changes - -## Documentation - - - Many updates across documentation made to match v0.10.0 of `admiral` [PR #51](https://github.com/pharmaverse/admiraltemplate/pull/51), including: - - Links were fixed on the website - - Templates were aligned to current `admiral` standards - - Package dependencies were updated - - Explanation on how to use family/keywords have been provided - -## Various - - - Renamed from `admiralext` to `admiraltemplate` - -# admiraltemplate 0.0.1 - -## New Features - - - You can link the GitHub Issue to Changelog by using (#ISSUE-NUMBER) - -## Updates of Existing Functions - - - Updates that you have made for this version (#ISSUE-NUMBER) - -## Breaking Changes - - - Deprecated functions. (#ISSUE-NUMBER) - - Bug Fixes (#ISSUE-NUMBER) - -## Documentation - - - Stuff that you did (#ISSUE-NUMBER) - -## Various - - - Stuff that you did (#ISSUE-NUMBER) +- Initial package release focused on <> +Note that after first release you should then start maintaining this `NEWS.md` file for every user-facing update. +You should categorise the updates under title sections for New Features, Updates of Existing Functions, +Breaking Changes, Documentation, Various. +Each update should also reference the original issue by adding at the end: (#ISSUE-NUMBER) From c9f53fa27c05664dcb9492333af330c7b42b6d48 Mon Sep 17 00:00:00 2001 From: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com> Date: Fri, 31 May 2024 09:52:55 +0100 Subject: [PATCH 02/16] Update NEWS.md --- NEWS.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index ad1cce1..6231a62 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,6 @@ # admiraltemplate 0.1.0 -- Initial package release focused on <> +- Initial package release focused on `<>` Note that after first release you should then start maintaining this `NEWS.md` file for every user-facing update. You should categorise the updates under title sections for New Features, Updates of Existing Functions, From fb95f67677cb1760003052c1a1584bfc3e97e288 Mon Sep 17 00:00:00 2001 From: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com> Date: Fri, 31 May 2024 09:55:09 +0100 Subject: [PATCH 03/16] #71 make clear the sections the pkg ext teams needs to update --- LICENSE.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/LICENSE.md b/LICENSE.md index 37d7bd9..b92cefd 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -179,7 +179,7 @@ recommend that a file or class name and description of purpose be included on the same “printed page” as the copyright notice for easier identification within third-party archives. - Copyright 2021 F. Hoffmann-La Roche AG and GlaxoSmithKline LLC + Copyright `<>` `<>` Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. From d087f9941c25036288f06ff4bdb402692f8cc295 Mon Sep 17 00:00:00 2001 From: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com> Date: Fri, 31 May 2024 10:00:18 +0100 Subject: [PATCH 04/16] #71 brought in line with admiralpeds latest --- DESCRIPTION | 32 ++++++++++++++------------------ 1 file changed, 14 insertions(+), 18 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 821ca55..9bfbbd9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package -Package: admiraltemplate -Title: ADaM in R Asset Library - Extension -Version: 0.0.3 +Package: `<>' +Title: ADaM in R Asset Library - Extension Package for `<>` +Version: 0.1.0 Authors@R: person("Open", "Source", , "admiraltemplate@pharmaverse.com", role = c("aut", "cre")) Description: A toolbox for programming Clinical Data Standards Interchange @@ -11,16 +11,17 @@ Description: A toolbox for programming Clinical Data Standards Interchange Administration (FDA). Analysis derivations are implemented in accordance with the "Analysis Data Model Implementation Guide" (CDISC Analysis Data Model Team, 2021, - ). + ). The package is + an extension package of the 'admiral' package. License: Apache License (>= 2) URL: https://pharmaverse.github.io/admiraltemplate, https://github.com/pharmaverse/admiraltemplate Depends: - R (>= 3.5) + R (>= 4.1) Imports: - admiral (>= 0.10.0), - admiraldev (>= 0.5.0), - dplyr (>= 0.8.4), + admiral (>= 1.0.0), + admiraldev (>= 1.0.0), + dplyr (>= 1.0.5), hms (>= 0.5.3), lifecycle (>= 0.1.0), lubridate (>= 1.7.4), @@ -31,22 +32,17 @@ Imports: tidyr (>= 1.0.2), tidyselect (>= 1.1.0) Suggests: - covr, - devtools, diffdf, DT, + htmltools, knitr, - lintr, methods, - miniUI, - pharmaversesdtm, - pkgdown, + pharmaversesdtm (>= 0.2.0), + reactable, + readxl, rmarkdown, - roxygen2, - spelling, testthat (>= 3.0.0), - tibble, - usethis + tibble VignetteBuilder: knitr Config/testthat/edition: 3 From 9d4fcdfb139b4a82764323180312b0f5d5b80125 Mon Sep 17 00:00:00 2001 From: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com> Date: Fri, 31 May 2024 10:04:01 +0100 Subject: [PATCH 05/16] #71 bring in line with latest --- _pkgdown.yml | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/_pkgdown.yml b/_pkgdown.yml index 035a488..25b07bb 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -12,6 +12,10 @@ repo: user: https://github.com/ news: cran_dates: true + +development: + mode: auto + reference: - title: Derivations for Adding Variables @@ -53,6 +57,7 @@ reference: navbar: structure: left: [getstarted, reference, articles, news] + right: [search, slack, history, newissue, github] components: getstarted: text: Get Started @@ -65,3 +70,15 @@ navbar: menu: - text: Creating ADXX href: articles/adxx.html + history: + icon: fa-history + href: articles/website-versions.html + aria-label: Previous Release Websites + slack: + icon: fa-slack + href: https://app.slack.com/client/T028PB489D3/C02M8KN8269 + aria-label: Slack + newissue: + icon: fa-bug + href: https://github.com/pharmaverse/admiraltemplate/issues/new/choose + aria-label: New Issue From d4bc0086bdae87d900ba12bed68ff37db541af5a Mon Sep 17 00:00:00 2001 From: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com> Date: Fri, 31 May 2024 10:07:59 +0100 Subject: [PATCH 06/16] #71 we no longer use staged dependencies --- staged_dependencies.yaml | 12 ------------ 1 file changed, 12 deletions(-) delete mode 100644 staged_dependencies.yaml diff --git a/staged_dependencies.yaml b/staged_dependencies.yaml deleted file mode 100644 index 6cebdb1..0000000 --- a/staged_dependencies.yaml +++ /dev/null @@ -1,12 +0,0 @@ ---- -current_repo: - repo: pharmaverse/admiraltemplate - host: https://github.com -upstream_repos: - - repo: pharmaverse/admiral - host: https://github.com - - repo: pharmaverse/pharmaversesdtm - host: https://github.com - - repo: pharmaverse/admiraldev - host: https://github.com -downstream_repos: From f70c37b1c4543e7afd4ba74e5ff84daaa5d62bca Mon Sep 17 00:00:00 2001 From: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com> Date: Fri, 31 May 2024 10:12:54 +0100 Subject: [PATCH 07/16] #71 add save data step at end --- inst/templates/ad_adxx.R | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/inst/templates/ad_adxx.R b/inst/templates/ad_adxx.R index 297c40d..df6ede1 100644 --- a/inst/templates/ad_adxx.R +++ b/inst/templates/ad_adxx.R @@ -7,3 +7,13 @@ library(admiral) library(pharmaversesdtm) # Contains example datasets from the CDISC pilot project # Add your template ADaM script code + +# Save output ---- + +# Change to whichever directory you want to save the dataset in +dir <- tools::R_user_dir("admiraltemplate_templates_data", which = "cache") +if (!file.exists(dir)) { + # Create the folder + dir.create(dir, recursive = TRUE, showWarnings = FALSE) +} +save(adxx, file = file.path(dir, "adxx.rda"), compress = "bzip2") From 7caf1a965475e08fddc17a36a97039f599ab77b3 Mon Sep 17 00:00:00 2001 From: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com> Date: Fri, 31 May 2024 10:13:14 +0100 Subject: [PATCH 08/16] Update ad_adxx.R --- inst/templates/ad_adxx.R | 1 + 1 file changed, 1 insertion(+) diff --git a/inst/templates/ad_adxx.R b/inst/templates/ad_adxx.R index df6ede1..ca371f8 100644 --- a/inst/templates/ad_adxx.R +++ b/inst/templates/ad_adxx.R @@ -3,6 +3,7 @@ # Label: XXX # # Input: xx, xx, xx + library(admiral) library(pharmaversesdtm) # Contains example datasets from the CDISC pilot project From b3a7ca18ed7ce349321debdff554164467072b5b Mon Sep 17 00:00:00 2001 From: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com> Date: Fri, 31 May 2024 10:15:18 +0100 Subject: [PATCH 09/16] #71 add support link --- vignettes/admiraltemplate.Rmd | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/vignettes/admiraltemplate.Rmd b/vignettes/admiraltemplate.Rmd index 5e61078..0bea69b 100644 --- a/vignettes/admiraltemplate.Rmd +++ b/vignettes/admiraltemplate.Rmd @@ -19,3 +19,7 @@ library(admiraltemplate) ``` Introduction to how to use the package extension... + +# Support + +Support is provided via [pharmaverse Slack](https://pharmaverse.slack.com/). From 0ef7f2450f72b74299d8652931693f281483c1b9 Mon Sep 17 00:00:00 2001 From: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com> Date: Fri, 31 May 2024 10:18:09 +0100 Subject: [PATCH 10/16] #71 add few more standard sections --- vignettes/adxx.Rmd | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/vignettes/adxx.Rmd b/vignettes/adxx.Rmd index e9f700f..b847846 100644 --- a/vignettes/adxx.Rmd +++ b/vignettes/adxx.Rmd @@ -18,3 +18,13 @@ knitr::opts_chunk$set( # Introduction This article describes creating an `ADXX` ADaM. + +# Programming Workflow + +Steps involved to create an `ADXX` ADaM. + +# Example Scripts + +ADaM | Sourcing Command +---- | -------------- +ADXX | `admiral::use_ad_template("ADXX", package = "admiraltemplate")` From 73e6fc41c4bc14c953d9e848e98a0cea30ffe68c Mon Sep 17 00:00:00 2001 From: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com> Date: Fri, 31 May 2024 10:26:26 +0100 Subject: [PATCH 11/16] #71 add data-raw example --- data-raw/xx.R | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 data-raw/xx.R diff --git a/data-raw/xx.R b/data-raw/xx.R new file mode 100644 index 0000000..b981e62 --- /dev/null +++ b/data-raw/xx.R @@ -0,0 +1,7 @@ +# Dataset: xx +# Description: xx test SDTM dataset for xx + +Add code to create test dataset xx and update this in `R/data.R` + +# Save dataset ---- +usethis::use_data(xx, overwrite = TRUE) From 7a960ed2ec0a99167e306994a0354acfe0ba51c7 Mon Sep 17 00:00:00 2001 From: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com> Date: Fri, 31 May 2024 10:27:22 +0100 Subject: [PATCH 12/16] #71 placeholder folder for test data --- data/xx.rda | 1 + 1 file changed, 1 insertion(+) create mode 100644 data/xx.rda diff --git a/data/xx.rda b/data/xx.rda new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/data/xx.rda @@ -0,0 +1 @@ + From 3639e7219668fd8c1a575eb1a6c7666900a93e03 Mon Sep 17 00:00:00 2001 From: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com> Date: Fri, 31 May 2024 10:28:19 +0100 Subject: [PATCH 13/16] #71 add data.R --- R/data.R | 6 ++++++ 1 file changed, 6 insertions(+) create mode 100644 R/data.R diff --git a/R/data.R b/R/data.R new file mode 100644 index 0000000..e0c31be --- /dev/null +++ b/R/data.R @@ -0,0 +1,6 @@ +#' xx Dataset +#' +#' An xx test dataset for xx +#' @keywords datasets +#' @family datasets +"xx" From a59bd898eb3c1cddb0647ba6028ab34d96c0a397 Mon Sep 17 00:00:00 2001 From: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com> Date: Fri, 31 May 2024 10:31:07 +0100 Subject: [PATCH 14/16] #71 remove renv --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 7b47836..e72af7a 100644 --- a/README.md +++ b/README.md @@ -47,8 +47,8 @@ The repository template includes the following: - License file (Apache 2.0 - but company co-developers need to be added to copyright section) -- Required folders (R; test; templates; vignettes; renv; etc) -- Set-up files (DESCRIPTION; NAMESPACE; renv.lock; etc) +- Required folders (R; test; templates; vignettes; etc) +- Set-up files (DESCRIPTION; NAMESPACE; etc) - Issue Templates (Bug Template; Feature Request; Documentation Request/Update; Onboarding) - Pull Request Template From 79124b07fc1504ab2273c0b40d458af78d44fc3c Mon Sep 17 00:00:00 2001 From: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com> Date: Fri, 31 May 2024 11:20:50 +0100 Subject: [PATCH 15/16] #71 slack link replace --- _pkgdown.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index 25b07bb..379b934 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -76,7 +76,7 @@ navbar: aria-label: Previous Release Websites slack: icon: fa-slack - href: https://app.slack.com/client/T028PB489D3/C02M8KN8269 + href: https://pharmaverse.slack.com/ aria-label: Slack newissue: icon: fa-bug From aae005896c83a53a2a34cc5dfaa98d8f6acab6db Mon Sep 17 00:00:00 2001 From: Ben Straub Date: Mon, 3 Jun 2024 09:04:39 -0400 Subject: [PATCH 16/16] Update .Rbuildignore --- .Rbuildignore | 2 -- 1 file changed, 2 deletions(-) diff --git a/.Rbuildignore b/.Rbuildignore index 409b610..7e8e3a5 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,5 +1,3 @@ -^renv$ -^renv\.lock$ ^.*\.Rproj$ ^.*\.lycheeignore$ ^\.Rproj\.user$