From e1c301142995e20d239355a4a0018457994c0d65 Mon Sep 17 00:00:00 2001 From: Adam Forys Date: Mon, 20 Nov 2023 10:30:32 +0000 Subject: [PATCH 01/10] Add staged_dependencies for admiraldev --- staged_dependencies.yaml | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 staged_dependencies.yaml diff --git a/staged_dependencies.yaml b/staged_dependencies.yaml new file mode 100644 index 00000000..a5f533e9 --- /dev/null +++ b/staged_dependencies.yaml @@ -0,0 +1,10 @@ +--- +upstream_repos: +- repo: pharmaverse/admiraldev + host: https://github.com + +downstream_repos: + +current_repo: + repo: pharmaverse/admiral + host: https://github.com \ No newline at end of file From 707ea80d0dca3ff90fb35e7c802d5ce3e66864cd Mon Sep 17 00:00:00 2001 From: Adam Forys Date: Mon, 20 Nov 2023 10:33:02 +0000 Subject: [PATCH 02/10] Add new line --- staged_dependencies.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/staged_dependencies.yaml b/staged_dependencies.yaml index a5f533e9..72a49b08 100644 --- a/staged_dependencies.yaml +++ b/staged_dependencies.yaml @@ -6,5 +6,6 @@ upstream_repos: downstream_repos: current_repo: - repo: pharmaverse/admiral - host: https://github.com \ No newline at end of file + repo: pharmaverse/sdtm.oak + host: https://github.com + \ No newline at end of file From 79590409a25bb246a9c8abe2a3281a96dc48f9c7 Mon Sep 17 00:00:00 2001 From: Adam Forys Date: Mon, 20 Nov 2023 10:42:30 +0000 Subject: [PATCH 03/10] Fix admiraldev links. --- .github/CONTRIBUTING.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index df42b284..8a1ba358 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -3,7 +3,7 @@ This outlines how to propose a change to the aok package. For more detailed info about contributing to {oak}, and other [pharmaverse packages](https://pharmaverse.org/), please see the [development process -guide](https://pharmaverse.github.io/admiraldev/main/articles/development_process.html) +guide](https://pharmaverse.github.io/admiraldev/articles/development_process.html) as well as other Developer Guides in the Articles section of the [{admiral} website](https://pharmaverse.github.io/admiral/cran-release/index.html) @@ -23,7 +23,7 @@ feedback. Since we are not a 100% fully resourced software development team it might be that some issues will take longer to respond to depending on the amount of overall issues. - * Familiarize yourself with our [programming strategy](https://pharmaverse.github.io/admiraldev/main/articles/programming_strategy.html), guidance for [GitHub usage](https://pharmaverse.github.io/admiraldev/main/articles/git_usage.html) and [unit testing](https://pharmaverse.github.io/admiraldev/main/articles/unit_test_guidance.html). + * Familiarize yourself with our [programming strategy](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html), guidance for [GitHub usage](https://pharmaverse.github.io/admiraldev/articles/git_usage.html) and [unit testing](https://pharmaverse.github.io/admiraldev/articles/unit_test_guidance.html). * All newly [created issues](https://github.com/pharmaverse/oak/issues) will be reviewed within the next backlog meeting and the creator will receive an From 11ab81dba67129ceef876629aeaf4399b7d9d06e Mon Sep 17 00:00:00 2001 From: Adam Forys Date: Mon, 20 Nov 2023 10:45:30 +0000 Subject: [PATCH 04/10] Fix admiraldev articles links. --- .github/pull_request_template.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md index f49a5340..e32853fc 100644 --- a/.github/pull_request_template.md +++ b/.github/pull_request_template.md @@ -1,6 +1,6 @@ Thank you for your Pull Request! We have developed this task checklist from the [Development Process -Guide](https://pharmaverse.github.io/admiraldev/devel/articles/development_process.html) +Guide](https://pharmaverse.github.io/admiraldev/articles/development_process.html) to help with the final steps of the process. Completing the below tasks helps to ensure our reviewers can maximize their time on your code as well as making sure the oak codebase remains robust and consistent. @@ -18,13 +18,13 @@ Request Title (Use Edit button in top-right if you need to update) - [ ] Updated relevant unit tests or have written new unit tests, which should consider realistic data scenarios and edge cases, e.g. empty datasets, errors, boundary cases etc. - See -[Unit Test Guide](https://pharmaverse.github.io/admiraldev/devel/articles/unit_test_guidance.html#tests-should-be-robust-to-cover-realistic-data-scenarios) +[Unit Test Guide](https://pharmaverse.github.io/admiraldev/articles/unit_test_guidance.html#tests-should-be-robust-to-cover-realistic-data-scenarios) - [ ] If you removed/replaced any function and/or function parameters, did you fully follow the -[deprecation guidance](https://pharmaverse.github.io/admiraldev/devel/articles/programming_strategy.html#deprecation)? +[deprecation guidance](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html#deprecation)? - [ ] Update to all relevant roxygen headers and examples, including keywords and families. Refer to the -[categorization of functions](https://pharmaverse.github.io/admiraldev/devel/articles/programming_strategy.html#categorization-of-functions) to tag appropriate keyword/family. +[categorization of functions](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html#categorization-of-functions) to tag appropriate keyword/family. - [ ] Run `devtools::document()` so all `.Rd` files in the `man` folder and the `NAMESPACE` file in the project root are updated appropriately - [ ] Address any updates needed for vignettes and/or templates From 900d3eaf923a7b27ed5a4ace73cfaace9e3a600a Mon Sep 17 00:00:00 2001 From: Adam Forys Date: Mon, 20 Nov 2023 11:59:41 +0000 Subject: [PATCH 05/10] Remove R 4.1 a it causing dependencies issues. We want to use purrr >= 1.0.0 --- .Rprofile | 2 +- .devcontainer/4.1/devcontainer.json | 95 -- .github/workflows/r-renv-lock.yml | 1 - DESCRIPTION | 6 +- renv/profiles/4.1/renv.lock | 1254 -------------------------- renv/profiles/4.1/renv/.gitignore | 7 - renv/profiles/4.1/renv/settings.json | 21 - 7 files changed, 4 insertions(+), 1382 deletions(-) delete mode 100644 .devcontainer/4.1/devcontainer.json delete mode 100644 renv/profiles/4.1/renv.lock delete mode 100644 renv/profiles/4.1/renv/.gitignore delete mode 100644 renv/profiles/4.1/renv/settings.json diff --git a/.Rprofile b/.Rprofile index a94c4d6f..062e3271 100644 --- a/.Rprofile +++ b/.Rprofile @@ -27,7 +27,7 @@ Sys.setenv("RENV_CONFIG_AUTO_SNAPSHOT" = FALSE) if (!Sys.getenv("RENV_AUTOLOADER_ENABLED") %in% c("false", "FALSE")) { .renv_profile <- paste(R.version$major, substr(R.version$minor, 1, 1), sep = ".") if (!file.exists("./renv/profile")) { - if (.renv_profile %in% c("4.1", "4.2", "4.3")) { + if (.renv_profile %in% c("4.2", "4.3")) { message("Set renv profile to `", .renv_profile, "`") Sys.setenv("RENV_PROFILE" = .renv_profile) } else { diff --git a/.devcontainer/4.1/devcontainer.json b/.devcontainer/4.1/devcontainer.json deleted file mode 100644 index e60b4fd9..00000000 --- a/.devcontainer/4.1/devcontainer.json +++ /dev/null @@ -1,95 +0,0 @@ -{ - // https://containers.dev/implementors/json_reference/ - "name": "sdtm.oak (RStudio) container", - "image": "ghcr.io/pharmaverse/sdtm.oak-4.1:latest", - // Install Dev Container Features. More info: https://containers.dev/features - "containerEnv": { - "ROOT": "true", - "PASSWORD": "rstudio", - "DISABLE_AUTH": "true", - "RENV_AUTOLOADER_ENABLED": "false" - }, - "features": { - "./ca-cert": {}, - "ghcr.io/rocker-org/devcontainer-features/r-rig:1": { - "version": "none", - "vscodeRSupport": "full", - "installRadian": true, - "installVscDebugger": true - }, - "ghcr.io/rocker-org/devcontainer-features/renv-cache:latest": {}, - "ghcr.io/devcontainers/features/common-utils:2": { - "installZsh": true, - "configureZshAsDefaultShell": false, - "installOhMyZsh": true, - "username": "rstudio", - "upgradePackages": false - }, - "ghcr.io/mikaello/devcontainer-features/modern-shell-utils:1": {} - }, - "overrideFeatureInstallOrder": [ - "./ca-cert", - "./arm64-repos", - "ghcr.io/devcontainers/features/common-utils", - "ghcr.io/rocker-org/devcontainer-features/renv-cache", - "ghcr.io/rocker-org/devcontainer-features/r-rig", - "ghcr.io/mikaello/devcontainer-features/modern-shell-utils" - ], - "init": true, - "overrideCommand": false, - - "postCreateCommand": "bash ./.devcontainer/postCreateCommand.sh", - - "postAttachCommand": "rstudio || true", - - "customizations": { - "codespaces": { - "repositories": { - "pharmaverse/mint": { - "permissions": "write-all" - }, - "pharmaverse/raw.synthetic.data": { - "permissions": "write-all" - } - } - }, - "vscode": { - "settings": { - "r.rterm.linux": "/usr/local/bin/radian", - "r.bracketedPaste": true, - "editor.bracketPairColorization.enabled": true, - "editor.guides.bracketPairs": "active" - }, - "extensions": [ - "vsls-contrib.codetour", - "GitHub.copilot", - "GitHub.copilot-chat", - // R extensions - "ikuyadeu.r", - "REditorSupport.r-lsp", - // Extra extension - "streetsidesoftware.code-spell-checker", - "eamodio.gitlens", - "cweijan.vscode-office", - "donjayamanne.githistory", - "GitHub.vscode-github-actions", - "GitHub.vscode-pull-request-github", - "GitHub.remotehub", - "alefragnani.Bookmarks", - "vscode-icons-team.vscode-icons" - ] - } - }, - - // RStudio ports - "forwardPorts": [8787], - "portsAttributes": { - "8787": { - "label": "Rstudio", - "requireLocalPort": true, - "onAutoForward": "openBrowser" - } - }, - // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root - "remoteUser": "rstudio" -} diff --git a/.github/workflows/r-renv-lock.yml b/.github/workflows/r-renv-lock.yml index fd5015d4..d07747e0 100644 --- a/.github/workflows/r-renv-lock.yml +++ b/.github/workflows/r-renv-lock.yml @@ -22,7 +22,6 @@ jobs: fail-fast: false matrix: config: - - {os: ubuntu-20.04, r: '4.1', repos: 'https://packagemanager.posit.co/cran/2022-03-10/'} - {os: ubuntu-20.04, r: '4.2', repos: 'https://packagemanager.posit.co/cran/2023-03-15/'} - {os: ubuntu-20.04, r: '4.3', repos: 'https://packagemanager.posit.co/cran/2023-04-20/'} diff --git a/DESCRIPTION b/DESCRIPTION index 4509f099..d115078b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -19,11 +19,11 @@ Encoding: UTF-8 LazyData: true Roxygen: list(markdown = TRUE) RoxygenNote: 7.2.3 -Depends: R (>= 4.1) +Depends: R (>= 4.2) Imports: admiraldev, - dplyr, - purrr, + dplyr (>= 1.0.0), + purrr (>= 1.0.0), rlang (>= 1.0.0), stringr, tibble diff --git a/renv/profiles/4.1/renv.lock b/renv/profiles/4.1/renv.lock deleted file mode 100644 index 5b858691..00000000 --- a/renv/profiles/4.1/renv.lock +++ /dev/null @@ -1,1254 +0,0 @@ -{ - 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"bioconductor.version": null, - "external.libraries": [], - "ignored.packages": [ - "admiraldev" - ], - "package.dependency.fields": [ - "Imports", - "Depends", - "LinkingTo" - ], - "ppm.enabled": null, - "ppm.ignored.urls": [], - "r.version": null, - "snapshot.type": "custom", - "use.cache": true, - "vcs.ignore.cellar": true, - "vcs.ignore.library": true, - "vcs.ignore.local": true, - "vcs.manage.ignores": true -} From db0ebe9c759936b7ea0bd26ad6e473d255f9b5fe Mon Sep 17 00:00:00 2001 From: Adam Forys Date: Mon, 20 Nov 2023 12:47:00 +0000 Subject: [PATCH 06/10] Test latest lintr --- .github/workflows/common.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/common.yml b/.github/workflows/common.yml index a8c9a5d3..786fa938 100644 --- a/.github/workflows/common.yml +++ b/.github/workflows/common.yml @@ -78,10 +78,11 @@ jobs: ^cran-release$|^main$|^v([0-9]+\\.)?([0-9]+\\.)?([0-9]+)$ linter: name: Lint - uses: pharmaverse/admiralci/.github/workflows/lintr.yml@main + uses: pharmaverse/admiralci/.github/workflows/lintr.yml@lintr-latest-cran if: github.event_name == 'pull_request' with: r-version: "4.3" + latest-lintr: "true" links: name: Links uses: pharmaverse/admiralci/.github/workflows/links.yml@main From 2d3e101438ab2f230a08e864229c5340c9492a6a Mon Sep 17 00:00:00 2001 From: Adam Forys Date: Mon, 20 Nov 2023 13:27:55 +0000 Subject: [PATCH 07/10] Test lintr with install package locally From eeaec18a89773f86e4f7a0317b0af0f617afeb91 Mon Sep 17 00:00:00 2001 From: Adam Forys Date: Mon, 20 Nov 2023 13:33:24 +0000 Subject: [PATCH 08/10] Add install pacakge variable for lintr --- .github/workflows/common.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/common.yml b/.github/workflows/common.yml index 786fa938..87c7d7ae 100644 --- a/.github/workflows/common.yml +++ b/.github/workflows/common.yml @@ -83,6 +83,7 @@ jobs: with: r-version: "4.3" latest-lintr: "true" + install-package: "true" links: name: Links uses: pharmaverse/admiralci/.github/workflows/links.yml@main From 457c7f03c265f6d1ca20a4735b4a9b2c42cda509 Mon Sep 17 00:00:00 2001 From: Adam Forys Date: Mon, 20 Nov 2023 13:48:15 +0000 Subject: [PATCH 09/10] Skip multi version pkgdown workflow. --- .github/workflows/common.yml | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/.github/workflows/common.yml b/.github/workflows/common.yml index 87c7d7ae..f4aacbb0 100644 --- a/.github/workflows/common.yml +++ b/.github/workflows/common.yml @@ -71,11 +71,7 @@ jobs: # Whether to skip multiversion docs # Note that if you have multiple versions of docs, # your URL links are likely to break due to path changes - skip-multiversion-docs: false - latest-tag-alt-name: cran-release - multiversion-docs-landing-page: cran-release - branches-or-tags-to-list: >- - ^cran-release$|^main$|^v([0-9]+\\.)?([0-9]+\\.)?([0-9]+)$ + skip-multiversion-docs: true linter: name: Lint uses: pharmaverse/admiralci/.github/workflows/lintr.yml@lintr-latest-cran From 061f9282b92f6445fee500568796e3607bf0b825 Mon Sep 17 00:00:00 2001 From: Ramiro Magno Date: Mon, 20 Nov 2023 17:43:40 +0000 Subject: [PATCH 10/10] R build ignore staged_dependencies.yaml --- .Rbuildignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.Rbuildignore b/.Rbuildignore index 4bca79b1..41c60f38 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -12,3 +12,4 @@ ^LICENSE\.md$ ^\.lintr$ ^data-raw$ +^staged_dependencies.yaml$