From 1feeced933bdbea7db90bd876af10a021af47102 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Adam=20Fory=C5=9B?= Date: Tue, 15 Aug 2023 16:28:47 +0000 Subject: [PATCH 1/6] Replace admiral.test with pharmaversesdtm --- .Rprofile | 2 +- .github/workflows/propagate.yml | 2 +- .github/workflows/r-renv-lock.yml | 10 +++++----- vignettes/lock_and_prop.Rmd | 2 +- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/.Rprofile b/.Rprofile index 51ad0fdc..d059c2fc 100644 --- a/.Rprofile +++ b/.Rprofile @@ -19,7 +19,7 @@ )) ) ) - packages[!(packages %in% c("admiral", "admiraldev", "admiralci", "admiral.test", getwd()))] + packages[!(packages %in% c("admiral", "admiraldev", "admiralci", "admiral.test", "pharmaversesdtm", getwd()))] } options(renv.snapshot.filter = .get_dependencies) diff --git a/.github/workflows/propagate.yml b/.github/workflows/propagate.yml index 144cbfee..08a1c49a 100644 --- a/.github/workflows/propagate.yml +++ b/.github/workflows/propagate.yml @@ -77,7 +77,7 @@ jobs: cicdguy bms63 bundfussr - - name: admiral.test + - name: pharmaversesdtm target-branch: devel reviewers: |- bms63 diff --git a/.github/workflows/r-renv-lock.yml b/.github/workflows/r-renv-lock.yml index 5822cf6e..d0f7392c 100644 --- a/.github/workflows/r-renv-lock.yml +++ b/.github/workflows/r-renv-lock.yml @@ -99,7 +99,7 @@ jobs: )) ) ) - packages[!(packages %in% c("admiral", "admiraldev", "admiralci", "admiral.test", getwd()))] + packages[!(packages %in% c("admiral", "admiraldev", "admiralci", "admiral.test", "pharmaversesdtm", getwd()))] } options(renv.snapshot.filter = .get_dependencies) @@ -108,7 +108,7 @@ jobs: loc_path <- find.package("admiraldev", lib.loc = .libPaths(), quiet = TRUE) suggests <- renv:::renv_dependencies_discover_description(loc_path, fields = "Suggests")[["Package"]] - suggests <- suggests[!(suggests %in% c("admiral", "admiraldev", "admiralci", "admiral.test"))] + suggests <- suggests[!(suggests %in% c("admiral", "admiraldev", "admiralci", "admiral.test", "pharmaversesdtm"))] renv::install(suggests, repos = options("repos")) } @@ -126,12 +126,12 @@ jobs: renv::install("openpharma/staged.dependencies", repos = options("repos")) # Packages from stage dependencies to ignore - renv::settings$ignored.packages(c("admiral", "admiraldev", "admiral.test", "admiralci")) + renv::settings$ignored.packages(c("admiral", "admiraldev", "admiral.test", "admiralci", "pharmaversesdtm")) - renv::install("pharmaverse/admiral.test@devel", repos = options("repos")) + renv::install("pharmaverse/pharmaversesdtm@devel", repos = options("repos")) renv::install("pharmaverse/admiraldev@devel", repos = options("repos")) renv_install_suggests("admiraldev") - renv_install_suggests("admiral.test") + renv_install_suggests("pharmaversesdtm") # Install dependencies renv::settings$snapshot.type("explicit") diff --git a/vignettes/lock_and_prop.Rmd b/vignettes/lock_and_prop.Rmd index 48f5a866..6dca810e 100644 --- a/vignettes/lock_and_prop.Rmd +++ b/vignettes/lock_and_prop.Rmd @@ -46,7 +46,7 @@ The first step for requesting an update for a R package in the `renv.lock` file ## Propagation Process -Through GitHub Actions we have developed the ability to **propagate** updated lock files with our preferred versions of R and R packages throughout the family of admiral packages. This ensures that developers working on `{admiral.test}` and `{admiralonco}` have the same common environment as those working on `{admiraldev}` and `{admiralvaccines}`. +Through GitHub Actions we have developed the ability to **propagate** updated lock files with our preferred versions of R and R packages throughout the family of admiral packages. This ensures that developers working on `{pharmaversesdtm}` and `{admiralonco}` have the same common environment as those working on `{admiraldev}` and `{admiralvaccines}`. The file that does the propagation process is called [`propagate.yml`](https://github.com/pharmaverse/admiralci/blob/main/.github/workflows/propagate.yml) located in the `.github/workflows` folder of the [admiralci repository](https://github.com/pharmaverse/admiralci/). From 595996bba780eb40c2f64393939a3fe2c05da05e Mon Sep 17 00:00:00 2001 From: galachad Date: Tue, 15 Aug 2023 16:42:28 +0000 Subject: [PATCH 2/6] Automatic renv profile update. --- renv/profiles/4.1/renv/settings.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/renv/profiles/4.1/renv/settings.json b/renv/profiles/4.1/renv/settings.json index 3462f3b0..4922677e 100644 --- a/renv/profiles/4.1/renv/settings.json +++ b/renv/profiles/4.1/renv/settings.json @@ -5,7 +5,8 @@ "admiral", "admiraldev", "admiral.test", - "admiralci" + "admiralci", + "pharmaversesdtm" ], "package.dependency.fields": [ "Imports", From fda66d9be504efc25c0af3109c65882adcfa7b9b Mon Sep 17 00:00:00 2001 From: galachad Date: Tue, 15 Aug 2023 16:50:15 +0000 Subject: [PATCH 3/6] Automatic renv profile update. --- renv/profiles/4.2/renv/settings.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/renv/profiles/4.2/renv/settings.json b/renv/profiles/4.2/renv/settings.json index 3462f3b0..4922677e 100644 --- a/renv/profiles/4.2/renv/settings.json +++ b/renv/profiles/4.2/renv/settings.json @@ -5,7 +5,8 @@ "admiral", "admiraldev", "admiral.test", - "admiralci" + "admiralci", + "pharmaversesdtm" ], "package.dependency.fields": [ "Imports", From 96f7c180230dd65960b0780ce40e0823857f9a6f Mon Sep 17 00:00:00 2001 From: galachad Date: Tue, 15 Aug 2023 16:56:36 +0000 Subject: [PATCH 4/6] Automatic renv profile update. --- renv/profiles/4.3/renv/settings.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/renv/profiles/4.3/renv/settings.json b/renv/profiles/4.3/renv/settings.json index 3462f3b0..4922677e 100644 --- a/renv/profiles/4.3/renv/settings.json +++ b/renv/profiles/4.3/renv/settings.json @@ -5,7 +5,8 @@ "admiral", "admiraldev", "admiral.test", - "admiralci" + "admiralci", + "pharmaversesdtm" ], "package.dependency.fields": [ "Imports", From d0ca916337c073c5cf371686e9bd27a15c0a9661 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Adam=20Fory=C5=9B?= Date: Wed, 16 Aug 2023 14:27:42 +0000 Subject: [PATCH 5/6] Propagation trigger From 7e830359ce6beb16a4063362a09e028e1cec4689 Mon Sep 17 00:00:00 2001 From: Zelos Zhu Date: Fri, 25 Aug 2023 15:17:36 +0000 Subject: [PATCH 6/6] get around personal access token --- .Rprofile | 2 +- renv/profiles/4.1/renv/settings.json | 1 - renv/profiles/4.2/renv/settings.json | 1 - renv/profiles/4.3/renv/settings.json | 1 - renv/settings.json | 4 ++-- 5 files changed, 3 insertions(+), 6 deletions(-) diff --git a/.Rprofile b/.Rprofile index d059c2fc..51f55c19 100644 --- a/.Rprofile +++ b/.Rprofile @@ -19,7 +19,7 @@ )) ) ) - packages[!(packages %in% c("admiral", "admiraldev", "admiralci", "admiral.test", "pharmaversesdtm", getwd()))] + packages[!(packages %in% c("admiral", "admiraldev", "admiralci", "pharmaversesdtm", getwd()))] } options(renv.snapshot.filter = .get_dependencies) diff --git a/renv/profiles/4.1/renv/settings.json b/renv/profiles/4.1/renv/settings.json index 4922677e..0c8943c5 100644 --- a/renv/profiles/4.1/renv/settings.json +++ b/renv/profiles/4.1/renv/settings.json @@ -4,7 +4,6 @@ "ignored.packages": [ "admiral", "admiraldev", - "admiral.test", "admiralci", "pharmaversesdtm" ], diff --git a/renv/profiles/4.2/renv/settings.json b/renv/profiles/4.2/renv/settings.json index 4922677e..0c8943c5 100644 --- a/renv/profiles/4.2/renv/settings.json +++ b/renv/profiles/4.2/renv/settings.json @@ -4,7 +4,6 @@ "ignored.packages": [ "admiral", "admiraldev", - "admiral.test", "admiralci", "pharmaversesdtm" ], diff --git a/renv/profiles/4.3/renv/settings.json b/renv/profiles/4.3/renv/settings.json index 4922677e..0c8943c5 100644 --- a/renv/profiles/4.3/renv/settings.json +++ b/renv/profiles/4.3/renv/settings.json @@ -4,7 +4,6 @@ "ignored.packages": [ "admiral", "admiraldev", - "admiral.test", "admiralci", "pharmaversesdtm" ], diff --git a/renv/settings.json b/renv/settings.json index 3462f3b0..0c8943c5 100644 --- a/renv/settings.json +++ b/renv/settings.json @@ -4,8 +4,8 @@ "ignored.packages": [ "admiral", "admiraldev", - "admiral.test", - "admiralci" + "admiralci", + "pharmaversesdtm" ], "package.dependency.fields": [ "Imports",