diff --git a/404.html b/404.html index 6b930c4..6769fce 100644 --- a/404.html +++ b/404.html @@ -32,7 +32,7 @@ rworkflows - 1.0.3 + 1.0.5 diff --git a/articles/bioconductor.html b/articles/bioconductor.html index d68d56a..3583acb 100644 --- a/articles/bioconductor.html +++ b/articles/bioconductor.html @@ -32,7 +32,7 @@ rworkflows - 1.0.3 + 1.0.5 @@ -183,7 +183,7 @@

## runner_os: ${{ runner.os }} ## cache_version: cache-v1 ## docker_registry: ghcr.io -
## Saving yaml ==> /tmp/RtmpDVZM22/rworkflows.devel.yml
+
## Saving yaml ==> /tmp/RtmprytOGa/rworkflows.devel.yml

@@ -250,7 +250,7 @@

## runner_os: ${{ runner.os }} ## cache_version: cache-v1 ## docker_registry: ghcr.io -
## Saving yaml ==> /tmp/RtmpDVZM22/rworkflows.RELEASE_3_17.yml
+
## Saving yaml ==> /tmp/RtmprytOGa/rworkflows.RELEASE_3_17.yml

@@ -297,7 +297,7 @@

Session Info## [1] stats graphics grDevices utils datasets methods base ## ## other attached packages: -## [1] rworkflows_1.0.3 +## [1] rworkflows_1.0.5 ## ## loaded via a namespace (and not attached): ## [1] gtable_0.3.6 jsonlite_1.8.9 renv_1.0.11 diff --git a/articles/depgraph.html b/articles/depgraph.html index 3f17046..8283289 100644 --- a/articles/depgraph.html +++ b/articles/depgraph.html @@ -32,7 +32,7 @@ rworkflows - 1.0.3 + 1.0.5

diff --git a/articles/docker.html b/articles/docker.html index bd511c0..41f32de 100644 --- a/articles/docker.html +++ b/articles/docker.html @@ -32,7 +32,7 @@ rworkflows - 1.0.3 + 1.0.5 @@ -196,7 +196,7 @@

Session Info## [1] stats graphics grDevices utils datasets methods base ## ## other attached packages: -## [1] rworkflows_1.0.3 +## [1] rworkflows_1.0.5 ## ## loaded via a namespace (and not attached): ## [1] gtable_0.3.6 jsonlite_1.8.9 renv_1.0.11 diff --git a/articles/index.html b/articles/index.html index 223ed2a..90522f7 100644 --- a/articles/index.html +++ b/articles/index.html @@ -17,7 +17,7 @@ rworkflows - 1.0.3 + 1.0.5 diff --git a/articles/repos.html b/articles/repos.html index 7bebf06..cd1b113 100644 --- a/articles/repos.html +++ b/articles/repos.html @@ -32,7 +32,7 @@ rworkflows - 1.0.3 + 1.0.5 diff --git a/articles/rworkflows.html b/articles/rworkflows.html index 4746df6..d58a2f4 100644 --- a/articles/rworkflows.html +++ b/articles/rworkflows.html @@ -32,7 +32,7 @@ rworkflows - 1.0.3 + 1.0.5 @@ -147,7 +147,7 @@

dynamic action force_new = TRUE, ## Use default save_dir in practice save_dir = tempdir()) -
## Saving yaml ==> /tmp/RtmpK5rZv5/rworkflows.yml
+
## Saving yaml ==> /tmp/RtmpBgFOqP/rworkflows.yml

static workflow @@ -164,7 +164,7 @@

static workflow force_new = TRUE, ## Use default save_dir in practice save_dir = tempdir())

-
## Saving yaml ==> /tmp/RtmpK5rZv5/rworkflows_static.yml
+
## Saving yaml ==> /tmp/RtmpBgFOqP/rworkflows_static.yml
@@ -184,7 +184,7 @@ 

## Adding codecov.
## Adding authors.
## When refs is provided, paths must have the same length (or be set to NULL). Setting paths=NULL.
-
License: GPL-3 +
License: GPL-3
R build status @@ -206,7 +206,7 @@ 

 ## Use default save_dir in practice
 dockerfile <- rworkflows::use_dockerfile(save_dir = tempdir())
-
## Creating new Docker file ==> /tmp/RtmpK5rZv5/Dockerfile
+
## Creating new Docker file ==> /tmp/RtmpBgFOqP/Dockerfile

Templates @@ -224,7 +224,7 @@

README 
 ## Use default save_dir in practice
 readme <- rworkflows::use_readme(save_dir = tempdir())
-
## Creating new README file ==> /tmp/RtmpK5rZv5/README.Rmd
+
## Creating new README file ==> /tmp/RtmpBgFOqP/README.Rmd

Vignette: Get started @@ -235,7 +235,7 @@

Vignette: Get started## Use default save_dir in practice vignette1 <- rworkflows::use_vignette_getstarted(package = "mypackage", save_dir = tempdir())

-
## Creating new vignette file ==> /tmp/RtmpK5rZv5/vignettes/mypackage.Rmd
+
## Creating new vignette file ==> /tmp/RtmpBgFOqP/vignettes/mypackage.Rmd

Vignette: docker @@ -258,7 +258,7 @@

Vignette: docker## Use default save_dir in practice vignette2 <- rworkflows::use_vignette_docker(docker_org = "neurogenomics", save_dir = tempdir())

-
## Creating new vignette file ==> /tmp/RtmpK5rZv5/vignettes/docker.Rmd
+
## Creating new vignette file ==> /tmp/RtmpBgFOqP/vignettes/docker.Rmd
@@ -346,7 +346,7 @@

Using Python## runner_os: ${{ runner.os }} ## cache_version: cache-v1 ## docker_registry: ghcr.io -
## Saving yaml ==> /tmp/RtmpK5rZv5/rworkflows.yml
+
## Saving yaml ==> /tmp/RtmpBgFOqP/rworkflows.yml

Using conda @@ -459,7 +459,7 @@

Using conda## docker_registry: ghcr.io ## miniforge_variant: '' ## environment_file: /__w/rworkflows/rworkflows/myenv_conda.yml -
## Saving yaml ==> /tmp/RtmpK5rZv5/rworkflows.yml
+
## Saving yaml ==> /tmp/RtmpBgFOqP/rworkflows.yml
 ## Cleanup files
 try({file.remove(environment_file)})
@@ -494,7 +494,7 @@

Session Info## [1] stats graphics grDevices utils datasets methods base ## ## other attached packages: -## [1] rworkflows_1.0.3 +## [1] rworkflows_1.0.5 ## ## loaded via a namespace (and not attached): ## [1] gtable_0.3.6 jsonlite_1.8.9 renv_1.0.11 diff --git a/authors.html b/authors.html index ef9e089..842c2c6 100644 --- a/authors.html +++ b/authors.html @@ -17,7 +17,7 @@ rworkflows - 1.0.3 + 1.0.5

diff --git a/index.html b/index.html index 9a16e2c..496f728 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ rworkflows - 1.0.3 + 1.0.5 @@ -90,7 +90,7 @@
-
License: GPL-3

R build status R build status R build status

+
License: GPL-3

R build status R build status R build status

Authors: Brian Schilder, Alan Murphy, Nathan Skene

@@ -356,7 +356,7 @@

## [22] munsell_0.5.1 pillar_1.9.0 RColorBrewer_1.1-3 ## [25] rlang_1.1.4 utf8_1.2.4 badger_0.2.4 ## [28] xfun_0.49 fs_1.6.5 cli_3.6.3 -## [31] magrittr_2.0.3 rworkflows_1.0.3 digest_0.6.37 +## [31] magrittr_2.0.3 rworkflows_1.0.5 digest_0.6.37 ## [34] grid_4.4.1 lifecycle_1.0.4 vctrs_0.6.5 ## [37] evaluate_1.0.1 glue_1.8.0 data.table_1.16.4 ## [40] fansi_1.0.6 colorspace_2.1-1 tools_4.4.1 diff --git a/news/index.html b/news/index.html index d18783c..b7007df 100644 --- a/news/index.html +++ b/news/index.html @@ -17,7 +17,7 @@ rworkflows - 1.0.3 + 1.0.5

@@ -69,6 +69,13 @@

Changelog

Source: NEWS.md
+
+

rworkflows 1.0.5

+
+

New features

+
  • New arg force_install allows users to bypass cache while installing dependencies.
    • +
+

rworkflows 1.0.4

diff --git a/pkgdown.yml b/pkgdown.yml index 8875286..af3dd63 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -7,4 +7,4 @@ articles: docker: docker.html repos: repos.html rworkflows: rworkflows.html -last_built: 2024-12-18T14:34Z +last_built: 2024-12-18T15:42Z diff --git a/reference/bioc_r_versions.html b/reference/bioc_r_versions.html index fcde141..48c0fcf 100644 --- a/reference/bioc_r_versions.html +++ b/reference/bioc_r_versions.html @@ -18,7 +18,7 @@ rworkflows - 1.0.3 + 1.0.5
diff --git a/reference/biocpkgtools_db.html b/reference/biocpkgtools_db.html index 53a179c..1fa0c8b 100644 --- a/reference/biocpkgtools_db.html +++ b/reference/biocpkgtools_db.html @@ -19,7 +19,7 @@ rworkflows - 1.0.3 + 1.0.5
diff --git a/reference/check_cont.html b/reference/check_cont.html index f341e5e..2ce61b9 100644 --- a/reference/check_cont.html +++ b/reference/check_cont.html @@ -17,7 +17,7 @@ rworkflows - 1.0.3 + 1.0.5 diff --git a/reference/check_miniconda_args.html b/reference/check_miniconda_args.html index 34f145d..be02e37 100644 --- a/reference/check_miniconda_args.html +++ b/reference/check_miniconda_args.html @@ -17,7 +17,7 @@ rworkflows - 1.0.3 + 1.0.5 diff --git a/reference/check_registry.html b/reference/check_registry.html index fce1d27..e4af847 100644 --- a/reference/check_registry.html +++ b/reference/check_registry.html @@ -17,7 +17,7 @@ rworkflows - 1.0.3 + 1.0.5 diff --git a/reference/conda_export.html b/reference/conda_export.html index 49cb255..fc04952 100644 --- a/reference/conda_export.html +++ b/reference/conda_export.html @@ -18,7 +18,7 @@ rworkflows - 1.0.3 + 1.0.5 diff --git a/reference/construct_authors.html b/reference/construct_authors.html index cc134a9..3912a7c 100644 --- a/reference/construct_authors.html +++ b/reference/construct_authors.html @@ -18,7 +18,7 @@ rworkflows - 1.0.3 + 1.0.5 diff --git a/reference/construct_conda_yml.html b/reference/construct_conda_yml.html index aa50048..d61cd9b 100644 --- a/reference/construct_conda_yml.html +++ b/reference/construct_conda_yml.html @@ -18,7 +18,7 @@ rworkflows - 1.0.3 + 1.0.5 @@ -139,7 +139,7 @@

Examples

return_path = FALSE, ## Writing to temp only for example save_path=tempfile(fileext="myenv_conda.yml")) -#> Saving yaml ==> /tmp/RtmposGs9v/file19b21468061bmyenv_conda.yml +#> Saving yaml ==> /tmp/RtmppaN4bb/file11e2144aaf25myenv_conda.yml diff --git a/reference/construct_cont.html b/reference/construct_cont.html index 3ed3e25..3f1f78f 100644 --- a/reference/construct_cont.html +++ b/reference/construct_cont.html @@ -17,7 +17,7 @@ rworkflows - 1.0.3 + 1.0.5 diff --git a/reference/construct_runners.html b/reference/construct_runners.html index 331306c..192ced7 100644 --- a/reference/construct_runners.html +++ b/reference/construct_runners.html @@ -18,7 +18,7 @@ rworkflows - 1.0.3 + 1.0.5 diff --git a/reference/dt_to_desc.html b/reference/dt_to_desc.html index 08539f6..c3e3bf2 100644 --- a/reference/dt_to_desc.html +++ b/reference/dt_to_desc.html @@ -19,7 +19,7 @@ rworkflows - 1.0.3 + 1.0.5 diff --git a/reference/fill_description.html b/reference/fill_description.html index 934efe7..e27a484 100644 --- a/reference/fill_description.html +++ b/reference/fill_description.html @@ -32,7 +32,7 @@ rworkflows - 1.0.3 + 1.0.5 @@ -282,7 +282,7 @@

Examples

#> Updating: biocViews --> Genetics, SystemsBiology #> Updating: URL --> https://github.com/OwnerName/MyPackageName #> Updating: BugReports --> https://github.com/OwnerName/MyPackageName/issues -#> Saving updated file: /tmp/RtmposGs9v/file19b247c518dcDESCRIPTION +#> Saving updated file: /tmp/RtmppaN4bb/file11e260993437DESCRIPTION diff --git a/reference/get_authors.html b/reference/get_authors.html index 87f1e4f..ecd9650 100644 --- a/reference/get_authors.html +++ b/reference/get_authors.html @@ -17,7 +17,7 @@ rworkflows - 1.0.3 + 1.0.5 diff --git a/reference/get_description.html b/reference/get_description.html index ee9657a..72a59cb 100644 --- a/reference/get_description.html +++ b/reference/get_description.html @@ -24,7 +24,7 @@ rworkflows - 1.0.3 + 1.0.5 diff --git a/reference/get_description_repo.html b/reference/get_description_repo.html index ddcc9d6..bf09afb 100644 --- a/reference/get_description_repo.html +++ b/reference/get_description_repo.html @@ -20,7 +20,7 @@ rworkflows - 1.0.3 + 1.0.5 diff --git a/reference/get_github_url_db.html b/reference/get_github_url_db.html index 2b04e8f..42d0637 100644 --- a/reference/get_github_url_db.html +++ b/reference/get_github_url_db.html @@ -18,7 +18,7 @@ rworkflows - 1.0.3 + 1.0.5 diff --git a/reference/get_hex.html b/reference/get_hex.html index 16aedf8..71f1e03 100644 --- a/reference/get_hex.html +++ b/reference/get_hex.html @@ -17,7 +17,7 @@ rworkflows - 1.0.3 + 1.0.5 diff --git a/reference/gha_python_versions.html b/reference/gha_python_versions.html index 0368da0..4ada76e 100644 --- a/reference/gha_python_versions.html +++ b/reference/gha_python_versions.html @@ -17,7 +17,7 @@ rworkflows - 1.0.3 + 1.0.5 diff --git a/reference/index.html b/reference/index.html index 6c8411f..dd3e19a 100644 --- a/reference/index.html +++ b/reference/index.html @@ -17,7 +17,7 @@ rworkflows - 1.0.3 + 1.0.5 diff --git a/reference/infer_biocviews.html b/reference/infer_biocviews.html index f3648bf..4b25f95 100644 --- a/reference/infer_biocviews.html +++ b/reference/infer_biocviews.html @@ -23,7 +23,7 @@ rworkflows - 1.0.3 + 1.0.5 diff --git a/reference/infer_deps.html b/reference/infer_deps.html index 8681702..9c81fa0 100644 --- a/reference/infer_deps.html +++ b/reference/infer_deps.html @@ -17,7 +17,7 @@ rworkflows - 1.0.3 + 1.0.5 diff --git a/reference/infer_docker_org.html b/reference/infer_docker_org.html index 8213f26..7581fa6 100644 --- a/reference/infer_docker_org.html +++ b/reference/infer_docker_org.html @@ -17,7 +17,7 @@ rworkflows - 1.0.3 + 1.0.5 diff --git a/reference/is_gha.html b/reference/is_gha.html index d042793..3382a5c 100644 --- a/reference/is_gha.html +++ b/reference/is_gha.html @@ -18,7 +18,7 @@ rworkflows - 1.0.3 + 1.0.5 diff --git a/reference/message_parallel.html b/reference/message_parallel.html index 9d814eb..5a5a66e 100644 --- a/reference/message_parallel.html +++ b/reference/message_parallel.html @@ -17,7 +17,7 @@ rworkflows - 1.0.3 + 1.0.5 diff --git a/reference/messager.html b/reference/messager.html index 8ac82a7..c413307 100644 --- a/reference/messager.html +++ b/reference/messager.html @@ -20,7 +20,7 @@ rworkflows - 1.0.3 + 1.0.5 diff --git a/reference/stopper.html b/reference/stopper.html index 499c0f7..3780467 100644 --- a/reference/stopper.html +++ b/reference/stopper.html @@ -20,7 +20,7 @@ rworkflows - 1.0.3 + 1.0.5 diff --git a/reference/use_badges.html b/reference/use_badges.html index 2a3cc6c..75214e4 100644 --- a/reference/use_badges.html +++ b/reference/use_badges.html @@ -19,7 +19,7 @@ rworkflows - 1.0.3 + 1.0.5 @@ -285,7 +285,7 @@

Examples

#> When refs is provided, paths must have the same length (or be set to NULL). Setting paths=NULL. #> <img src='https://github.com/neurogenomics/rworkflows/raw/master/inst/hex/hex.png' title='Hex sticker for rworkflows' height='300'><br> #> [![License: GPL-3](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://cran.r-project.org/web/licenses/GPL-3) -#> [![](https://img.shields.io/badge/devel%20version-1.0.3-black.svg)](https://github.com/neurogenomics/rworkflows) +#> [![](https://img.shields.io/badge/devel%20version-1.0.5-black.svg)](https://github.com/neurogenomics/rworkflows) #> [![](https://img.shields.io/github/languages/code-size/neurogenomics/rworkflows.svg)](https://github.com/neurogenomics/rworkflows) #> [![](https://img.shields.io/github/last-commit/neurogenomics/rworkflows.svg)](https://github.com/neurogenomics/rworkflows/commits/master) #> <br> diff --git a/reference/use_codespace.html b/reference/use_codespace.html index ddfaf4a..051ec4d 100644 --- a/reference/use_codespace.html +++ b/reference/use_codespace.html @@ -18,7 +18,7 @@ rworkflows - 1.0.3 + 1.0.5 @@ -145,7 +145,7 @@

Value

Examples

path <- use_codespace(save_dir=tempdir())
-#> Creating new dev container config file ==> /tmp/RtmposGs9v/devcontainer.json
+#> Creating new dev container config file ==> /tmp/RtmppaN4bb/devcontainer.json
diff --git a/reference/use_dockerfile.html b/reference/use_dockerfile.html index 0381aed..82f21c6 100644 --- a/reference/use_dockerfile.html +++ b/reference/use_dockerfile.html @@ -18,7 +18,7 @@ rworkflows - 1.0.3 + 1.0.5 @@ -124,7 +124,7 @@

Value

Examples

path <- use_dockerfile(save_dir=tempdir())
-#> Creating new Docker file ==> /tmp/RtmposGs9v/Dockerfile
+#> Creating new Docker file ==> /tmp/RtmppaN4bb/Dockerfile
diff --git a/reference/use_issue_template.html b/reference/use_issue_template.html index e693ff2..97bc128 100644 --- a/reference/use_issue_template.html +++ b/reference/use_issue_template.html @@ -17,7 +17,7 @@ rworkflows - 1.0.3 + 1.0.5 @@ -122,9 +122,9 @@

Value

Examples

path <- use_issue_template(save_dir=tempdir())
-#> Creating new Issue Template ==> /tmp/RtmposGs9v/bug_report.yml
-#> Creating new Issue Template ==> /tmp/RtmposGs9v/feature_request.yml
-#> Creating new Issue Template ==> /tmp/RtmposGs9v/config.yml
+#> Creating new Issue Template ==> /tmp/RtmppaN4bb/bug_report.yml
+#> Creating new Issue Template ==> /tmp/RtmppaN4bb/feature_request.yml
+#> Creating new Issue Template ==> /tmp/RtmppaN4bb/config.yml
diff --git a/reference/use_readme.html b/reference/use_readme.html index 3a89607..9ba7a82 100644 --- a/reference/use_readme.html +++ b/reference/use_readme.html @@ -18,7 +18,7 @@ rworkflows - 1.0.3 + 1.0.5 @@ -120,7 +120,7 @@

Value

Examples

## use default save_dir in practice
 path <- use_readme(save_dir = tempdir()) 
-#> Creating new README file ==> /tmp/RtmposGs9v/README.Rmd
+#> Creating new README file ==> /tmp/RtmppaN4bb/README.Rmd
diff --git a/reference/use_vignette_docker.html b/reference/use_vignette_docker.html index c8da18a..08761f2 100644 --- a/reference/use_vignette_docker.html +++ b/reference/use_vignette_docker.html @@ -19,7 +19,7 @@ rworkflows - 1.0.3 + 1.0.5 @@ -194,7 +194,7 @@

Examples

docker_org = "neurogenomics", ## use default save_dir in practice save_dir = tempdir()) -#> Creating new vignette file ==> /tmp/RtmposGs9v/vignettes/docker.Rmd +#> Creating new vignette file ==> /tmp/RtmppaN4bb/vignettes/docker.Rmd diff --git a/reference/use_vignette_getstarted.html b/reference/use_vignette_getstarted.html index 18d9df7..cb9a0a2 100644 --- a/reference/use_vignette_getstarted.html +++ b/reference/use_vignette_getstarted.html @@ -17,7 +17,7 @@ rworkflows - 1.0.3 + 1.0.5 @@ -141,7 +141,7 @@

Examples

path <- use_vignette_getstarted(package = "mypackage",
                                 ## use default save_dir in practice
                                 save_dir = tempdir())
-#> Creating new vignette file ==> /tmp/RtmposGs9v/vignettes/mypackage.Rmd
+#> Creating new vignette file ==> /tmp/RtmppaN4bb/vignettes/mypackage.Rmd
diff --git a/reference/use_workflow.html b/reference/use_workflow.html index 6c3961a..b3145a3 100644 --- a/reference/use_workflow.html +++ b/reference/use_workflow.html @@ -19,7 +19,7 @@ rworkflows - 1.0.3 + 1.0.5 @@ -380,7 +380,7 @@

Value

Examples

path <- use_workflow(save_dir = file.path(tempdir(),".github","workflows"))
-#> Saving yaml ==> /tmp/RtmposGs9v/.github/workflows/rworkflows.yml
+#> Saving yaml ==> /tmp/RtmppaN4bb/.github/workflows/rworkflows.yml