Skip to content

Commit

Permalink
Update readme. update rworkflows
Browse files Browse the repository at this point in the history
  • Loading branch information
@bschilder
bschilder committed Nov 5, 2023
1 parent e462f48 commit b89a974
Show file tree
Hide file tree
Showing 3 changed files with 77 additions and 120 deletions.
23 changes: 14 additions & 9 deletions .github/workflows/rworkflows.yml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,16 +4,17 @@ name: rworkflows
branches:
- master
- main
- devel
- RELEASE_**
pull_request:
branches:
- master
- main
- devel
- RELEASE_**
jobs:
rworkflows:
permissions:
contents: write
permissions: write-all
runs-on: ${{ matrix.config.os }}
name: ${{ matrix.config.os }} (${{ matrix.config.r }})
container: ${{ matrix.config.cont }}
Expand All @@ -22,16 +23,20 @@ jobs:
matrix:
config:
- os: ubuntu-latest
r: devel
bioc: devel
cont: bioconductor/bioconductor_docker:devel
rspm: https://packagemanager.rstudio.com/cran/__linux__/focal/release
r: auto
cont: ghcr.io/bioconductor/bioconductor_docker:devel
rspm: ~
- os: macOS-latest
r: latest
bioc: release
r: auto
cont: ~
rspm: ~
- os: windows-latest
r: latest
bioc: release
r: auto
cont: ~
rspm: ~
steps:
- uses: neurogenomics/rworkflows@master
with:
Expand All @@ -43,10 +48,10 @@ jobs:
run_covr: ${{ true }}
run_pkgdown: ${{ true }}
has_runit: ${{ false }}
has_latex: ${{ false }}
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
run_docker: ${{ true }}
docker_user: bschilder
docker_org: neurogenomicslab
DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
runner_os: ${{ runner.os }}
cache_version: cache-v1
docker_registry: ghcr.io
52 changes: 20 additions & 32 deletions README.Rmd
View file
Original file line number Diff line number Diff line change
Expand Up @@ -11,13 +11,13 @@ output:
```{r, echo=FALSE, include=FALSE}
pkg <- read.dcf("DESCRIPTION", fields = "Package")[1]
title <- read.dcf("DESCRIPTION", fields = "Title")[1]
description <- read.dcf("DESCRIPTION", fields = "Description")[1]
description <- gsub("\n"," ",read.dcf("DESCRIPTION", fields = "Description")[1])
URL <- read.dcf('DESCRIPTION', fields = 'URL')[1]
owner <- strsplit(URL,"/")[[1]][4]
repo <- strsplit(URL,"/")[[1]][5]
```

*\<---(Start of section that can be deleted after forking the template)---\>*
**\<---⬇️⬇️⬇️(Start of section that can be deleted after forking the template)⬇️⬇️⬇️---\>**

## Citation

Expand All @@ -34,31 +34,32 @@ please cite:
- **DESCRIPTION, vignettes/, tests/, R/, man/, inst/**: Basic skeleton for the package itself.
- **README.Rmd**: Auto-populates based on the *DESCRIPTION* file (that can be knit to create *README.md*). Also contains [badges](https://github.com/GuangchuangYu/badger) that automatically update themselves.
- **inst/hex/hexSticker.Rmd**: Template for creating [hex stickers](https://github.com/GuangchuangYu/hexSticker).
- **.github/workflows/\*.yml**: [GitHub Actions](https://docs.github.com/en/actions/learn-github-actions/understanding-github-actions) workflow files that will automatically trigger code checks and pushing images to [DockerHub](https://hub-stage.docker.com/) every time you make a push to your GitHub repo (from [`r_workflows`](https://github.com/neurogenomics/r_workflows)).
- **inst/CITATIONS** : Allows users of your package to call `citation("<packageName>")`. Also used to auto-populate the *README.Rmd*.
- **.github/workflows/\*.yml**: [GitHub Actions](https://docs.github.com/en/actions/learn-github-actions/understanding-github-actions) workflow files that will automatically trigger code checks and pushing images to [DockerHub](https://hub-stage.docker.com/) every time you make a push to your GitHub repo (from [`rworkflows`](https://github.com/neurogenomics/rworkflows)).
- **inst/CITATION** : Allows users of your package to call `citation("<packageName>")`. Also used to auto-populate the *README.Rmd*.

To get started, simply click on the green **Use this template** button at the top right of the `templateR` repo.
To get started, simply click on the green **Use this template** button
at the top right of the `templateR` repo.

### GitHub Secrets

Before pushing changes to your new R package,
you will need to add two [GitHub Secrets](https://docs.github.com/en/actions/security-guides/encrypted-secrets):

1. `PAT_GITHUB`: Speeds up installations and gives access to private repos on GitHub Actions. You can generate your very own Personal Authentication Token using [these instructions](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token).
2. `CODECOV_TOKEN`: Allows [code coverage](https://app.codecov.io/) results to be displayed via the `rworkflows::use_badges()` at the top of the *README.Rmd*. This [Codecov](https://app.codecov.io/) token is repository-specific and can be found [here](https://app.codecov.io/gh/`r owner`/`r pkg`).
3. `DOCKER_TOKEN`: Allows GitHub Actions to push to the [neurogenomicslab DockerHub](https://hub.docker.com/orgs/neurogenomicslab) account. Ask a fellow [Neurogenomics Lab](https://www.neurogenomics.co.uk/) member for this token.
### GitHub Secrets

To use certain features of `rworkflows`, you may need to set up one or more [GitHub Secrets](https://docs.github.com/en/actions/security-guides/encrypted-secrets):

- `PAT_GITHUB` [Optional]: Can grant access to private repos on GitHub
Actions. You can generate your very own Personal Authentication Token
with `usethis::create_github_token()`. See the [GitHub
docs](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token)
for details.
- `DOCKER_TOKEN` [Optional]: Allows GitHub Actions to push to a
[DockerHub](https://hub.docker.com) account.

### GitHub Pages

The [GitHub Actions](https://docs.github.com/en/actions/learn-github-actions/understanding-github-actions) workflows included in this template will automatically create a documentation website for your package via [GitHub Pages](https://pages.github.com/). This requires several initial setup steps (you only need to do these once per repo):

1. After *check-bioc-docker.yml* has successfully run on Ubuntu for the first, a new branch will appear in your repo called "gh-pages".
2. In the **Settings** tab of your repo, go to **Pages** on the left. Then under **Source** select `"branch: gh-pages"` and `"root"` from the respective dropdown menus. Finally, click the **Save** button.
The [GitHub Actions](https://docs.github.com/en/actions/learn-github-actions/understanding-github-actions) workflows included in this template will automatically create a documentation website for your package via [GitHub Pages](https://pages.github.com/).

*Note*: If you don't have admin access to your repo, you will need to ask someone who does to change this for you.
After the **`rworkflows` action** has successfully run on Ubuntu for the
first time, a new branch will appear in your repo called "gh-pages".

*\<---(End of section that can be deleted after forking the template)---\>*
**\<---⬆️⬆️⬆️(End of section that can be deleted after forking the template)⬆️⬆️⬆️---\>**

## ``r pkg``: `r gsub("\n","",title)`

Expand All @@ -84,19 +85,6 @@ library(`r pkg`)

<hr>

## Contact

### [Neurogenomics Lab](https://www.neurogenomics.co.uk/)

UK Dementia Research Institute
Department of Brain Sciences
Faculty of Medicine
Imperial College London
[GitHub](https://github.com/neurogenomics)
[DockerHub](https://hub.docker.com/orgs/neurogenomicslab)

<br>

## Session Info

<details>
Expand Down
122 changes: 43 additions & 79 deletions README.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,13 +15,13 @@ status](https://github.com/neurogenomics/templateR/workflows/rworkflows/badge.sv
Authors: <i>yourGivenName yourFamilyName</i>
</h4>
<h4>
README updated: <i>Sep-01-2023</i>
README updated: <i>Nov-05-2023</i>
</h4>

<!-- To modify Package/Title/Description/Authors fields, edit the DESCRIPTION file -->

*\<—(Start of section that can be deleted after forking the
template)—\>*
**\<—⬇️⬇️⬇️(Start of section that can be deleted after forking the
template)⬇️⬇️⬇️—\>**

## Citation

Expand Down Expand Up @@ -53,8 +53,8 @@ easy by providing:
workflow files that will automatically trigger code checks and pushing
images to [DockerHub](https://hub-stage.docker.com/) every time you
make a push to your GitHub repo (from
[`r_workflows`](https://github.com/neurogenomics/r_workflows)).
- **inst/CITATIONS** : Allows users of your package to call
[`rworkflows`](https://github.com/neurogenomics/rworkflows)).
- **inst/CITATION** : Allows users of your package to call
`citation("<packageName>")`. Also used to auto-populate the
*README.Rmd*.

Expand All @@ -63,44 +63,31 @@ at the top right of the `templateR` repo.

### GitHub Secrets

Before pushing changes to your new R package, you will need to add two
[GitHub
To use certain features of `rworkflows`, you may need to set up one or
more [GitHub
Secrets](https://docs.github.com/en/actions/security-guides/encrypted-secrets):

1. `PAT_GITHUB`: Speeds up installations and gives access to private
repos on GitHub Actions. You can generate your very own Personal
Authentication Token using [these
instructions](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token).
2. `CODECOV_TOKEN`: Allows [code coverage](https://app.codecov.io/)
results to be displayed via the `rworkflows::use_badges()` at the
top of the *README.Rmd*. This [Codecov](https://app.codecov.io/)
token is repository-specific and can be found
[here](https://app.codecov.io/gh/neurogenomics/templateR).
3. `DOCKER_TOKEN`: Allows GitHub Actions to push to the
[neurogenomicslab
DockerHub](https://hub.docker.com/orgs/neurogenomicslab) account.
Ask a fellow [Neurogenomics Lab](https://www.neurogenomics.co.uk/)
member for this token.
- `PAT_GITHUB` \[Optional\]: Can grant access to private repos on GitHub
Actions. You can generate your very own Personal Authentication Token
with `usethis::create_github_token()`. See the [GitHub
docs](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token)
for details.
- `DOCKER_TOKEN` \[Optional\]: Allows GitHub Actions to push to a
[DockerHub](https://hub.docker.com) account.

### GitHub Pages

The [GitHub
Actions](https://docs.github.com/en/actions/learn-github-actions/understanding-github-actions)
workflows included in this template will automatically create a
documentation website for your package via [GitHub
Pages](https://pages.github.com/). This requires several initial setup
steps (you only need to do these once per repo):
Pages](https://pages.github.com/).

1. After *check-bioc-docker.yml* has successfully run on Ubuntu for the
first, a new branch will appear in your repo called “gh-pages”.
2. In the **Settings** tab of your repo, go to **Pages** on the left.
Then under **Source** select `"branch: gh-pages"` and `"root"` from
the respective dropdown menus. Finally, click the **Save** button.
After the **`rworkflows` action** has successfully run on Ubuntu for the
first time, a new branch will appear in your repo called “gh-pages”.

*Note*: If you don’t have admin access to your repo, you will need to
ask someone who does to change this for you.

*\<—(End of section that can be deleted after forking the template)—\>*
**\<—⬆️⬆️⬆️(End of section that can be deleted after forking the
template)⬆️⬆️⬆️—\>**

## `templateR`: packageTitle

Expand Down Expand Up @@ -130,19 +117,6 @@ library(templateR)

<hr>

## Contact

### [Neurogenomics Lab](https://www.neurogenomics.co.uk/)

UK Dementia Research Institute
Department of Brain Sciences
Faculty of Medicine
Imperial College London
[GitHub](https://github.com/neurogenomics)
[DockerHub](https://hub.docker.com/orgs/neurogenomicslab)

<br>

## Session Info

<details>
Expand All @@ -151,49 +125,39 @@ Imperial College London
utils::sessionInfo()
```

## R version 4.2.1 (2022-06-23)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur ... 10.16
## R version 4.3.1 (2023-06-16)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Sonoma 14.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
## BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## time zone: Europe/London
## tzcode source: internal
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## loaded via a namespace (and not attached):
## [1] here_1.0.1 rprojroot_2.0.3 digest_0.6.31
## [4] utf8_1.2.3 BiocFileCache_2.6.1 R6_2.5.1
## [7] stats4_4.2.1 RSQLite_2.3.1 evaluate_0.21
## [10] httr_1.4.6 ggplot2_3.4.2 pillar_1.9.0
## [13] yulab.utils_0.0.6 rworkflows_0.99.13 biocViews_1.66.3
## [16] rlang_1.1.1 curl_5.0.0 data.table_1.14.8
## [19] rstudioapi_0.14 whisker_0.4.1 blob_1.2.4
## [22] DT_0.28 RUnit_0.4.32 rmarkdown_2.22
## [25] desc_1.4.2 readr_2.1.4 stringr_1.5.0
## [28] htmlwidgets_1.6.2 dlstats_0.1.7 BiocPkgTools_1.16.1
## [31] igraph_1.5.0.1 RCurl_1.98-1.12 bit_4.0.5
## [34] munsell_0.5.0 compiler_4.2.1 xfun_0.39
## [37] pkgconfig_2.0.3 BiocGenerics_0.44.0 rorcid_0.7.0
## [40] htmltools_0.5.5 tidyselect_1.2.0 tibble_3.2.1
## [43] httpcode_0.3.0 XML_3.99-0.14 fansi_1.0.4
## [46] dplyr_1.1.2 tzdb_0.4.0 dbplyr_2.3.2
## [49] bitops_1.0-7 rappdirs_0.3.3 crul_1.4.0
## [52] grid_4.2.1 RBGL_1.74.0 jsonlite_1.8.4
## [55] gtable_0.3.3 lifecycle_1.0.3 DBI_1.1.3
## [58] magrittr_2.0.3 scales_1.2.1 graph_1.76.0
## [61] cli_3.6.1 stringi_1.7.12 cachem_1.0.8
## [64] renv_0.17.3 fauxpas_0.5.2 xml2_1.3.4
## [67] rvcheck_0.2.1 filelock_1.0.2 generics_0.1.3
## [70] vctrs_0.6.2 gh_1.4.0 RColorBrewer_1.1-3
## [73] tools_4.2.1 bit64_4.0.5 Biobase_2.58.0
## [76] glue_1.6.2 hms_1.1.3 fastmap_1.1.1
## [79] yaml_2.3.7 colorspace_2.1-0 BiocManager_1.30.20
## [82] rvest_1.0.3 memoise_2.0.1 badger_0.2.3
## [85] knitr_1.43
## [1] gtable_0.3.4 jsonlite_1.8.7 renv_1.0.3
## [4] dplyr_1.1.3 compiler_4.3.1 BiocManager_1.30.22
## [7] tidyselect_1.2.0 rvcheck_0.2.1 scales_1.2.1
## [10] yaml_2.3.7 fastmap_1.1.1 here_1.0.1
## [13] ggplot2_3.4.4 R6_2.5.1 generics_0.1.3
## [16] knitr_1.45 yulab.utils_0.1.0 tibble_3.2.1
## [19] desc_1.4.2 dlstats_0.1.7 rprojroot_2.0.3
## [22] munsell_0.5.0 pillar_1.9.0 RColorBrewer_1.1-3
## [25] rlang_1.1.1 utf8_1.2.4 cachem_1.0.8
## [28] badger_0.2.3 xfun_0.41 fs_1.6.3
## [31] memoise_2.0.1.9000 cli_3.6.1 magrittr_2.0.3
## [34] rworkflows_1.0.0 digest_0.6.33 grid_4.3.1
## [37] rstudioapi_0.15.0 lifecycle_1.0.3 vctrs_0.6.4
## [40] data.table_1.14.8 evaluate_0.23 glue_1.6.2
## [43] fansi_1.0.5 colorspace_2.1-0 rmarkdown_2.25
## [46] tools_4.3.1 pkgconfig_2.0.3 htmltools_0.5.6.1

</details>

0 comments on commit b89a974

Please sign in to comment.