From 81ac5f5c6cbf0a057b47d61774ebb259cd65a6dc Mon Sep 17 00:00:00 2001 From: bschilder Date: Fri, 1 Sep 2023 17:33:28 +0100 Subject: [PATCH] Add rworkflows and deprecation warning --- .Rbuildignore | 1 + .github/workflows/rworkflows.yml | 57 ++++++++++++++++++++++++++++++++ .gitignore | 1 + DESCRIPTION | 45 +++++++++++++++++-------- R/data.r | 3 +- Readme.Rmd | 6 +++- Readme.md | 4 +++ 7 files changed, 101 insertions(+), 16 deletions(-) create mode 100644 .github/workflows/rworkflows.yml diff --git a/.Rbuildignore b/.Rbuildignore index 91114bf..dd2032e 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,2 +1,3 @@ ^.*\.Rproj$ ^\.Rproj\.user$ +.github diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml new file mode 100644 index 0000000..34df233 --- /dev/null +++ b/.github/workflows/rworkflows.yml @@ -0,0 +1,57 @@ +name: rworkflows +'on': + push: + branches: + - master + - main + - devel + - RELEASE_** + pull_request: + branches: + - master + - main + - devel + - RELEASE_** +jobs: + rworkflows: + permissions: + contents: write + runs-on: ${{ matrix.config.os }} + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + container: ${{ matrix.config.cont }} + strategy: + fail-fast: ${{ false }} + matrix: + config: + - os: ubuntu-latest + bioc: devel + r: auto + cont: bioconductor/bioconductor_docker:devel + rspm: https://packagemanager.rstudio.com/cran/__linux__/focal/release + - os: macOS-latest + bioc: release + r: auto + cont: ~ + rspm: ~ + - os: windows-latest + bioc: release + r: auto + cont: ~ + rspm: ~ + steps: + - uses: neurogenomics/rworkflows@master + with: + run_bioccheck: ${{ false }} + run_rcmdcheck: ${{ true }} + as_cran: ${{ true }} + run_vignettes: ${{ true }} + has_testthat: ${{ true }} + run_covr: ${{ true }} + run_pkgdown: ${{ true }} + has_runit: ${{ false }} + has_latex: ${{ false }} + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + run_docker: ${{ false }} + DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }} + runner_os: ${{ runner.os }} + cache_version: cache-v1 diff --git a/.gitignore b/.gitignore index c066a39..8e3a7fd 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,2 @@ inst/doc +.Rproj.user diff --git a/DESCRIPTION b/DESCRIPTION index 5592630..ac8e2c5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,18 +1,35 @@ Package: One2One Type: Package -Title: What the Package Does (Title Case) -Version: 0.1.1 -Author: Who wrote it -Maintainer: The package maintainer -Description: More about what it does (maybe more than one line) - Use four spaces when indenting paragraphs within the Description. -License: What license is it under? +Title: Convert 1:1 Orthologs +Version: 0.99.0 +Authors@R: + c( + person(given = "Nathan", + family = "Skene", + role = c("aut","cre"), + email = "nathan.skene@gmail.com", + comment = c(ORCID = "0000-0002-6807-3180"))) +Description: This package is used to get 1:1 orthologs based on + MGI homology data. +URL: https://github.com/NathanSkene/One2One/ +BugReports: https://github.com/NathanSkene/One2One/issues Encoding: UTF-8 -LazyData: true -Imports: - dplyr, - magrittr -Suggests: knitr, - rmarkdown +Depends: R (>= 4.0) +biocViews: +Imports: + dplyr, + magrittr +Suggests: + rworkflows, + methods, + markdown, + rmarkdown, + remotes, + knitr, + BiocStyle, + testthat (>= 3.0.0), + utils +RoxygenNote: 7.2.3 VignetteBuilder: knitr -RoxygenNote: 7.1.1 +License: GPL-3 +Config/testthat/edition: 3 diff --git a/R/data.r b/R/data.r index 055d1d0..6136e52 100644 --- a/R/data.r +++ b/R/data.r @@ -1,6 +1,7 @@ #' Table of 1:1 Human-->Mouse orthologs #' -#' A dataset containing the MGI and HGNC symbols. This table was generated using this package. +#' A dataset containing the MGI and HGNC symbols. +#' This table was generated using this package. #' #' @source #' The code to prepare the .Rda file file from the marker file is: diff --git a/Readme.Rmd b/Readme.Rmd index 766f663..f01ddf6 100644 --- a/Readme.Rmd +++ b/Readme.Rmd @@ -1,5 +1,5 @@ --- -title: "One2one Orthologs" +title: "One2One Orthologs" author: "Nathan Skene" date: "`r Sys.Date()`" output: rmarkdown::github_document @@ -9,6 +9,10 @@ vignette: > %\VignetteEncoding{UTF-8} --- +# :warning: :warning: +## `One2One` is now deprecated. Please use [`orthogene`](https://github.com/neurogenomics/orthogene) instead. +# :warning: :warning: + This package is used to get 1:1 orthologs based on MGI homology data from http://www.informatics.jax.org/homology.shtml The data is processed within the package but for key species comparisons is also stored in the data diff --git a/Readme.md b/Readme.md index 26b356d..09d46ac 100644 --- a/Readme.md +++ b/Readme.md @@ -3,6 +3,10 @@ One2one Orthologs Nathan Skene 2018-01-17 +# :warning: :warning: +## `One2One` is now deprecated. Please use [`orthogene`](https://github.com/neurogenomics/orthogene) instead. +# :warning: :warning: + This package is used to get 1:1 orthologs based on MGI homology data from The data is processed within the package but for key species comparisons is also stored in the data