Add rworkflows and deprecation warning

.Rbuildignore

@@ -1,2 +1,3 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+.github

.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

.gitignore

@@ -1 +1,2 @@
 inst/doc
+.Rproj.user

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 <yourself@somewhere.net>
-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

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:

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

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 <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