Merge pull request #17 from ropensci/dev

Dev -> main

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

README.Rmd

@@ -26,6 +26,7 @@ knitr::opts_chunk$set(
 # GLMMcosinor <a href='https://docs.ropensci.org/GLMMcosinor/'><img src='man/figures/logo.png' align="right" height="139" /></a>
 
 <!-- badges: start -->
+[![cranlogs](https://www.r-pkg.org/badges/version/GLMMcosinor)](https://CRAN.R-project.org/package=GLMMcosinor)
 [![R-CMD-check](https://github.com/ropensci/GLMMcosinor/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ropensci/GLMMcosinor/actions/workflows/R-CMD-check.yaml)
 [![Codecov test coverage](https://codecov.io/gh/ropensci/GLMMcosinor/branch/main/graph/badge.svg)](https://app.codecov.io/gh/ropensci/GLMMcosinor?branch=main)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
@@ -64,10 +65,10 @@ is described [here](https://doi.org/10.18637/jss.v070.i05) [@Kristensen2016TMB].
 
 ```{r, include=FALSE}
 source("vignettes/fixtures/methods-table.R")
-flextable::save_as_image(
-  dat,
-  file.path("man", "figures", "methods-table.png")
-)
+# flextable::save_as_image(
+#   dat,
+#   file.path("man", "figures", "methods-table.png")
+# )
 ```
 
 <img src="man/figures/methods-table.png" width="=900px" alt="flextable formats" align="center" /> 

README.md

@@ -5,6 +5,7 @@
 
 <!-- badges: start -->
 
+[![cranlogs](https://www.r-pkg.org/badges/version/GLMMcosinor)](https://CRAN.R-project.org/package=GLMMcosinor)
 [![R-CMD-check](https://github.com/ropensci/GLMMcosinor/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ropensci/GLMMcosinor/actions/workflows/R-CMD-check.yaml)
 [![Codecov test
 coverage](https://codecov.io/gh/ropensci/GLMMcosinor/branch/main/graph/badge.svg)](https://app.codecov.io/gh/ropensci/GLMMcosinor?branch=main)

_pkgdown.yml

@@ -1,5 +1,4 @@
 url: https://docs.ropensci.org/GLMMcosinor/
 template:
   bootstrap: 5
-  params:
-    mathjax: true
+  math-rendering: katex