From 08222b82475c3b0e1fa7d74c2a00632257df628a Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.johnson@arjohnsonau.com>
Date: Wed, 22 Mar 2023 10:38:28 +0200
Subject: [PATCH] Update gitignore and DESCRIPTION, add testing workflow

---
 .Rbuildignore                      |  1 +
 .github/.gitignore                 |  1 +
 .github/workflows/R-CMD-check.yaml | 50 ++++++++++++++++++++++++++++++
 .gitignore                         |  1 -
 DESCRIPTION                        | 11 ++++---
 NAMESPACE                          |  3 +-
 R/bayes4psy-package.R              |  3 +-
 README.md                          |  3 ++
 inst/include/stan_meta_header.hpp  |  1 +
 9 files changed, 67 insertions(+), 7 deletions(-)
 create mode 100644 .github/.gitignore
 create mode 100644 .github/workflows/R-CMD-check.yaml
 create mode 100644 inst/include/stan_meta_header.hpp

diff --git a/.Rbuildignore b/.Rbuildignore
index 6f55499..e206297 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -6,3 +6,4 @@ cran-comments.md
 ^doc$
 ^Meta$
 ^CRAN-RELEASE$
+^\.github$
diff --git a/.github/.gitignore b/.github/.gitignore
new file mode 100644
index 0000000..2d19fc7
--- /dev/null
+++ b/.github/.gitignore
@@ -0,0 +1 @@
+*.html
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
new file mode 100644
index 0000000..600f7ac
--- /dev/null
+++ b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master, develop]
+  pull_request:
+    branches: [main, master, develop]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          error-on: '"error"'
diff --git a/.gitignore b/.gitignore
index 06bacdc..cf4f1c4 100644
--- a/.gitignore
+++ b/.gitignore
@@ -41,6 +41,5 @@ vignettes/*.pdf
 *.o
 *.so
 *.cc
-*.hpp
 doc
 Meta
diff --git a/DESCRIPTION b/DESCRIPTION
index 1e7072d..d4506f7 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -30,8 +30,9 @@ Imports:
     mcmcse (>= 1.4.1),
     scales (>= 1.1.1),
     stats (>= 4.0.0),
-    utils (>= 4.0.0)
-Suggests: 
+    utils (>= 4.0.0),
+    RcppParallel
+Suggests:
     testthat (>= 3.0.0),
     rmarkdown (>= 2.5.0),
     knitr (>= 1.30.0)
@@ -40,10 +41,12 @@ LinkingTo:
     rstan (>= 2.21.0),
     BH (>= 1.72.0.3),
     Rcpp (>= 1.0.5),
-    RcppEigen (>= 0.3.3.7.0)
+    RcppEigen (>= 0.3.3.7.0),
+    RcppParallel
 SystemRequirements: GNU make
 VignetteBuilder: knitr
 NeedsCompilation: yes
-RoxygenNote: 7.2.1
+UseLTO: true
+RoxygenNote: 7.2.3
 URL: https://github.com/bstatcomp/bayes4psy
 BugReports: https://github.com/bstatcomp/bayes4psy/issues
diff --git a/NAMESPACE b/NAMESPACE
index 1d848f0..cf2e3c6 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -32,6 +32,7 @@ import(dplyr)
 import(ggplot2)
 import(methods)
 import(rstan)
-import(rstantools)
+importFrom(RcppParallel,RcppParallelLibs)
 importFrom(rstan,sampling)
+importFrom(rstantools,rstan_config)
 useDynLib(bayes4psy, .registration = TRUE)
diff --git a/R/bayes4psy-package.R b/R/bayes4psy-package.R
index 504881e..3074171 100644
--- a/R/bayes4psy-package.R
+++ b/R/bayes4psy-package.R
@@ -8,7 +8,8 @@
 #' @useDynLib bayes4psy, .registration = TRUE
 #' @import methods
 #' @import Rcpp
-#' @import rstantools
+#' @importFrom rstantools rstan_config
+#' @importFrom RcppParallel RcppParallelLibs
 #' @importFrom rstan sampling
 #'
 #' @references
diff --git a/README.md b/README.md
index 1ac550f..d91309f 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,9 @@
 # bayes4psy—User Friendly Bayesian Data Analysis for Psychology
 
+<!-- badges: start -->
+[![R-CMD-check](https://github.com/bstatcomp/bayes4psy/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/bstatcomp/bayes4psy/actions/workflows/R-CMD-check.yaml)
 [![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/bayes4psy?color=blue)](https://CRAN.R-project.org/package=bayes4psy)[![Downloads](http://cranlogs.r-pkg.org/badges/bayes4psy?color=blue)](https://CRAN.R-project.org/package=bayes4psy)
+<!-- badges: end -->
 
 ## Authors
 
diff --git a/inst/include/stan_meta_header.hpp b/inst/include/stan_meta_header.hpp
new file mode 100644
index 0000000..3b914da
--- /dev/null
+++ b/inst/include/stan_meta_header.hpp
@@ -0,0 +1 @@
+// Insert all #include<foo.hpp> statements here