run tests gh actions.

Author: jeliason

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,55 @@
+# 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]
+  pull_request:
+    branches: [main]
+
+name: tests
+
+jobs:
+  tests:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: ubuntu-latest,   r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          extra-repositories: 'https://mc-stan.org/r-packages/'
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::cmdstanr
+            any::testthat
+            local::.
+
+      - name: Install CmdStan
+        shell: Rscript {0}
+        run: |
+          cmdstanr::check_cmdstan_toolchain(fix = TRUE)
+          cmdstanr::install_cmdstan()
+
+      - name: Run tests
+        run: |
+          testthat::test_dir("tests/testthat", reporter = "summary")
+        shell: Rscript {0}

.github/workflows/render-vignettes.yaml

@@ -10,6 +10,4 @@ inst/stan/**/*.EXE
 *.dll
 *.Rproj
 *_cache/
-*_files/
 .DS_Store
-*.html

.github/workflows/tests.yaml

@@ -1,7 +1,7 @@
 # SHADE: Spatial Hierarchical Asymmetry via Directional Estimation
 
 <!-- badges: start -->
-[![R-CMD-check](https://github.com/jeliason/SHADE/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jeliason/SHADE/actions/workflows/R-CMD-check.yaml)
+[![tests](https://github.com/jeliason/SHADE/actions/workflows/tests.yaml/badge.svg)](https://github.com/jeliason/SHADE/actions/workflows/tests.yaml)
 <!-- badges: end -->
 
 SHADE is an R package for modeling asymmetric spatial associations between cell types in tissue images using a multilevel Bayesian framework.

.gitignore

@@ -1,9 +0,0 @@
-# Settings from /etc/R/Makeconf with "non-portable flag(s):"
-# ‘-Wdate-time’ ‘-Werror=format-security’ ‘-Wformat’ replaced by -Wall -pedantic
-# and without -fdebug-prefix-map=... 
-CFLAGS = -g -O2 -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 $(LTO)
-CXXFLAGS = -g -O2 -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 $(LTO)
-CXX98FLAGS = -g -O2 -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2
-CXX11FLAGS = -g -O2 -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2
-CXX14FLAGS = -g -O2 -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2
-CXX17FLAGS = -g -O2 -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2