From 8818b8c546e9dec5c881cc453b91050c0aa4374e Mon Sep 17 00:00:00 2001
From: Jim Thorson <50178738+James-Thorson-NOAA@users.noreply.github.com>
Date: Wed, 23 Aug 2023 20:55:37 -0700
Subject: [PATCH] add testthat CI

---
 .github/.gitignore                 |  1 +
 .github/workflows/R-CMD-check.yaml | 29 +++++++++++++++
 tests/testthat.R                   | 10 ++++++
 tests/testthat/test-platform.R     | 57 ++++++++++++++++++++++++++++++
 4 files changed, 97 insertions(+)
 create mode 100644 .github/.gitignore
 create mode 100644 .github/workflows/R-CMD-check.yaml
 create mode 100644 tests/testthat.R
 create mode 100644 tests/testthat/test-platform.R

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..f4b17a4
--- /dev/null
+++ b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,29 @@
+# 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]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          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
diff --git a/tests/testthat.R b/tests/testthat.R
new file mode 100644
index 0000000..ee84583
--- /dev/null
+++ b/tests/testthat.R
@@ -0,0 +1,10 @@
+
+
+library(testthat)
+library(dsem)
+
+# Run tests
+testthat::test_check("dsem")
+
+# Run from local directory
+# testthat::test_dir( "C:/Users/James.Thorson/Desktop/Git/dsem/tests/testthat/", reporter="check" )
diff --git a/tests/testthat/test-platform.R b/tests/testthat/test-platform.R
new file mode 100644
index 0000000..915cf34
--- /dev/null
+++ b/tests/testthat/test-platform.R
@@ -0,0 +1,57 @@
+
+
+context("Testing cross platform and R version compatibility")
+
+# Eastern Bering Sea pollcok
+test_that("dsem example is working ", {
+  #skip_on_ci()
+  sem = "
+    Profits -> Consumption, 0, a2
+    Profits -> Consumption, -1, a3
+    Priv_wage -> Consumption, 0, a4
+    Gov_wage -> Consumption, 0, a4
+    Consumption <-> Consumption, 0, v1
+    Consumption -> Consumption, -1, ar1
+    Consumption -> Consumption, -2, ar2
+    Profits -> Investment, 0, b2
+    Profits -> Investment, -1, b3
+    Capital_stock -> Investment, -1, b4
+    Investment <-> Investment, 0, v2
+    neg_Gov_wage <-> neg_Gov_wage, 0, v3
+    GNP -> Priv_wage, 0, c2
+    Taxes -> Priv_wage, 0, c2
+    neg_Gov_wage -> Priv_wage, 0, c2
+    GNP -> Priv_wage, -1, c3
+    Taxes -> Priv_wage, -1, c3
+    neg_Gov_wage -> Priv_wage, -1, c3
+    Time -> Priv_wage, 0, c4
+    Priv_wage <-> Priv_wage, 0, v4
+    GNP <-> GNP, 0, v5
+    Profits <-> Profits, 0, v6
+    Capital_stock <-> Capital_stock, 0, v7
+    Taxes <-> Taxes, 0, v8
+    Time <-> Time, 0, v9
+    Gov_wage <-> Gov_wage, 0, v10
+    Gov_expense <-> Gov_expense, 0, v11
+  "
+
+  # Load data
+  data(KleinI, package="AER")
+  Data = as.data.frame(KleinI)
+  Data = cbind( Data, "time" = seq(1,22)-11 )
+  colnames(Data) = sapply( colnames(Data), FUN=switch,
+             "consumption"="Consumption", "invest"="Investment",
+             "cprofits"="Profits", "capital"="Capital_stock", "gwage"="Gov_wage",
+             "pwage"="Priv_wage", "gexpenditure"="Gov_expense", "taxes"="Taxes",
+             "time"="Time", "gnp"="GNP")
+  Z = ts( cbind(Data, "neg_Gov_wage"=-1*Data[,'Gov_wage']) )
+
+  # Fit model
+  fit = dsem( sem=sem, tsdata=Z )
+  # Check objective function
+  expect_equal( as.numeric(fit$opt$obj), 587.4755, tolerance=1e-2 )
+
+  # Convert and plot using phylopath
+  as_fitted_DAG(fit)
+})
+