Adding tests and refactor pkgdown action

Author: gvegayon

.github/workflows/pkgdown.yaml

@@ -11,16 +11,27 @@ on:
 
 name: pkgdown
 
+# Sets permissions of the GITHUB_TOKEN
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+  pull-requests: write
+  actions: read
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
 jobs:
-  pkgdown:
+  build:
     runs-on: ubuntu-latest
-    # Only restrict concurrency for non-PR jobs
-    concurrency:
-      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -39,10 +50,39 @@ jobs:
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
-      - name: Deploy to GitHub pages 🚀
-        if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+      # Upload artifact for GitHub Pages deployment (only for pushes to main/master)
+      - name: Upload Pages artifact
+        if: github.event_name != 'pull_request' && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master')
+        uses: actions/upload-pages-artifact@v3
         with:
-          clean: false
-          branch: gh-pages
-          folder: docs
+          path: docs
+
+      # Upload artifact for PR preview (only for pull requests)
+      - name: Upload PR artifact
+        if: github.event_name == 'pull_request'
+        uses: actions/upload-artifact@v4
+        with:
+          name: pkgdown-site
+          path: docs
+
+      # Post comment with link to artifact on PRs
+      - name: Post artifact link to PR
+        if: github.event_name == 'pull_request'
+        uses: CDCgov/cfa-actions/post-artifact@v1.2.0
+        with:
+          artifact-name: pkgdown-site
+          gh-token: ${{ secrets.GITHUB_TOKEN }}
+          message: 'Thank you for your contribution @${{ github.actor }} :rocket:! The pkgdown site preview is ready for review :point_right: [Download here]({ artifact-url }) :point_left:!'
+
+  # Deployment job - only runs on pushes to main/master
+  deploy:
+    if: github.event_name != 'pull_request' && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master')
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

inst/tinytest/test_defm.R

@@ -12,6 +12,20 @@ init_defm(mymodel)
 
 ans <- defm_mle(mymodel)
 
+# Checking texreg fancy
+expect_stdout({
+  print(texreg_fancy(
+    ans, texreg::screenreg,
+    skip_intercept = TRUE
+    ))
+}, "Model 1")
+
+expect_stdout({
+  print(summary_table(ans))
+  },
+  "pvalues"
+)
+
 # Fitting individual models for each outcome
 ans_alcohol <- glm(
   alcohol ~ Hispanic, data = valentesns,

inst/tinytest/test_sim_defm.R

@@ -8,6 +8,10 @@ id <- cbind(rep(1L:n_id, each = n_T))
 Y <- matrix(0L, nrow = n_T * n_id, ncol = n_Y)
 X <- matrix(rnorm(n_K * n_T * n_id), ncol = n_K)
 
+# ------------------------------------------------------------------------------
+# new_defm
+# ------------------------------------------------------------------------------
+
 expect_error({
   d_model_formula <- new_defm(id = id, Y = Y, X = X, order = 1)
 })
@@ -40,6 +44,10 @@ td_logit_intercept(
 
 init_defm(d_model_formula)
 
+# ------------------------------------------------------------------------------
+# Stats
+# ------------------------------------------------------------------------------
+
 expect_silent({
   Y_stats <- get_stats(d_model_formula)
 })
@@ -57,4 +65,50 @@ expect_stdout(
 )
 
 expect_equal(get_Y_names(d_model_formula), colnames(Y_sim))
-expect_equal(get_X_names(d_model_formula), colnames(X))
+expect_equal(get_X_names(d_model_formula), colnames(X))
+
+# ------------------------------------------------------------------------------
+# Motif census
+# ------------------------------------------------------------------------------
+expect_stdout({
+  print(motif_census(d_model_formula, c(0,1)))
+}, "census for variable")
+
+
+# ------------------------------------------------------------------------------
+# Log odds
+# ------------------------------------------------------------------------------
+expect_silent({
+  lo <- logodds(d_model_formula, c(-1, -.5, .5, 1), i=1, j=1)
+})
+
+
+# ------------------------------------------------------------------------------
+# Counters
+# ------------------------------------------------------------------------------
+expect_stdout({
+  print(get_counters(d_model_formula))
+}, "Counters \\(4\\)")
+
+expect_stdout({
+  print(get_counters(d_model_formula)[1])
+}, "Counter[:]")
+
+
+set_counter_info(
+  counter = get_counters(d_model_formula)[1],
+  new_name = "lame", new_desc = "whatever"
+  )
+
+tmp <- get_counters(d_model_formula)[1] |>
+  as.list()
+
+expect_equal(
+  list(name = "lame", description = "whatever"),
+  tmp[[1]]
+)
+
+# ------------------------------------------------------------------------------
+# Misc
+# ------------------------------------------------------------------------------
+expect_inherits(as.list(get_counters(d_model_formula)), "list")