Add vignette on how to handle deprecations with $format()

R/model.R

@@ -914,6 +914,9 @@ format <- function(overwrite_file = FALSE,
     out_file <- self$stan_file()
   }
   cat(run_log$stdout, file = out_file, sep = "\n")
+  if (isTRUE(overwrite_file)) {
+    private$stan_code_ <- readLines(self$stan_file())
+  }
 
   invisible(TRUE)
 }

_pkgdown.yml

@@ -71,6 +71,7 @@ articles:
     contents:
       - cmdstanr-internals
       - r-markdown
+      - deprecations
       - profiling
       - articles-online-only/opencl
 

docs/articles/deprecations_files/header-attrs-2.11/header-attrs.js

@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});

docs/articles/deprecations_files/header-attrs-2.9/header-attrs.js

@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});