Merge pull request #1527 from rstudio/knitr-format-exceptions

knitr eng: format captured exceptions

NEWS.md

@@ -1,13 +1,18 @@
 # reticulate (development version)
 
+- The knitr python engine now formats captured python exceptions to include the 
+  exception type and any exception notes when chunk options 
+  `error = TRUE` is set (reported in #1520, fixed in #1527).
+
 - R external pointers (EXTPTRSXP objects) now round-trip through 
   `py_to_r(r_to_py(x))` successfully.
   (reported in #1511, fixed in #1519, contributed by @llaniewski).
 
 - Fixed issue where `virtualenv_create()` would error on Ubuntu 22.04 when
   using the system python as a base. (#1495, fixed in #1496).
 
-- Fixed issue where `csc_matrix` objects with unsorted indices could not be converted to a dgCMatrix. (related to #727, fixed in #1524, contributed by @rcannood).
+- Fixed issue where `csc_matrix` objects with unsorted indices could not be 
+  converted to a dgCMatrix. (related to #727, fixed in #1524, contributed by @rcannood).
 
 # reticulate 1.34.0
 

R/knitr-engine.R

@@ -252,8 +252,25 @@ eng_python <- function(options) {
     compile_mode <- if (suppress) "exec" else "single"
 
     # run code and capture output
-    captured_stdout <- if (capture_errors)
-      tryCatch(py_compile_eval(snippet, compile_mode), error = identity)
+    captured_stdout <- if (capture_errors) {
+      tryCatch(
+        py_compile_eval(snippet, compile_mode),
+        error = function(e) {
+
+          # if the chunk option is error = FALSE (the default).
+          # we'll need to bail and not evaluate to the next python expression.
+          if (identical(options$error, FALSE))
+            had_error <- TRUE
+
+          # format the exception object
+          etype <- py_get_attr(e, "__class__")
+          traceback <- import("traceback")
+          paste0(traceback$format_exception_only(etype, e),
+                 collapse = "")
+        }
+      )
+
+    }
     else
       py_compile_eval(snippet, compile_mode)
 
@@ -304,10 +321,9 @@ eng_python <- function(options) {
       pending_source_index <- range[2] + 1
 
       # bail if we had an error with 'error=FALSE'
-      if (identical(options$error, FALSE) && inherits(captured, "error")) {
-        had_error <- TRUE
+      if (had_error && identical(options$error, FALSE))
         break
-      }
+
 
     }
   }

tests/testthat/resources/eng-reticulate-example.Rmd

@@ -8,15 +8,20 @@ library(reticulate)
 knitr::knit_engines$set(python = eng_python)
 
 # use specific environment if available
-python <- "~/.virtualenvs/python-3.7.7-venv/bin/python"
-if (file.exists(python))
-  reticulate::use_python(python, required = TRUE)
+# python <- "~/.virtualenvs/python-3.7.7-venv/bin/python"
+# if (file.exists(python))
+#   reticulate::use_python(python, required = TRUE)
 
 # use rlang error handler
 if (requireNamespace("rlang", quietly = TRUE))
   options(error = rlang::entrace)
 ```
 
+```{r}
+reticulate::py_config()
+```
+
+
 Python variables live across chunk boundaries.
 
 ```{python}
@@ -129,6 +134,25 @@ raise RuntimeError("oops!")
 print("This line is still reached.")
 ```
 
+Ensure that Exceptions are formatted w/ the type and notes.
+```{python, error=TRUE}
+class CustomException(Exception):
+  pass
+
+e = CustomException("oops!")
+
+# BaseException.add_note() added in Python 3.11
+import sys
+if sys.version_info >= (3, 11):
+  e.add_note("note 1: extra oopsy oops")
+  e.add_note("note 2: in the future avoid oopsies")
+else:
+  print(sys.version_info)
+
+raise e
+print("This line is still reached.")
+```
+
 Ensure that lines with multiple statements are only run once.
 
 ```{python}