By default, raise errors on IOPub timeouts

See the following links for details on the issues with IOPub and
nbconvert's ExecutePreprocessor:

- nteract/papermill#426 (comment)
- jupyter/nbconvert#994

README.md

@@ -44,7 +44,8 @@ nbexec --max-depth 3 path/to/directory-of-notebooks
 
 ``` 
 usage: nbexec [-h] [--max-depth MAX_DEPTH] [--timeout TIMEOUT]
-              [--kernel-name KERNEL_NAME] [--quiet] [--stdout]
+              [--allow-iopub-timeout] [--kernel-name KERNEL_NAME] [--quiet]
+              [--stdout]
               notebooks [notebooks ...]
 
 Execute Jupyter notebooks on the command line.
@@ -60,6 +61,9 @@ optional arguments:
                         (default: 1)
   --timeout TIMEOUT     How long to wait, in seconds, for any given notebook
                         cell to before raising an exception. (default: None)
+  --allow-iopub-timeout
+                        Don't raise an error on IOPub timeouts. (default:
+                        False)
   --kernel-name KERNEL_NAME
                         The name of the kernel to use, e.g., 'python3'. If
                         None, nbexec uses the kernel specified in the

nbexec/cli.py

@@ -38,6 +38,12 @@ def parse_args(args):
         help = "How long to wait, in seconds, for any given notebook cell to before raising an exception."
     )
 
+    parser.add_argument(
+        "--allow-iopub-timeout",
+        action = "store_true",
+        help = "Don't raise an error on IOPub timeouts."
+    )
+
     parser.add_argument(
         "--kernel-name",
         default = DEFAULTS["kernel_name"],

nbexec/core.py

@@ -16,7 +16,8 @@
 DEFAULTS = {
     "timeout": None,
     "kernel_name": None,
-    "stdout": False
+    "stdout": False,
+    "allow_iopub_timeout": True,
 }
 
 class NBExecError(Exception):
@@ -42,6 +43,7 @@ def exec_nb(path, **kwargs):
 
     ep = ExecutePreprocessor(
         timeout = settings["timeout"],
+        raise_on_iopub_timeout = not settings["allow_iopub_timeout"],
         kernel_name = kernel_name
     )