Merge pull request voila-dashboards#544 from davidbrochart/show_timeout

Show timeout error in cell output

.github/workflows/main.yml

@@ -26,14 +26,12 @@ jobs:
     - name: Add conda to $PATH
       run: echo ::add-path::$CONDA/condabin
 
-    - name: Update conda on Mac
+    - name: Fix permissions on Mac
       if: matrix.os == 'macos-latest'
       run: |
-        # sudo required?
-        sudo conda update -y -n base conda setuptools
-        
-    - name: Update conda on Linux
-      if: matrix.os == 'ubuntu-latest'
+        sudo chmod -R a+rw /usr/local/miniconda
+
+    - name: Update conda
       run: |
         conda update -y -n base conda setuptools
     

tests/app/timeout_test.py

@@ -0,0 +1,20 @@
+import pytest
+
+import os
+
+
+@pytest.fixture
+def voila_notebook(notebook_directory):
+    return os.path.join(notebook_directory, 'sleep.ipynb')
+
+
+@pytest.fixture
+def voila_args_extra():
+    return ['--VoilaExecutePreprocessor.timeout=1', '--KernelManager.shutdown_wait_time=0.1']
+
+
+@pytest.mark.gen_test
+def test_timeout(http_client, base_url):
+    response = yield http_client.fetch(base_url)
+    html_text = response.body.decode('utf-8')
+    assert 'Cell execution timed out' in html_text

tests/notebooks/sleep.ipynb

@@ -0,0 +1,35 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import time\n",
+    "time.sleep(10)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

voila/execute.py

@@ -8,10 +8,7 @@
 #############################################################################
 import collections
 import logging
-try:
-    from time import monotonic  # Py 3
-except ImportError:
-    from time import time as monotonic  # Py 2
+from time import monotonic
 
 from nbconvert.preprocessors import ClearOutputPreprocessor
 from nbconvert.preprocessors.execute import CellExecutionError, ExecutePreprocessor
@@ -21,11 +18,6 @@
 from traitlets import Unicode
 from ipykernel.jsonutil import json_clean
 
-try:
-    TimeoutError  # Py 3
-except NameError:
-    TimeoutError = RuntimeError  # Py 2
-
 
 def strip_code_cell_warnings(cell):
     """Strip any warning outputs and traceback from a code cell."""
@@ -131,6 +123,14 @@ class VoilaExecutePreprocessor(ExecutePreprocessor):
         )
     )
 
+    cell_timeout_instruction = Unicode(
+        'Please run Voila with --VoilaExecutePreprocessor.interrupt_on_timeout=True to continue executing the rest of the notebook.',
+        config=True,
+        help=(
+            'instruction given to user to continue execution on timeout'
+        )
+    )
+
     def __init__(self, **kwargs):
         super(VoilaExecutePreprocessor, self).__init__(**kwargs)
         self.output_hook_stack = collections.defaultdict(list)  # maps to list of hooks, where the last is used
@@ -154,6 +154,10 @@ def preprocess_cell(self, cell, resources, cell_index, store_history=True):
             # TODO: pass store_history as a 5th argument when we can require nbconver >=5.6.1
             # result = super(VoilaExecutePreprocessor, self).preprocess_cell(cell, resources, cell_index, store_history)
             result = super(VoilaExecutePreprocessor, self).preprocess_cell(cell, resources, cell_index)
+        except TimeoutError as e:
+            self.log.error(e)
+            self.show_code_cell_timeout(cell)
+            raise e
         except CellExecutionError as e:
             self.log.error(e)
             result = (cell, resources)
@@ -321,6 +325,18 @@ def run_cell(self, cell, cell_index=0, store_history=False):
 
         return execute_reply, cell.outputs
 
+    def show_code_cell_timeout(self, cell):
+        """Show a timeout error output in a code cell."""
+
+        timeout_message = 'Cell execution timed out, aborting notebook execution. {}'.format(self.cell_timeout_instruction)
+
+        output = {'output_type': 'error',
+                  'ename': 'TimeoutError',
+                  'evalue': 'Timeout error',
+                  'traceback': [timeout_message]}
+
+        cell['outputs'] = [output]
+
 
 def executenb(nb, cwd=None, km=None, **kwargs):
     resources = {}

voila/handler.py

@@ -140,9 +140,16 @@ def _jinja_cell_generator(self, nb, kernel_id):
         nb, resources = ClearOutputPreprocessor().preprocess(nb, {'metadata': {'path': self.cwd}})
         ep = VoilaExecutePreprocessor(config=self.traitlet_config)
 
+        stop_execution = False
         with ep.setup_preprocessor(nb, resources, km=km):
             for cell_idx, cell in enumerate(nb.cells):
-                res = ep.preprocess_cell(cell, resources, cell_idx, store_history=False)
+                if stop_execution:
+                    break
+                try:
+                    res = ep.preprocess_cell(cell, resources, cell_idx, store_history=False)
+                except TimeoutError:
+                    res = (cell, resources)
+                    stop_execution = True
 
                 yield res[0]