added option jupyter_timeout for the first code chunk in a session (#30)

CHANGELOG.md

@@ -1,7 +1,8 @@
 # Change Log
 
-## v0.5.0 (2020-05-??)
+## v0.5.0 (dev)
 
+* Added option `jupyter_timeout` for the first code chunk in a session (#30).
 * Fixed Pandoc 2.8+ compatibility by using `-raw_attribute` in intermediate
   Markdown.  Code output in raw format (interpreted as Markdown) is no longer
   lost when converting to document formats other than Markdown (#26).

README.md

@@ -305,6 +305,9 @@ session is in use).
   kernel.  Except when otherwise specified, Jupyter kernels should be usable
   just like the built-in code execution system.
 
+* `jupyter_timeout`={int} — Jupyter kernel timeout per code chunk in seconds.
+  The default is 60.
+
 
 #### Execution
 

codebraid/codeprocessors/base.py

@@ -137,6 +137,7 @@ def __init__(self, session_key):
         self.lang_def = None
         self.executable = None
         self.jupyter_kernel = None
+        self.jupyter_timeout = None
 
         self.code_options = None
         self.code_chunks = []
@@ -170,6 +171,7 @@ def append(self, code_chunk):
             jupyter_kernel = code_chunk.options['first_chunk_options'].get('jupyter_kernel')
             if jupyter_kernel is not None:
                 self.jupyter_kernel = jupyter_kernel
+                self.jupyter_timeout = code_chunk.options['first_chunk_options'].get('jupyter_timeout')
             else:
                 self.lang_def = self.code_processor.language_definitions[self.lang]
                 self.executable = code_chunk.options['first_chunk_options'].get('executable')
@@ -1081,7 +1083,7 @@ def _run_jupyter(self, session):
 
         # https://jupyter-client.readthedocs.io/en/stable/api/client.html
         # https://jupyter-client.readthedocs.io/en/stable/messaging.html#messages-on-the-iopub-pub-sub-channel
-        kernel_name = session.code_chunks[0].options['first_chunk_options']['jupyter_kernel']
+        kernel_name = session.jupyter_kernel
         try:
             import jupyter_client
         except ImportError:
@@ -1130,7 +1132,7 @@ def shutdown_kernel():
                 external_file_mime_types = set(['image/png', 'image/jpeg', 'image/svg+xml', 'application/pdf'])
                 while True:
                     try:
-                        msg = jupyter_client.iopub_channel.get_msg(timeout=60)
+                        msg = jupyter_client.iopub_channel.get_msg(timeout=session.jupyter_timeout or 60)
                     except queue.Empty:
                         chunk_runtime_source_error_dict[cc.session_output_index].append('Jupyter kernel "{0}" timed out during execution"'.format(kernel_name))
                         errors = True

codebraid/converters/base.py

@@ -319,7 +319,8 @@ def finalize_after_copy(self):
                             for kw in ('first_number', 'line_numbers', 'rewrap_lines', 'rewrap_width', 'expand_tabs', 'tab_size')])
     _first_chunk_execute_keywords = set(['executable', 'jupyter_kernel'])
     _first_chunk_save_keywords = set(['save', 'save_as'])
-    _first_chunk_keywords = _first_chunk_execute_keywords | _first_chunk_save_keywords
+    _first_chunk_other_keywords = set(['jupyter_timeout'])
+    _first_chunk_keywords = _first_chunk_execute_keywords | _first_chunk_save_keywords | _first_chunk_other_keywords
 
     keywords = _base_keywords | _layout_keywords | _first_chunk_keywords
 
@@ -420,8 +421,15 @@ def _option_first_chunk_string_error(self, key, value):
             else:
                 first_chunk_options[key] = value
 
+    def _option_first_chunk_int_warning(self, key, value):
+        if not isinstance(value, int):
+            self.code_chunk.source_warnings.append('Invalid "{0}" value "{1}"'.format(key, value))
+        else:
+            self['first_chunk_options'][key] = value
+
     _option_executable = _option_first_chunk_string_error
     _option_jupyter_kernel = _option_first_chunk_string_error
+    _option_jupyter_timeout = _option_first_chunk_int_warning
     _option_save = _option_first_chunk_bool_error
     _option_save_as = _option_first_chunk_string_error
 

codebraid/converters/pandoc.py

@@ -183,6 +183,7 @@ def keyval_namespace(code_chunk, options, key, value):
                                     **expand_tabs,
                                     **first_number,
                                     **include,
+                                    'jupyter_timeout': keyval_int,
                                     **line_anchors,
                                     **line_numbers,
                                     'name': keyval_generic,

codebraid/version.py

@@ -1,4 +1,4 @@
 # -*- coding: utf-8 -*-
 
 from .fmtversion import get_version_plus_info
-__version__, __version_info__ = get_version_plus_info(0, 5, 0, 'dev', 3)
+__version__, __version_info__ = get_version_plus_info(0, 5, 0, 'dev', 4)