fix swi call leak

improve yapi
reformat

packages/python/yap_kernel/CMakeLists.txt

@@ -1,53 +1,53 @@
 
     set (EXTRAS
-      MANIFEST.in
-        YAP_KERNEL.md
-    )
+            MANIFEST.in
+            YAP_KERNEL.md
+            )
 
     set (PYTHON_SOURCES
-    yap_kernel_launcher.py
-    data_kernelspec/kernel.json
-    yap_kernel/__init__.py
-    yap_kernel/__main__.py
-    yap_kernel/_version.py
-    yap_kernel/codeutil.py
-    yap_kernel/connect.py
+            yap_kernel_launcher.py
+            data_kernelspec/kernel.json
+            yap_kernel/__init__.py
+            yap_kernel/__main__.py
+            yap_kernel/_version.py
+            yap_kernel/codeutil.py
+            yap_kernel/connect.py
             yap_kernel/datapub.py
-    yap_kernel/displayhook.py
-    yap_kernel/embed.py
-    yap_kernel/eventloops.py
-    yap_kernel/heartbeat.py
-    yap_kernel/interactiveshell.py
-    yap_kernel/iostream.py
-    yap_kernel/jsonutil.py
-    yap_kernel/kernelapp.py
-    yap_kernel/kernelbase.py
-    yap_kernel/kernelspec.py
-    yap_kernel/log.py
-    yap_kernel/parentpoller.py
-    yap_kernel/pickleutil.py
-    yap_kernel/serialize.py
-    yap_kernel/yapkernel.py
-    yap_kernel/zmqshell.py
-    yap_kernel/comm/__init__.py
-    yap_kernel/comm/comm.py
-    yap_kernel/comm/manager.py
-    yap_kernel/gui/__init__.py
-    yap_kernel/gui/gtk3embed.py
-    yap_kernel/gui/gtkembed.py
-    yap_kernel/inprocess/__init__.py
-    yap_kernel/inprocess/blocking.py
-    yap_kernel/inprocess/channels.py
-    yap_kernel/inprocess/client.py
-    yap_kernel/inprocess/ipkernel.py
-    yap_kernel/inprocess/manager.py
-    yap_kernel/inprocess/socket.py
-    yap_kernel/pylab/__init__.py
-    yap_kernel/pylab/backend_inline.py
-    yap_kernel/pylab/config.py
-      )
+            yap_kernel/displayhook.py
+            yap_kernel/embed.py
+            yap_kernel/eventloops.py
+            yap_kernel/heartbeat.py
+            yap_kernel/interactiveshell.py
+            yap_kernel/iostream.py
+            yap_kernel/jsonutil.py
+            yap_kernel/kernelapp.py
+            yap_kernel/kernelbase.py
+            yap_kernel/kernelspec.py
+            yap_kernel/log.py
+            yap_kernel/parentpoller.py
+            yap_kernel/pickleutil.py
+            yap_kernel/serialize.py
+            yap_kernel/yapkernel.py
+            yap_kernel/zmqshell.py
+            yap_kernel/comm/__init__.py
+            yap_kernel/comm/comm.py
+            yap_kernel/comm/manager.py
+            yap_kernel/gui/__init__.py
+            yap_kernel/gui/gtk3embed.py
+            yap_kernel/gui/gtkembed.py
+            yap_kernel/inprocess/__init__.py
+            yap_kernel/inprocess/blocking.py
+            yap_kernel/inprocess/channels.py
+            yap_kernel/inprocess/client.py
+            yap_kernel/inprocess/ipkernel.py
+            yap_kernel/inprocess/manager.py
+            yap_kernel/inprocess/socket.py
+            yap_kernel/pylab/__init__.py
+            yap_kernel/pylab/backend_inline.py
+            yap_kernel/pylab/config.py
+            )
 
-      configure_file(setup.py.in ${CMAKE_CURRENT_BINARY_DIR}/setup.py)
+    configure_file(setup.py.in ${CMAKE_CURRENT_BINARY_DIR}/setup.py)
 
     file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/yap_kernel/resources)
     file(COPY  yap_kernel DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
@@ -61,12 +61,12 @@
     set(SETUP_PY ${CMAKE_CURRENT_BINARY_DIR}/setup.py)
 
     add_custom_target( YAPKernel ALL
-      COMMAND ${PYTHON_EXECUTABLE}  ${SETUP_PY} sdist
-      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-    )
+            COMMAND ${PYTHON_EXECUTABLE}  ${SETUP_PY} sdist
+            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+            )
 
     install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} -m pip install  --no-index -f dist yap_kernel
     WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})")
 
-#    install(FILES jupyter.yap
-#    DESTINATION ${libpl} )
+    #    install(FILES jupyter.yap
+    #    DESTINATION ${libpl} )

packages/python/yap_kernel/examples/embedding/ipkernel_qtapp.py

@@ -28,6 +28,7 @@ from internal_yapkernel import InternalYAPKernel
 class SimpleWindow(Qt.QWidget, InternalYAPKernel):
 
     def __init__(self, app):
+        # type: (object) -> object
         Qt.QWidget.__init__(self)
         self.app = app
         self.add_widgets()

packages/python/yap_kernel/examples/embedding/ipkernel_wxapp.py

@@ -36,6 +36,7 @@ class MyFrame(wx.Frame, InternalYAPKernel):
     """
 
     def __init__(self, parent, title):
+        # type: (object, object) -> object
         wx.Frame.__init__(self, parent, -1, title,
                           pos=(150, 150), size=(350, 285))
 

packages/python/yap_kernel/setup.py.in

@@ -85,10 +85,6 @@ if 'develop' in sys.argv or any(a.startswith('bdist') for a in sys.argv):
 
 setuptools_args = {}
 install_requires = setuptools_args['install_requires'] = [
-    'ipython>=4.0.0',
-    'traitlets>=4.1.0',
-    'jupyter_client',
-    'tornado>=4.0',
 ]
 
 if any(a.startswith(('bdist', 'build', 'install')) for a in sys.argv):

packages/python/yap_kernel/yap_kernel/comm/comm.py

@@ -48,6 +48,7 @@ class Comm(LoggingConfigurable):
     _closed = Bool(True)
 
     def __init__(self, target_name='', data=None, metadata=None, buffers=None, **kwargs):
+        # type: (object, object, object, object, object) -> object
         if target_name:
             kwargs['target_name'] = target_name
         super(Comm, self).__init__(**kwargs)

packages/python/yap_kernel/yap_kernel/displayhook.py

@@ -18,6 +18,7 @@ class ZMQDisplayHook(object):
     topic = b'execute_result'
 
     def __init__(self, session, pub_socket):
+        # type: (object, object) -> object
         self.session = session
         self.pub_socket = pub_socket
         self.parent_header = {}

packages/python/yap_kernel/yap_kernel/eventloops.py

@@ -138,6 +138,7 @@ def loop_wx(kernel):
     # We make the Frame hidden when we create it in the main app below.
     class TimerFrame(wx.Frame):
         def __init__(self, func):
+            # type: (object) -> object
             wx.Frame.__init__(self, None, -1)
             self.timer = wx.Timer(self)
             # Units for the timer are in milliseconds
@@ -184,6 +185,7 @@ def loop_tk(kernel):
     # For Tkinter, we create a Tk object and call its withdraw method.
     class Timer(object):
         def __init__(self, func):
+            # type: (object) -> object
             self.app = Tk()
             self.app.withdraw()
             self.func = func

packages/python/yap_kernel/yap_kernel/gui/gtk3embed.py

@@ -27,6 +27,7 @@ class GTKEmbed(object):
     """A class to embed a kernel into the GTK main event loop.
     """
     def __init__(self, kernel):
+        # type: (object) -> object
         self.kernel = kernel
         # These two will later store the real gtk functions when we hijack them
         self.gtk_main = None

packages/python/yap_kernel/yap_kernel/gui/gtkembed.py

@@ -25,6 +25,7 @@ class GTKEmbed(object):
     """A class to embed a kernel into the GTK main event loop.
     """
     def __init__(self, kernel):
+        # type: (object) -> object
         self.kernel = kernel
         # These two will later store the real gtk functions when we hijack them
         self.gtk_main = None

packages/python/yap_kernel/yap_kernel/heartbeat.py

@@ -30,6 +30,7 @@ class Heartbeat(Thread):
     "A simple ping-pong style heartbeat that runs in a thread."
 
     def __init__(self, context, addr=None):
+        # type: (object, object) -> object
         if addr is None:
             addr = ('tcp', localhost(), 0)
         Thread.__init__(self)

packages/python/yap_kernel/yap_kernel/inprocess/blocking.py

@@ -27,6 +27,7 @@ from .client import InProcessKernelClient
 class BlockingInProcessChannel(InProcessChannel):
 
     def __init__(self, *args, **kwds):
+        # type: (object, object) -> object
         super(BlockingInProcessChannel, self).__init__(*args, **kwds)
         self._in_queue = Queue()
 

packages/python/yap_kernel/yap_kernel/inprocess/channels.py

@@ -16,6 +16,7 @@ class InProcessChannel(object):
     proxy_methods = []
 
     def __init__(self, client=None):
+        # type: (object) -> object
         super(InProcessChannel, self).__init__()
         self.client = client
         self._is_alive = False
@@ -70,6 +71,7 @@ class InProcessHBChannel(object):
     time_to_dead = 3.0
 
     def __init__(self, client=None):
+        # type: (object) -> object
         super(InProcessHBChannel, self).__init__()
         self.client = client
         self._is_alive = False

packages/python/yap_kernel/yap_kernel/inprocess/ipkernel.py

@@ -70,6 +70,7 @@ class InProcessKernel(YAPKernel):
     stdin_socket = Instance(DummySocket, ())
 
     def __init__(self, **traits):
+        # type: (object) -> object
         super(InProcessKernel, self).__init__(**traits)
 
         self._underlying_iopub_socket.observe(self._io_dispatch, names=['message_sent'])

packages/python/yap_kernel/yap_kernel/interactiveshell.py

@@ -98,6 +98,7 @@ class YAPInteraction:
     """An enhanced, interactive shell for YAP."""
 
     def __init__(self, shell, **kwargs):
+        # type: (object, object) -> object
         try:
             if self.yapeng:
                 return

packages/python/yap_kernel/yap_kernel/iostream.py

@@ -43,6 +43,7 @@ class IOPubThread(object):
     """
 
     def __init__(self, socket, pipe=False):
+        # type: (object, object) -> object
         """Create IOPub thread
 
         Parameters
@@ -220,6 +221,7 @@ class BackgroundSocket(object):
     io_thread = None
     
     def __init__(self, io_thread):
+        # type: (object) -> object
         self.io_thread = io_thread
     
     def __getattr__(self, attr):
@@ -261,6 +263,7 @@ class OutStream(TextIOBase):
     encoding = 'UTF-8'
 
     def __init__(self, session, pub_thread, name, pipe=None):
+        # type: (object, object, object, object) -> object
         if pipe is not None:
             warnings.warn("pipe argument to OutStream is deprecated and ignored",
                 DeprecationWarning)

packages/python/yap_kernel/yap_kernel/kernelbase.py

@@ -134,6 +134,7 @@ class Kernel(SingletonConfigurable):
     control_msg_types = msg_types + ['clear_request', 'abort_request']
 
     def __init__(self, **kwargs):
+        # type: (object) -> object
         super(Kernel, self).__init__(**kwargs)
 
         # Build dict of handlers for message types

packages/python/yap_kernel/yap_kernel/log.py

@@ -10,6 +10,7 @@ class EnginePUBHandler(PUBHandler):
     engine=None
 
     def __init__(self, engine, *args, **kwargs):
+        # type: (object, object, object) -> object
         PUBHandler.__init__(self,*args, **kwargs)
         self.engine = engine
 

packages/python/yap_kernel/yap_kernel/parentpoller.py

@@ -25,6 +25,7 @@ class ParentPollerUnix(Thread):
     """
 
     def __init__(self):
+        # type: () -> object
         super(ParentPollerUnix, self).__init__()
         self.daemon = True
 
@@ -50,6 +51,7 @@ class ParentPollerWindows(Thread):
     """
 
     def __init__(self, interrupt_handle=None, parent_handle=None):
+        # type: (object, object) -> object
         """ Create the poller. At least one of the optional parameters must be
         provided.
 

packages/python/yap_kernel/yap_kernel/pickleutil.py

@@ -127,6 +127,7 @@ def use_cloudpickle():
 
 class CannedObject(object):
     def __init__(self, obj, keys=[], hook=None):
+        # type: (object, object, object) -> object
         """can an object for safe pickling
         
         Parameters
@@ -167,6 +168,7 @@ class CannedObject(object):
 class Reference(CannedObject):
     """object for wrapping a remote reference by name."""
     def __init__(self, name):
+        # type: (object) -> object
         if not isinstance(name, string_types):
             raise TypeError("illegal name: %r"%name)
         self.name = name
@@ -185,6 +187,7 @@ class Reference(CannedObject):
 class CannedCell(CannedObject):
     """Can a closure cell"""
     def __init__(self, cell):
+        # type: (object) -> object
         self.cell_contents = can(cell.cell_contents)
     
     def get_object(self, g=None):
@@ -197,6 +200,7 @@ class CannedCell(CannedObject):
 class CannedFunction(CannedObject):
 
     def __init__(self, f):
+        # type: (object) -> object
         self._check_type(f)
         self.code = f.__code__
         if f.__defaults__:
@@ -239,6 +243,7 @@ class CannedFunction(CannedObject):
 class CannedClass(CannedObject):
 
     def __init__(self, cls):
+        # type: (object) -> object
         self._check_type(cls)
         self.name = cls.__name__
         self.old_style = not isinstance(cls, type)
@@ -263,6 +268,7 @@ class CannedClass(CannedObject):
 
 class CannedArray(CannedObject):
     def __init__(self, obj):
+        # type: (object) -> object
         from numpy import ascontiguousarray
         self.shape = obj.shape
         self.dtype = obj.dtype.descr if obj.dtype.fields else obj.dtype.str
@@ -300,6 +306,7 @@ class CannedBytes(CannedObject):
     wrap = staticmethod(buffer_to_bytes)
 
     def __init__(self, obj):
+        # type: (object) -> object
         self.buffers = [obj]
     
     def get_object(self, g=None):

packages/python/yap_kernel/yap_kernel/tests/test_message_spec.py

@@ -61,6 +61,7 @@ class Reference(HasTraits):
 
 class Version(Unicode):
     def __init__(self, *args, **kwargs):
+        # type: (object, object) -> object
         self.min = kwargs.pop('min', None)
         self.max = kwargs.pop('max', None)
         kwargs['default_value'] = self.min

packages/python/yap_kernel/yap_kernel/yapkernel.py

@@ -35,6 +35,7 @@ class YAPKernel(KernelBase):
     _sys_eval_input = Any()
 
     def __init__(self, **kwargs):
+        # type: (object) -> object
         super(YAPKernel, self).__init__(**kwargs)
 
         # Initialize the InteractiveShell subclass
@@ -376,6 +377,7 @@ class YAPKernel(KernelBase):
 
 class Kernel(YAPKernel):
     def __init__(self, *args, **kwargs):
+        # type: (object, object) -> object
         import warnings
         warnings.warn('Kernel is a deprecated alias of yap_kernel.yapkernel.YAPKernel',
                       DeprecationWarning)