{"action":"created","issue":{"url":"https://api.github.com/repos/robclewley/pydstool/issues/110","labels_url":"https://api.github.com/repos/robclewley/pydstool/issues/110/labels{/name}","comments_url":"https://api.github.com/repos/robclewley/pydstool/issues/110/comments","events_url":"https://api.github.com/repos/robclewley/pydstool/issues/110/events","html_url":"https://github.com/robclewley/pydstool/issues/110","id":90776026,"number":110,"title":"Solvers other than Vode are not working in ipython notebook","user":{"login":"fccoelho","id":140123,"avatar_url":"https://avatars.githubusercontent.com/u/140123?v=3","gravatar_id":"","url":"https://api.github.com/users/fccoelho","html_url":"https://github.com/fccoelho","followers_url":"https://api.github.com/users/fccoelho/followers","following_url":"https://api.github.com/users/fccoelho/following{/other_user}","gists_url":"https://api.github.com/users/fccoelho/gists{/gist_id}","starred_url":"https://api.github.com/users/fccoelho/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fccoelho/subscriptions","organizations_url":"https://api.github.com/users/fccoelho/orgs","repos_url":"https://api.github.com/users/fccoelho/repos","events_url":"https://api.github.com/users/fccoelho/events{/privacy}","received_events_url":"https://api.github.com/users/fccoelho/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-06-24T20:44:31Z","updated_at":"2015-06-24T20:56:56Z","closed_at":null,"body":"I am trying the example from the tutorial (calcium channel) but I will only work with the Vode_ODESystem. If I try with Dopri I get the following error:\r\n\r\n```python\r\nUnsupportedOperation                      Traceback (most recent call last)\r\n<ipython-input-166-62fb45b0f9e8> in <module>()\r\n      1 DSargs.tdomain = [0,30]                         # set the range of integration.\r\n----> 2 ode  = dst.Generator.Dopri_ODEsystem(DSargs)     # an instance of the 'Generator' class.\r\n      3 traj = ode.compute('polarization')              # integrate ODE\r\n      4 pts  = traj.sample(dt=0.1)                      # Data for plotting\r\n      5 \r\n\r\n/usr/local/lib/python3.4/dist-packages/PyDSTool/Generator/Dopri_ODEsystem.py in __init__(self, kw)\r\n    368             print(\"stages using the makeLibSource and compileLib methods.\")\r\n    369         else:\r\n--> 370             self.makeLib()\r\n    371 \r\n    372     @property\r\n\r\n/usr/local/lib/python3.4/dist-packages/PyDSTool/Generator/mixins.py in makeLib(self, libsources, libdirs, include)\r\n    100             self.forceLibRefresh()\r\n    101         self.makeLibSource(include)\r\n--> 102         self.compileLib(libsources, libdirs)\r\n    103 \r\n    104     @property\r\n\r\n/usr/local/lib/python3.4/dist-packages/PyDSTool/Generator/mixins.py in compileLib(self, libsources, libdirs)\r\n     80           precompiled libraries.\r\n     81 \r\n---> 82         self._builder.build(libsources, libdirs, self._compiler)\r\n     83 \r\n     84     def forceLibRefresh(self):\r\n\r\n/usr/local/lib/python3.4/dist-packages/PyDSTool/Generator/mixins.py in build(self, libsources, libdirs, compiler)\r\n    184             libraries=self.libs\r\n    185         )\r\n--> 186         with RedirectStdout(os.path.join(self.tempdir, 'build.log')):\r\n    187             setup(name=self.description,\r\n    188                 author=\"PyDSTool (automatically generated)\",\r\n\r\n/usr/lib/python3.4/contextlib.py in __enter__(self)\r\n     57     def __enter__(self):\r\n     58         try:\r\n---> 59             return next(self.gen)\r\n     60         except StopIteration:\r\n     61             raise RuntimeError(\"generator didn't yield\") from None\r\n\r\n/usr/local/lib/python3.4/dist-packages/PyDSTool/core/context_managers.py in _stdchannel_redirected(stdchannel, dest_filename, mode)\r\n     27             yield iter([None])\r\n     28         else:\r\n---> 29             oldstdchannel = os.dup(stdchannel.fileno())\r\n     30             dest_file = open(dest_filename, mode)\r\n     31             os.dup2(dest_file.fileno(), stdchannel.fileno())\r\n\r\n/usr/local/lib/python3.4/dist-packages/IPython/kernel/zmq/iostream.py in fileno(self)\r\n    203 \r\n    204     def fileno(self):\r\n--> 205         raise UnsupportedOperation(\"IOStream has no fileno.\")\r\n    206 \r\n    207     def write(self, string):\r\n\r\nUnsupportedOperation: IOStream has no fileno.\r\n```"},"comment":{"url":"https://api.github.com/repos/robclewley/pydstool/issues/comments/115010102","html_url":"https://github.com/robclewley/pydstool/issues/110#issuecomment-115010102","issue_url":"https://api.github.com/repos/robclewley/pydstool/issues/110","id":115010102,"user":{"login":"robclewley","id":4868709,"avatar_url":"https://avatars.githubusercontent.com/u/4868709?v=3","gravatar_id":"","url":"https://api.github.com/users/robclewley","html_url":"https://github.com/robclewley","followers_url":"https://api.github.com/users/robclewley/followers","following_url":"https://api.github.com/users/robclewley/following{/other_user}","gists_url":"https://api.github.com/users/robclewley/gists{/gist_id}","starred_url":"https://api.github.com/users/robclewley/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/robclewley/subscriptions","organizations_url":"https://api.github.com/users/robclewley/orgs","repos_url":"https://api.github.com/users/robclewley/repos","events_url":"https://api.github.com/users/robclewley/events{/privacy}","received_events_url":"https://api.github.com/users/robclewley/received_events","type":"User","site_admin":false},"created_at":"2015-06-24T20:56:56Z","updated_at":"2015-06-24T20:56:56Z","body":"Hi, this is a known issue with our way of redirecting output in python 3.4. For now, please just comment out the line \"with RedirectStdout(...\" in mixins.py and re-indent the block accordingly."}}