{"action":"created","issue":{"url":"https://api.github.com/repos/BlueBrain/RTNeuron/issues/9","repository_url":"https://api.github.com/repos/BlueBrain/RTNeuron","labels_url":"https://api.github.com/repos/BlueBrain/RTNeuron/issues/9/labels{/name}","comments_url":"https://api.github.com/repos/BlueBrain/RTNeuron/issues/9/comments","events_url":"https://api.github.com/repos/BlueBrain/RTNeuron/issues/9/events","html_url":"https://github.com/BlueBrain/RTNeuron/issues/9","id":339432738,"node_id":"MDU6SXNzdWUzMzk0MzI3Mzg=","number":9,"title":"Errors and problems on the 'Code examples' page.","user":{"login":"alex4200","id":12729291,"node_id":"MDQ6VXNlcjEyNzI5Mjkx","avatar_url":"https://avatars3.githubusercontent.com/u/12729291?v=4","gravatar_id":"","url":"https://api.github.com/users/alex4200","html_url":"https://github.com/alex4200","followers_url":"https://api.github.com/users/alex4200/followers","following_url":"https://api.github.com/users/alex4200/following{/other_user}","gists_url":"https://api.github.com/users/alex4200/gists{/gist_id}","starred_url":"https://api.github.com/users/alex4200/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/alex4200/subscriptions","organizations_url":"https://api.github.com/users/alex4200/orgs","repos_url":"https://api.github.com/users/alex4200/repos","events_url":"https://api.github.com/users/alex4200/events{/privacy}","received_events_url":"https://api.github.com/users/alex4200/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2018-07-09T12:41:05Z","updated_at":"2018-09-28T12:38:41Z","closed_at":null,"author_association":"NONE","body":"Errors and problems found on the site http://bluebrain.github.io/RTNeuron-3.0/python/gallery.html\r\n\r\n\r\n **1.- DONE**  In 'Getting Started': Not clear what the 'snapshot' function does:\r\n  `rtneuron.snapshot_to_notebook(rtneuron.engine.views[0])`\r\n\r\n **2.-** In 'Getting Started' 7th code block I get a bunch of output that is not clear to me:\r\n    ````In [5]: rtneuron.display_circuit(blueconfig, 6523)\r\n   ...: # This function doesn't directly accept a dictionary for the attributes, it has to be\r\n   ...: # an AttributeMap instead.\r\n   ...: rtneuron.display_synapses(\r\n   ...:     6523, attributes=rtneuron.AttributeMap({'color': [1, 1, 0, 1], 'radius': 3}))\r\n   ...: rtneuron.snapshot_to_notebook(rtneuron.engine.views[0])\r\n   ...: \r\n```\r\n['/gpfs/bbp.cscs.ch/project/proj3/resources/circuits/ReleaseL2_fixed']\r\nTrying to load blue config: /gpfs/bbp.cscs.ch/project/proj3/resources/circuits/ReleaseL2_fixed... done\r\nError starting Servus client: Can't setup avahi client: Daemon not running\r\nError starting Servus client: Can't setup avahi client: Daemon not running\r\nError starting Servus client: Can't setup avahi client: Daemon not running\r\nError starting Servus client: Can't setup avahi client: Daemon not running\r\nCreating 1 neurons\r\n0%   10   20   30   40   50   60   70   80   90   100%\r\n|----|----|----|----|----|----|----|----|----|----|\r\n***************************************************\r\nAdding 1 neurons to the scene\r\n0%   10   20   30   40   50   60   70   80   90   100%\r\n|----|----|----|----|----|----|----|----|----|----|\r\n***************************************************\r\n    1533 Only unmerged synapse files found for /gpfs/bbp.cscs.ch/release/l2/2012.07.23/circuit/O1/merged_circuit/ncsFunctionalAllRecipePathways/nrn_positions.h5; consider using merged files for better performance.\r\n 11444 No merged file found in \"/gpfs/bbp.cscs.ch/release/l2/2012.07.23/circuit/O1/merged_circuit/ncsFunctionalAllRecipePathways\" to build lookup index; loading data will be very slow\r\n```\r\n    Also it takes quite a long time (>1 minute) which is way too long for an user. It should be mentioned on the \r\n\r\n **3.- DONE** In 'Getting Started the command\r\n   `view.attributes.help()`\r\n   does not show anything.  \r\n\r\n **4.- DONE** In 'Coloring and Modes', code block 4: Syntax error, one bracket too much:\r\n   `layer_ids.append(simulation.gids('Layer%d' % i)))`\r\n   \r\n\r\n **5.- DONE** in Meshes and models, fifth code block:\r\n    `scene.addMesh(vertices, indices, colors=colors, attributes=attributes)`\r\n     AttributeError: 'Scene' object has no attribute 'addMesh'\r\n **6.- DONE** This happens also in 'Getting Started' Cell 12.\r\n\r\n **7.- DONE** In \"Simulation playback', block 1:  `rtneuron.display_circuit(brain.test.blue_config, ('MiniColumn_[0-5]', attributes))`\r\n   `AttributeError: 'module' object has no attribute 'test'`\r\n\r\n\r\n **8.-**  In \"Simulation playback', block 1, first line (`rtneuron.apply_spike_data(rtneuron.simulation, view)`):\r\n   `RuntimeError: IO error reading spike times file: /out.dat`\r\n   Unable to test remainder of the page ...\r\n\r\n **9.-** In 'Synaptic afferent projections': `blue.test` again not defined. Also unable to load the `blueconfig` defined in other pages (Error: `AttributeError: 'exceptions.RuntimeError' object has no attribute 'msg'`).\r\n      Unable to test remainder of the page ..."},"comment":{"url":"https://api.github.com/repos/BlueBrain/RTNeuron/issues/comments/425422343","html_url":"https://github.com/BlueBrain/RTNeuron/issues/9#issuecomment-425422343","issue_url":"https://api.github.com/repos/BlueBrain/RTNeuron/issues/9","id":425422343,"node_id":"MDEyOklzc3VlQ29tbWVudDQyNTQyMjM0Mw==","user":{"login":"hernando","id":791427,"node_id":"MDQ6VXNlcjc5MTQyNw==","avatar_url":"https://avatars3.githubusercontent.com/u/791427?v=4","gravatar_id":"","url":"https://api.github.com/users/hernando","html_url":"https://github.com/hernando","followers_url":"https://api.github.com/users/hernando/followers","following_url":"https://api.github.com/users/hernando/following{/other_user}","gists_url":"https://api.github.com/users/hernando/gists{/gist_id}","starred_url":"https://api.github.com/users/hernando/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hernando/subscriptions","organizations_url":"https://api.github.com/users/hernando/orgs","repos_url":"https://api.github.com/users/hernando/repos","events_url":"https://api.github.com/users/hernando/events{/privacy}","received_events_url":"https://api.github.com/users/hernando/received_events","type":"User","site_admin":false},"created_at":"2018-09-28T12:38:41Z","updated_at":"2018-09-28T12:38:41Z","author_association":"COLLABORATOR","body":"Number should now be resolved."}}
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