Errors and problems on the 'Code examples' page.

[alex4200]

Errors and problems found on the site http://bluebrain.github.io/RTNeuron-3.0/python/gallery.html

1.- DONE In 'Getting Started': Not clear what the 'snapshot' function does: rtneuron.snapshot_to_notebook(rtneuron.engine.views[0])

2.- In 'Getting Started' 7th code block I get a bunch of output that is not clear to me:

   ...: # This function doesn't directly accept a dictionary for the attributes, it has to be
   ...: # an AttributeMap instead.
   ...: rtneuron.display_synapses(
   ...:     6523, attributes=rtneuron.AttributeMap({'color': [1, 1, 0, 1], 'radius': 3}))
   ...: rtneuron.snapshot_to_notebook(rtneuron.engine.views[0])
   ...: 

['/gpfs/bbp.cscs.ch/project/proj3/resources/circuits/ReleaseL2_fixed'] Trying to load blue config: /gpfs/bbp.cscs.ch/project/proj3/resources/circuits/ReleaseL2_fixed... done Error starting Servus client: Can't setup avahi client: Daemon not running Error starting Servus client: Can't setup avahi client: Daemon not running Error starting Servus client: Can't setup avahi client: Daemon not running Error starting Servus client: Can't setup avahi client: Daemon not running Creating 1 neurons 0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----|

---

Adding 1 neurons to the scene 0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----|

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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.

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

    Also it takes quite a long time (>1 minute) which is way too long for an user. It should be mentioned on the 

 **3.- DONE** In 'Getting Started the command
   `view.attributes.help()`
   does not show anything.  

 **4.- DONE** In 'Coloring and Modes', code block 4: Syntax error, one bracket too much:
   `layer_ids.append(simulation.gids('Layer%d' % i)))`

 **5.- DONE** in Meshes and models, fifth code block:
    `scene.addMesh(vertices, indices, colors=colors, attributes=attributes)`
     AttributeError: 'Scene' object has no attribute 'addMesh'
 **6.- DONE** This happens also in 'Getting Started' Cell 12.

 **7.-** In "Simulation playback', block 1:  `rtneuron.display_circuit(brain.test.blue_config, ('MiniColumn_[0-5]', attributes))`
   `AttributeError: 'module' object has no attribute 'test'`

 **8.-**  In "Simulation playback', block 1, first line (`rtneuron.apply_spike_data(rtneuron.simulation, view)`):
   `RuntimeError: IO error reading spike times file: /out.dat`
   Unable to test remainder of the page ...

 **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'`).
      Unable to test remainder of the page ...

[hernando]

So far I have addressed 1, 3, 4, 5, 6 and 9. All the others that have to do with the simulation/circuit config will take longer. I wish there was a public dataset I could use instead.

[alex4200]

@hernando Item 9 does not yet seem to work. I still get the same error..

[hernando]

True, I didn't fully resolve it because blue.test is still not defined. You should be able to load some other configuration, however, I forgot to update the deployment. I'll get back to you when you can test again, should be done in a couple of hours.

[hernando]

You can try again now

[alex4200]

Hi,

I still get the same error when I follow the instructions...

Alex

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From: hernando notifications@github.com Sent: Monday, August 6, 2018 5:04:16 PM To: BlueBrain/RTNeuron Cc: Dietz Alexander; Author Subject: Re: [BlueBrain/RTNeuron] Errors and problems on the 'Code examples' page. (#9)

You can try again now

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/BlueBrain/RTNeuron/issues/9#issuecomment-410739749, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AMI7y0KWdDZgbHgi8d1UWCuPbndtXxHFks5uOFrwgaJpZM4VHonx.

[hernando]

Number 7 should now be resolved.

[hernando]

Sorry, it isn't. I what confused by a build recipe used in CI that contains the test data. The recipe used in deployment doesn't contain it.