alleninstitute/swdb_2017

course materials for the 2017 Summer Workshop on the Dynamic Brain

SWDB_2017

This is the repository for the course materials for the 2017 Summer Workshop on the Dynamic Brain.

Support Policy

We are releasing this code as part of the 2017 Summer Workshop on the Dynamic Brain and will only be supporting and developing it for the context of this workshop. The community is welcome to submit issues, but you should not expect an active response outside of the context of the course.

Copyright 2017 Allen Institute

swdb_2017's Issues

biophysical simulation cannot be run more than once in a notebook in aws

something about neuron or modelingsdk is not closing a file in the sim_results directory, so when it is removed, it isn't fully removed and so the shutil.rmdir call falls the second time you start the simulation.

The workaround is to restart the kernel, which will cause the .nfs file to go away and the command clears the directory just fine.

OSErrorTraceback (most recent call last)
<ipython-input-54-99cbe447b962> in <module>()
----> 1 run_sim('config.json')

<ipython-input-53-87e04acd2127> in run_sim(config_file)
     13 def run_sim(config_file):
     14     conf = config.from_json(config_file) # Build a configuration paths
---> 15     io.setup_output_dir(conf)            # Create output directory tree structure
     16 
     17     nrn.load_neuron_modules(conf)        # Load NMODL mechanisms,hoc templates

/opt/conda/envs/py27/lib/python2.7/site-packages/modelingsdk-0.0.4-py2.7.egg/modelingsdk/simulator/bionet/io.pyc in setup_output_dir(conf)
    279 
    280                 if conf["run"]['overwrite_output_dir']==True:
--> 281                     shutil.rmtree(conf["output"]["output_dir"])
    282                     print('Overwriting the output directory %s:' %conf["output"]["output_dir"]) # must print to stdout because the log file is not created yet
    283                 else:

/opt/conda/envs/py27/lib/python2.7/shutil.pyc in rmtree(path, ignore_errors, onerror)
    245             mode = 0
    246         if stat.S_ISDIR(mode):
--> 247             rmtree(fullname, ignore_errors, onerror)
    248         else:
    249             try:

/opt/conda/envs/py27/lib/python2.7/shutil.pyc in rmtree(path, ignore_errors, onerror)
    254         os.rmdir(path)
    255     except os.error:
--> 256         onerror(os.rmdir, path, sys.exc_info())
    257 
    258 

/opt/conda/envs/py27/lib/python2.7/shutil.pyc in rmtree(path, ignore_errors, onerror)
    252                 onerror(os.remove, fullname, sys.exc_info())
    253     try:
--> 254         os.rmdir(path)
    255     except os.error:
    256         onerror(os.rmdir, path, sys.exc_info())

OSError: [Errno 39] Directory not empty: '/home/forrestc/SWDB_2017/DynamicBrain/Modeling/biophysical_notebook/sim_results_001/cellvars'```

Deprecation Warning in Cell Types notebook

The line

ephys_features_df = ctc.get_ephys_features(dataframe=True)
ephys_features_df.head(1)

issues a deprecation warning about the 'dataframe' argument. Is there a new, approved way of doing this?