Neuronvisio 0.7.0 released

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Michele Mattioni

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Nov 3, 2011, 9:22:18 AM11/3/11
to neuronvisio
Dear all,

I'm very happy to announce the release of Neuronvisio 0.7.0

This release features the contribution of Uri Cohen
(https://github.com/uricohen), which has provided an integration for
Neuronvisio with ModelDB
(http://mattions.github.com/neuronvisio/gettingstarted.html#modeldb-integration).
A whole brand new tab will make easy to navigate the models written
for NEURON on ModelDB, and with one clcik, you will be able to
download the model, extract it, compile it and install it.

You can get the latest release from Pipy
(http://pypi.python.org/pypi/neuronvisio/0.7.0), or just pull the
latest src from master as usual.
(https://github.com/mattions/neuronvisio)

If you have any issues report them to the MailingList, or open one
(https://github.com/mattions/neuronvisio/issues) and point us to it.

Thanks for using Neuronvisio.

Cheers,
Michele.

Mike Vella

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Nov 8, 2011, 9:10:37 AM11/8/11
to neuro...@googlegroups.com
using pip --upgrade didn't work for me, here's the trace:

mike@jarvis:~$ sudo pip install neuronvisio --upgrade
[sudo] password for mike:
Downloading/unpacking neuronvisio
Running setup.py egg_info for package neuronvisio
some tasks could not not be imported.
no previously-included directories found matching 'docs/_build'
Downloading/unpacking distribute (from neuronvisio)
Downloading distribute-0.6.24.tar.gz (620Kb): 620Kb downloaded
Running setup.py egg_info for package distribute
warning: no files found matching 'Makefile' under directory 'docs'
warning: no files found matching 'indexsidebar.html' under directory 'docs'
Installing collected packages: distribute, neuronvisio
Found existing installation: distribute 0.6.24
Uninstalling distribute:
Successfully uninstalled distribute
Running setup.py install for distribute
Before install bootstrap.
Scanning installed packages
Setuptools installation detected at /usr/local/lib/python2.6/dist-packages
Non-egg installation
Removing elements out of the way...
Already patched.
/usr/local/lib/python2.6/dist-packages/setuptools-0.6c11-py2.6.egg-info
already patched.
warning: no files found matching 'Makefile' under directory 'docs'
warning: no files found matching 'indexsidebar.html' under directory 'docs'
Installing easy_install script to /usr/local/bin
Installing easy_install-2.6 script to /usr/local/bin
After install bootstrap.
/usr/local/lib/python2.6/dist-packages/setuptools-0.6c11-py2.6.egg-info
already exists
Found existing installation: neuronvisio 0.5.2
Uninstalling neuronvisio:
Successfully uninstalled neuronvisio
Running setup.py install for neuronvisio
some tasks could not not be imported.
no previously-included directories found matching 'docs/_build'
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/home/mike/build/neuronvisio/setup.py", line 7, in <module>
paver.tasks.main()
File "paver-minilib.zip/paver/tasks.py", line 621, in main
File "paver-minilib.zip/paver/tasks.py", line 604, in _launch_pavement
File "paver-minilib.zip/paver/tasks.py", line 569, in _process_commands
File "paver-minilib.zip/paver/setuputils.py", line 146, in __call__
File "/usr/lib/python2.6/distutils/dist.py", line 995, in run_command
cmd_obj.run()
File "/usr/local/lib/python2.6/dist-packages/setuptools/command/install.py",
line 53, in run
return _install.run(self)
File "/usr/lib/python2.6/distutils/command/install.py", line 615, in run
self.run_command('build')
File "/usr/lib/python2.6/distutils/cmd.py", line 333, in run_command
self.distribution.run_command(command)
File "/usr/lib/python2.6/distutils/dist.py", line 995, in run_command
cmd_obj.run()
File "/usr/lib/python2.6/distutils/command/build.py", line 135, in run
self.run_command(cmd_name)
File "/usr/lib/python2.6/distutils/cmd.py", line 333, in run_command
self.distribution.run_command(command)
File "/usr/lib/python2.6/distutils/dist.py", line 995, in run_command
cmd_obj.run()
File "/usr/lib/python2.6/distutils/command/build_scripts.py",
line 53, in run
self.copy_scripts()
File "/usr/lib/python2.6/distutils/command/build_scripts.py",
line 70, in copy_scripts
if not self.force and not newer(script, outfile):
File "/usr/lib/python2.6/distutils/dep_util.py", line 23, in newer
os.path.abspath(source))
distutils.errors.DistutilsFileError: file
'/home/mike/build/neuronvisio/src/nrnvisio' does not exist
Complete output from command /usr/bin/python -c "import
setuptools; __file__='/home/mike/build/neuronvisio/setup.py';
execfile('/home/mike/build/neuronvisio/setup.py')" install
--single-version-externally-managed --record
/tmp/pip-Rk9O2I-record/install-record.txt:
some tasks could not not be imported.

running install

running build

running build_py

running egg_info

writing requirements to neuronvisio.egg-info/requires.txt

writing neuronvisio.egg-info/PKG-INFO

writing top-level names to neuronvisio.egg-info/top_level.txt

writing dependency_links to neuronvisio.egg-info/dependency_links.txt

writing entry points to neuronvisio.egg-info/entry_points.txt

reading manifest file 'neuronvisio.egg-info/SOURCES.txt'

reading manifest template 'MANIFEST.in'

no previously-included directories found matching 'docs/_build'

writing manifest file 'neuronvisio.egg-info/SOURCES.txt'

running build_scripts

Traceback (most recent call last):

File "<string>", line 1, in <module>

File "/home/mike/build/neuronvisio/setup.py", line 7, in <module>

paver.tasks.main()

File "paver-minilib.zip/paver/tasks.py", line 621, in main

File "paver-minilib.zip/paver/tasks.py", line 604, in _launch_pavement

File "paver-minilib.zip/paver/tasks.py", line 569, in _process_commands

File "paver-minilib.zip/paver/setuputils.py", line 146, in __call__

File "/usr/lib/python2.6/distutils/dist.py", line 995, in run_command

cmd_obj.run()

File "/usr/local/lib/python2.6/dist-packages/setuptools/command/install.py",
line 53, in run

return _install.run(self)

File "/usr/lib/python2.6/distutils/command/install.py", line 615, in run

self.run_command('build')

File "/usr/lib/python2.6/distutils/cmd.py", line 333, in run_command

self.distribution.run_command(command)

File "/usr/lib/python2.6/distutils/dist.py", line 995, in run_command

cmd_obj.run()

File "/usr/lib/python2.6/distutils/command/build.py", line 135, in run

self.run_command(cmd_name)

File "/usr/lib/python2.6/distutils/cmd.py", line 333, in run_command

self.distribution.run_command(command)

File "/usr/lib/python2.6/distutils/dist.py", line 995, in run_command

cmd_obj.run()

File "/usr/lib/python2.6/distutils/command/build_scripts.py", line 53, in run

self.copy_scripts()

File "/usr/lib/python2.6/distutils/command/build_scripts.py", line
70, in copy_scripts

if not self.force and not newer(script, outfile):

File "/usr/lib/python2.6/distutils/dep_util.py", line 23, in newer

os.path.abspath(source))

distutils.errors.DistutilsFileError: file
'/home/mike/build/neuronvisio/src/nrnvisio' does not exist

----------------------------------------
Rolling back uninstall of neuronvisio
Command /usr/bin/python -c "import setuptools;
__file__='/home/mike/build/neuronvisio/setup.py';
execfile('/home/mike/build/neuronvisio/setup.py')" install
--single-version-externally-managed --record
/tmp/pip-Rk9O2I-record/install-record.txt failed with error code 1
Storing complete log in /home/mike/.pip/pip.log

Michele Mattioni

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Nov 8, 2011, 11:08:01 AM11/8/11
to neuro...@googlegroups.com
Hi Mike,

that's because the binary script is called nrnvisio.py instead of nrnvisio ...
I'll fix and I will release a new release ASAP.

Thanks for spotting that :)

Michele Mattioni

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Nov 8, 2011, 11:16:14 AM11/8/11
to neuro...@googlegroups.com
I've released the 0.7.1 bugfix and uploaded the new package on PiPy.

Can you try again and let me know?

Thanks,
Michele.

Mike Vella

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Nov 8, 2011, 11:35:51 AM11/8/11
to neuro...@googlegroups.com
Hey Michele,

I'm still getting the same problem - I'm using neuronvisio 0.5.2,
could that be the problem?

Mike

Here is the trace I'm getting, think it's identical to the one I posted earlier:

mike@jarvis:~$ sudo pip install neuronvisio --upgrade

/tmp/pip-D2I0vr-record/install-record.txt:

running install

running build

running build_py

running egg_info

writing requirements to neuronvisio.egg-info/requires.txt

writing neuronvisio.egg-info/PKG-INFO

writing dependency_links to neuronvisio.egg-info/dependency_links.txt

reading manifest file 'neuronvisio.egg-info/SOURCES.txt'

reading manifest template 'MANIFEST.in'

writing manifest file 'neuronvisio.egg-info/SOURCES.txt'

running build_scripts

paver.tasks.main()

cmd_obj.run()

return _install.run(self)

self.run_command('build')

self.distribution.run_command(command)

cmd_obj.run()

self.run_command(cmd_name)

self.distribution.run_command(command)

cmd_obj.run()

self.copy_scripts()

os.path.abspath(source))

/tmp/pip-D2I0vr-record/install-record.txt failed with error code 1


Storing complete log in /home/mike/.pip/pip.log

Michele Mattioni

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Nov 8, 2011, 11:58:13 AM11/8/11
to neuro...@googlegroups.com
Hey Mike,

I've tried the latest version on a virtualenvs, and it works here.

It seems pip is not downloading the latest version.
Try to uninstall the old 0.5.2 and install the 0.7.1

pip uninstall neuronvisio

and then

pip install neuronvisio


the first lines should be:

Downloading/unpacking neuronvisio
Downloading neuronvisio-0.7.1.tar.gz (2.6Mb): 2.6Mb downloaded
...

HIH,
Michele.

Mike Vella

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Nov 8, 2011, 12:29:02 PM11/8/11
to neuro...@googlegroups.com
That worked, but now neuronvisio is broken, here's what I get:

>>> from neuronvisio.controls import Controls
NEURON -- Release 7.1 (359:7f113b76a94b) 2009-10-26
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008
See http://www.neuron.yale.edu/credits.html

WARNING neuronvisio.controls 57 You must use the Qt4 backend to be
able to use Neuronvisio.
Check your backend in ~/.matplotlib/matplotlibrc and set it to Qt4Agg


Traceback (most recent call last):

File "<stdin>", line 1, in <module>
File "/usr/local/lib/python2.6/dist-packages/neuronvisio/controls.py",
line 70, in <module>
from modeldb.ModelDB import Models
ImportError: No module named modeldb.ModelDB

Michele Mattioni

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Nov 8, 2011, 12:53:50 PM11/8/11
to neuro...@googlegroups.com
Ok,

Paver was not picking up the new module. I had too add it to the pavement.
https://github.com/mattions/neuronvisio/commit/38ed6c25c9e267f0d964857d8ff62ee94e890a91

I've released 0.7.2.

Hopefully we have fixed all the packaging problem.

P.S.: Big thanks for testing this :)

Mike Vella

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Nov 8, 2011, 6:39:40 PM11/8/11
to neuro...@googlegroups.com
That worked!

As a side-note: For some reason after pip uninstall neuronvisio you
still have to do pip install --upgrade, if you just do pip install it
says

Requirement already satisfied (use --upgrade to upgrade): neuronvisio
in /usr/local/lib/python2.6/dist-packages
Requirement already satisfied (use --upgrade to upgrade): distribute
in /usr/local/lib/python2.6/dist-packages (from neuronvisio)
Cleaning up...

I'm not sure why that is.

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