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@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
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 :)
Can you try again and let me know?
Thanks,
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
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.
>>> 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
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 :)
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.