ImportError: cannot import name tools about bioblend

[afgane]

Hi James,
Did you update an existing installation of bioblend or did a previous installation exist on the system? Did you install it into a virtualenv? Maybe try removing any current installation and giving it fresh go inside a virtualenv.
The reason I'm suggesting that is because the most recent code works fine on my OS X with python 2.7.2. I also launched a clean Ubuntu 12.04 instance and installed the library directly from github repo and the import works fine as well (this is with python 2.7.3).
Let us know how it goes.

[jdiggans]

It was installing in a fresh python install on the windows machine - I'll give the virtualenv route a go and let you know. For the sake of completeness, I also get a similar error when trying to import galaxy.libraries:

>>> from bioblend.galaxy import (tools,libraries)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "build\bdist.win-amd64\egg\bioblend\galaxy\__init__.py", line 9, in <module>
ImportError: cannot import name libraries

[effect]

Just want to notice I have the same issue.
I've installed everything on ubuntu with virtualenv (--nosudo option) and still can not run bcbio_nextgen. It fails with ImportError: cannot import name tools.

[jdiggans]

No go with virtualenv - created a clean env, activated it, moved to the git clone location for the bioblend repo and ran:

python setup.py clean
python setup.py install

Installation did not produce any errors and my virtualenv site-packages now has the 'bioblend-0.2.4_dev-py2.7.egg' egg present. Activating the python interpreter again in the virtual env, I still get the error:

PS H:\tmp\venvtest> .\Scripts\activate
(venvtest) PS H:\tmp\venvtest> python
Python 2.7.5 (default, May 15 2013, 22:44:16) [MSC v.1500 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> from bioblend import galaxy
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "build\bdist.win-amd64\egg\bioblend\galaxy\__init__.py", line 9, in <module>
ImportError: cannot import name tools
>>>

Full output of install is below:

(venvtest) PS H:\software\bioblend> python setup.py clean
running clean
(venvtest) PS H:\software\bioblend> python setup.py install
running install
running bdist_egg
running egg_info
writing requirements to bioblend.egg-info\requires.txt
writing bioblend.egg-info\PKG-INFO
writing top-level names to bioblend.egg-info\top_level.txt
writing dependency_links to bioblend.egg-info\dependency_links.txt
reading manifest file 'bioblend.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '*.swp' found anywhere in distribution
warning: no previously-included files matching '.gitignore' found anywhere in distribution
writing manifest file 'bioblend.egg-info\SOURCES.txt'
installing library code to build\bdist.win-amd64\egg
running install_lib
running build_py
creating build\bdist.win-amd64\egg
creating build\bdist.win-amd64\egg\bioblend
copying build\lib\bioblend\__init__.py -> build\bdist.win-amd64\egg\bioblend
copying build\lib\bioblend\config.py -> build\bdist.win-amd64\egg\bioblend
creating build\bdist.win-amd64\egg\bioblend\cloudman
copying build\lib\bioblend\cloudman\__init__.py -> build\bdist.win-amd64\egg\bioblend\cloudman
copying build\lib\bioblend\cloudman\launch.py -> build\bdist.win-amd64\egg\bioblend\cloudman
creating build\bdist.win-amd64\egg\bioblend\galaxy
copying build\lib\bioblend\galaxy\__init__.py -> build\bdist.win-amd64\egg\bioblend\galaxy
copying build\lib\bioblend\galaxy\client.py -> build\bdist.win-amd64\egg\bioblend\galaxy
creating build\bdist.win-amd64\egg\bioblend\galaxy\datasets
copying build\lib\bioblend\galaxy\datasets\__init__.py -> build\bdist.win-amd64\egg\bioblend\galaxy\datasets
creating build\bdist.win-amd64\egg\bioblend\galaxy\histories
copying build\lib\bioblend\galaxy\histories\__init__.py -> build\bdist.win-amd64\egg\bioblend\galaxy\histories
creating build\bdist.win-amd64\egg\bioblend\galaxy\libraries
copying build\lib\bioblend\galaxy\libraries\__init__.py -> build\bdist.win-amd64\egg\bioblend\galaxy\libraries
creating build\bdist.win-amd64\egg\bioblend\galaxy\users
copying build\lib\bioblend\galaxy\users\__init__.py -> build\bdist.win-amd64\egg\bioblend\galaxy\users
creating build\bdist.win-amd64\egg\bioblend\galaxy\genomes
copying build\lib\bioblend\galaxy\genomes\__init__.py -> build\bdist.win-amd64\egg\bioblend\galaxy\genomes
creating build\bdist.win-amd64\egg\bioblend\galaxy\workflows
copying build\lib\bioblend\galaxy\workflows\__init__.py -> build\bdist.win-amd64\egg\bioblend\galaxy\workflows
creating build\bdist.win-amd64\egg\bioblend\util
copying build\lib\bioblend\util\__init__.py -> build\bdist.win-amd64\egg\bioblend\util
byte-compiling build\bdist.win-amd64\egg\bioblend\__init__.py to __init__.pyc
byte-compiling build\bdist.win-amd64\egg\bioblend\config.py to config.pyc
byte-compiling build\bdist.win-amd64\egg\bioblend\cloudman\__init__.py to __init__.pyc
byte-compiling build\bdist.win-amd64\egg\bioblend\cloudman\launch.py to launch.pyc
byte-compiling build\bdist.win-amd64\egg\bioblend\galaxy\__init__.py to __init__.pyc
byte-compiling build\bdist.win-amd64\egg\bioblend\galaxy\client.py to client.pyc
byte-compiling build\bdist.win-amd64\egg\bioblend\galaxy\datasets\__init__.py to __init__.pyc
byte-compiling build\bdist.win-amd64\egg\bioblend\galaxy\histories\__init__.py to __init__.pyc
byte-compiling build\bdist.win-amd64\egg\bioblend\galaxy\libraries\__init__.py to __init__.pyc
byte-compiling build\bdist.win-amd64\egg\bioblend\galaxy\users\__init__.py to __init__.pyc
byte-compiling build\bdist.win-amd64\egg\bioblend\galaxy\genomes\__init__.py to __init__.pyc
byte-compiling build\bdist.win-amd64\egg\bioblend\galaxy\workflows\__init__.py to __init__.pyc
byte-compiling build\bdist.win-amd64\egg\bioblend\util\__init__.py to __init__.pyc
creating build\bdist.win-amd64\egg\EGG-INFO
copying bioblend.egg-info\PKG-INFO -> build\bdist.win-amd64\egg\EGG-INFO
copying bioblend.egg-info\SOURCES.txt -> build\bdist.win-amd64\egg\EGG-INFO
copying bioblend.egg-info\dependency_links.txt -> build\bdist.win-amd64\egg\EGG-INFO
copying bioblend.egg-info\requires.txt -> build\bdist.win-amd64\egg\EGG-INFO
copying bioblend.egg-info\top_level.txt -> build\bdist.win-amd64\egg\EGG-INFO
zip_safe flag not set; analyzing archive contents...
creating 'dist\bioblend-0.2.4_dev-py2.7.egg' and adding 'build\bdist.win-amd64\egg' to it
removing 'build\bdist.win-amd64\egg' (and everything under it)
Processing bioblend-0.2.4_dev-py2.7.egg
Copying bioblend-0.2.4_dev-py2.7.egg to h:\tmp\venvtest\lib\site-packages
Adding bioblend 0.2.4-dev to easy-install.pth file

Installed h:\tmp\venvtest\lib\site-packages\bioblend-0.2.4_dev-py2.7.egg
Processing dependencies for bioblend==0.2.4-dev
Searching for PyYAML==3.10
Best match: PyYAML 3.10
Adding PyYAML 3.10 to easy-install.pth file

Using h:\tmp\venvtest\lib\site-packages
Searching for mock==1.0.1
Best match: mock 1.0.1
Adding mock 1.0.1 to easy-install.pth file

Using h:\tmp\venvtest\lib\site-packages
Searching for nose==1.3.0
Best match: nose 1.3.0
Adding nose 1.3.0 to easy-install.pth file
Installing nosetests-script.py script to H:\tmp\venvtest\Scripts
Installing nosetests.exe script to H:\tmp\venvtest\Scripts
Installing nosetests.exe.manifest script to H:\tmp\venvtest\Scripts
Installing nosetests-2.7-script.py script to H:\tmp\venvtest\Scripts
Installing nosetests-2.7.exe script to H:\tmp\venvtest\Scripts
Installing nosetests-2.7.exe.manifest script to H:\tmp\venvtest\Scripts

Using h:\tmp\venvtest\lib\site-packages
Searching for boto==2.9.5
Best match: boto 2.9.5
Adding boto 2.9.5 to easy-install.pth file

Using h:\tmp\venvtest\lib\site-packages
Searching for simplejson==3.3.0
Best match: simplejson 3.3.0
Adding simplejson 3.3.0 to easy-install.pth file

Using h:\tmp\venvtest\lib\site-packages
Searching for poster==0.8.1
Best match: poster 0.8.1
Adding poster 0.8.1 to easy-install.pth file

Using h:\tmp\venvtest\lib\site-packages
Searching for requests==1.2.3
Best match: requests 1.2.3
Adding requests 1.2.3 to easy-install.pth file

Using h:\tmp\venvtest\lib\site-packages
Finished processing dependencies for bioblend==0.2.4-dev

[jdiggans]

Also note that if I am in the directory where bioblend was built (with the virtualenv active or not), the import statement works just fine:

(venvtest) PS H:\software\bioblend> python
Python 2.7.5 (default, May 15 2013, 22:44:16) [MSC v.1500 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> from bioblend import galaxy
>>>

[chapmanb]

James and Pavel;
Can you try this branch to see if the fix I checked into setup.py resolves the problem for you?

https://github.com/chapmanb/bioblend

Thanks for all the helpful debug information which helped isolate (hopefully) the problem.

Enis, #21 is the fix pull request.

[jdiggans]

Works like a charm - thanks @chapmanb (and to @afgane for writing bioblend!).