Using virtualenv with Chimera

Adding python packages to Chimera is possible and a great way to do this, while preserving the state of the Chimera distribution, is to use ​virtualenv. First, add easy_install add then add the virtualenv package into the Chimera python installation, like so:

$CHIMERA/bin/easy_install virtualenv
$CHIMERA/bin/virtualenv --help

Now that virtualenv is installed in the Chimera python distribution, we can setup any additional custom virtual environments to add python packages into our custom development environment. As a regular user, the following will create a Chimera-specific development environment in ~/src/chimera-virtualenv:

mkdir -p ~/src
cd ~/src
${CHIMERA}/bin/virtualenv --distribute ${HOME}/src/chimera-virtualenv
ls -al ${HOME}/src/chimera-virtualenv/

Once this virtual environment is created, it can be activated and deactivated with the following commands (note how the system prompt changes to indicate that we have entered and left the virtual environment).

source ~/src/chimera-virtualenv/bin/activate
deactivate

VirtualEnv Python Development for Chimera

Now you can start the Chimera build of python and import the chimera module. First activate the virtualenv and confirm that it's using the right python.

source $HOME/src/chimera-virtualenv/bin/activate
cd $HOME/src/chimera-virtualenv
export CHIMERA=$(cd $HOME/src/Chimera64-daily && pwd -P)
#export CHIMERA=$(cd $HOME/src/Chimera64-build && pwd -P)
export LD_LIBRARY_PATH=$CHIMERA/lib
cat > chimeraImportStartup.py <<END
import sys
import os
print os.getenv('CHIMERA')
sys.path.append(os.path.join(os.getenv('CHIMERA'), 'share'))
sys.path.append(os.path.join(os.getenv('CHIMERA'), 'lib'))
import chimera
print chimera.version.version
for s in sys.path:
    print s
END
export PYTHONSTARTUP=./chimeraImportStartup.py
python

An interactive terminal session might look like this:

$ source ~/src/chimera-virtualenv/bin/activate
(chimera-virtualenv)$ which python
/home/dweber/src/chimera-virtualenv/bin/python
(chimera-virtualenv)$ python
Python 2.7 (r27:82500, Aug 23 2010, 21:16:26) 
[GCC 4.2.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> import os
>>> os.getenv('CHIMERA')
'/home/dweber/src/Chimera64-daily'
>>> sys.path.append(os.path.join(os.getenv('CHIMERA'), 'share'))
>>> sys.path.append(os.path.join(os.getenv('CHIMERA'), 'lib'))
>>> import chimera
>>> chimera.version.version
'alpha version 1.5 (build 31253) 2010-08-24 01:28:28 GMT'
>>> for s in sys.path: print s
... 

/home/dweber/src/chimera-virtualenv/lib/python2.7/site-packages/distribute-0.6.10-py2.7.egg
/home/dweber/src/chimera-virtualenv/lib/python2.7/site-packages/pip-0.7.2-py2.7.egg
/home/dweber/src/chimera-virtualenv/lib/python27.zip
/home/dweber/src/chimera-virtualenv/lib/python2.7
/home/dweber/src/chimera-virtualenv/lib/python2.7/plat-linux2
/home/dweber/src/chimera-virtualenv/lib/python2.7/lib-tk
/home/dweber/src/chimera-virtualenv/lib/python2.7/lib-old
/home/dweber/src/chimera-virtualenv/lib/python2.7/lib-dynload
/home/dweber/src/Chimera64-daily/lib/python2.7
/home/dweber/src/Chimera64-daily/lib/python2.7/plat-linux2
/home/dweber/src/Chimera64-daily/lib/python2.7/lib-tk
/home/dweber/src/chimera-virtualenv/lib/python2.7/site-packages
/home/dweber/src/Chimera64-daily/lib/python2.7/site-packages/distribute-0.6.14-py2.7.egg
/home/dweber/src/Chimera64-daily/lib/python2.7/site-packages/virtualenv-1.4.9-py2.7.egg
/home/dweber/src/Chimera64-daily/lib/python2.7/site-packages
/home/dweber/src/Chimera64-daily/lib/python2.7/site-packages/PIL
/home/dweber/src/Chimera64-daily/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg-info
/home/dweber/src/Chimera64-daily/share
/home/dweber/src/Chimera64-daily/lib
>>> 
(chimera-virtualenv)$ deactivate 
$ 

To add additional packages into the virtual environment, try using pip.

$ source ~/src/chimera-virtualenv/bin/activate
(chimera-virtualenv)$ pip --help
Usage: pip COMMAND [OPTIONS]

Options:
  --version             show program's version number and exit
  -h, --help            Show help
  -E DIR, --environment=DIR
                        virtualenv environment to run pip in (either give the
                        interpreter or the environment base directory)
  -s, --enable-site-packages
                        Include site-packages in virtualenv if one is to be
                        created. Ignored if --environment is not used or the
                        virtualenv already exists.
  -v, --verbose         Give more output
  -q, --quiet           Give less output
  --log=FILENAME        Log file where a complete (maximum verbosity) record
                        will be kept
  --proxy=PROXY         Specify a proxy in the form
                        user:passwd@proxy.server:port. Note that the
                        user:password@ is optional and required only if you
                        are behind an authenticated proxy.  If you provide
                        user@proxy.server:port then you will be prompted for a
                        password.
  --timeout=SECONDS, --default-timeout=SECONDS
                        Set the socket timeout (default 15 seconds)

Commands available:
  bundle: Create pybundles (archives containing multiple packages)
  freeze: Output all currently installed packages (exact versions) to stdout
  help: Show available commands
  install: Install packages
  search: Search PyPI
  uninstall: Uninstall packages
  unzip: Unzip individual packages
  zip: Zip individual packages