Upgrade From 2.0.x¶

Download myami 2.1.x source code¶

Download myami (contains Appion and Leginon) using one of the following options:

Option 1: 3.4 version (Current release)¶

• We have switched to git for version control.
  

  git clone -b myami-3.4 https://emg.nysbc.org/git/myami myami
  

  
  Note: If you are installing these files on a microscope Windows PC, you may use Git for Windows to clone the files. See notes on configuration note in Here Check compatibility as newer version does not support Windows XP.

Option 2: beta-release version (Used and updated at NRAMM daily with newest features that may not yet documented)¶

• We have switched to git for version control.
  

  git clone -b myami-beta https://emg.nysbc.org/git/myami myami
  

  
  Note: If you are installing these files on a microscope Windows PC, you may use Git for Windows to clone the files. See notes on configuration note in Here Check compatibility as newer version does not support Windows XP.

Option 3: Development version (For true developer to play with)¶

• We have switched to git for version control recently. trunk and future release branches will be available with git clone
• unstable with latest features

 
This contains features that may still be under development. It is not supported and may not be stable. Use at your own risk.

git clone -b trunk https://your_redmine_username@emg.nysbc.org/git/myami myami

• your_redmine_username is required if you intend and have permission to push changes to our repository. Please ask the development team if you would like to contribute.*

Note: If you are installing these files on a microscope Windows PC, you may use Git for Windows to clone the files. See notes on configuration note in Here Check compatibility as newer version does not support Windows XP.

Install myami 2.1.x packages¶

cd /path/to/myami-VERSION/myami
sudo ./pysetup.sh install

That will install each package, and report any failures. To determine the cause of failure, see the generated log file "pysetup.log".

Packages installed by pysetup.sh¶

Package Path:
pyami
myami_test
sinedon
leginon
pyscope
imageviewer
modules/numextension
modules/radermacher
modules/libcv

alternatively, install a specific package in turn¶

If necessary, you can enter a specific package directory and run the python setup command manually. For example, if pyami failed to install, you can try again like this:

cd pyami
sudo python setup.py install

python-site-package-path: where the installed python packages went:¶

Python installer put the packages you installed into its site-packages directory. This enables all users on the same computer to access them. The easiest way to discover where your installed package is loaded from by python is to load a module from the package using interactive python command lines like this:

Start the python command line from shell:

python

Import a module from the package. Let's try pyami here. All packages installed through the above setup.py script should go to the same place.
At the python prompt (python>) type:

import pyami

If the module is loaded successfully, call the module attribute path (two underscrolls before "path" and two underscrolls after) will return the location of the module it is loaded from

pyami.__path__
['/usr/lib/python2.6/site-packages/pyami']

In this case, /usr/lib/python2.6/site-packages/ is your python-site-package-path. If you go to that directory, you will find all the packages you just installed.

Save this value as an environment variable for use later, for bash:

export PYTHONSITEPKG='/usr/lib/python2.6/site-packages'

or C shell

setenv PYTHONSITEPKG '/usr/lib/python2.6/site-packages'