Leginon

Another bit of feedback:

leginon]# python syscheck.py


Python XML module:
importing xml module...
Traceback (most recent call last):
File "syscheck.py", line 183, in <module>
mystr = xml.__version__
AttributeError: 'module' object has no attribute '__version__'


Then looking inside the xml module that I can import:

@
leginon]# python
Python 2.7.1 |CUSTOM| (r271:86832, Nov 29 2010, 13:51:37)

import xml
dir(xml)

['_MINIMUM_XMLPLUS_VERSION', '__all__', '__builtins__', '__doc__', '__file__', '__name__', '__package__', '__path__']

xml._MINIMUM_XMLPLUS_VERSION

(0, 8, 4)
@

It seems that version was dropped in the XML module in Python 2.7. It is still there in Python 2.6.

Ian

Thanks so much for the feedback Ian! This is really helpful informatation. I'll take a look at each of these, reply with answers to any questions, and update the docs where needed.

I've updated the documentation.

Ian Stokes-Rees wrote:

Here is some feedback on my installation experience so far. I'm now looking at this page:

http://emg.nysbc.org/projects/appion/wiki/Install_Appion_Packages

The first thing it says is:

"The pysetup.py script above did not install the appion package."

However I never ran pysetup.py "above", so either I've missed a step or the documentation here needs to be changed.

We swapped the sections for pysetup.py and setup.py without editing that sentance. You have not missed any steps.

Next, the "setup.py install" part works fine, but I got confused on the next step. Seeing "cd myami" made me think this was similar to the "cd appion" step above, so I did "cd my<TAB>" (like I think many people do), and this resulted in "cd myamiweb". Looking around the directory I then saw "pyami" and thought maybe your instructions had a typo. Only then did I realize that the "pysetup.sh" script was in the current directory which I was already in.

I think the two things that would have helped me would have been to put:

cd /path/to/myami-VERSION

in front of both the "setup.py install" line, and the "pysetup.sh" line.

I have modified the docs to reflect this suggestion.

Things then proceeded fairly smoothly until this step:

http://emg.nysbc.org/projects/appion/wiki/Compile_FindEM

I don't know where to put the findem*.exe binaries. There are no instructions on where to install/copy these. Anywhere? In fact, it looks like the earlier installation step of "--install-scripts" already copied these.

Same issue for ace2

Yes, these were already included in the previous installation steps, so if the tests for FindEM and ace2 work, you do not need to do anything else for these programs. I modified the doc, hopefully that is more clear.

Finally, testing: first part worked fine (EMAN, Matlab, and Chimera errors, as expected), but the 3rd party check script doesn't exist:

myami-2.1.3]# find . | grep check3rdPartyPackages.py

Where can I find this script, or has it changed names in the MyAMI v2.1.3 tarball?

My bad. I added the check3rdPartyPackages.py test script to the code after the 2.1.3 release, so it is not available to you with the code that you have.
If you are having any problems running a 3rd party package you can download the script from here:
http://emg.nysbc.org/projects/appion/repository/changes/trunk/appion/test/check3rdPartyPackages.py

It should tell you if you are missing anything critical for any of the packages to run.

The next several steps proceed pretty well, but once I get here:

http://emg.nysbc.org/projects/appion/wiki/Install_the_MRC_PHP_Extension

I start having problems again. I'm told to go to the "myami/php_mrc" directory. This doesn't exist. Instead, I have two directories:

/myami-2.1.3/programs/php_mrc
/myami-2.1.3/programs/php_mrc-5.3

It is not clear which I should try to install -- I opted for php_mrc, since my assumption is that php_mrc-5.3 is for PHP 5.3 (and I'm using 5.1).

Yes, you are correct to chose /myami-2.1.3/programs/php_mrc. We updated the file structure and forgot to update this bit of documentation.

regarding xml version in syscheck.py:

In recent versions of python, the xml module is part of the standard library, so this may explain why version is not important anymore. Only the version of python is now important. We may have to add an "if" to syscheck.py to only check xml version for python 2.4 and earlier. Or maybe the version of xml is not important anyway, and we can get away with only checking that it will import.
Jim