[Ifeffit] updating iXAFS in place (it ain't pretty)

[Bruce Ravel]

On Monday 30 August 2010 10:11:06 am Bruce Ravel wrote:
> On Saturday 28 August 2010 02:47:11 pm Brandon Reese wrote:
> > I am running iXAFS 2.1 b1, is there any way to update the
> > Athena/Artemis versions, or would I have to an source install?
> 
> That is actually a question I need to know the answer to as well.  In
> fact, our group's post-doc has  the same question, so I plan to look
> into it this week.  (Since I did not make the iXAFS package, I am not
> 100% clear on how it works -- which is actually true of most things on
> a Mac!)
> 
> I believe the answer is yes, but I'll let you know what I know more.
> 
> B

Hi Brandon,

I just managed to update Athena and Artemis in situ on a colleague's
Mac laptop.  It is possible, but it is not pretty.  I will give the
steps below, but BY FAR the better solution would be to say really
nice things to Ken and Jeff so that they will update the iXAFS package
to include the latest versions.

It is certainly true that I have only figured out *a way* of doing
this.  I have certainly not found *the best way* of doing so.  I
should also say that I was sitting next to one of my linux computers
while working on this.  That + a memory stick made step 1 very easy.
I have never used svn on a Mac and cannot advise you about how to
install it or how to get it to work on that platform.

1. To begin, you need to download a copy of the horae package from its
   svn repository.  

     svn export http://cars9.uchicago.edu/svn/horae/trunk horae

   In a terminal window, go into the newly made horae folder and run
   the scripts "mkartemis.PL", "mkathena.PL" and "mkhephaestus.PL".
   This will generate the athena, artmeis, and hephaestus programs and
   place them in the bin folder.  Those are perl scripts and will only
   work if perl works on your computer.

2. Open the copy of the athena program that is in this folder in a
   text editor:
     /Applications/iXAFS/Contents/Resources/bin
   Copy (in the sense of copy in Edit menu) the lines that appear
   between    

     #!/usr/bin/perl

   and the first line containing only hash marks (#).  


3. Copy the three programs from the bin folder into
     /Applications/iXAFS/Contents/Resources/bin
   This will overwrite the old version.

4. Edit each of the three files that you just copied.  Place the lines
   from step 2 after

     #!/usr/bin/perl

   in each of the three files.  Those cryptic lines are absolutely
   essential to making the programs work.  Crazy, but true.

5. Copy all the .pm files from lib/Ifeffit/ folder into this folder:
     /Applications/iXAFS/Contents/Resources/lib/perl5/site_perl/5.8.8/darwin-
thread-multi-2level/Ifeffit/


6. Copy this file:
     http://cars9.uchicago.edu/svn/libperlxray/Absorption/lib/Xray/FluorescenceEXAFS.pm
   into 
     /Applications/iXAFS/Contents/Resources/lib/perl5/site_perl/5.8.8/darwin-
thread-multi-2level/Xray/

7. Edit the file FluorecenceEXAFS.pm that you just installed in a text
   editor (*not* a word processor).  Remove the line that says 

      use Readonly;

   and edit the line that says

      Readonly my $ETOK => 0.2624682917;

   to instead read

      my $ETOK = 0.2624682917;


Having done all those things, my colleague's computer was up to date
and all the programs seemed to work normally.

Obviously, all of that is not for the casual user of my software.
Please remember that I am not your computer administrator and it is
not my responsibility to walk you through all these steps.  Typing up
this email is already more than I actually feel responsible for.

Really ... make nice to Ken and Jeff.  That's a much better solution.
Or, volunteer to help maintain the iXAFS package.  That's the best
solution of them all!


B



-- 

 Bruce Ravel  ------------------------------------ bravel at bnl.gov

 National Institute of Standards and Technology
 Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
 Building 535A
 Upton NY, 11973

 My homepage:    http://xafs.org/BruceRavel
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/