[SDM-SPA] Re: [kepler-dev] RFC new directory structure

[Ilkay Altintas]

For Chad's comments on 4&5:
  I'm not using those files so I aggree.

Ilkay

-----Original Message-----
From: sdm-dev-admin at sdsc.edu [mailto:sdm-dev-admin at sdsc.edu]On Behalf Of
Chad Berkley
Sent: Thursday, March 18, 2004 8:30 AM
To: Xiaowen Xin
Cc: sdm-dev at sdsc.edu; kepler-dev at ecoinformatics.org
Subject: [SDM-SPA] Re: [kepler-dev] RFC new directory structure


Hello,

See my comments below:

Xiaowen Xin wrote:
> Hi,
> 
> David, Ilkay, Zhengang, Dan and I have discussed on the phone and over
> email the last couple of days about the directory hierarchy
> reorganization and have come to a rough consensus.  This will be a long
> email, so please bear with me =)
> 
> The problem basically is that there is currently no clear organization
> of the files in the CVS repository.  Workflows are scattered around the
> lib/ directory for example, and it's not clear, looking at the
> repository, which files relate to SPA and which to one of the other
> projects.
> 
> Here's a pictorial view of how we would like to reorganize the
> repository.  I will be talking mostly about SPA, but the concepts should
> carry over to the other Kepler projects as well.
> 
> - copyright.txt
> - README
> - build.xml
> - bin
>         - runVergil.bat
>         - runVergil.sh
> - build (directory used for compiling the sources)
> - docs
> - lib
>         - jar (directory for all the jars)
>         - dll (directory for all the dlls)
> - src
>         - org
>                 - ecoinformatics
>                 - geon
>                 - sdm
>                         - spa (directory for all the spa-related actors)
> 			- util
> - test
> - workflows
>         - spa (directory for spa workflows)
>         - seek
>         - geon
> 

this seems good to me, but it might be better to move the workflows 
directory under lib.  it's just nicer to have fewer top level directories.

> 
> So all the SPA related actors will be in the org.sdm.spa package. 
> Currently there are some SPA actors in edu.ncsu.sdm, but this doesn't
> make much conceptual sense.  There's no reason to divide up SPA source
> files according to the organization that developed it, since all of SPA
> will be working closely together to create _one_ set of interrelated
> actors.  Zhengang will work on moving the actors from edu.ncsu.sdm to
> org.sdm.spa.  It's better to divide up the source files by project
> rather than by organization because the boundary between organizations
> is artificial and only serves to confuse things.
> 
> Currently, there's a util/ directory in src/.  This isn't really
> consistent with our naming convention so far (i.e. putting source files
> in packages that reflect which project made them).  The argument for
> having a util/ directory has been that we'd like to put useful classes
> in there that can be shared between the projects.  However, this
> argument doesn't make much sense because theoretically, all of our
> actors could be shared between the projects.  So we'd like to move the
> files in util/ to org/sdm/spa/util.  If another project requires the
> functionality of those two classes, then it would have to include the
> org.sdm.spa.util package instead of simply the util package.
> 
> After making these changes, all the SPA source files will be in
> org/sdm/spa, thus making it much easier to distinguish SPA and its
> contribution to Kepler.
> 
> Currently, all the workflows are in lib/ and there are some that are not
> in CVS at all.  We would like create a top-level workflows/ directory to
> store all of the workflows.  spa, seek, and geon would be subdirectories
> under there.  Thus all SPA workflows will be put in workflows/spa/. 
> Similarly, GEON and SEEK should probably do the same with their
> workflows.
> 
> With this directory structure, it would be easy to tell which workflows
> are designed for which project, but we must also remember to check all
> of our workflows into CVS, and update them when/if they break.  Having
> PIW-full.xml, PIW-full_new_matt.xml, PIW-int-ex0.xml, and
> PIW-full_new.xml, as we do right now is just plain confusing!
> 
> Currently the lib/ directory is a mess.  It appears to be the garbage
> bin, where everything is dumped if the author can't find a better
> container for it.  So we propose a series of steps to clean this up.
> 
> 1. There are two dll's in lib/.  There should probably be a subdirectory
> called dll/ under lib/ that contains these dll's.  The person who put
> these there should probably move them ...
> 

yeah, i'll do that.

> 2. demos.htm and ptolemy-index.html should probably be moved out of lib/
> and into a more appropriate folder, probably into src/.

ptolemy-index.html isn't a demo.  it's the startup view for kepler.  it 
gets copied into the ptolemy directory as kepler-index.html.  I think 
it's fine in lib.

> 
> 3. Ilkay will dispose of lib/forBerkeley/ and lib/forSB/ folders or move
> them into the top-level test/ folder since they contain testing material
> and so don't belong in lib/.  Whoever's responsible for
> lib/ecoPipelines/ should probably do the same because that's testing
> material also as I understand it.

the ecoPipelines directory just contains some random seek stuff i was 
working on.  i can put them under the workflows directory, whereever it 
ends up.

> 
> 4. Is everyone ok with our deleting makefile and makefile.lib from
> lib/?  These are also not library files, and we're not using makefiles
> any more.

I have no problem with that.  ilkay or efrat?

> 
> 5. We should move runVergil.bat and runVergil.sh into a top-level bin/
> directory.

they aren't really binary, but sure.  Efrat and Ilkay, are you still 
using these?

> 
> 6. Does anyone know what lib/sample.dat and lib/scew-0.3.1.tar.gz are? 
> Can we delete them?

please do not delete these.  they go with the garp stuff i've been 
working on.  i can move sample.dat into testdata/garp.  scew is in there 
so i had access to the version that I know compiles with the garp cpp code.

> 
> 7. We will delete the lib/soap directory because it's empty, and there's
> already a lib/jar/soap that contains jar files.
> 
> 8. We need to do something about lib/testdata/ because it's not a
> library file.  I personally think it should be moved into the global
> test/ directory.

i personally think it's fine where it is, though it would also be fine 
in a test directory.  the test directory was supposed to be for junit 
tests, but more structure could be created under that as not many junit 
tests have been created yet.

> 
> 9. We will move lib/workflow/ into the top-level workflows/ directory.
> 
> The existence of src/exp/ seems a bit questionable.  It seems to stand
> for "experimental".  Maybe it's time to either make it stable and
> incorporate it into an existing project, or delete it ...

the stuff in exp was was some stuff we were messing around with to 
extend the type system.  it hasn't been used yet but may be in the 
future.  please leave it there.

> 
> Please comment!  If nobody objects to the proposed restructuring here, I
> can do nothing but assume everybody loves it =)  We'd like to get this
> finalized as soon as possible, which would make it easier to create a
> distribution.  Matt will be back next week from travel I believe, and it
> would be wonderful to have some kind of rudimentary installer for him.

Thanks a lot for looking into this.  the messiness of it's been bugging 
me as well.

chad


> 
> Xiaowen
> 
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