Complete Minimal CellBlender about cellblender

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I started working on this Friday, and I can run the simple cube intro tutorial 
totally from within Blender.

It generates both the viz and rxn files (very simple versions), and it runs 
mcell with a "hard-coded" path after it exports the MDL files.

So there's a bit more work to get it operating more properly.

Original comment by [email protected] on 11 Mar 2013 at 7:51

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It looks like Jacob's recent changes supersede mine ... and I suspect he did a 
much better job.

Note that this version was created as a local git branch named 
"minimal_full_blender_interface" and it had not been pushed to github at the 
time of Jacob's changes.

Original comment by [email protected] on 13 Mar 2013 at 1:05

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Your version exports reaction and visualization data output, which both my 
branch and the master branch are currently lacking. You could still push your 
branch, and hopefully we could merge our changes together without too much 
trouble. What do you think?

Original comment by [email protected] on 13 Mar 2013 at 3:52

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I'm in the process of merging our two branches together.

Original comment by [email protected] on 14 Mar 2013 at 5:12

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Thanks Jacob!!!

Please post when they're merged so I can try it out!!!

Original comment by [email protected] on 14 Mar 2013 at 8:56

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Sorry for the delay. I was almost done when I posted that message this morning, 
and then a million little things came up to stop me from finishing it. Anyway, 
I merged it into a new branch called combine_runner_viz_rxn_output (my branch 
names are a mouthful apparently). It was actually pretty painless. I cut out 
what I thought were debug print statements in case we merge this into the 
master branch soon. If you want/need them for any reason, just add them back.

Original comment by [email protected] on 14 Mar 2013 at 10:24

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I've had trouble getting the merged version to work, so I've continued on with 
the "minimal_full_blender_interface" branch. Maybe we can merge them early next 
week.

I've added an MCell path setting mechanism (the earlier versions were 
hard-coded to my own path as mentioned in the first comment). But there are 
still some open questions about what it means to set a "Project Directory".

Original comment by [email protected] on 16 Mar 2013 at 4:17

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What exactly isn't working? Does the Run Simulation panel not show up? Do you 
get an error? The changes to the interface can be seen in the attached image.

Original comment by [email protected] on 21 Mar 2013 at 1:40

Attachments:

• export_and_run2.png

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I updated the Visualization Output Settings panel so that the user can select 
which molecules are visualized and over what frames. I also started doing some 
similar work on the Reaction Output Settings panel and should hopefully be 
pushing that shortly.

Original comment by [email protected] on 25 Mar 2013 at 6:33

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It looks like the recent changes have been merged and it seems to be functional.

But the mcell executable path doesn't seem to be remembered between runs.

Also, we still don't really have a good definition of which paths are supposed 
to follow which settings. For example, when I change the project path, it 
doesn't seem to update the viz path (and possibly other paths).

Having said that, I think this task is completed. I think we have a working 
version of CellBlender that can run minimal simulations without leaving 
Blender. So I suggest that we close this task and create new tasks for 
additional features/fixes (like saving the mcell path in the .blend file and 
defining path policies in general).

Original comment by [email protected] on 28 Mar 2013 at 6:04

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I agree. There are definitely other features to add and bugs to fix, but we at 
least fulfill the original purpose of this issue:

"This task is intended to offer just enough support for simple projects, but 
hand-editing of MDL may still be required to take advantage of more advanced 
MCell features."

I'm marking this as "Done" with the understanding that new features and 
bug-fixes will become new issues.

Original comment by [email protected] on 28 Mar 2013 at 9:56

• Changed state: Done