[cctbxbb] simtbx

Wed May 3 08:28:08 PDT 2017

"simtbx" is the name we are giving to my diffraction image simulation 
codes.  You may or may not of heard of their standalone versions as 
MLFSOM, fastBragg (now nanoBragg), nonBragg and nearBragg.  Nick and I 
thought the capability of creating absolutely realistic diffraction data 
from a completely independent code base would be an excellent way to 
generate test data for cctbx, dials, phenix, and even third-party 
packages.  There is also the idea of fitting a simulation directly to 
diffraction images, which I have had some success doing independently, 
but we hope this will work better under cctbx.  Until recently, all this 
was standalone c code, with home pages here:

http://bl831.als.lbl.gov/~jamesh/mlfsom/
http://bl831.als.lbl.gov/~jamesh/nanoBragg/
http://bl831.als.lbl.gov/~jamesh/nearBragg/
http://bl831.als.lbl.gov/~jamesh/nonBragg/

I have spent the bulk of my time for three months trying to wire these 
codes into the boost/Python framework of cctbx.  I put docstrings into 
every single one of my objects, but since I am new to Python I don't 
know where people look for documentation.

Again, sorry this broke everything.  It's been in there since February 
and I was surprised to find that a new developer here couldn't access 
it.  This is why I've been asking so many questions about tests I should 
perform before checking things in, but apparently it was all for naught.

-James

On 5/3/2017 7:57 AM, Pavel Afonine wrote:
> Same questions here as Markus asked.. What is simtbx? First time hear 
> about it. How cctbx can benefit from it?
> Pavel
>
> On 5/3/17 07:53, markus.gerstel at diamond.ac.uk wrote:
>>
>> Hi Nick,
>>
>> Sorry, outsider perspective here. I don’t know what simtbx does or is 
>> supposed to do.
>>
>> What is the benefit of having code in a repository that, according to 
>> your earlier mail, is explicitly not used in the project?
>>
>> Or more bluntly: We (and ccp4) distribute dials and, as part of it, 
>> the cctbx_project repository.
>>
>> Why should we ship dead code?
>>
>> -Markus
>>
>> *From:*cctbxbb-bounces at phenix-online.org 
>> [mailto:cctbxbb-bounces at phenix-online.org] *On Behalf Of *Nicholas Sauter
>> *Sent:* 03 May 2017 15:52
>> *To:* cctbx mailing list <cctbxbb at phenix-online.org>
>> *Subject:* Re: [cctbxbb] simtbx
>>
>> Markus,
>>
>> We want option c.  simtbx should be in the cctbx_project directory.  
>> No separate git repository.  We need to double check we've gotten all 
>> the files in cctbx_project, then remove them from the separate repo.  
>> James, could you look into this?
>>
>> Nick
>>
>>
>> Nicholas K. Sauter, Ph. D.
>> Senior Scientist, Molecular Biophysics & Integrated Bioimaging Division
>>
>> Lawrence Berkeley National Laboratory
>> 1 Cyclotron Rd., Bldg. 33R0345
>> Berkeley, CA 94720
>> (510) 486-5713
>>
>> On Wed, May 3, 2017 at 7:49 AM, <markus.gerstel at diamond.ac.uk 
>> <mailto:markus.gerstel at diamond.ac.uk>> wrote:
>>
>>     Hi James,
>>
>>     It looks that you now have two separate places where simtbx code
>>     is kept. One is in the simtbx repository, where you fixed the
>>     sign earlier, and the other one is in the cctbx repository, where
>>     you just now fixed it again.
>>
>>     Simtbx repo: https://github.com/dials/simtbx
>>
>>     Simtbx folder in cctbx repo:
>>     https://github.com/cctbx/cctbx_project/tree/master/simtbx
>>
>>     I guess suppose there are three options here:
>>
>>     a.move simtbx into the module directory, add simtbx to the
>>     bootstrap script so it is initialised correctly.
>>
>>     b.leave simtbx inside the cctbx_project directory and repository,
>>     but as its own git repository (using git submodule)
>>
>>     c.leave simtbx inside the cctbx_project directory, delete the
>>     separate git repository
>>
>>     NB: This issue is independent of resolving the dials-dependency
>>     issue.
>>
>>     -Markus
>>
>>     *From:*cctbxbb-bounces at phenix-online.org
>>     <mailto:cctbxbb-bounces at phenix-online.org>
>>     [mailto:cctbxbb-bounces at phenix-online.org
>>     <mailto:cctbxbb-bounces at phenix-online.org>] *On Behalf Of *James
>>     Holton
>>     *Sent:* 03 May 2017 15:40
>>     *To:* Winter, Graeme (DLSLtd,RAL,LSCI)
>>     <Graeme.Winter at Diamond.ac.uk
>>     <mailto:Graeme.Winter at Diamond.ac.uk>>; cctbxbb at phenix-online.org
>>     <mailto:cctbxbb at phenix-online.org>
>>     *Subject:* Re: [cctbxbb] simtbx
>>
>>
>>     Yesterday, Aaron and I were trying to set things up so that
>>     simtbx would be available to people who aren't James Holton. 
>>     It's been checked in and working for over a month now, and only a
>>     few days ago I discovered that a fresh "bootstrap" has a broken
>>     simtbx, despite my "git status" telling me all my files are up to
>>     date.  I asked Aaron and Nick for help with this.
>>
>>       I thought what we did was make cctbx.xfel depends on simtbx,
>>     since fitting simulations to stills is the whole reason for
>>     porting my stuff into python.
>>
>>     I set up simtbx with a constructor that takes a dxtbx detector as
>>     input, but does that make it depend on dials?  I did not expect that.
>>
>>     Sorry, didn't mean to break anything!  Would much appreciate any
>>     help on this.
>>
>>     -James
>>
>>     On 5/3/2017 1:41 AM, Graeme.Winter at Diamond.ac.uk
>>     <mailto:Graeme.Winter at Diamond.ac.uk> wrote:
>>
>>         Hi Folks
>>
>>         We have noticed that simtbx, part of the core cctbx now,
>>         depends on dials
>>
>>         This means if you do not have a dials build your cctbx will
>>         be broken
>>
>>         This is probably not the way we want things?
>>
>>         I thought simtbx was a separate repo?
>>
>>         Cheerio Graeme
>>
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