[cctbxbb] simtbx

Graeme.Winter at diamond.ac.uk Graeme.Winter at diamond.ac.uk
Wed May 3 07:59:00 PDT 2017


HI Markus

I think over this side of the project we are more keen on splitting things up i.e. xia2, dials, i19 modules which could all be considered as “one thing”

Looks like the DIALS-West side approach is to have all things under one roof i.e.

[gw56 at ws133 cctbx_project]$ ls
boost_adaptbx    cma_es   dox.sphinx  iota    prime      site.py     tbxx
cbflib_adaptbx   cootbx   dxtbx       iotbx   README.md  site.pyc    ucif
cctbx            crys3d   fable       libtbx  rstbx      smtbx       wxtbx
chiltbx          cudatbx  fftw3tbx    mmtbx   scitbx     sphinx      xfel
clipper_adaptbx  dox      gltbx       omptbx  simtbx     spotfinder
[gw56 at ws133 cctbx_project]$ cd ../

[gw56 at ws133 modules]$ ls
allsvn           ccp4io            dials_scratch       phenix_regression
annlib           ccp4io_adaptbx    dlstbx              scons
annlib_adaptbx   cctbx_project     eigen               tntbx
bestmx           clipper           gui_resources       xia2
boost            cxi_user          i19                 xia2_regression
bpcx_regression  dials             labelit
cbflib           dials_regression  labelit_regression

so more projects in cctbx_project than in my modules directory…

To CCP4 / DIALS this could be “dead code” but to cctbx.xfel crew this is bread and butter stuff

That said, I can see some argument to bundling fewer things in cctbx_project…

Best wishes Graeme

From: cctbxbb-bounces at phenix-online.org [mailto:cctbxbb-bounces at phenix-online.org] On Behalf Of markus.gerstel at diamond.ac.uk
Sent: 03 May 2017 15:54
To: cctbxbb at phenix-online.org
Subject: Re: [cctbxbb] simtbx

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> [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<mailto: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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