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@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@ws133 cctbx_project]$ cd ../

 

[gw56@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: [email protected] [mailto:[email protected]] On Behalf Of [email protected]
Sent: 03 May 2017 15:54
To: [email protected]
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: [email protected] [mailto:[email protected]] On Behalf Of Nicholas Sauter
Sent: 03 May 2017 15:52
To: cctbx mailing list <[email protected]>
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, <[email protected]> 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: [email protected] [mailto:[email protected]] On Behalf Of James Holton
Sent: 03 May 2017 15:40
To: Winter, Graeme (DLSLtd,RAL,LSCI) <[email protected]>; [email protected]
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, [email protected] 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

 

-- 

This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd.
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
 

 

 

-- 

This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd.
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
 


_______________________________________________
cctbxbb mailing list
[email protected]
http://phenix-online.org/mailman/listinfo/cctbxbb

 

 

-- 

This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd.
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom