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Thu Aug 3 09:23:59 PDT 2017


Another happy side effect is this would allow e.g. libtbx.bootstrap to exist...

Cheers Graeme

On 19 Jan 2018, at 14:10, Winter, Graeme (DLSLtd,RAL,LSCI) <graeme.winter at diamond.ac.uk<mailto:graeme.winter at diamond.ac.uk>> wrote:

Hi Rob

Interesting question. I have sympathy for your point of view. Some thoughts, from a conversation here in DIALS land…

(i) dxtbx is not only there to support DIALS - cctbx image viewer, bits of iotbx, cctbx.xfel also use it (I think)

(ii) from where I am sat this is a wider question - if I have a look in cctbx_project I see more “non core code" than just dxtbx:

Graemes-MBP-5:cctbx_project graeme$ ls
README.md cootbx fftw3tbx omptbx sphinx
boost_adaptbx crys3d gltbx prime spotfinder
cbflib_adaptbx cudatbx iota rstbx tbxx
cctbx dox iotbx scitbx ucif
chiltbx dox.sphinx libtbx simtbx wxtbx
clipper_adaptbx dxtbx mmtbx site.pyc xfel
cma_es fable msvc9.0_include smtbx

So, in here we have several things which probably do not “belong” in the world view you present below, for example fable, prime, simtbx, xfel etc.

(iii) If we are visiting this stuff, should we be visiting the wider build system which I understand is one of the “blockers” for e.g. pip install cctbx

I appreciate that this is a wider question than can we pull dxtbx out, but is essentially derived…

Best wishes Graeme






On 18 Jan 2018, at 15:56, Dr. Robert Oeffner <rdo20 at cam.ac.uk<mailto:rdo20 at cam.ac.uk>> wrote:

Hi all,

I'm wondering if we could make efforts to refactor code modules in the cctbx_project so as making it have the minimum number of dependencies. This would be helpful to other users of the CCTBX that wishes to develop code on top of it. In the longer term it would also make it easier for us to deploy CCTBX as a Python wheel installer and by implication, spread the gospel of the wonders of the CCTBX.

What is currently complicating this is the inclusion of the dxtbx module within the cctbx_project. It is being used by Dials. So my question is if it would be possible to move this project into the Dials code?

If the dxtbx was just another small module it wouldn't be much of a problem. But the dxtbx depends on the cbflib and HDF5 components. If you want to build CCTBX from sources that's cumbersome. Why? Because CCTBX as deployed from CCI on http://cci.lbl.gov/cctbx_build/ is only built for a few select platforms. Building CCTBX on a different platform from those with bootstrap compels us to also build cbflib and HDF5 from scratch. Although this is not impossible it does increase the entry barrier for other potential users of the CCTBX who wish to incorporate the CCTBX in their programs: If all a user wants is to calculate allowed origins and symmetry sites for a given space group then an alternative to CCTBX might be preferable rather than having to massively expand their project with the seemingly unrelated HDF5 component. In other words, as it stands now the CCTBX is not straightforward for others to adopt.

What do other people think?


Regards,

Rob


--
Robert Oeffner, Ph.D.
Research Associate, The Read Group
Department of Haematology,
Cambridge Institute for Medical Research
University of Cambridge
Cambridge Biomedical Campus
Wellcome Trust/MRC Building
Hills Road
Cambridge CB2 0XY

www.cimr.cam.ac.uk/investigators/read/index.html<http://www.cimr.cam.ac.uk/investigators/read/index.html>
tel: +44(0)1223 763234
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