[cctbxbb] simtbx

Nicholas Sauter nksauter at lbl.gov
Wed May 3 07:57:56 PDT 2017


Markus,

This is an old argument, not a new one.  But the same logic, you would have
us remove all our xfel code, since it has dials dependency.  The fact is
cctbx is a multipurpose repo contributed by several groups for different
purposes.  Not dead code.

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 7:53 AM, <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@
> 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> 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@
> 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>;
> 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 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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