[cctbxbb] Tidy up CCTBX

Fri Jan 26 03:58:10 PST 2018

Folks,

Two concerns with these:
 - I am not sure that these address the biggest problem i.e. iotbx depends_on dxtbx
 - Will we end up getting bug reports where DIALS programs can’t read e.g. Eiger, CBF images?

The latter worries me more, as it could be a tricky one to diagnose…

Best wishes Graeme

On 25 Jan 2018, at 19:20, Aaron Brewster <asbrewster at lbl.gov<mailto:asbrewster at lbl.gov>> wrote:

I've created the issues:

https://github.com/cctbx/cctbx_project/issues/125
https://github.com/cctbx/cctbx_project/issues/126

-Aaron

On Tue, Jan 23, 2018 at 10:50 AM, Paul Adams <pdadams at lbl.gov<mailto:pdadams at lbl.gov>> wrote:
Hi Aaron,

  thanks for the email. I think your proposal to remove the compile time dependencies by moving code to extension modules is great. I think this would be greatly appreciated by Rob and others.
  Fable, contrary to recent rumors, is actually often used by others outside of the cctbx community. While it is true that we wrote it for mainly one task, it turns out there are lots of people with old f77 code they’d like to translate. Given that we don’t seem to have any dependency or support issues with the code I’d recommend it stays - making and supporting a separate package would be too much.

  Cheers,
        Paul

> On Jan 23, 2018, at 9:53 AM, Aaron Brewster <asbrewster at lbl.gov<mailto:asbrewster at lbl.gov>> wrote:
>
> Hi folks,
>
> There are lots of threads in this email.  Pulling a couple of them...
>       • The LBL team runs the libtbx/phil/tst_interface.py test nightly in buildbot as part of testing phenix, so the test is exercised (and it passed last night).  Whether it should be moved to phenix_regression is another issue (I don't think it's necessary, the has_module call seems clear to me).
>       • I think there are many projects that shouldn't be moved out of cctbx_project.  IOTA, xfel, prime, simtbx, and dxtbx are all under active development and are useful to many crystallographers.  cctbx is a toolbox after all.  It just has a lot of tools.
>       • That said, It may be worth having a discussion about fable, and maybe one or two of the others.  That can be done in separate threads for each project?
>       • I would like to break compile-time dependencies on external packages in dxtbx as identified by Rob.  If the C++ code in dxtbx/iotbx that imports cbf.h and hdf5.h is moved to separate boost-python extension modules (some of this is done already), then the SConscript can be made smarter and compile only the libraries it can find headers for.  I'd be in favor of making two issues to track this work, one for cbflib and one for hdf5.  That would be a step in the direction restoring the 'standaloneness' of the cctbx package.
> -Aaron
>
> On Tue, Jan 23, 2018 at 3:16 AM, <markus.gerstel at diamond.ac.uk<mailto:markus.gerstel at diamond.ac.uk>> wrote:
> Hi Marcin
>
> Hmm, so in other words "his free / open source software cannot be fully tested without agreeing to this license"?
>
> No, still doesn't make sense to me. It only raises more questions. Such as: does Travis have a phenix license?
>
> Currently we don't run these tests at all - although we *should* run all tests on libtbx - because we don't have phenix installed during cctbx tests.
> Either the required test data should fully go into libtbx or the test should fully go into phenix. Distributing a test in two parts is no good to anyone.
>
> -Markus
>
> ________________________________________
> From: cctbxbb-bounces at phenix-online.org<mailto:cctbxbb-bounces at phenix-online.org> [cctbxbb-bounces at phenix-online.org<mailto:cctbxbb-bounces at phenix-online.org>] on behalf of Marcin Wojdyr [wojdyr at gmail.com<mailto:wojdyr at gmail.com>]
> Sent: Tuesday, January 23, 2018 10:55
> To: cctbx mailing list
> Cc: Randy Read
> Subject: Re: [cctbxbb] Tidy up CCTBX
>
> Hi Graeme,
>
> > Turns out that the assert that libtbx has no dependencies is not strictly true:
> >
>
> >   if (not libtbx.env.has_module(name="phenix")):
> >     print "phenix module not available: skipping advanced tests"
> >     return
>
> This is optional dependency (cctbx optionally uses Phenix for testing
> in various places) and doesn't cause problems.
> If you'd like to do disentangling, dxtbx-iotbx would be a good
> starting point as it really causes problems.
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Paul Adams
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Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab
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