[cctbxbb] Tidy up CCTBX

Thu Jan 25 11:20:56 PST 2018

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> 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> 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> 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 [cctbxbb-bounces at phenix-
> online.org] on behalf of Marcin Wojdyr [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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> >
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> --
> Paul Adams
> Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence
> Berkeley Lab
> Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley
> Lab
> Adjunct Professor, Department of Bioengineering, U.C. Berkeley
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