[cctbxbb] Tidy up CCTBX

Thu Jan 25 12:41:50 PST 2018

My 2 cents: when talking about creating PyPI CCTBX modules it may be 
worthwhile to start by thinking smaller. For instance, while planning 
out how to interface my (largely NumPy-based by necessity) application 
to PHENIX, it would be an enormous help if I could, say, 'pip install 
flex_array' and 'pip install phil'.

On 2018-01-25 19:20, Aaron Brewster wrote:
> I've created the issues:
> 
> https://github.com/cctbx/cctbx_project/issues/125 [6]
> 
> https://github.com/cctbx/cctbx_project/issues/126 [7]
> 
> -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
>> Vice President for Technology, the Joint BioEnergy Institute
>> Laboratory Research Manager, ENIGMA Science Focus Area
>> 
>> Building 33, Room 347
>> Building 978, Room 4126
>> Tel: 1-510-486-4225 [2], Fax: 1-510-486-5909 [3]
>> http://cci.lbl.gov/paul [4]
>> 
>> Lawrence Berkeley Laboratory
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>> Berkeley, CA 94720, USA.
>> 
>> Executive Assistant: Louise Benvenue [ LBenvenue at lbl.gov ][
>> 1-510-495-2506 [5] ]
>> --
>> 
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> 
> 
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> [5] tel:%5B%201-510-495-2506
> [6] https://github.com/cctbx/cctbx_project/issues/125
> [7] https://github.com/cctbx/cctbx_project/issues/126
> 
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