Re: r24323 - in /branches/disp_spin_speed: dep_check.py target_functions/relax_disp.py -- June 27, 2014 - 10:53

Hi Troels,

This is ok.  If you would like to have the relax numpy dependency
increased to 1.6, then you'll just have to blacklist all system tests
that do not work, so they obtain a printout at the end that X number
of tests were skipped due to numpy < 1.6.  Then on the website and in
the manual, we tell users to use numpy < 1.6 at their own risk.  We
could even block the relaxation dispersion analysis in the pipe.create
user function via a RelaxError if numpy < 1.6, if all models are
affected.  But if this is the case, then maybe we make numpy >= 1.6 an
essential dependency which is checked in dep_check, calling sys.exit()
if not.

Regards,

Edward


On 27 June 2014 10:34, Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx> wrote:
> Hi ed.
>
> I have already been looking at the systemtests.
>
> Our server has numpy 1.4.1
>
> But some of the analytical models fails as well, since 1.4.1 does not
> recognise the 'out' keyword.
>
> Sigh...
>
> 2014-06-26 17:26 GMT+02:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> > Hi,
> >
> > I can look at it later.  For requiring numpy 1.6, the following could be 
> > done:
> >
> > - If you could delete the printout in dep_check, that would be good.
> > The printouts are only used for the essential packages before calling
> > sys.exit().  If you are interested in a message to the user, the
> > message needs to be modified to say something like "numpy >= 1.6 is
> > required for...", rather than "numpy einsum is not installed", and
> > this needs to be used like the C_module_exp_fn_mesg variable in the
> > dep_check and info modules rather than calling sys.stderr.write().
> >
> > - Blacklist the system tests requiring this.  This is absolutely
> > essential for me to release the changes in a new relax version.  Maybe
> > you could tackle that one, as the problem is of your own doing ;)
> > It's just a simple duplication of code in the setUp() method.  Do you
> > have a system with numpy < 1.6 to test on?
> >
> > - A RelaxError in the relax_disp.select_model user function for just
> > these models.  Could you give a list of these models, as I don't know
> > if all numeric models are affected, or if non-numeric models are
> > affected.  The best would be to create a new variable in
> > specific_analyses.relax_disp.variables for this model list.
> >
> > - A GUI error blocking the execution of the analysis.  This would
> > require the model list in specific_analyses.relax_disp.variables to
> > identify the problem.  But I can look at this one.
> >
> > Cheers,
> >
> > Edward
> >
> >
> >
> > On 25 June 2014 20:14, Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx> wrote:
> > > Hi Edward.
> > >
> > > Do you fix this?
> > >
> > > Thanks.
> > >
> > > Best
> > > Troels
> > >
> > >
> > > 2014-06-25 20:06 GMT+02:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> > > > Hi Troels,
> > > >
> > > > For this change, it might be better to not output a message to
> > > > sys.stderr.  For relax users who are not interested in a dispersion
> > > > analysis, there is no need to bother them.  What I would suggest for
> > > > safety is, in the backend for the relax_disp.select_model user
> > > > function, that we raise a RelaxError if one of these models are
> > > > selected but numpy.einsum does not exist.  The RelaxError message
> > > > could be that numpy version 1.6 or greater is required for the numeric
> > > > dispersion models.  A message could also appear in the GUI when the
> > > > execute button is clicked on, if these models have been selected.
> > > > That should be the best for the user experience when they have numpy <
> > > > 1.6.
> > > >
> > > > Regards,
> > > >
> > > > Edward
> > > >
> > > >
> > > >
> > > > On 25 June 2014 19:31,  <tlinnet@xxxxxxxxxxxxx> wrote:
> > > > > Author: tlinnet
> > > > > Date: Wed Jun 25 19:31:40 2014
> > > > > New Revision: 24323
> > > > >
> > > > > URL: http://svn.gna.org/viewcvs/relax?rev=24323&view=rev
> > > > > Log:
> > > > > Implemented a dependency check for numpy einsum, so relax can still
> > > > > start.
> > > > >
> > > > > Task #7807 (https://gna.org/task/index.php?7807): Speed-up of 
> > > > > dispersion
> > > > > models for Clustered analysis.
> > > > >
> > > > > Modified:
> > > > >     branches/disp_spin_speed/dep_check.py
> > > > >     branches/disp_spin_speed/target_functions/relax_disp.py
> > > > >
> > > > > Modified: branches/disp_spin_speed/dep_check.py
> > > > > URL:
> > > > > http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/dep_check.py?rev=24323&r1=24322&r2=24323&view=diff
> > > > >
> > > > > ==============================================================================
> > > > > --- branches/disp_spin_speed/dep_check.py       (original)
> > > > > +++ branches/disp_spin_speed/dep_check.py       Wed Jun 25 19:31:40 
> > > > > 2014
> > > > > @@ -57,6 +57,14 @@
> > > > >
> > > > >  # Optional packages.
> > > > >  ####################
> > > > > +
> > > > > +# numpy einsum import.
> > > > > +try:
> > > > > +    from numpy import einsum
> > > > > +    einsum_module = True
> > > > > +except ImportError:
> > > > > +    sys.stderr.write("The dependency 'numpy einsum' has not been
> > > > > installed.  Numerical models in dispersion analysis will not be
> > > > > possible.\n")
> > > > > +    einsum_module = False
> > > > >
> > > > >  # Bmrblib python package check.
> > > > >  try:
> > > > >
> > > > > Modified: branches/disp_spin_speed/target_functions/relax_disp.py
> > > > > URL:
> > > > > http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=24323&r1=24322&r2=24323&view=diff
> > > > >
> > > > > ==============================================================================
> > > > > --- branches/disp_spin_speed/target_functions/relax_disp.py
> > > > > (original)
> > > > > +++ branches/disp_spin_speed/target_functions/relax_disp.py     Wed Jun
> > > > > 25 19:31:40 2014
> > > > > @@ -30,6 +30,7 @@
> > > > >  from numpy.ma import masked_equal
> > > > >
> > > > >  # relax module imports.
> > > > > +import dep_check
> > > > >  from lib.dispersion.b14 import r2eff_B14
> > > > >  from lib.dispersion.cr72 import r2eff_CR72
> > > > >  from lib.dispersion.dpl94 import r1rho_DPL94
> > > > > @@ -40,13 +41,7 @@
> > > > >  from lib.dispersion.m61b import r1rho_M61b
> > > > >  from lib.dispersion.mp05 import r1rho_MP05
> > > > >  from lib.dispersion.mmq_cr72 import r2eff_mmq_cr72
> > > > > -from lib.dispersion.ns_cpmg_2site_3d import r2eff_ns_cpmg_2site_3D
> > > > >  from lib.dispersion.ns_cpmg_2site_expanded import
> > > > > r2eff_ns_cpmg_2site_expanded
> > > > > -from lib.dispersion.ns_cpmg_2site_star import r2eff_ns_cpmg_2site_star
> > > > > -from lib.dispersion.ns_mmq_3site import r2eff_ns_mmq_3site_mq,
> > > > > r2eff_ns_mmq_3site_sq_dq_zq
> > > > > -from lib.dispersion.ns_mmq_2site import r2eff_ns_mmq_2site_mq,
> > > > > r2eff_ns_mmq_2site_sq_dq_zq
> > > > > -from lib.dispersion.ns_r1rho_2site import ns_r1rho_2site
> > > > > -from lib.dispersion.ns_r1rho_3site import ns_r1rho_3site
> > > > >  from lib.dispersion.ns_matrices import r180x_3d
> > > > >  from lib.dispersion.tp02 import r1rho_TP02
> > > > >  from lib.dispersion.tap03 import r1rho_TAP03
> > > > > @@ -56,6 +51,14 @@
> > > > >  from target_functions.chi2 import chi2, chi2_rankN
> > > > >  from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_DQ,
> > > > > EXP_TYPE_CPMG_MQ, EXP_TYPE_CPMG_PROTON_MQ, EXP_TYPE_CPMG_PROTON_SQ,
> > > > > EXP_TYPE_CPMG_SQ, EXP_TYPE_CPMG_ZQ, EXP_TYPE_LIST_CPMG, EXP_TYPE_R1RHO,
> > > > > MODEL_B14, MODEL_B14_FULL, MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94,
> > > > > MODEL_IT99, MODEL_LIST_CPMG, MODEL_LIST_CPMG_FULL, MODEL_LIST_FULL,
> > > > > MODEL_LIST_MMQ, MODEL_LIST_MQ_CPMG, MODEL_LIST_R1RHO, 
> > > > > MODEL_LIST_R1RHO_FULL,
> > > > > MODEL_LM63, MODEL_LM63_3SITE, MODEL_M61, MODEL_M61B, MODEL_MP05,
> > > > > MODEL_MMQ_CR72, MODEL_NOREX, MODEL_NS_CPMG_2SITE_3D,
> > > > > MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED,
> > > > > MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL, 
> > > > > MODEL_NS_MMQ_2SITE,
> > > > > MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_2SITE,
> > > > > MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR, MODEL_TAP03, 
> > > > > MODEL_TP02,
> > > > > MODEL_TSMFK01
> > > > >
> > > > > +# Check if eisum is available for numerical models.
> > > > > +if dep_check.einsum_module:
> > > > > +    from lib.dispersion.ns_cpmg_2site_3d import r2eff_ns_cpmg_2site_3D
> > > > > +    from lib.dispersion.ns_cpmg_2site_star import
> > > > > r2eff_ns_cpmg_2site_star
> > > > > +    from lib.dispersion.ns_mmq_3site import r2eff_ns_mmq_3site_mq,
> > > > > r2eff_ns_mmq_3site_sq_dq_zq
> > > > > +    from lib.dispersion.ns_mmq_2site import r2eff_ns_mmq_2site_mq,
> > > > > r2eff_ns_mmq_2site_sq_dq_zq
> > > > > +    from lib.dispersion.ns_r1rho_2site import ns_r1rho_2site
> > > > > +    from lib.dispersion.ns_r1rho_3site import ns_r1rho_3site
> > > > >
> > > > >  class Dispersion:
> > > > >      def __init__(self, model=None, num_params=None, num_spins=None,
> > > > > num_frq=None, exp_types=None, values=None, errors=None, missing=None,
> > > > > frqs=None, frqs_H=None, cpmg_frqs=None, spin_lock_nu1=None,
> > > > > chemical_shifts=None, offset=None, tilt_angles=None, r1=None,
> > > > > relax_times=None, scaling_matrix=None, recalc_tau=True):
> > > > >
> > > > >
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