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Re: [ddlm-group] Relationship asmong CIF2, STAR,CIF1 and Python. .

Dear Simon,

   No apologies are needed.  We are all doing our best to
achieve the best possible result.  We differ and we make
mistakes because we care.

   I would prefer not to risk circular reasoning, so I find it
safer to settle on objectives before considering whether
a particular feature does or does not meet those objectives,
but I think it is likely that much of what has gone into
the more recent CIF2 decisions has made preservation of CIF1
difficult.

   Regards,
     Herbert

=====================================================
  Herbert J. Bernstein, Professor of Computer Science
    Dowling College, Kramer Science Center, KSC 121
         Idle Hour Blvd, Oakdale, NY, 11769

                  +1-631-244-3035
                  yaya@dowling.edu
=====================================================

On Sun, 16 Jan 2011, SIMON WESTRIP wrote:

> Unfortunately Herbert, I've been guilty of a lack of clarity in my 
> messages (again): I wasnt attempting to state the design objectives of 
> CIF2; rather I was reviewing some of the CIF2 changes as drafted. By 
> "enhance CIF as data source" I meant the addition of unicode, list 
> structures, table structures, for use within a CIF file, and did not 
> mean to imply that this was necessarily a goal, let alone prioritize it. 
> Likewise, I did not intend any inference about the nature of the 
> original objectives nor their priority.
> 
> That said, pehaps listing the objectives and relating them to CIF2 as
> drafted would be a useful
> exercise.
> 
> Cheers
> 
> Simon
> 
> 
> ____________________________________________________________________________
> From: Herbert J. Bernstein <yaya@bernstein-plus-sons.com>
> To: Group finalising DDLm and associated dictionaries <ddlm-group@iucr.org>
> Sent: Sunday, 16 January, 2011 12:26:28
> Subject: Re: [ddlm-group] Relationship asmong CIF2, STAR, CIF1 and Python. .
> 
> Dear Simon,
> 
>   If I read your message correctly, you seem to be saying that the design
> objectives of CIF2 are:
> 
>   1.  enchance CIF as a data source
>   2.  accomodate DDLm
>   3.  do 1 and 2 in a way that does not complicate CIF as a data source
> 
>   I don't understand what you mean by "enhance CIF as a data source". This
> is the first time I recall hearing that objective.  Please clarify.
> 
> In terms of present practice, I had thought that the major current uses of
> CIF to be:
> 
>   1.  As a language for publication of papers in IUCr journals;
>   2.  As a language for submission of data to CCDC;
>   3.  As a language for submission of data to the PDB;
>   4.  As a data harvest language for CCP4; and
>   5.  As a language for formatting image data from Dectris detectors,
> with some emerging use for data management of synchrotron data
>   ( Please fill in uses I have missed ...)
> 
> which would seem to me to represent a large current investment in data
> management software that depends critically on stability and reliability of
> CIF representation of both numeric data and text.  As I understand it, DDLm
> and dREL can contribute to these current uses by enhancing the reliabiity of
> validation of data in these contexts, especially in uses 1, 2 and 3, above. 
> To me, that would  seem to change the objectives to:
> 
>   1.  Accomodate DDLm and dREL; and
>   2.  Do this in a way that keeps required changes to existing
> archives to a minimum; and
>   3.  Do this in a way that allows as much existing CIF software
> as possible to continue to operate reliably; and
>   4.  To the extent that changes will be needed in archives and
> software, provide a clearly understood mechanism for making
> those changes, with as much support software as possible; and
>   5.  Subordinate to the above, add new features to CIF that may
> encourage broader use and more software support
> 
> Please tell me what I have misunderstood in this.
> 
> Regards,
>   Herbert
> 
> =====================================================
> Herbert J. Bernstein, Professor of Computer Science
>   Dowling College, Kramer Science Center, KSC 121
>         Idle Hour Blvd, Oakdale, NY, 11769
> 
>                 +1-631-244-3035
>                 yaya@dowling.edu
> =====================================================
> 
> On Sun, 16 Jan 2011, SIMON WESTRIP wrote:
> 
> > I believe that the CIF2 syntax changes enhance CIF as data source,
> > even with the restriction to the contents of  ' and " delimited values,
> > which
> > I suspect will be the main source of incompatability between archived CIFs
> > and CIF2. What we havent acheived is 100% compatability of CIF1 with CIF2,
> > but having agreed that CIF2 is distinct from CIF1 and minimized the
> > incompatability,
> > I do not see the changes as disruptive or retrograde.
> >
> > DDLm methods will not be applicable to a significant percentage of a CIF
> > data source
> > (those 'free text' fields used to report experimental details etc.). I
> > believe other approaches
> > will be needed to enhance their content (referencing other data items from
> > an item etc).
> > Unicode support in CIF2 is beneficial in this area, and the new
> alternative
> > delimiters may
> > prove convenient. The list and table structures may also be exploited.
> >
> > So from my point of view, though I understood the aim of CIF2 was to
> > accommodate DDLm,
> > it turns out that it does offer a little bit more. I would still like the
> > problem of including all delimiters
> > in a value to be solved, and line-folding to be included. On my 'wish
> list'
> > are value concatenation
> > and a value-referencing mechanism for use with CIF as a data source.
> >
> > I know this doesnt really answer your question. What we are *not* trying
> to
> > do is complicate
> >  CIF as a data source?
> >
> > Cheers
> >
> > Simon
> >
> >___________________________________________________________________________
> _
> > From: Herbert J. Bernstein <yaya@bernstein-plus-sons.com>
> > To: Group finalising DDLm and associated dictionaries
> <ddlm-group@iucr.org>
> > Sent: Sunday, 16 January, 2011 2:05:59
> > Subject: Re: [ddlm-group] Relationship asmong CIF2, STAR, CIF1 and Python.
> .
> >
> > Dear Simon,
> >
> >   I have reviewed the record on this, and I have trouble finding
> > a strong basis for most of the decisions made other than arguments
> > from the authority of established past practice in STAR and dREL.
> > Now that those arguments have turned out not to have been what they
> > seemed, I have trouble accepting the resulting conclusions without
> > new, clearly stated arguments based in the functionality we are
> > trying to achieve, but it is now not even clear what functionality we
> > are
> > trying to achieve.
> >
> >   Perhaps you can help me -- what are we trying to do in defining
> > CIF2?
> >
> >   Regards,
> >     Herbert
> >
> >
> > At 11:55 PM +0000 1/15/11, SIMON WESTRIP wrote:
> > >That's a question I asked myself when I first joined this discussion
> group
> > :-)
> > >
> > >To be honest Herbert, I do not feal qualified to contest anything to do
> > with
> > >dREL, nor DDLm, given that I havent worked on them and respecting the
> > >years of effort that went into development thus far. The same is
> > >true with respect to some of
> > >the changes to CIF syntax that invalidate CIF1: I have accepted that
> > >they are necessary
> > >to facilitate implementation of dREL methods.
> > >
> > >Cheers
> > >
> > >Simon
> > >
> > >
> > >
> > >From: Herbert J. Bernstein <yaya@bernstein-plus-sons.com>
> > >To: Group finalising DDLm and associated dictionaries
> <ddlm-group@iucr.org>
> > >Sent: Saturday, 15 January, 2011 23:14:36
> > >Subject: Re: [ddlm-group] Relationship asmong CIF2, STAR, CIF1 and
> Python.
> > .
> > >
> > >Why not?  It is almost that right now.
> > >
> > >
> > >At 11:08 PM +0000 1/15/11, SIMON WESTRIP wrote:
> > >>True - but I can't see dREL becoming pyREL at this stage?
> > >>
> > >>
> > >>
> > >>From: Herbert J. Bernstein
> > >><<mailto:yaya@bernstein-plus-sons.com>yaya@bernstein-plus-sons.com>
> > >>To: Group finalising DDLm and associated dictionaries
> > >><<mailto:ddlm-group@iucr.org>ddlm-group@iucr.org>
> > >>Sent: Saturday, 15 January, 2011 22:57:17
> > >>Subject: Re: [ddlm-group] Relationship asmong CIF2, STAR, CIF1 and
> Python.
> > .
> > >>
> > >>Dear Simon,
> > >>
> > >>  But dREL already shares much of Python syntax and data structures,
> > >>but, being significantly mutated, lacks the software support and
> > >>documentation that Python has.  Anyone who has to work with the
> > >>methods in a DDLm dictionary would be much better off if we
> > >>simply made Python work with DDLm.  We would gain large libraries
> > >>of pre-written utilities, tools to test code fragments interactively,
> > >>and a lot more time to do science or whatever we are actually
> > >>funded to do.
> > >>
> > >>  Regards,
> > >>    Herbert
> > >>
> > >>
> > >>
> > >>At 10:35 PM +0000 1/15/11, SIMON WESTRIP wrote:
> > >>>As far as I can see, parsing DDLm into an object stucture is fairly
> > >>>uncomplicated;
> > >>>the hurdle is parsing the dREL script as a method of the object.
> > >>>Unless working with python, I'm not sure that adopting python syntax
> > >>>for DDLm/CIF
> > >>>is of any great benefit; likewise for dREL.
> > >>>
> > >>>That said, I have yet to actually do anything with DDLm, let alone
> > >>>dREL, so I may be
> > >>>well off the mark. But even if this is the case, I suspect there
> > >>>will be non-python programmers out
> > >>>there that have cause to work with CIF and similarly will see no
> > >>>obvious benefit in
> > >>>CIF sharing python syntax (especially if it only adopts it for one
> > >>>set of delimiters at the
> > >>>data-source level).
> > >>>
> > >>>Cheers
> > >>>
> > >>>Simon
> > >>>
> > >>>
> > >>>
> > >>>From: Herbert J. Bernstein
> >>>><<mailto:<mailto:yaya@bernstein-plus-sons.com>yaya@bernstein-plus-sons.c
> 
> > om><mailto:yaya@bernstein-plus-sons.com>yaya@bernstein-plus-sons.com>
> > >>>To: Group finalising DDLm and associated dictionaries
> >>>><<mailto:<mailto:ddlm-group@iucr.org>ddlm-group@iucr.org><mailto:ddlm-gr
> 
> > oup@iucr.org>ddlm-group@iucr.org>
> > >>>Sent: Saturday, 15 January, 2011 21:16:59
> > >>>Subject: Re: [ddlm-group] Relationship asmong CIF2, STAR, CIF1 and
> > Python. .
> > >>>
> > >>>At 12:43 PM +0000 1/15/11, Brian McMahon wrote:
> > >>>>It might be worth remarking (again) that dREL is being developed as a
> > >>>>canonical methods description language, and not necessarily the
> runtime
> > >  >>>methods evaluator of choice for future applications. It may be that
> in
> > >>>>practice future methods are initially developed and most frequently
> > >>>>executed directly in Python or some other language. As I see it, the
> > >>>>goal of CIF and DDL evolution is not to exclude such a possibility.
> > >>>
> > >>>If we are trying to be Python friendly and much of dREL is derived
> > >>>from a Jython implementation, I don't understand why we are not
> > >>>conforming dREL, DDLm and CIF2 to Python conventions as closely as
> > >>>possible.
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>At 12:43 PM +0000 1/15/11, Brian McMahon wrote:
> > >>>>On Thu, Jan 13, 2011 at 05:35:21PM -0600, Bollinger, John C wrote:
> > >>>>>
> > >>>>>  (snip)
> > >>>>>
> > >>>>>  CIF2 <=> CIF1:
> > >>>>>  To the greatest extent feasible, well-formed CIF1 documents should
> be
> > >>>>>  well-formed CIF2 documents (modulo a CIF version identification
> > >>>>>  signature) having the same meaning.
> > >>>>
> > >>>>Agreed.
> > >>>>
> > >>>>>  CIF2 <=> STAR:
> > >>>>>  Inasmuch as CIF1 is derived from STAR, I think it appropriate for
> > CIF2
> > >>>>>  to look first to STAR, including its post-CIF1 development, for new
> > >>>>>  features it may need.  Even if CIF2 is not 100% compatible with
> STAR,
> > it
> > >>>>>  is worthwhile to avoid diverging without compelling reason.
> > >>>>
> > >>>>Agreed
> > >>>>
> > >>>>>  CIF2 <=> Python:
> > >>>>>  I see no particular reason for any formal relationship here beyond
> > >>>>>  Python's role as the indirect inspiration for CIF2's new
> > >>>>>  triple-quote syntax.  I am wary of the idea of tying CIF tightly to
> > >>>>>  a particular language.  CIF2 documents are not and never will be
> > >>>>>  Python programs.  I could imagine embedding Python in CIF or vise
> > >>  >>>  versa, but I have seen no evidence to suggest that greater
> > similarity
> > >>>>>  between the two languages' syntax and semantics would benefit
> efforts
> > >>>>>  such as those.
> > >>>>
> > >>>>Agreed. As I mention elsewhere, there is a greater influence on the
> > >>>>prototype dREL (arising from the initial Jython implementation), and
> > >>>>the list and table data types doubtless arise from that also.
> > >>>>
> > >>>>It might be worth remarking (again) that dREL is being developed as a
> > >>>>canonical methods description language, and not necessarily the
> runtime
> > >>>>methods evaluator of choice for future applications. It may be that in
> > >>>  >practice future methods are initially developed and most frequently
> > >>>>executed directly in Python or some other language. As I see it, the
> > >>>>goal of CIF and DDL evolution is not to exclude such a possibility.
> > >>>>
> > >>>>Regards
> > >>>>Brian
> > >>>>_______________________________________________
> > >>>>ddlm-group mailing list
> >>>>><mailto:<mailto:<mailto:ddlm-group@iucr.org>ddlm-group@iucr.org><mailto
> 
> >:ddlm-group@iucr.org>ddlm-group@iucr.org><mailto:<mailto:ddlm-group@iucr.or
> 
> > g>ddlm-group@iucr.org><mailto:ddlm-group@iucr.org>ddlm-group@iucr.org
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> 
> > http://scripts.iucr.org/mailman/listinfo/ddlm-group
> > >>>
> > >>>
> > >>>--
> > >>>=====================================================
> > >>>  Herbert J. Bernstein, Professor of Computer Science
> > >>>    Dowling College, Kramer Science Center, KSC 121
> > >>>        Idle Hour Blvd, Oakdale, NY, 11769
> > >>>
> > >>>                  +1-631-244-3035
> > >>>
> >>>><mailto:<mailto:<mailto:yaya@dowling.edu>yaya@dowling.edu><mailto:yaya@d
> 
> >owling.edu>yaya@dowling.edu><mailto:<mailto:yaya@dowling.edu>yaya@dowling.e
> 
> > du><mailto:yaya@dowling.edu>yaya@dowling.edu
> > >>>=====================================================
> > >>>_______________________________________________
> > >>>ddlm-group mailing list
> >>>><mailto:<mailto:<mailto:ddlm-group@iucr.org>ddlm-group@iucr.org><mailto:
> 
> >ddlm-group@iucr.org>ddlm-group@iucr.org><mailto:<mailto:ddlm-group@iucr.org
> 
> > >ddlm-group@iucr.org><mailto:ddlm-group@iucr.org>ddlm-group@iucr.org
> >>>><<<http://scripts.iucr.org/mailman/listinfo/ddlm-group>http://scripts.iu
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> >cr.org/mailman/listinfo/ddlm-group><http://scripts.iucr.org/mailman/listinf
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> > >  >>
> > >>>
> > >>>_______________________________________________
> > >>>ddlm-group mailing list
> >>>><mailto:<mailto:ddlm-group@iucr.org>ddlm-group@iucr.org><mailto:ddlm-gro
> 
> > up@iucr.org>ddlm-group@iucr.org
> >>>><<http://scripts.iucr.org/mailman/listinfo/ddlm-group>http://scripts.iuc
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> > >>
> > >>
> > >>--
> > >>=====================================================
> > >>  Herbert J. Bernstein, Professor of Computer Science
> > >>    Dowling College, Kramer Science Center, KSC 121
> > >>        Idle Hour Blvd, Oakdale, NY, 11769
> > >>
> > >>                  +1-631-244-3035
> > >>
> >>><mailto:<mailto:yaya@dowling.edu>yaya@dowling.edu><mailto:yaya@dowling.ed
> 
> > u>yaya@dowling.edu
> > >>=====================================================
> > >>_______________________________________________
> > >>ddlm-group mailing list
> >>><mailto:<mailto:ddlm-group@iucr.org>ddlm-group@iucr.org><mailto:ddlm-grou
> 
> > p@iucr.org>ddlm-group@iucr.org
> >>><<http://scripts.iucr.org/mailman/listinfo/ddlm-group>http://scripts.iucr
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> >.org/mailman/listinfo/ddlm-group><http://scripts.iucr.org/mailman/listinfo/
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> > >>
> > >>
> > >>_______________________________________________
> > >>ddlm-group mailing list
> > >><mailto:ddlm-group@iucr.org>ddlm-group@iucr.org
> >>><http://scripts.iucr.org/mailman/listinfo/ddlm-group>http://scripts.iucr.
> 
> > org/mailman/listinfo/ddlm-group
> > >
> > >
> > >--
> > >=====================================================
> > >  Herbert J. Bernstein, Professor of Computer Science
> > >    Dowling College, Kramer Science Center, KSC 121
> > >        Idle Hour Blvd, Oakdale, NY, 11769
> > >
> > >                  +1-631-244-3035
> > >                  <mailto:yaya@dowling.edu>yaya@dowling.edu
> > >=====================================================
> > >_______________________________________________
> > >ddlm-group mailing list
> > ><mailto:ddlm-group@iucr.org>ddlm-group@iucr.org
> >><http://scripts.iucr.org/mailman/listinfo/ddlm-group>http://scripts.iucr.o
> 
> > rg/mailman/listinfo/ddlm-group
> > >
> > >
> > >_______________________________________________
> > >ddlm-group mailing list
> > >ddlm-group@iucr.org
> > >http://scripts.iucr.org/mailman/listinfo/ddlm-group
> >
> >
> > --
> > =====================================================
> >   Herbert J. Bernstein, Professor of Computer Science
> >     Dowling College, Kramer Science Center, KSC 121
> >         Idle Hour Blvd, Oakdale, NY, 11769
> >
> >                   +1-631-244-3035
> >                   yaya@dowling.edu
> > =====================================================
> > _______________________________________________
> > ddlm-group mailing list
> > ddlm-group@iucr.org
> > http://scripts.iucr.org/mailman/listinfo/ddlm-group
> >
> >
> 
>
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