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Re: [ddlm-group] CIF 1.5

Dear Colleagues,

   I respectfully disagree.  Indeed, I strongly disagree with almost every
aspect of the recent CIF 2 decisions.  However, I have had my say.  Let
us finish the design of something and get it into use.

   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 Tue, 1 Dec 2009, David Brown wrote:

> Before we close off the discussion on CIF1.5 I just want to put in my final 2 cents
> worth.
> 
> As I mentioned before, I see no point in introducing CIF1.5 which will only muddy the
> waters and lead to total confusion.  CIF1.5 is quite unnecessary.
> 
> 1. Legacy software will not be able to read CIF1.5 any more than it will be able to
> read CIF2.0 files, so we might as well go directly to  CIF 2.0.  And how quickly will
> the legacy software be converted to output CIF1.5 files anyway.  You need a 10 year
> lead time for changes in packages such as SHELX and another decade before people
> upload the latest version.  Even then they will produce CIF1.1 output that they can
> load into their other programs.
> 
> 2. For the forseable future DDLm applications will have to have a CIF1.1 lexer and a
> preparser to convert legacy files into CIF2.0 mode.
> 
> 3. What dictionaries will be used for files written in CIF1.5?  It will be difficult
> enough to find volunteers to convert DDL1 to DDLm, and I have no idea if there are
> any plans to convert DDL2 to DDLm dictionaries.  If CIF1.5 will use DDLm then why not
> just go straight to CIF2.0?
> 
> 4. CIF2.0 datafiles can look almost exactly like CIF1.1 datafiles except for a few
> datanames and some undelimited data values that include forbidden characters.  Most
> people will not notice the difference between CIF2.0 files and regular old fashioned
> CIFs.  Indeed many CIF1.1 data files could probably be read in with CIF2.0 parsers
> without a problem.  The biggest problem are the DDL2 datanames that contain
> 'U[1][2]', but these are not found in DDL1.  Since the whole DDL2 data archive is
> centrally held I assume could it could be easily converted (if it was thought
> worthwhile),  If there are problems in DDL1 they are confined to one or two
> datanamens.  Undelimited data values containing illegal characters could be a
> problem.  The CIF1.1 lexer and preparser mentioned in 2 above will deal with all of
> these.
> 
> 5. DDLm does not require that its lists, vectors and matrices be entered as arrays. 
> dREL allows all of these new CIF2.0 constructs to be reconstituted from their
> primitives as required.
> 
> The future as I foresea it will see everone carrying on with current software and
> CIF1.1 datafiles as long as they want.  CIF2.0 software will be developed to take
> advantage of the new features, but with a CIF1.1 front end to carry out the minimal
> required conversion to CIF2.0, such applications will be able to read all existing
> and future CIFs of every stripe.  Eventually CIF1.1 legacy software will die or be
> converted to CIF2.0 and the rest of the world will painlessly convert to to CIF2.0
> data files, probably without the ueser even noticing.
> 
> I think we are imagining monsters lurking behind trees even in a treeless desert.
> 
> CIF1.5 should be dropped and not resurrected, and I am prepared to debate this with
> Herbert privately (so as not te waste everyone else's time) if he is not convinced.
> 
> David
> 
> 
> 
> Brian McMahon wrote:
> 
> Dear Colleagues
> 
> I agree with James. The remit of this group was to finalise DDLm. An
> early conclusion was that this necessarily involved syntax changes at
> the STAR level, and the consequent discussions have revolved around
> the idea of providing a specification for CIF (essentially at the
> syntax level) that took advantage of these syntactic changes and
> allowed uniform handling of CIF data files and DDLm dictionaries. For
> me, the immediate benefit of these discussions has been a much more
> complete account of what needs to be done upstream, at the STAR level,
> to accommodate the changes that are desirable in downstream (CIF and
> DDLm applications) at some point.
> 
> So, for example, the STAR spec needs formally to be revised to allow
> Unicode character sets (certainly UTF-8, which is what we settled on
> for CIF; as far as I recall, it's still possible that the STAR
> revision could allow other Unicode encodings that Herbert needs
> for imgCIF, and I'd be interested in knowing whether the new spec
> could also allow the inclusion of full binary data streams so that
> CBF could properly become one of the STAR family of formats). There
> must also be the new delimiter characters and formal rules for
> handling list items.
> 
> We've developed these conclusions by using various use cases and
> Gedankenexperimente, but we've not, in the main, been driven by the
> need to meet real problems currently difficult of solution in the
> community. Indeed, recent work with embedded visualisation scripts and
> incorporation of TeX mathematical fragments into CIFs destined for
> publication in Acta show that there's much more that can still be
> achieved within the existing syntactic framework.
> 
> So let us complete the job of finalising the specifications (STAR++,
> DDLm, CIF2.0), and then involve the wider community in discussing
> how, when and if they are to be implemented.
> 
> Brian
> 
> On Tue, Dec 01, 2009 at 02:30:09PM +1100, James Hester wrote:
> 
> Dear Herbert and colleagues,
> 
> Little quibble: I wrote 'one more type' rather than 'more than one type'.
> 
> Anyway, I suggest that we concentrate on finalising CIF2.0 syntax, then put
> a draft out for discussion in the broader community, and if there is
> sufficient feedback to the effect of 'we need an intermediate format', then
> we can address the issue of CIF1.5.  Addressing it now distracts us from the
> task of putting CIF2.0 to bed, which we will still need to do in any case.
> 
> On Tue, Dec 1, 2009 at 11:17 AM, Herbert J. Bernstein <
> yaya@bernstein-plus-sons.com> wrote:
> 
> Dear James,
>
>  Please look at the following part of your first paragraph:
> 
> 
> "with a commitment to support CIF1.1 for the long term and a guaranteed way
> to distinguish the two types of data files."
> 
> and please look at the following part of your second paragraph
> 
> 
> "Furthermore, they now have to support one more type of file going into the
> future."
> 
> I seem to be missing something.  If we are going to support CIF 1.1 for
> the long term and we are going to have CIF 2 be a very different file type,
> then it is not CIF 1.5 that will cause software devlopers to have
> to support one more file type going into the future, but the fundamental
> decisions made by this group.
> 
> If you support CIF 1.1 and a very different CIF 2, then you are going to
> end up with mixed files, i.e. multiple ad hoc CIF 1.5 (or actually CIF
> 1.55) files.  All I am doing is proposing to formalize what is going to
> happen anyway.
>
>  I've had my say.
> 
>
>  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 Tue, 1 Dec 2009, James Hester wrote:
>
>  (Note to those reading this later: this continues a thread started within
> 
> the 'space as
> list item separator' thread.  I recommend reading those messages before
> continuing on
> here).
> 
> (For those who came in late:
> We flirted with the idea of a minimally disruptive path from CIF1.1 to
> CIF2.0 back in the
> beginning of this group (late September/early October, I believe) , and
> ended up choosing
> to define one maximally disruptive CIF2.0 standard together with a
> commitment to support
> CIF1.1 for the long term and a guaranteed way to distinguish the two types
> of data files.)
> 
> Picking up the CIF1.5 discussion...
> Introducing CIF1.5 is a further source of confusion.  Apart from this, it
> produces extra
> workload for software authors.  Herb has essentially defined CIF1.5 as
> CIF1.1 plus new
> syntactical elements (or in other words CIF2.0 minus character set
> limitations and UTF8).
> So in order to support CIF1.5, authors of both CIF reading and CIF writing
> software have
> to add this new syntax.  Then when they decide to support CIF2.0, they
> have to once again
> revisit their software.  I would have thought it far more sensible to ask
> them to update
> and distribute their software only once.  Furthermore, they now have to
> support one more
> type of file going into the future.
> 
> I see absolutely no benefit in this idea.
> 
> On Tue, Dec 1, 2009 at 9:40 AM, Herbert J. Bernstein <
> yaya@bernstein-plus-sons.com> wrote:
>      Dear James,
>
>       The point is that we will need to make it easy for people working
> with
>      CIF 1 and CIF 1.1 based tools to cobble together valid CIF 2 data.
>  The
>      most important bit will be a way to include vectors and matrices in
> their
>      data.  This will allow them to do it.
>
>       Please note that it hase taken several years to just get to the
> point
>      where we are beginning to rigorously define CIF 2.  If we are lucky,
> it
>      will only take a few years to have a full set of tools to allow users
>      and software writers to reliably produce true CIF 2 data.
>
>       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 Tue, 1 Dec 2009, James Hester wrote:
>
>      Dear Herbert: as CIF 1.1 doesn't define lists, I'm not sure why you
>      suggest that the
>      example below is a valid tag.
>
>      On Tue, Dec 1, 2009 at 12:36 AM, Herbert J. Bernstein
>      <yaya@bernstein-plus-sons.com>
>      wrote:
>           Sorry something got lost in the prior message.  It should have
>           read:
>
>                 Dear Colleagues,
>
>                  Back to the question of commas.  If you accept the
>                  desirability of having a CIF 1.5, commas in lists
>                  become very useful. Someone with
>                  a CIF 1.1 editor will be able to prepare a CIF 1.5 file
>                  for many useful cases by doing all lists with commas
>                  and no embedded blanks as long as they can make their
>                  lists fit on single lines.
>
>                  In CIF 1.1
>
>                 [[1,2,3],[4,5,6],[7,8,9]]
>
>                 is a valid value for a tag, but
>
>                 [[1 2 3] [4 5 6] [7 8 9]]
>      is not.
>
>      No, neither example is a valid CIF 1.1 tag.  CIF 1.1 explicitly
>      excludes brackets as the first character of a non-delimited string.
> 
>
>                 Having the option of commas in lists will help to smooth
>                 the transition for at least some people.
> 
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> 
> 
> 
>
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