Re: Mathematica Notebook Organiztion

*To*: mathgroup at smc.vnet.net*Subject*: [mg56825] Re: [mg56816] Mathematica Notebook Organiztion*From*: DrBob <drbob at bigfoot.com>*Date*: Sat, 7 May 2005 04:16:38 -0400 (EDT)*References*: <200505060701.DAA06272@smc.vnet.net>*Reply-to*: drbob at bigfoot.com*Sender*: owner-wri-mathgroup at wolfram.com

WRI, please take notice. David is truly a guru on visual presentation and organization of information. Bobby On Fri, 6 May 2005 03:01:35 -0400 (EDT), David Park <djmp at earthlink.net> wrote: > I've made this a new topic because we have rather drifted off from the > subject of writing packages to the subject of using notebooks in the best > manner. > > It is my view that Mathematica notebooks (and similar such entities) are an > entirely new publishing form. They FAR SURPASS printed books and articles > because of the ability to interactively meld text, calculations, graphics > and animations in one document. Theodore Gray deserves a lot of credit for > his work on this concept. We are still learning how to use this media. But > things are not perfect yet and Professor Siegman has touched on some issues. > > There is no reason that the Initialization and Routines Sections couldn't be > at the end of the notebook. The Input cells in these Sections should be made > into Initialization cells (and choose NOT to save as an AutoSave package). > That way one doesn't have to necessarily evaluate a notebook from the top. > The initializations are automatically performed when the first statement, > anywhere, is evaluated. I like to make my notebooks such that a reader can > start at any Section and begin evaluating. If this is not possible because > of a rigid progression in the sections then the reader should be so > instructed. > > Often I will select the Initialization and Routine section headings and > change the FontColor to Gray. I also often add "Automatically Initialized". > This subdues the sections and tells the reader he can generally ignore them. > > Sections are not automatically opened when Initialization cells are > evaluated. My experience is that the sections remain closed. Also you can > select a Section and completely evaluate it without ever opening it, or > seeing the results. (I've had super geniuses complain that they evaluated my > notebook but got no results, simply because they didn't know how to open > Sections!) > > Graphics code can be put in closed cells in the running sections. It doesn't > necessarily have to be put in the Routines section. That way you can > intermix text, calculations and graphics in a smooth manner. The only > problem is getting the reader to evaluate the closed cells, even if it has > been carefully explained in an Introduction. They are so thin and small new > readers often overlook them. It might be nice if one had the option of > having a closed cell display a cell tag. It would also be nice if closed > cells could be opened and closed in the same way as Sections. > > It is also possible to generate proofs, derivations or step by step > calculations by interspersing Print statements with %% referenced > statements. These can also be put in closed cells so that the main code is > hidden. > > For printing (It will take some time for people to give up the security > blanket of printed documents - inferior as they are!) there is no reason why > some Sections can't be open and others closed. > > Professor Siegman's case: > > Section > Text (a few paragraphs introducing the section) > Subsection > Subsection > > is a good point. I don't see any direct way around it other than making the > Text an Introductory Subsection, which may be objectionable because it is so > short, or manually closing these Text cells, but this is too difficult for > the reader to work with. Perhaps there might be a FrontEnd command that > gives the "outline view". > > Another approach would be to make a Table of Contents Section. The various > items in the Table of Contents could actually be links to the corresponding > sections of the notebook. This is like pdf documents where there is often a > table of contents with links in the side bar. It requires extra work to > write the sections, but then it also requires extra work in a pdf document. > > It would also be nice to have the following construction: > > Section > Text and Input cells > BoxSection > Text and Input cells > End of BoxSection marker > Text and Input cells > > where the BoxSection could be closed or terminated, and subsequent Text and > Input cells would NOT be part of the BoxSection, but part of the containing > section. The BoxSections would be like boxes in textbooks which contain a > side discussion without interrupting the main flow of material. (Possibly > there could be a way to have manual grouping only in some subsection of a > notebook, but I would much prefer a more versatile automatic grouping > because manual grouping is too subject to abuse.) > > I have only looked a little at the Author's Tools application. It does give > information about constructing Help documentation, which I omitted to > mention in an earlier posting. But otherwise I haven't figured out just what > Author's Tools does for one in the way of constructing better notebooks for > readers. I wish WRI had provided a short elegant example with the > application. > > It might also be nice to have the ability to construct stand alone browsers. > Then the categories in the browser would be like the table of contents. In > essence, authors would write Mathematica browsers, in which Mathematica > notebooks formed the various chapters and sections. > > I wish that there were better standard notebook styles supplied with > Mathematica. I find many of the standard ones useless. WRI needs to hire > Edward Tufte, or someone equivalent, to design some notebook styles. It > certainly is preferable to use a standard style because then one can count > on readers having it. > > I would like to see one more Section level in notebooks. I would like to see > the default to have GroupOpenCloseIcons on all the Section levels - but NOT > on anything else. (Especially not on Input/Output groups.) The triangular > open/close icons are intuitive to new readers - the cell brackets are not. I > would like to see a better balance, actually a smaller range, of font sizes. > In the Default style, for instance, I think the Title font size is much too > large, and the Text font size is too small. The Text, Input and Output font > sizes should be reasonably close in size. After all, text cells and > Input/Output cells are of equal importance (IMHO) and should better blend. > Look at any technical article or book and you will see that the equations > and text have roughly comparable font sizes. > > David Park > djmp at earthlink.net > http://home.earthlink.net/~djmp/ > > > From: AES [mailto:siegman at stanford.edu] To: mathgroup at smc.vnet.net > > Agreed, this is the sensible way to [include routines in notebooks], and how > I generally do it. > But two gripes about the result: > > 1) In PhD dissertations, journal papers, books, reports, the (sometimes > lengthy) "Routines" are most commonly are sent to the end, e.g. are > stuck in Appendices, and the Initialization (or Introduction) section is > immediately followed by the important (to the reader) sections such as > Calculations and Results. Among other things that lets you easily > select and print the Introduction, the Calculations and the Results to > toss in a file folder or (three-hole-type) notebook, leaving off the > lengthy Routines stuff. > > Mathematica doesn't make it easy to organize its notebooks that way. > > 2) In my (limited) experience if I use Automatic Grouping and try to > close groups to see only the section headings (to get an overview of the > notebook structure and faster scrolling to , this doesn't work right > (i.e., the way I want it!) unless the cell structure is strictly > hierarchical. E.g., if I have repeated cell sequences in the form > > Section > Text (a few paragraphs introducing the section) > Subsection > Subsection > > closing these groups so I'll see just the Section headings does not > close the Text cells, although it does close the Subsections (maybe I'm > not doing things right?). > > Also, closing the Routines section, then running the notebook from the > top (to get a fresh start) opens the Routines section, doesn't it? > > > > > > > -- DrBob at bigfoot.com

**Follow-Ups**:**Re: Re: Mathematica Notebook Organiztion***From:*Josef Karthauser <joe@tao.org.uk>

**References**:**Mathematica Notebook Organiztion***From:*"David Park" <djmp@earthlink.net>

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