VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed May 20 2020 - 10:26:21 CDT

Giacomo,
  Thanks for the concrete feedback.
The tab completion feature for linenoise requires that the caller
(VMD) register a callback to be triggered any time the user presses
the completion key (tab, in this case). I haven't implemented
tab completion in the version of the code I sent you.

To implement tab completion, I would likely use the Tcl command
"info commands" to get a list of all global Tcl commands, which would
include Tcl-intrinsic commands, VMD-internal commands, and VMD plugin
commands added to the global namespace. I could use that to provide
a large fraction of the completion candidates in an automatic way
without hard-coding a bunch of Tcl-specific stuff there.

As with tab completion, I also didn't yet implement the "hint" callback
described in the linenoise README doc.

The linenoise code appeals to me because of the BSD license
and minimalist implementation (3% of the size of GNU readline).

Another more full-featured option would be the BSD libedit
library, which is apparently what Apple uses (along with a shim)
to emulate GNU readline (since they can't ship the real readline
lib due to GPL). I haven't looked at how clean/portable libedit is
outside of BSD OSes, but that might be another option for those
that expect a more featureful line editing implementation.

The implementation I made for linenoise should serve as a proof of
concept for implementing support for any of the other line editing libs.

Best,
  John

On Wed, May 20, 2020 at 11:06:50AM -0400, Giacomo Fiorin wrote:
> Hi John, I just built VMD using the -DVMDLINENOISE flag and linenoise.c
> added to the Makefile, and manually edited the "vmd" launcher script after
> building to remove rlwrap.
> I can confirm that with linenoise I can access the history of VMD commands
> by using the up and down arrows, and move the cursor left or right using
> the corresponding arrows. Two of the most basic readline keys (Ctrl-a
> and Crtr-e, equivalent to Home and End) are able to navigate at the
> beginning and the end of the current line.  Also, Ctrl-h and Backspace
> delete the last character and Ctrl-l correctly clears the screen.
> Here are several things that differ from readline (details may be specific
> to my build on CentOS 7 with gcc 4.8):
>
> * Word navigation (Alt-f and Alt-b, or Ctrl-Left and Ctrl-Right) is not
> supported.
> * Ctrl-k (kill aka cut) is supported, but not Ctrl-y (yank, aka paste).
> * Tab inserts a tab, and does not autocomplete. There may be something
> wrong in my build, since this is actually an advertised feature in the
> linenoise README.
> * There is no persistent history (people's opinions on the importance of
> this feature may differ).
>
> I used vmd -dispdev text, both with TERM=xterm-256color (default in
> gnome-terminal) and with TERM=xterm set by hand.
> Assuming that tab completion can be fixed, I'm frustrated by the lack of
> an explicit list of supported features: IMO, "the usual key bindings" is
> not sufficient. Also IMO, word navigation and copy/paste are essential
> features of command-line editing.
> Overall, I would still prefer using rlwrap over linenoise given the
> choice.
> I would definitely welcome the ability to turn rlwrap on/off based on an
> environment variable, the default value of which should be based on most
> people's preference. One quirk that I noticed was that rlwrap was
> interfering with the input/output channels handled by GNU parallel, which
> I use sometimes to process a bunch of trajectory files using the same
> script. Using a custom vmd script where I stripped the rlwrap part fixed
> that problem for me, but I would very much welcome an environment variable
> for this.
> Thanks for pointing out this feature to us, please let me know if I can
> provide anything else.
> Giacomo
> On Wed, May 20, 2020 at 3:55 AM John Stone <[1]johns_at_ks.uiuc.edu> wrote:
>
> Axel, et al.,
> Â Since people have recently been begging me to include
> 'rlwrap' with VMD by default I revisited the current crop
> of GNU readline alternatives unencumbered by problematic
> licenses.
>
> To my delight, I managed to find an input editing library
> that is very minimalistic-but-usable, with a BSD license,
> called "linenoise":
> Â [2]https://github.com/antirez/linenoise
>
> I've made initial modifications to VMD to support it,
> and thought I'd see what people think about this as an
> alternative to our current strategy of 'rlwrap' autodetection.Â
> It's in the current publically accessible VMD CVS tree, but I've
> also attached the current TclTextInterp.[Ch] files.
>
> If people think this is as good as rlwrap, and it holds up in testing,
> I would like to consider changing the behavior of the VMD
> startup scripts to use rlwrap only when the user requests it
> specifically (e.g. via a special env variable), which would
> also disable the built-in command editing at the same time.
>
> I've made an effort to maintain proper special handling of
> console redirection, MPI builds of VMD, and other cases by
> integrating the new console support with our existing code,
> but I need to run tests on several parallel MPI platforms and
> such to validate that it works as expected in these special cases.
>
> The new code is enabled by compiling with -DVMDLINENOISE
> and hacking in linenoise.c to the generated VMD
> Makefile manually at present.
>
> I haven't yet done a Windows build with this library,
> so that remains a future challenge when I get myh Windows x64
> build system completely setup.
>
> Best,
> Â John
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [3]http://www.ks.uiuc.edu/~johns/Â Â Â Â Â Â Phone: 217-244-3349
> [4]http://www.ks.uiuc.edu/Research/vmd/Â Â Â
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Research collaborator, National Institutes of Health, Bethesda, MD
> [5]http://goo.gl/Q3TBQU
> [6]https://github.com/giacomofiorin
>
> References
>
> Visible links
> 1. mailto:johns_at_ks.uiuc.edu
> 2. https://github.com/antirez/linenoise
> 3. http://www.ks.uiuc.edu/~johns/
> 4. http://www.ks.uiuc.edu/Research/vmd/
> 5. http://goo.gl/Q3TBQU
> 6. https://github.com/giacomofiorin 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/