Re: Guile + SWIG

[Paul Emsley]

Hi Linas,

Thanks for your reply.

Let me clarify if I can. I have many C++ functions that I would like to use 
from scheme. I am using
SWIG to generate wrappers for these functions, and these get added
at the "root module"

    http://www.swig.org/Doc3.0/Guile.html

    The default linkage is the simplest; nothing special is done. In this case
    the function SWIG_init() is exported. Simple linkage can be used in several 
ways:

    Embedded Guile, no modules. You want to embed a Guile interpreter into your
    program; all bindings made by SWIG shall show up in the root module. Then 
call
    SWIG_init() in the inner_main() function

So that is what I was trying to do. My understanding was that 
enhanced-ligand-coot-p
and its friends would be added so that their usage would be no different to 
list, string?,
map and any number of basic scheme functions. However something is amiss.

If I try this:
./coot
Enter `,help' for help.
scheme@(guile-user)> (load "test-embedding.scm")
(55555555555555 #f)

Now, if I install that in $prefix/share/guile/site
If I try this:
./coot
Enter `,help' for help.
scheme@(guile-user)> (use-modules (test-embedding))
While compiling expression:
In procedure module-lookup: Unbound variable: enhanced-ligand-coot-p
scheme@(guile-user)> 

Is that because the "compiler" doesn't know where enhanced-ligand-coot-p is? 
Maybe the compiler
is not my application, so that's why it's not there?

If that is the case, then can I not compile my .scm files? How to do that? Or 
can I somehow say
"don't worry that it's not there now, when the application runs, it will be 
there"?

Thanks,

Paul.

p.s. It's quite likely that Coot was used in the analysis of spike proteins 
from coronavirus
that lead to 2P and hexapro stabilization mutants, and they have been taken up 
by the pharmaceutical
companies and embedded into the mRNA or more conventional preps. So you can 
have some guile-1.8.8-based
technology squirted into your arm next week.


On Mon, 2021-04-05 at 10:27 -0500, Linas Vepstas wrote:
> Hi Paul,
> 
> Conventionally, a guile module would look something like
> 
> 
>  (define-module (test-embedding))
>  (use-modules (srfi srfi-1)) ; .. etc
> 
>  (define (enhanced-ligand-coot-p) #t) ; etc.
> 
>  (export enhanced-ligand-coot-p)
> 
> 
> In your example, you never explained how "enhanced-ligand-coot-p"
> magically showed up in your environment.
> 
> When a module is defined, it starts with a new environment. The module
> cannot access stuff you've defined previously; you would have to import
> it somehow.
> 
> --linas
> 
> 
> On Mon, 2021-04-05 at 11:24 +0100, Paul Emsley wrote:
> > Hi,
> > 
> > I am trying to bring my swigged Gtk2 + guile 1.8.8 + guile-gtk
> > application up to date and I'd like some help please.
> > 
> > My SWIG usage wraps many function, including
> > enhanced_coot_ligand_p(). I am confused between the difference
> > between
> > functions that are available from C/C++ and those from a scheme
> > script:
> > 
> > if my inner_main looks like this:
> > 
> > void inner_main(void *closure, int argc, char **argv) {
> > 
> >    SWIG_init();
> >    std::string handler_string = "(lambda (key . args) ";
> >    handler_string += "(display (list \"Error in proc:\" key \" args:
> > \" args)) (newline))";
> >    SCM handler = scm_c_eval_string(handler_string.c_str());
> >    std::string thunk_str = "(lambda() (display (list
> > 444444444444444444 (enhanced-ligand-coot-p))) (newline))\n";
> >    SCM thunk = scm_c_eval_string(thunk_str.c_str());
> >    scm_catch(SCM_BOOL_T, thunk, handler);
> >    gtk_main();
> > 
> > }
> > 
> > then I get on the terminal what I expected:
> > 
> > (444444444444444444 #f)
> > 
> > (i.e. enhanced-ligand-coot-p is evaluated)
> > 
> > 
> > if my inner_main looks like this:
> > void inner_main(void *closure, int argc, char **argv) {
> > 
> >    SWIG_init();
> >    std::string handler_string = "(lambda (key . args) ";
> >    handler_string += "(display (list \"Error in proc:\" key \" args:
> > \" args)) (newline))";
> >    SCM handler = scm_c_eval_string(handler_string.c_str());
> >    std::string thunk_str = "(use-modules (test-
> > embedding))\n";  //////////// different ///////////////
> >    SCM thunk = scm_c_eval_string(thunk_str.c_str());
> >    scm_catch(SCM_BOOL_T, thunk, handler);
> >    gtk_main();
> > 
> > }
> > 
> > then I get:
> > 
> > ;; compiling /home/paule/autobuild/Linux-pen-pre-release-
> > gtk3/share/guile/site/test-embedding.scm
> > ;;; test-embedding.scm:21:30: warning: possibly unbound variable
> > `enhanced-ligand-coot-p'
> > ;;; compiled /home/paule/.cache/guile/ccache/2.2-LE-8-
> > 3.A/home/paule/autobuild/Linux-pen-pre-release-
> > gtk3/share/guile/site/test-embedding.scm.go
> > ------------------- test embedding! -----------------------
> > Backtrace:
> >           18 (apply-smob/1 #<catch-closure 7f98d1436b20>)
> > In ice-9/boot-9.scm:
> >    2312:4 17 (save-module-excursion _)
> > In ice-9/eval-string.scm:
> >      38:6 16 (read-and-eval #<input: string 7f98d08acbd0> #:lang _)
> > In ice-9/eval.scm:
> >    721:20 15 (primitive-eval _)
> > In ice-9/psyntax.scm:
> >   1262:36 14 (expand-top-sequence _ _ _ #f _ _ _)
> >   1209:24 13 (parse _ (("placeholder" placeholder)) ((top) #(# # …))
> > …)
> >    285:10 12 (parse _ (("placeholder" placeholder)) (()) _ c&e (eval)
> > …)
> > In ice-9/boot-9.scm:
> >   3377:20 11 (process-use-modules _)
> >    222:17 10 (map1 (((test-embedding))))
> >   3378:31  9 (_ ((test-embedding)))
> >   2800:17  8 (resolve-interface (test-embedding) #:select _ #:hide _
> > …)
> > In ice-9/threads.scm:
> >     390:8  7 (_ _)
> > In ice-9/boot-9.scm:
> >   2726:13  6 (_)
> > In ice-9/threads.scm:
> >     390:8  5 (_ _)
> > In ice-9/boot-9.scm:
> >   2994:20  4 (_)
> >    2312:4  3 (save-module-excursion _)
> >   3014:26  2 (_)
> > In unknown file:
> >            1 (primitive-load-path "test-embedding" #<procedure
> > 7f98d…>)
> > In test-embedding.scm:
> >      19:0  0 (_)
> > 
> > test-embedding.scm:4:0: In procedure module-lookup: Unbound variable:
> > enhanced-ligand-coot-p
> > 
> > 
> > 
> > test-embedding.scm looks like this and is installed in
> > $prfx/share/guile/site
> > 
> > (display "------------- test embedding! ------------\n")
> > (display (list 55555555555555 (enhanced-ligand-coot-p)))
> > (newline)
> > 
> > 
> > So, inner_main() knows that enhanced-ligand-coot-p is available, but
> > the scheme script does not. I don't know how to
> > resolve this.
> > 
> > How do I get a list of the available functions?
> > 
> > Thanks in advance for your help.
> > 
> > Paul.
> > 
> > 
> >