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Re: Need some help packaging parts of a scientific workflow


From: Kyle
Subject: Re: Need some help packaging parts of a scientific workflow
Date: Wed, 29 Mar 2023 04:46:37 +0000

Thanks, Philip! Your descriptions really made it click for me.

Might you give a small example of what you mean by adding an error phase? That 
sounds like an important debugging strategy, but I can't quite grasp what it 
would actually look like. I'm curious what kinds of data you are printing out. 

On March 23, 2023 5:30:11 PM EDT, Philip McGrath <philip@philipmcgrath.com> 
wrote:
>Hi Kyle,
>
>On Wed, Mar 22, 2023, at 5:29 PM, Kyle Andrews wrote:
>> Dear Guix,
>>
>> Part of my scientific workflow involves compiling a small Racket script
>> for a command line program into its executable and placing that on
>> PATH.
>
>I am always glad to hear of more people using Guix and Racket together!
>
>> I had bundled this script inside an R package which made sure it
>> got compiled and everything was correctly configured at library load
>> time.
>>
>
>Tangential to your actual question, I think this is not necessarily a terrible 
>practice. There is not much difference between running `my-script` and running 
>`racket -y "path/to/my-script.rkt"`, and, if you do that or `raco make` during 
>the build process of your R package, you'll get compiled files properly. There 
>are tradeoffs to weigh, including support for R users without Guix. But there 
>are also good reasons to decide to separate the Racket script from the R 
>library, so that's what I'll explain below.
>
>> From reading the documentation a lot, I think the actual compilation
>> step can be done using the "invoke" procedure like so:
>>
>> ```
>> (invoke "raco" "exe" "{package_location}/custom-shell-tool.rkt")
>> ```
>>
>> What I'm struggling with the most is understanding all the boilerplate
>> code I need to place around that fundamental call.
>>
>
>I'll start with a working example suitable for `guix build -f`, then answer 
>your specific questions.
>
>```
>;; SPDX-License-Identifier: (CC0-1.0 OR (Apache-2.0 OR MIT))
>;; SPDX-FileCopyrightText: Philip McGrath <philip@philipmcgrath.com>
>
>(use-modules
> (gnu packages racket)
> (guix build-system copy)
> (guix gexp)
> (guix packages))
>
>(package
>  (name "racket-hello")
>  (version "1.0")
>  (source (plain-file "hello.rkt"
>                      "#lang racket (displayln '|Hello from Racket!|)"))
>  (inputs (list racket))
>  (build-system copy-build-system)
>  (arguments
>   (list
>    #:install-plan #~'(("hello" "bin/"))
>    #:phases
>    #~(modify-phases %standard-phases
>        (add-before 'install 'build
>          (lambda args
>            (invoke "raco" "exe" "hello.rkt"))))))
>  (home-page #f)
>  (synopsis "Hello world in Racket")
>  (description
>   "This is a trivial example of using @code{raco exe} with Guix.")
>  (license #f))
>```
>
>In fact this package would be a reasonable candidate for 
>`trivial-build-system`, but I've stuck with `copy-build-system` because the 
>boilerplate for `trivial-build-system` is very different than for all other 
>build systems.
>
>Likewise, I'm assuming you know how you want to build your executable, but you 
>might consider the `--launcher` flag for `raco exe` and an explicit call to 
>`raco make`: in particular, it might take use less total disk space than an 
>ELF executable.
>
>Note that you do have to use `racket`, not `racket-minimal`, because 
>`racket-minimal` doesn't include the `raco exe` command.
>
>>  (source
>>   (local-file "package_location")) ; how to refer to local files?
>
>In general, `local-file` is the right mechanism; specifics depend on your 
>situation, including how you are expecting your package definition to be used. 
>For a single file, `(local-file "path/to/script.rkt")` is probably what you 
>want, where the path is relative to the Guile file containing the `local-file` 
>expression. For a directory, consider the `#:recursive?` and `#:select?` 
>arguments.
>
>>         (invoke "raco" "exe"
>>          (string-append
>>           #$package-folder ; how to refer to the build itself?
>>           "custom-shell-tool.rkt"))))))
>
>The `unpack` phase from `gnu-build-system` handles this: if the package source 
>is a directory, you're inside a copy of it; if it's a file, you're in a 
>temporary directory containing it.
>
>>
>> I'm especially interested in figuring out how I can productively learn
>> to experiment productively with this stuff for myself.
>>
>
>Personally, I often insert a phase that calls `error` to stop the build, 
>perhaps printing out interesting values first, and use `guix build 
>--keep-failed` to explore the build environment.
>
>-Philip


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