a guile based build tool at the base of a guile-build-system

a guile based build tool at the base of a guile-build-system

[Catonano]

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2018-04-23 10:20 GMT+02:00 Ludovic Courtès <ludovic.courtes@inria.fr>:

> Hello Ricardo & all!
>
> Ricardo Wurmus <rekado@elephly.net> skribis:
>
> > I’m happy to announce that the group I’m working with has released a
> > preprint of a paper on reproducibility with the title:
> >
> >     Reproducible genomics analysis pipelines with GNU Guix
> >     https://www.biorxiv.org/content/early/2018/04/11/298653
> >
> > We built a collection of bioinformatics pipelines and packaged them with
> > GNU Guix, and then looked at the degree to which the software achieves
> > bit-reproducibility (spoiler: ~98%), analysed sources of non-determinism
> > (e.g. time stamps), discussed experimental reproducibility at runtime
> > (e.g. random number generators, kernel+glibc interface, etc) and
> > commented on the idea of using “containers” (or application bundles)
> > instead.
>
> Very impressive piece of work!  I think it’s important to stress that
> reproducible builds is a crucial foundation for reproducible
> computational experiments, and this paper does a great job at this.
>
> Also nice that you show you can have these bit-reproducible pipelines
> formalized in Guix *and* produce a ready-to-use “container image.”
>
> Hopefully we can soon address the remaining sources of non-determinism
> shown in Table 3 (I think you already addressed some of them in the
> meantime, didn’t you?).
>
> The bit I’m less comfortable with is Autotools.  I do understand how it
> helps capture configure-time dependencies, and how it generally helps
> people package and use the software; I think it’s one of the best tools
> for the job.  However it’s also hard to learn and, whether it’s
> justified or not, it’s considered “scary.”
>
> Given the intended audience, I wonder how we could provide a simpler
> path to achieve the same goal.  It could be a set of Autoconf macros
> leading to high-level ‘configure.ac’ files without any line of shell
> code, or it could be Guix interpreting a top-level .scm or JSON file,
> both of which would ideally be easier to write for bioinformaticians.
>
> What are your thoughts on this?
>

I have explored the possibility to create a guile based tool for building
guile packages

That could be easily expanded to support non guile based projects

It could reproduce all thhe tests that Autoconf generated scripts perform

I thought it would be nice to reproduce the record format used in Guildhall

It seems to me that the pacages defined in pkg-list.scm files are not using
the standard srfi-9 syntax

I also noticed that the guix/records.scm file

So I embarked in the process of learning how the guile macros are used there

It was a tumble, substantially

I couldn't read the code, too much and too articulated

The guile manual was not very helpfful

So I took this article
https://www.cs.indiana.edu/~dyb/pubs/tr356.pdf

to a print shop to have it printed and be able to read it peacefully

I read it. so now I know at least what the whole thing is about

I made this little (< 7 Mb) footage of me expanding a guix defined macro
for creating a record
http://catonano.v22018025836661967.nicesrv.de/resources/videos/expanding.flv

Too bad, it expands the thing completely, so I end up with some code
creating and manipulating structures, rather than srffi-9 records

I remebered aout a macroexpand-1 macro doing only one pass of expansion but
that's in Clojure !
I remembered incorrectly !

So this is where I'm at and where I've been

A stumble in yakk shaving, substantially.

I could give up on macros and use srfi-9 records for now.

The next step would be to test if some guile deps are available (calling
the line I already have briefly discussed here)

should anyone be working on a guile based buld tool, I'd love them to make
their efforts known to the community, maybe publish a repo somewhere


>
> Anyway, kudos on this, thank you!
>
> Ludo’.
>
>

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