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Subject: bug#74015: 'guix shell --export-manifest' fails for some transformations
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Hi,

I notice this:

--8<---------------cut here---------------start------------->8---
$ cat manifest.scm
(use-modules (guix transformations) (guix packages)
             (guix download) (guix build-system r))

(define r-knitr
  (specification->package "r-knitr"))

(define r-knitr-other
  (package
    (inherit r-knitr)
    (version "1.47")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "knitr" version))
              (sha256
               (base32
                "1kx6g8ddbigwx3bmq771gwi3din3fxjn59l801904kjaz6dq9pgs"))))))

(define r-ggplot2
  (package
    (inherit
     ((package-input-rewriting `((,r-knitr . ,r-knitr-other)))
      (specification->package "r-ggplot2")))
    (name "my-ggplot")))

(define transform
  (options->transformation
    '((with-c-toolchain . "r-minimal=3Dgcc-toolchain@12")
      (with-c-toolchain . "r=3Dgcc-toolchain@12"))))

(packages->manifest
 (append
  (map specification->package
       (list "python" "python-numpy"))
  (map transform
       (list (specification->package "r")
             r-ggplot2))))

$ guix shell -m manifest.scm --export-manifest
guix shell: warning: transformation 'with-c-toolchain' had no effect on my-=
ggplot@HIDDEN
;; What follows is a "manifest" equivalent to the command line you gave.
;; You can store it in a file that you may then pass to any 'guix' command
;; that accepts a '--manifest' (or '-m') option.

(use-modules (guix transformations))

(define transform1
  (options->transformation
    '((with-c-toolchain . "r-minimal=3Dgcc-toolchain@12")
      (with-c-toolchain . "r=3Dgcc-toolchain@12"))))

(packages->manifest
  (list (specification->package "python")
        (specification->package "python-numpy")
        (transform1 (specification->package "r"))
        (transform1 (specification->package "my-ggplot"))))
--8<---------------cut here---------------end--------------->8---

Well, this is incorrect.  While I understand the approximation when
dealing with profiles built over time in the imperative way, here I am
missing why the transformation of =E2=80=99r-ggplot2=E2=80=99 is skipped.  =
And even the
export manifest is broken.

It=E2=80=99s skipped because:

--8<---------------cut here---------------start------------->8---
$ guix shell -m manifest.scm
$ grep ggplot $GUIX_ENVIRONMENT/manifest
     ("my-ggplot"
      "/gnu/store/x0jbmvg0nbl7lyk8zd938rq2c7c9qkn4-my-ggplot-3.5.1"
--8<---------------cut here---------------end--------------->8---

Please note that if the symbol =E2=80=99r-ggplot2=E2=80=99 is not named =E2=
=80=9Cmy-ggplot=E2=80=9D but
kept as =E2=80=99r-ggplot2=E2=80=9C:

        (define r-ggplot2
          ((package-input-rewriting `((,r-knitr . ,r-knitr-other)))
              (specification->package "r-ggplot2")))

then the bug is maybe worse because the exported manifest =E2=80=9Cworks=E2=
=80=9D but
without the transformation=E2=80=A6 which can be misleading and hard to det=
ect.

Well, I understand it=E2=80=99s hard to capture this kind of transformation.
Still, it appears to me as an half-baked feature. :-)

That=E2=80=99s annoying in some context as =E2=80=9Cguix pack --save-proven=
ance=E2=80=9D [1].
Even, it defeats the idea of a self-contained reproducible binary
container. ;-)

Maybe, aside the profile =E2=80=99manifest=E2=80=99 file, we could store al=
l the
manifests provided by the command line.  Something as:

    /gnu/store/xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx-profile/manifest
    /gnu/store/xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx-profile/manifest.orig1
    /gnu/store/xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx-profile/manifest.orig2
    =E2=80=A6

where manifest.orig1 and manifest.orig2 are the copy of files =E2=80=99foo.=
scm=E2=80=99
and =E2=80=99bar.scm=E2=80=99 from:

    -m foo.scm -m bar.scm

This way, the option --export-manifest could be improved.

WDYT?

Cheers,
simon

1: https://hpc.guix.info/blog/2021/10/when-docker-images-become-fixed-point

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From: help-debbugs@HIDDEN (GNU bug Tracking System)
To: Simon Tournier <zimon.toutoune@HIDDEN>
Subject: bug#74015: Acknowledgement ('guix shell --export-manifest' fails
 for some transformations)
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Date: Fri, 25 Oct 2024 17:09:02 +0000

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Subject: bug#74015: 'guix shell --export-manifest' fails for some transformations
Resent-From: Ludovic =?UTF-8?Q?Court=C3=A8s?= <ludo@HIDDEN>
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From: Ludovic =?UTF-8?Q?Court=C3=A8s?= <ludo@HIDDEN>
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 Oct 2024 19:08:17 +0200")
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Date: Sun, 10 Nov 2024 12:38:50 +0100
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Hi,

Simon Tournier <zimon.toutoune@HIDDEN> skribis:

> $ guix shell -m manifest.scm --export-manifest

=E2=80=98--export-manifest=E2=80=99 is meant to =E2=80=9Ctranslate=E2=80=9D=
 a command line, which it can
do faithfully; there=E2=80=99s no way it could possibly =E2=80=9Crecreate=
=E2=80=9D what
=E2=80=98manifest.scm=E2=80=99, which may contain arbitrary Scheme code (an=
d someone who
already has a =E2=80=98manifest.scm=E2=80=99 file probably doesn=E2=80=99t =
need
=E2=80=98--export-manifest=E2=80=99).

It=E2=80=99s necessarily a lossy process.  Some of the transformations
=E2=80=98manifest.scm=E2=80=99 uses may be recorded as metadata in manifest=
 entries, but
others, such as uses of =E2=80=98package-input-rewriting=E2=80=99 here, ine=
vitably get
lost.

I would close it as not-a-bug; WDYT?

Ludo=E2=80=99.

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Subject: bug#74015: 'guix shell --export-manifest' fails for some transformations
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From: Simon Tournier <zimon.toutoune@HIDDEN>
In-Reply-To: <87v7wvwc6t.fsf@HIDDEN> ("Ludovic =?UTF-8?Q?Court=C3=A8s?="'s message of "Sun, 10 Nov 2024 12:38:50 +0100")
References: <87a5eshzzy.fsf@HIDDEN> <87v7wvwc6t.fsf@HIDDEN>
Date: Sun, 10 Nov 2024 14:06:16 +0100
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Hi,

On Sun, 10 Nov 2024 at 12:38, Ludovic Court=C3=A8s <ludo@HIDDEN> wrote:

>> $ guix shell -m manifest.scm --export-manifest
>
> =E2=80=98--export-manifest=E2=80=99 is meant to =E2=80=9Ctranslate=E2=80=
=9D a command line, which it can
> do faithfully; there=E2=80=99s no way it could possibly =E2=80=9Crecreate=
=E2=80=9D what
> =E2=80=98manifest.scm=E2=80=99, which may contain arbitrary Scheme code (=
and someone who
> already has a =E2=80=98manifest.scm=E2=80=99 file probably doesn=E2=80=99=
t need
> =E2=80=98--export-manifest=E2=80=99).

Yes, one might need. :-)

As I explained: =C2=AB That=E2=80=99s annoying in some context as =E2=80=9C=
guix pack
--save-provenance=E2=80=9D [1].  Even, it defeats the idea of a self-contai=
ned
reproducible binary container. =C2=BB

For sure, I understand it=E2=80=99s hard to capture this kind of transforma=
tion.
Still, an improvement appears to me possible (see below).

1: https://hpc.guix.info/blog/2021/10/when-docker-images-become-fixed-point


> It=E2=80=99s necessarily a lossy process.

This is where I disagree. :-) I mean, yes I agree that building
profile/manifest is somehow a lossy process because some Scheme is
potentially evaluated on the road.  However, I am proposing: Aside the
profile =E2=80=99manifest=E2=80=99 file (lossy process), we could store all=
 the
manifests provided by the command line.  Something as:

    /gnu/store/xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx-profile/manifest
    /gnu/store/xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx-profile/manifest.orig1
    /gnu/store/xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx-profile/manifest.orig2
    =E2=80=A6

where manifest.orig1 and manifest.orig2 are the copy of files =E2=80=99foo.=
scm=E2=80=99
and =E2=80=99bar.scm=E2=80=99 from:

    -m foo.scm -m bar.scm

This way, the option --export-manifest could be improved, eventually.

In other word, I think that saving as-is the manifests costs almost
nothing and it paves the way to more robust self-contained binary packs.

Well, maybe this extra work could be only done when there is an option
=E2=80=99--save-provenance=E2=80=99 applied.

> I would close it as not-a-bug; WDYT?

I still think it=E2=80=99s a feature that it=E2=80=99s possible to improve.

Cheers,
simon

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From: Suhail Singh <suhailsingh247@HIDDEN>
In-Reply-To: <87serzxmpj.fsf@HIDDEN> (Simon Tournier's message of "Sun, 10
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Simon Tournier <zimon.toutoune@HIDDEN> writes:

> However, I am proposing: Aside the profile =E2=80=99manifest=E2=80=99 fil=
e (lossy
> process), we could store all the manifests provided by the command
> line.  Something as:
>
>     /gnu/store/xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx-profile/manifest
>     /gnu/store/xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx-profile/manifest.orig1
>     /gnu/store/xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx-profile/manifest.orig2
>     =E2=80=A6
>
> where manifest.orig1 and manifest.orig2 are the copy of files =E2=80=99fo=
o.scm=E2=80=99
> and =E2=80=99bar.scm=E2=80=99 from:
>
>     -m foo.scm -m bar.scm
>
> ...
>
> Well, maybe this extra work could be only done when there is an option
> =E2=80=99--save-provenance=E2=80=99 applied.

For --save-provenance, is your proposal that in addition to saving the
additional manifests, the commandline that was used would also be saved?

--=20
Suhail

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From: Simon Tournier <zimon.toutoune@HIDDEN>
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Hi,

On Tue, 12 Nov 2024 at 10:33, Suhail Singh <suhailsingh247@HIDDEN> wrote:
> Simon Tournier <zimon.toutoune@HIDDEN> writes:
>
>> However, I am proposing: Aside the profile =E2=80=99manifest=E2=80=99 fi=
le (lossy
>> process), we could store all the manifests provided by the command
>> line.  Something as:
>>
>>     /gnu/store/xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx-profile/manifest
>>     /gnu/store/xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx-profile/manifest.orig1
>>     /gnu/store/xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx-profile/manifest.orig2
>>     =E2=80=A6
>>
>> where manifest.orig1 and manifest.orig2 are the copy of files =E2=80=99f=
oo.scm=E2=80=99
>> and =E2=80=99bar.scm=E2=80=99 from:
>>
>>     -m foo.scm -m bar.scm
>>
>> ...
>>
>> Well, maybe this extra work could be only done when there is an option
>> =E2=80=99--save-provenance=E2=80=99 applied.
>
> For --save-provenance, is your proposal that in addition to saving the
> additional manifests, the commandline that was used would also be saved?

We could save the command line too using another file. :-)

Cheers,
simon

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From: Suhail Singh <suhailsingh247@HIDDEN>
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Simon Tournier <zimon.toutoune@HIDDEN> writes:

>> For --save-provenance, is your proposal that in addition to saving the
>> additional manifests, the commandline that was used would also be saved?
>
> We could save the command line too using another file. :-)

That would be helpful :)

Given an image generated with --save-provenance enabled, making it
easier for it to be reconstructed by another would certainly be useful.

-- 
Suhail

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Hi,

Simon Tournier <zimon.toutoune@HIDDEN> skribis:

> On Sun, 10 Nov 2024 at 12:38, Ludovic Court=C3=A8s <ludo@HIDDEN> wrote:
>
>>> $ guix shell -m manifest.scm --export-manifest
>>
>> =E2=80=98--export-manifest=E2=80=99 is meant to =E2=80=9Ctranslate=E2=80=
=9D a command line, which it can
>> do faithfully; there=E2=80=99s no way it could possibly =E2=80=9Crecreat=
e=E2=80=9D what
>> =E2=80=98manifest.scm=E2=80=99, which may contain arbitrary Scheme code =
(and someone who
>> already has a =E2=80=98manifest.scm=E2=80=99 file probably doesn=E2=80=
=99t need
>> =E2=80=98--export-manifest=E2=80=99).
>
> Yes, one might need. :-)
>
> As I explained: =C2=AB That=E2=80=99s annoying in some context as =E2=80=
=9Cguix pack
> --save-provenance=E2=80=9D [1].  Even, it defeats the idea of a self-cont=
ained
> reproducible binary container. =C2=BB

I see, but if you have the source =E2=80=98manifest.scm=E2=80=99, best prac=
tice is to
publish it.

>> It=E2=80=99s necessarily a lossy process.
>
> This is where I disagree. :-)

You are free to disagree but it=E2=80=99s a fact.

> I mean, yes I agree that building profile/manifest is somehow a lossy
> process because some Scheme is potentially evaluated on the road.
> However, I am proposing: Aside the profile =E2=80=99manifest=E2=80=99 fil=
e (lossy
> process), we could store all the manifests provided by the command
> line.  Something as:
>
>     /gnu/store/xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx-profile/manifest
>     /gnu/store/xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx-profile/manifest.orig1
>     /gnu/store/xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx-profile/manifest.orig2
>     =E2=80=A6
>
> where manifest.orig1 and manifest.orig2 are the copy of files =E2=80=99fo=
o.scm=E2=80=99
> and =E2=80=99bar.scm=E2=80=99 from:
>
>     -m foo.scm -m bar.scm

Hmm yes, maybe =E2=80=98guix pack -m manifest.scm --save-provenance=E2=80=
=99 could
arrange to put =E2=80=98manifest.scm=E2=80=99 inside the pack, similar to h=
ow =E2=80=98guix
system reconfigure=E2=80=99 inserts =E2=80=98configuration.scm=E2=80=99 ins=
ide the system.

I=E2=80=99m all for it!

Thanks,
Ludo=E2=80=99.

Last modified: Sun, 12 Jan 2025 05:45:02 UTC

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