Re: Using an alternative python to build python modules

[Kyle Andrews]

Dear Edouard and Wojtek,

Thank you very much for your generous suggestions!

I would like to give you an update to share the state of my still
incomplete understanding after thinking about them.

With regards to this sort of thing:

```
(package-input-rewriting/spec
 `(("python-prompt-toolkit" . ,(const python-prompt-toolkit-2)))))
```

I did not try this yet because I don't understand it yet. My confusion
stems from the fact that python is not in the transitive inputs of any
python package. 

```
(use-modules (gnu packages) (gnu packages python))
,pretty-print (package-transitive-inputs python)
```

How could modifying the graph have any effect?

Instead I tried to go down the package-with-python2 route since it APTED
claimed it was tested on python 2.7. Unfortunately, I ran into many
other errors where different python packages in the transitive inputs of
python-numpy failed because they were using various python 3 syntaxes.

Now I am trying to figure out how to best go about trying with python 3
instead. One issue I am not sure how to get around is the
python?-variant property convention. It is not clear to me how to write
one for an inferior python for use with
`package-with-explicit-python'.

I will keep you posted if I make any breakthroughs. I'm really eager to
be able to replace conda with guix.

Best Regards,
Kyle

Edouard Klein <edou@rdklein.fr> writes:

> As an example in this line of thought, a long time ago I submitted a
> patch (since then reverted as it broke a lot of things) to use an
> obsolete version of a python module, which was the only one that worked
> with a specific module that hadn't updated its dependencies:
>
> https://git.savannah.gnu.org/cgit/guix.git/commit/?id=32ba87c14fd5e5b54d95211cd9a159d568ce7c67
>
> Look at the following lines:
>
> #+begin_src scheme
> (define-public prompt-toolkit-2-instead-of-prompt-toolkit
>   (package-input-rewriting/spec
>    `(("python-prompt-toolkit" . ,(const python-prompt-toolkit-2)))))
> #+end_src
>
> If instead of replacing "python-prompt-toolkit" with
> python-prompt-toolkit-2, you could replace "python" with the version of
> python you want to use, package-input-rewriting would then handle the
> work of changing the python package anywhere it appears in any
> dependency of your manifest.
>
> You can then end your manifest with
> (python-3.6-instead-of-python python-apted)
>
> Cheers,
>
> Edouard.
>
>
> Wojtek Kosior via <help-guix@gnu.org> writes:
>
>> [[PGP Signed Part:Undecided]]
>> Hi Kyle,
>>
>> Have you looked at the (package-input-rewriting) procedure described
>> towards the bottom of "Defining Package Variants"[1]?
>>
>> You might also like to look at the not-exported
>> (package-with-explicit-python) proc defined in
>> guix/build-system/python.scm[2]. It is used to produce python2 variants
>> of packages but I suppose it would also work for swapping the minor
>> versions of python3.
>>
>> Good luck with your task :)
>>
>> Wojtek
>>
>> [1] https://guix.gnu.org/manual/en/html_node/Defining-Package-Variants.html
>> [2] 
>> https://git.savannah.gnu.org/cgit/guix.git/tree/guix/build-system/python.scm?id=b544f460989a6189af111bb3ff6752cabdf23abc#n82
>>
>> -- (sig_start)
>> website: https://koszko.org/koszko.html
>> PGP: https://koszko.org/key.gpg
>> fingerprint: E972 7060 E3C5 637C 8A4F  4B42 4BC5 221C 5A79 FD1A
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>> c2luIHNlcGFyYXRlZCBtZSBmcm9tIEhpbQ==
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>> U2hhbGwgSSBiZWNvbWUgSGlzIGZyaWVuZD8=
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>>
>>
>> On Fri, 17 Feb 2023 21:27:39 +0000
>> Kyle Andrews <kyle@posteo.net> wrote:
>>
>>> Dear Guix,
>>>
>>> I want to use the python-apted package in my manifest. That package is
>>> not in Guix, but can readily be fetched from:
>>>
>>> ```
>>> guix import pypi APTED > python-apted.scm
>>> ```
>>>
>>> I just had to prefix the following modules to turn that into a package
>>> definition as well as a manifest.
>>>
>>> ```
>>> (use-modules (guix packages)
>>>          (guix download)
>>>          (guix licenses)
>>>          (guix profiles)
>>>          (gnu packages)
>>>          (guix build-system python))
>>> ```
>>>
>>> During my original testing of my scientific workflow I discovered that
>>> there was a bug introduced to the APTED package which was caused by a
>>> change in how python worked under the hood. As a result, the APTED
>>> package only advertises compatibility with python versions less than
>>> 3.7. So, I would like to use python 3.6 to be on the safe side.
>>>
>>> I also want to include 60+ other packages in my manifest which are
>>> "current" with the Guix repository and included within it. For
>>> situations like this it would be really convenient if it were possible
>>> to pass a version of python to python-build-system. Then, I hope all I
>>> would have to do is pass another another defined variant of the python
>>> package (e.g. called python-3.6) into that build-system argument.
>>>
>>> For example:
>>>
>>> ```
>>> (build-system python-build-system #:python python-3.6)
>>> ```
>>>
>>> That would be quite convenient and in line with the level of complexity
>>> I was faced with when I took the conda approach before trying to use
>>> Guix. Unfortunately, this functionality doesn't seem to be provided out
>>> of box and I am seeking help in the hopes that there is an easy way to
>>> do it.
>>>
>>> Am I thinking about this right?
>>>
>>> Thanks,
>>> Kyle
>>>
>>> P.S.
>>>
>>> APTED claims to also be able to run on top of python-2.7 so maybe that
>>> fact could be used to simplify this specific issue. I just wanted to
>>> discuss the general problem first because I really want Guix to gain
>>> broad traction within the scientific community.
>>>
>>> P.P.S.
>>>
>>> Here is a pretend manifest where I would love guidance on how to make
>>> python-apted get built in the context of python-2.7 or ideally
>>> python-3.6 even though the latest version of python is python-3.9 (where
>>> APTED doesn't always work).
>>>
>>> ```
>>> (use-modules (guix packages)
>>>          (guix download)
>>>          (guix licenses)
>>>          (guix profiles)
>>>          (gnu packages)
>>>          (guix build-system python))
>>>
>>> (define-public python-apted
>>>   (package
>>>     (name "python-apted")
>>>     (version "1.0.3")
>>>     (source (origin
>>>               (method url-fetch)
>>>               (uri (pypi-uri "apted" version))
>>>               (sha256
>>>                (base32
>>>             "1sawf6s5c64fgnliwy5w5yxliq2fc215m6alisl7yiflwa0m3ymy"))))
>>>     (build-system python-build-system)
>>>     (arguments '(#:tests? #f))
>>>     (home-page "https://github.com/JoaoFelipe/apted";)
>>>     (synopsis "APTED algorithm for the Tree Edit Distance")
>>>     (description "APTED algorithm for the Tree Edit Distance")
>>>     (license expat)))
>>>
>>> (concatenate-manifests
>>>  (list (specifications->manifest (list "r" "r-dplyr" "r-reticulate"))
>>>        (packages->manifest (list python-apted))))
>>> ```
>>>
>>
>>
>> [[End of PGP Signed Part]]