python package dependencies conflict, pydot, ipython and pyparsings

python package dependencies conflict, pydot, ipython and pyparsings

[OLIVER HENRIOT]

Hi Guix! 

I'm trying to use both python-pydot and python-ipython and I'm stumbling accross a dependency problem. Pydot specifies pyparsings 2.4.7 as a propagated input. Ipython requires version 3.0.6. 

guix package: error: profile contains conflicting entries for python-pyparsing 
guix package: error: first entry: python-pyparsing@2.4.7 /gnu/store/m7gzn7yw5g6f3ba3mrkc55pifl757hrb-python-pyparsing-2.4.7 
guix package: error: ... propagated from python-pydot@1.4.2 
guix package: error: second entry: python-pyparsing@3.0.6 /gnu/store/wlmf5spfdmsjiw6cx30h0rpydfpz3gil-python-pyparsing-3.0.6 
guix package: error: ... propagated from python-packaging@21.3 
guix package: error: ... propagated from python-sphinx@5.1.1 
guix package: error: ... propagated from python-numpydoc@1.5.0 
guix package: error: ... propagated from python-ipython@8.5.0 

I thought naively that both versions could coexist (they are both present in the store) but there is visibly some magic missing to make this work within my manifest. 

I did a dirty hack, copied the content of pydot from graphviz.scm to a personal channel repository package, edited to remove the reference to the pyparsing version and it installs nicely alongside ipython and all the other the packages in my manifest (I did have to disable the tests, `delete 'check)` instead of the existing `replace 'check) sequence as it genrated errors but it should have no impact on dependencies I presume and re-introducing checks "just" requires debugging). Relevant excerpt from my dirty hack package definition: 

(define-public my-python-pydot 
(package 
(name "my-python-pydot") 
(version "1.4.2") 
(source 
(origin 
(method url-fetch) 
(uri (pypi-uri "pydot" version)) 
(sha256 
(base32 
"0z80zwldf7ffkwrpm28hixsiqp3053j7g281xd6phmnbkfiq3014")))) 
(build-system python-build-system) 
(arguments 
'(#:phases 
(modify-phases %standard-phases 
;; checks disabled for testing 
(delete 'sanity-check) 
(delete 'check)))) 
(propagated-inputs 
(list python-pyparsing)) 
(home-page "https://github.com/pydot/pydot") 
(synopsis "Python interface to Graphviz's DOT language") 
(description 
"Pydot provides an interface to create, handle, modify and process 
graphs in Graphviz's DOT language, written in pure Python.") 
(license license:expat))) 

Pydot can then be imported in the python interpreter and a simple graph as given on the project's pypi page ( [ https://pypi.org/project/pydot/ | https://pypi.org/project/pydot/ ] ) works so I presume this is functionnal (haven't run further tests, I don't know pydot syntax well enough). Is there a reason I have missed to specify this precise version of pyparsings as a dependency for pydot in the official repo? If so, can I nonetheless have both ipython and pydot at the same time in my manifest using some magic trick? 

Thanks! 

Oliver 

Oliver Henriot OSUG - ISTerre 
ISDeform / RENAg 


1381 rue de la piscine 
33 (0)4 57 42 18 62 
[ https://www.isterre.fr/ | isterre.fr ] [ http://www.univ-grenoble-alpes.fr/ ] 

Re: python package dependencies conflict, pydot, ipython and pyparsings

[Simon Tournier]

Hi Oliver,

Sorry for the late reply.

On Mon, 17 Jul 2023 at 15:28, OLIVER HENRIOT <oliver.henriot@univ-grenoble-alpes.fr> wrote:

> guix package: error: profile contains conflicting entries for python-pyparsing 
> guix package: error: first entry: python-pyparsing@2.4.7 /gnu/store/m7gzn7yw5g6f3ba3mrkc55pifl757hrb-python-pyparsing-2.4.7 
> guix package: error: ... propagated from python-pydot@1.4.2 
> guix package: error: second entry: python-pyparsing@3.0.6 /gnu/store/wlmf5spfdmsjiw6cx30h0rpydfpz3gil-python-pyparsing-3.0.6 
> guix package: error: ... propagated from python-packaging@21.3 
> guix package: error: ... propagated from python-sphinx@5.1.1 
> guix package: error: ... propagated from python-numpydoc@1.5.0 
> guix package: error: ... propagated from python-ipython@8.5.0 
>
> I thought naively that both versions could coexist (they are both
> present in the store) but there is visibly some magic missing to make
> this work within my manifest.

Well, that is a “well-known“ issue coming from propagated-inputs.  And
sadly, there is few workarounds to my knowledge.


>                                       Is there a reason I have missed
> to specify this precise version of pyparsings as a dependency for
> pydot in the official repo?

Well, python-pyparsing@2.4.7 is the last version supporting Python 2,
but this should not be blocking and maybe removed.  However, the package
python-gixy contains the comment:

             ;; XXX: gixy is incompatible with pyparsing >= 3.x.
             ;; See <https://github.com/yandex/gixy/pull/132> and
             ;; <https://github.com/yandex/gixy/pull/122>.

and the package python-pydot contains the comment [1]:

     ;; XXX: Two test failures with 3.0+:
     ;; https://github.com/pydot/pydot/issues/277

Somehow the issue is upstream. ;-)

1: <https://git.savannah.gnu.org/cgit/guix.git/tree/gnu/packages/graphviz.scm?id=d1c811268d130041b5af1ba8f8b41cdafe8f08b5#n348>


>                             If so, can I nonetheless have both ipython
> and pydot at the same time in my manifest using some magic trick?  

Well, waiting a better solution, you can try --allow-collisions but (1)
there is no guarantee and (2) it can lead to “strange” behaviour.

Hope that helps,
simon