[bug#69579] [PATCH] gnu: python-joblib: Update to 1.3.2.

[Nicolas Graves]

On 2024-03-08 12:29, Vagrant Cascadian wrote:

> On 2024-03-06, Nicolas Graves wrote:
>> * gnu/packages/python-xyz.scm (python-joblib): Update to 1.3.2.
>> [build-system]: Update to pyproject-build-system.
>> [arguments]
>>   <#:phases>: Remove check phase.
>>   <#:test-flags>: Keep former test flag.
>> [propagated-inputs]: Add python-psutil.
>>
>> Change-Id: Ide110a19431b1d26e1d7dd8d1adc3b3f0f417749
>> ---
>>  gnu/packages/python-xyz.scm | 22 ++++++++--------------
>>  1 file changed, 8 insertions(+), 14 deletions(-)
>>
>> diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
>> index 46232d3c98..122dca6e4e 100644
>> --- a/gnu/packages/python-xyz.scm
>> +++ b/gnu/packages/python-xyz.scm
>> @@ -6169,26 +6169,20 @@ (define-public python-pystitcher
>>  (define-public python-joblib
>>    (package
>>      (name "python-joblib")
>> -    (version "1.1.1")
>> +    (version "1.3.2")
>>      (source (origin
>>                (method url-fetch)
>>                (uri (pypi-uri "joblib" version))
>>                (sha256
>>                 (base32
>> -                "0019p280s2k941mihl67l7y6amwx86639xp3zvpsg1lmyish67rh"))))
>> -    (build-system python-build-system)
>> +                "1cbjjzsh9hzaqr2cqja95673p7j88b8bd02hjpkq8xz147k6by4j"))))
>> +    (build-system pyproject-build-system)
>>      (arguments
>> -     `(#:phases
>> -       (modify-phases %standard-phases
>> -         (replace 'check
>> -           (lambda* (#:key tests? #:allow-other-keys)
>> -             (when tests?
>> -               (setenv "JOBLIB_MULTIPROCESSING" "0")
>> -               (invoke "pytest" "-v" "joblib"
>> -                       ;; We disable this test to avoid having to depend on 
>> ipython/jupyter
>> -                       "-k" "not 
>> test_parallel_call_cached_function_defined_in_jupyter")))))))
>> -    (native-inputs
>> -     (list python-pytest))
>> +     (list
>> +      #:test-flags  ; disabled to avoid having to depend on ipython/jupyter
>> +      #~(list "-k" "not 
>> test_parallel_call_cached_function_defined_in_jupyter")))
>> +    (native-inputs (list python-pytest))
>> +    (propagated-inputs (list python-psutil))
>>      (home-page "https://joblib.readthedocs.io/";)
>>      (synopsis "Using Python functions as pipeline jobs")
>>      (description
>> -- 
>> 2.41.0
>
> I did a local test build, and tried to build the moderately large list
> of dependents (~90 if I recall), which seems to fix some builds and
> introduces some new failures, and some still fail in both cases...

For the packages that were failing before but not after applying the
patch, I don't see why they're relevant, so I'll ignore them here.

For the following packages, they fail in both cases and are not about
this patch, I do not consider them in the review:

> `/gnu/store/1f7fjigxbran1bn1lwvy4v7vfdfz09rj-python-pingouin-0.5.2.drv',
> `/gnu/store/8gkvizln2kjpdjn4m89vws9xpj3f62dw-python-scikit-allel-1.3.5.drv',

The following packages build properly on my side, so they either failed
because of some determinism or system issue, or were simply fixes in the
meantime :

> `/gnu/store/ijg5hbhwj3h89bzh0n9l8zrg595bnscz-python-openturns-1.21.3.drv',
> `/gnu/store/cm2dr4npm0bn9w7xiyrfizcq097laibw-python-pyts-0.13.0.drv',
> `/gnu/store/n0f7flida4sag8ifsvmczg4r33r07ry8-python-pytorch-geometric-2.4.0.drv',
> `/gnu/store/yl5rndzgfprfr0lpcrhdwmvix61zyccr-python-poliastro-0.17.0.drv'

Now there are still some relevant failures, but they seem to come from
changes in the meantime, you probably have some patches differing
between both tries, since python-matplotlib-documentation is not the
same version between both.

> `/gnu/store/4g2r98m4d5zkwvlgghdqgvnda8p5b8lf-tadbit-1.0.1-1.5c4c1dd.drv',

>> File 
>> "/gnu/store/vkj58jsab13ybc871aiqrxdkmi54ijxn-tadbit-1.0.1-1.5c4c1dd/lib/python3.10/site-packages/pytadbit/mapping/restriction_enzymes.py",
>>  line 12, in <module>
>>    from scipy.stats import binom_test

The error in tadbit I get actually comes from scipy update. This should
be fixed in a tadbit-specific patch or update, rather than here.
    
> `/gnu/store/h5l1cymbzrz2havw6ygn0gafxwvf5k9m-python-matplotlib-documentation-3.8.2.drv',

This one is about missing python-pyyaml and unsubmitted python-sphinx-design
packages at least. This should be fixed in a matplotlib-specific patch,
rather than here.

I've also tried to rebuild all dependent packages on
447e9c96259e8fa15a828de9b2dd3400e2ffafe6, I also see the following
failures among dependents :
- music21@7.1.0 : missing dependency on numpy, to fix in a dedicated
patch 
- python-orange-canvas-core : probably some qt version mismatch here, to
fix in a dedicated patch

All in all, I don't see a precise reason why this patch is responsible
for any of the failures.

-- 
Best regards,
Nicolas Graves