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SciPy deprecation of "disp" in optimizer#3581

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skoudoro merged 3 commits intodipy:masterfrom
drammock:scipy-depr
Jun 28, 2025
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SciPy deprecation of "disp" in optimizer#3581
skoudoro merged 3 commits intodipy:masterfrom
drammock:scipy-depr

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@drammock drammock commented Jun 25, 2025

we're seeing an MNE-Python CI failure:

DeprecationWarning: scipy.optimize: The disp and iprint options of the L-BFGS-B solver are deprecated and will be removed in SciPy 1.18.0.

It's coming from the init of dipy.core.optimize.Optimizer. Full traceback:

Details 
        ../examples/inverse/morph_volume_stc.py failed leaving traceback:
    
        Traceback (most recent call last):
          File "/home/circleci/project/examples/inverse/morph_volume_stc.py", line 86, in <module>
            morph = mne.compute_source_morph(
                    ^^^^^^^^^^^^^^^^^^^^^^^^^
          File "<decorator-gen-501>", line 10, in compute_source_morph
          File "/home/circleci/project/mne/morph.py", line 258, in compute_source_morph
            shape, zooms, affine, pre_affine, sdr_morph = _compute_morph_sdr(
                                                          ^^^^^^^^^^^^^^^^^^^
          File "/home/circleci/project/mne/morph.py", line 1159, in _compute_morph_sdr
            ) = _compute_volume_registration(
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
          File "/home/circleci/project/mne/transforms.py", line 1862, in _compute_volume_registration
            moved_zoomed, reg_affine = affine_registration(
                                       ^^^^^^^^^^^^^^^^^^^^
          File "/home/circleci/python_env/lib/python3.12/site-packages/dipy/testing/decorators.py", line 201, in wrapper
            return convert_positional_to_keyword(func, args, kwargs)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
          File "/home/circleci/python_env/lib/python3.12/site-packages/dipy/testing/decorators.py", line 192, in convert_positional_to_keyword
            return func(*args, **kwargs)
                   ^^^^^^^^^^^^^^^^^^^^^
          File "/home/circleci/python_env/lib/python3.12/site-packages/dipy/align/_public.py", line 579, in affine_registration
            xform, xopt, fopt = affreg.optimize(
                                ^^^^^^^^^^^^^^^^
          File "/home/circleci/python_env/lib/python3.12/site-packages/dipy/testing/decorators.py", line 201, in wrapper
            return convert_positional_to_keyword(func, args, kwargs)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
          File "/home/circleci/python_env/lib/python3.12/site-packages/dipy/testing/decorators.py", line 192, in convert_positional_to_keyword
            return func(*args, **kwargs)
                   ^^^^^^^^^^^^^^^^^^^^^
          File "/home/circleci/python_env/lib/python3.12/site-packages/dipy/align/imaffine.py", line 1323, in optimize
            opt = Optimizer(
                  ^^^^^^^^^^
          File "/home/circleci/python_env/lib/python3.12/site-packages/dipy/testing/decorators.py", line 201, in wrapper
            return convert_positional_to_keyword(func, args, kwargs)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
          File "/home/circleci/python_env/lib/python3.12/site-packages/dipy/testing/decorators.py", line 192, in convert_positional_to_keyword
            return func(*args, **kwargs)
                   ^^^^^^^^^^^^^^^^^^^^^
          File "/home/circleci/python_env/lib/python3.12/site-packages/dipy/core/optimize.py", line 163, in __init__
            res = minimize(
                  ^^^^^^^^^
          File "/home/circleci/python_env/lib/python3.12/site-packages/scipy/optimize/_minimize.py", line 785, in minimize
            res = _minimize_lbfgsb(fun, x0, args, jac, bounds,
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
          File "/home/circleci/python_env/lib/python3.12/site-packages/scipy/optimize/_lbfgsb_py.py", line 381, in _minimize_lbfgsb
            warnings.warn("scipy.optimize: The `disp` and `iprint` options of the "
        DeprecationWarning: scipy.optimize: The `disp` and `iprint` options of the L-BFGS-B solver are deprecated and will be removed in SciPy 1.18.0.

This PR is my best guess as to the source of the problem, but I haven't yet looked closely to see if the same thing is happening elsewhere in dipy's codebase. Would be happy if a regular dipy contrib / maintainer took over this PR as it may be a while before I have time to do a thorough job of this.

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@drammock drammock mentioned this pull request Jun 25, 2025
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skoudoro commented Jun 25, 2025

Thank you for this @drammock.

Have these variables been replaced ? or completely removed ? I need to look at this

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drammock commented Jun 25, 2025

Have these variables been replaced ? or completely removed ?

I haven't investigated, so all I know is what the deprecation message said.

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skoudoro commented Jun 25, 2025

ok, Thank you for pointing that out, I will look into it 👍

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codecov bot commented Jun 25, 2025 •
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 83.86%. Comparing base (7547fe3) to head (92126b1).
Report is 11 commits behind head on master.

Additional details and impacted files

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@@            Coverage Diff             @@
##           master    #3581      +/-   ##
==========================================
- Coverage   83.87%   83.86%   -0.01%     
==========================================
  Files         161      161              
  Lines       24170    24181      +11     
  Branches     3640     3645       +5     
==========================================
+ Hits        20272    20279       +7     
- Misses       2935     2936       +1     
- Partials      963      966       +3
Files with missing lines Coverage Δ
dipy/align/imaffine.py 95.79% <100.00%> (ø)
dipy/reconst/qtdmri.py 93.50% <ø> (ø)

... and 3 files with indirect coverage changes

🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

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jhlegarreta commented Jun 26, 2025

Have not investigated the logs, but if any of the builds is using this version of scipy, an error should have been raised.

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skoudoro commented Jun 27, 2025

@drammock, Can you remove it here:

dipy/dipy/reconst/qtdmri.py

Line 1920 in 01c1abc

disp=False,
also

Then we can go ahead and merge this PR.

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skoudoro commented Jun 27, 2025

for backlog, related to scipy/scipy#23186

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drammock commented Jun 27, 2025

@drammock, Can you remove it here:

dipy/dipy/reconst/qtdmri.py

Line 1920 in 01c1abc

disp=False,

done

@skoudoro skoudoro added type:maintenance Maintenance tasks, such as release preparation type:backward compatibility Changes to maintain backward-compatibility labels Jun 28, 2025
@skoudoro skoudoro merged commit 984a2bb into dipy:master Jun 28, 2025
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skoudoro commented Jun 28, 2025

Thank you @drammock

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