Bug#1114722: symfit: FTBFS with NumPy 2.3

Mon Sep 8 20:44:42 BST 2025

Source: symfit
Version: 0.5.6-3
Severity: important
User: debian-python at lists.debian.org
Usertags: numpy2.3
Tags: ftbfs, forky, sid

Dear maintainer,

During a test rebuild for NumPy 2.3, symfit failed to rebuild.

Log Summary:
-------------------------------------------------------------------------------
[...]
  warn("IPython parent '{0}' is not a writable location,"
reading sources... [ 19%] examples/ex_ODEModel
reading sources... [ 22%] examples/ex_bivariate_likelihood
/usr/lib/python3/dist-packages/IPython/paths.py:69: UserWarning: IPython parent '../..' is not a writable location, using a temp directory.
  warn("IPython parent '{0}' is not a writable location,"
reading sources... [ 26%] examples/ex_fourier_series
reading sources... [ 30%] examples/ex_interactive_guesses_ODE
reading sources... [ 33%] examples/ex_interactive_guesses_nD
reading sources... [ 37%] examples/ex_interactive_guesses_vector_2D
reading sources... [ 41%] examples/ex_mexican_hat
/usr/lib/python3/dist-packages/IPython/paths.py:69: UserWarning: IPython parent '../..' is not a writable location, using a temp directory.
  warn("IPython parent '{0}' is not a writable location,"
reading sources... [ 44%] examples/ex_multidataset_likelihood
reading sources... [ 48%] examples/ex_ode_system
/usr/lib/python3/dist-packages/IPython/paths.py:69: UserWarning: IPython parent '../..' is not a writable location, using a temp directory.
  warn("IPython parent '{0}' is not a writable location,"

Notebook error!

Versions
========

* Platform:         linux; (Linux-6.1.0-38-amd64-x86_64-with-glibc2.41)
* Python version:   3.13.7 (CPython)
* Sphinx version:   8.2.3
* Docutils version: 0.21.2
* Jinja2 version:   3.1.6
* Pygments version: 2.18.0

Last Messages
=============

    reading sources... [ 41%]
    examples/ex_mexican_hat

    reading sources... [ 44%]
    examples/ex_multidataset_likelihood

    reading sources... [ 48%]
    examples/ex_ode_system

Loaded Extensions
=================

* sphinx.ext.mathjax (8.2.3)
* alabaster (0.7.16)
* sphinx.ext.autodoc.preserve_defaults (8.2.3)
* sphinx.ext.autodoc.type_comment (8.2.3)
* sphinx.ext.autodoc.typehints (8.2.3)
* sphinx.ext.autodoc (8.2.3)
* sphinx.ext.viewcode (8.2.3)
* sphinx.ext.intersphinx (8.2.3)
* nbsphinx (0.9.5)

Traceback
=========

      File "/usr/lib/python3/dist-packages/nbsphinx/__init__.py", line 641, in parse
        raise NotebookError('\n'.join(lines))
    nbsphinx.NotebookError: CellExecutionError in examples/ex_ode_system.ipynb:
    ------------------
    k1_f.min, k1_f.max = 0, 1
    k1_r.min, k1_r.max = 0, 1
    k2_f.min, k2_f.max = 0, 1
    k2_r.min, k2_r.max = 0, 1

    fit = Fit(model, t=tdata, MM=data[MM], F=data[F],
              FMMF=None, FMM=None,
              sigma_F=sigma_data, sigma_MM=sigma_data)
    fit_result = fit.execute()
    print(fit_result)
    ------------------

    [0;31m---------------------------------------------------------------------------[0m
    [0;31mAttributeError[0m                            Traceback (most recent call last)
    Cell [0;32mIn[4], line 9[0m
    [1;32m      4[0m k2_r[38;5;241m.[39mmin, k2_r[38;5;241m.[39mmax [38;5;241m=[39m [38;5;241m0[39m, [38;5;241m1[39m
    [1;32m      6[0m fit [38;5;241m=[39m Fit(model, t[38;5;241m=[39mtdata, MM[38;5;241m=[39mdata[MM], F[38;5;241m=[39mdata[F],
    [1;32m      7[0m           FMMF[38;5;241m=[39m[38;5;28;01mNone[39;00m, FMM[38;5;241m=[39m[38;5;28;01mNone[39;00m,
    [1;32m      8[0m           sigma_F[38;5;241m=[39msigma_data, sigma_MM[38;5;241m=[39msigma_data)
    [0;32m----> 9[0m fit_result [38;5;241m=[39m [43mfit[49m[38;5;241;43m.[39;49m[43mexecute[49m[43m([49m[43m)[49m
    [1;32m     10[0m [38;5;28mprint[39m(fit_result)

    File [0;32m/build/reproducible-path/symfit-0.5.6/symfit/core/fit.py:574[0m, in [0;36mFit.execute[0;34m(self, **minimize_options)[0m
    [1;32m    566[0m [38;5;250m[39m[38;5;124;03m"""[39;00m
    [1;32m    567[0m [38;5;124;03mExecute the fit.[39;00m
    [1;32m    568[0m 
    [0;32m   (...)[0m
    [1;32m    571[0m [38;5;124;03m:return: FitResults instance[39;00m
    [1;32m    572[0m [38;5;124;03m"""[39;00m
    [1;32m    573[0m minimizer_ans [38;5;241m=[39m [38;5;28mself[39m[38;5;241m.[39mminimizer[38;5;241m.[39mexecute([38;5;241m*[39m[38;5;241m*[39mminimize_options)
    [0;32m--> 574[0m minimizer_ans[38;5;241m.[39mcovariance_matrix [38;5;241m=[39m [38;5;28;43mself[39;49m[38;5;241;43m.[39;49m[43mcovariance_matrix[49m[43m([49m
    [1;32m    575[0m [43m    [49m[38;5;28;43mdict[39;49m[43m([49m[38;5;28;43mzip[39;49m[43m([49m[38;5;28;43mself[39;49m[38;5;241;43m.[39;49m[43mmodel[49m[38;5;241;43m.[39;49m[43mparams[49m[43m,[49m[43m [49m[43mminimizer_ans[49m[38;5;241;43m.[39;49m[43m_popt[49m[43m)[49m[43m)[49m
    [1;32m    576[0m [43m[49m[43m)[49m
    [1;32m    577[0m [38;5;66;03m# Overwrite the DummyModel with the current model[39;00m
    [1;32m    578[0m minimizer_ans[38;5;241m.[39mmodel [38;5;241m=[39m [38;5;28mself[39m[38;5;241m.[39mmodel

    File [0;32m/build/reproducible-path/symfit-0.5.6/symfit/core/fit.py:301[0m, in [0;36mHasCovarianceMatrix.covariance_matrix[0;34m(self, best_fit_params)[0m
    [1;32m    292[0m [38;5;250m        [39m[38;5;124;03m"""[39;00m
    [1;32m    293[0m [38;5;124;03m        Class which impersonates ``base``, but which returns zeros[39;00m
    [1;32m    294[0m [38;5;124;03m        for the models Hessian. This will effectively result in the[39;00m
    [1;32m    295[0m [38;5;124;03m        calculation of the approximate Hessian by calculating[39;00m
    [1;32m    296[0m [38;5;124;03m        outer(J.T, J) when calling ``base.eval_hessian``.[39;00m
    [1;32m    297[0m [38;5;124;03m        """[39;00m
    [1;32m    299[0m     objective [38;5;241m=[39m HessApproximation([38;5;28mself[39m[38;5;241m.[39mobjective[38;5;241m.[39mmodel,
    [1;32m    300[0m                                   [38;5;28mself[39m[38;5;241m.[39mobjective[38;5;241m.[39mdata)
    [0;32m--> 301[0m     cov_matrix [38;5;241m=[39m [38;5;28;43mself[39;49m[38;5;241;43m.[39;49m[43m_covariance_matrix[49m[43m([49m[43mbest_fit_params[49m[43m,[49m
    [1;32m    302[0m [43m                                         [49m[43mobjective[49m[38;5;241;43m=[39;49m[43mobjective[49m[43m)[49m
    [1;32m    304[0m [38;5;28;01mreturn[39;00m cov_matrix

    File [0;32m/build/reproducible-path/symfit-0.5.6/symfit/core/fit.py:256[0m, in [0;36mHasCovarianceMatrix._covariance_matrix[0;34m(self, best_fit_params, objective)[0m
    [1;32m    254[0m rss [38;5;241m=[39m [38;5;241m2[39m [38;5;241m*[39m objective([38;5;241m*[39m[38;5;241m*[39mkey2str(best_fit_params))
    [1;32m    255[0m [38;5;66;03m# Degrees of freedom[39;00m
    [0;32m--> 256[0m raw_dof [38;5;241m=[39m np[38;5;241m.[39msum([[43mnp[49m[38;5;241;43m.[39;49m[43mproduct[49m(shape) [38;5;28;01mfor[39;00m shape [38;5;129;01min[39;00m [38;5;28mself[39m[38;5;241m.[39mdata_shapes[[38;5;241m1[39m]])
    [1;32m    257[0m dof [38;5;241m=[39m raw_dof [38;5;241m-[39m [38;5;28mlen[39m([38;5;28mself[39m[38;5;241m.[39mmodel[38;5;241m.[39mparams)
    [1;32m    258[0m [38;5;28;01mif[39;00m [38;5;28mself[39m[38;5;241m.[39mabsolute_sigma:
    [1;32m    259[0m     [38;5;66;03m# When interpreting as measurement error, we do not rescale.[39;00m

    File [0;32m/usr/lib/python3/dist-packages/numpy/__init__.py:795[0m, in [0;36m__getattr__[0;34m(attr)[0m
    [1;32m    792[0m     [38;5;28;01mimport[39;00m [38;5;21;01mnumpy[39;00m[38;5;21;01m.[39;00m[38;5;21;01mchar[39;00m [38;5;28;01mas[39;00m [38;5;21;01mchar[39;00m
    [1;32m    793[0m     [38;5;28;01mreturn[39;00m char[38;5;241m.[39mchararray
    [0;32m--> 795[0m [38;5;28;01mraise[39;00m [38;5;167;01mAttributeError[39;00m([38;5;124mf[39m[38;5;124m"[39m[38;5;124mmodule [39m[38;5;132;01m{[39;00m[38;5;18m__name__[39m[38;5;132;01m!r}[39;00m[38;5;124m has no attribute [39m[38;5;132;01m{[39;00mattr[38;5;132;01m!r}[39;00m[38;5;124m"[39m)

    [0;31mAttributeError[0m: module 'numpy' has no attribute 'product'

    You can ignore this error by setting the following in conf.py:

        nbsphinx_allow_errors = True

The full traceback has been saved in:
/tmp/sphinx-err-hds5bofy.log

To report this error to the developers, please open an issue at <https://github.com/sphinx-doc/sphinx/issues/>. Thanks!
Please also report this if it was a user error, so that a better error message can be provided next time.
make[1]: *** [debian/rules:8: override_dh_auto_build] Error 2
make[1]: Leaving directory '/build/reproducible-path/symfit-0.5.6'
make: *** [debian/rules:4: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2025-09-08T12:14:15Z

-------------------------------------------------------------------------------

The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here (for the next 30 days):
https://debusine.debian.net/debian/developers-roehling.numpy/artifact/2457210/

About the archive rebuild: The build was made on debusine.debian.net,
using sbuild.

You can find the build task here:
https://debusine.debian.net/debian/developers-roehling.numpy/work-request/164154/

If this is really a bug in one of the build-depends, please use
reassign and affects, so that this is still visible in the BTS web
page for this package.

Cheers
Timo