Source: symfit
Version: 0.5.6-2
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: [email protected]
Usertags: ftbfs-20240319 ftbfs-trixie
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_test
> I: pybuild base:305: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build;
> python3.12 -m pytest tests
> ============================= test session starts
> ==============================
> platform linux -- Python 3.12.2, pytest-8.1.1, pluggy-1.4.0
> rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build
> configfile: pytest.ini
> collected 123 items
>
> tests/test_argument.py .... [
> 3%]
> tests/test_auto_fit.py ...... [
> 8%]
> tests/test_constrained.py .....s............ [
> 22%]
> tests/test_distributions.py .. [
> 24%]
> tests/test_finite_difference.py ........ [
> 30%]
> tests/test_fit_result.py .......... [
> 39%]
> tests/test_general.py .........s..............s...... [
> 64%]
> tests/test_global_opt.py .... [
> 67%]
> tests/test_minimize.py ...... [
> 72%]
> tests/test_minimizers.py F...... [
> 78%]
> tests/test_model.py ............ [
> 87%]
> tests/test_objectives.py ..... [
> 91%]
> tests/test_ode.py ........ [
> 98%]
> tests/test_support.py ..
> [100%]
>
> =================================== FAILURES
> ===================================
> ____________________________ test_custom_objective
> _____________________________
>
> recwarn = WarningsRecorder(record=True)
>
> def test_custom_objective(recwarn):
> """
> Compare the result of a custom objective with the symbolic result.
> :return:
> """
> # Create test data
> xdata = np.linspace(0, 100, 25) # From 0 to 100 in 100 steps
> a_vec = np.random.normal(15.0, scale=2.0, size=xdata.shape)
> b_vec = np.random.normal(100, scale=2.0, size=xdata.shape)
> ydata = a_vec * xdata + b_vec # Point scattered around the line 5 *
> x + 105
>
> # Normal symbolic fit
> a = Parameter('a', value=0, min=0.0, max=1000)
> b = Parameter('b', value=0, min=0.0, max=1000)
> x = Variable('x')
> y = Variable('y')
> model = {y: a * x + b}
>
> fit = Fit(model, xdata, ydata, minimizer=BFGS)
> fit_result = fit.execute()
>
> def f(x, a, b):
> return a * x + b
>
> def chi_squared(a, b):
> return np.sum((ydata - f(xdata, a, b))**2)
>
> # Should no longer raise warnings, because internally we practice
> # what we preach.
> fit_custom = BFGS(chi_squared, [a, b])
> > assert len(recwarn) == 0
> E assert 1 == 0
> E + where 1 = len(WarningsRecorder(record=True))
>
> tests/test_minimizers.py:120: AssertionError
> =============================== warnings summary
> ===============================
> symfit/core/operators.py:48
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/symfit/core/operators.py:48:
> SyntaxWarning: invalid escape sequence '\*'
> """
>
> symfit/core/support.py:296
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/symfit/core/support.py:296:
> SyntaxWarning: invalid escape sequence '\*'
> """
>
> symfit/core/printing.py:13
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/symfit/core/printing.py:13:
> DeprecationWarning: pkg_resources is deprecated as an API. See
> https://setuptools.pypa.io/en/latest/pkg_resources.html
> import pkg_resources
>
> ../../../../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:2871
> /usr/lib/python3/dist-packages/pkg_resources/__init__.py:2871:
> DeprecationWarning: Deprecated call to
> `pkg_resources.declare_namespace('mpl_toolkits')`.
> Implementing implicit namespace packages (as specified in PEP 420) is
> preferred to `pkg_resources.declare_namespace`. See
> https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
> declare_namespace(pkg)
>
> symfit/core/fit.py:32
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/symfit/core/fit.py:32:
> SyntaxWarning: invalid escape sequence '\_'
> """
>
> symfit/core/minimizers.py:211
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/symfit/core/minimizers.py:211:
> SyntaxWarning: invalid escape sequence '\*'
> '''
>
> symfit/core/minimizers.py:327
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/symfit/core/minimizers.py:327:
> SyntaxWarning: invalid escape sequence '\*'
> """
>
> symfit/core/minimizers.py:793
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/symfit/core/minimizers.py:793:
> SyntaxWarning: invalid escape sequence '\*'
> """
>
> symfit/core/fit_results.py:29
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/symfit/core/fit_results.py:29:
> SyntaxWarning: invalid escape sequence '\*'
> """
>
> symfit/core/objectives.py:389
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/symfit/core/objectives.py:389:
> SyntaxWarning: invalid escape sequence '\c'
> """
>
> tests/test_auto_fit.py: 3 warnings
> tests/test_constrained.py: 14 warnings
> tests/test_finite_difference.py: 1 warning
> tests/test_fit_result.py: 5 warnings
> tests/test_general.py: 16 warnings
> tests/test_minimizers.py: 2 warnings
> tests/test_objectives.py: 1 warning
> tests/test_ode.py: 1 warning
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/symfit/core/fit.py:278:
> DeprecationWarning: `product` is deprecated as of NumPy 1.25.0, and will be
> removed in NumPy 2.0. Please use `prod` instead.
> cov_matrix = self._covariance_matrix(best_fit_params,
>
> tests/test_auto_fit.py: 2 warnings
> tests/test_constrained.py: 13 warnings
> tests/test_finite_difference.py: 2 warnings
> tests/test_fit_result.py: 1 warning
> tests/test_general.py: 12 warnings
> tests/test_global_opt.py: 3 warnings
> tests/test_ode.py: 7 warnings
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/symfit/core/fit.py:301:
> DeprecationWarning: `product` is deprecated as of NumPy 1.25.0, and will be
> removed in NumPy 2.0. Please use `prod` instead.
> cov_matrix = self._covariance_matrix(best_fit_params,
>
> tests/test_general.py::test_likelihood_fitting_exponential
> /usr/lib/python3/dist-packages/_pytest/python.py:195: DeprecationWarning:
> `product` is deprecated as of NumPy 1.25.0, and will be removed in NumPy 2.0.
> Please use `prod` instead.
> result = testfunction(**testargs)
>
> -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
> =========================== short test summary info
> ============================
> FAILED tests/test_minimizers.py::test_custom_objective - assert 1 == 0
> ====== 1 failed, 119 passed, 3 skipped, 94 warnings in 102.13s (0:01:42)
> =======
> E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build; python3.12 -m pytest tests
> I: pybuild base:305: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build;
> python3.11 -m pytest tests
> ============================= test session starts
> ==============================
> platform linux -- Python 3.11.8, pytest-8.1.1, pluggy-1.4.0
> rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build
> configfile: pytest.ini
> collected 123 items
>
> tests/test_argument.py .... [
> 3%]
> tests/test_auto_fit.py ...... [
> 8%]
> tests/test_constrained.py .....s............ [
> 22%]
> tests/test_distributions.py .. [
> 24%]
> tests/test_finite_difference.py ........ [
> 30%]
> tests/test_fit_result.py .......... [
> 39%]
> tests/test_general.py .........s..............s...... [
> 64%]
> tests/test_global_opt.py .... [
> 67%]
> tests/test_minimize.py ...... [
> 72%]
> tests/test_minimizers.py F...... [
> 78%]
> tests/test_model.py ............ [
> 87%]
> tests/test_objectives.py ..... [
> 91%]
> tests/test_ode.py ........ [
> 98%]
> tests/test_support.py ..
> [100%]
>
> =================================== FAILURES
> ===================================
> ____________________________ test_custom_objective
> _____________________________
>
> recwarn = WarningsRecorder(record=True)
>
> def test_custom_objective(recwarn):
> """
> Compare the result of a custom objective with the symbolic result.
> :return:
> """
> # Create test data
> xdata = np.linspace(0, 100, 25) # From 0 to 100 in 100 steps
> a_vec = np.random.normal(15.0, scale=2.0, size=xdata.shape)
> b_vec = np.random.normal(100, scale=2.0, size=xdata.shape)
> ydata = a_vec * xdata + b_vec # Point scattered around the line 5 *
> x + 105
>
> # Normal symbolic fit
> a = Parameter('a', value=0, min=0.0, max=1000)
> b = Parameter('b', value=0, min=0.0, max=1000)
> x = Variable('x')
> y = Variable('y')
> model = {y: a * x + b}
>
> fit = Fit(model, xdata, ydata, minimizer=BFGS)
> fit_result = fit.execute()
>
> def f(x, a, b):
> return a * x + b
>
> def chi_squared(a, b):
> return np.sum((ydata - f(xdata, a, b))**2)
>
> # Should no longer raise warnings, because internally we practice
> # what we preach.
> fit_custom = BFGS(chi_squared, [a, b])
> > assert len(recwarn) == 0
> E assert 1 == 0
> E + where 1 = len(WarningsRecorder(record=True))
>
> tests/test_minimizers.py:120: AssertionError
> =============================== warnings summary
> ===============================
> symfit/core/operators.py:48
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/symfit/core/operators.py:48:
> DeprecationWarning: invalid escape sequence '\*'
> """
>
> symfit/core/support.py:296
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/symfit/core/support.py:296:
> DeprecationWarning: invalid escape sequence '\*'
> """
>
> symfit/core/printing.py:13
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/symfit/core/printing.py:13:
> DeprecationWarning: pkg_resources is deprecated as an API. See
> https://setuptools.pypa.io/en/latest/pkg_resources.html
> import pkg_resources
>
> ../../../../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:2871
> /usr/lib/python3/dist-packages/pkg_resources/__init__.py:2871:
> DeprecationWarning: Deprecated call to
> `pkg_resources.declare_namespace('mpl_toolkits')`.
> Implementing implicit namespace packages (as specified in PEP 420) is
> preferred to `pkg_resources.declare_namespace`. See
> https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
> declare_namespace(pkg)
>
> symfit/core/fit.py:32
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/symfit/core/fit.py:32:
> DeprecationWarning: invalid escape sequence '\_'
> """
>
> symfit/core/minimizers.py:211
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/symfit/core/minimizers.py:211:
> DeprecationWarning: invalid escape sequence '\*'
> '''
>
> symfit/core/minimizers.py:327
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/symfit/core/minimizers.py:327:
> DeprecationWarning: invalid escape sequence '\*'
> """
>
> symfit/core/minimizers.py:793
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/symfit/core/minimizers.py:793:
> DeprecationWarning: invalid escape sequence '\*'
> """
>
> symfit/core/fit_results.py:29
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/symfit/core/fit_results.py:29:
> DeprecationWarning: invalid escape sequence '\*'
> """
>
> symfit/core/objectives.py:389
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/symfit/core/objectives.py:389:
> DeprecationWarning: invalid escape sequence '\c'
> """
>
> tests/test_auto_fit.py: 5 warnings
> tests/test_constrained.py: 27 warnings
> tests/test_finite_difference.py: 3 warnings
> tests/test_fit_result.py: 6 warnings
> tests/test_general.py: 28 warnings
> tests/test_global_opt.py: 3 warnings
> tests/test_minimizers.py: 2 warnings
> tests/test_objectives.py: 1 warning
> tests/test_ode.py: 8 warnings
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/symfit/core/fit.py:256:
> DeprecationWarning: `product` is deprecated as of NumPy 1.25.0, and will be
> removed in NumPy 2.0. Please use `prod` instead.
> raw_dof = np.sum([np.product(shape) for shape in self.data_shapes[1]])
>
> tests/test_general.py::test_likelihood_fitting_exponential
> /usr/lib/python3/dist-packages/_pytest/python.py:195: DeprecationWarning:
> `product` is deprecated as of NumPy 1.25.0, and will be removed in NumPy 2.0.
> Please use `prod` instead.
> result = testfunction(**testargs)
>
> -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
> =========================== short test summary info
> ============================
> FAILED tests/test_minimizers.py::test_custom_objective - assert 1 == 0
> ====== 1 failed, 119 passed, 3 skipped, 94 warnings in 102.07s (0:01:42)
> =======
> E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build; python3.11 -m pytest tests
> dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12
> 3.11" returned exit code 13
The full build log is available from:
http://qa-logs.debian.net/2024/03/19/symfit_0.5.6-2_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20240319;[email protected]
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240319&[email protected]&allbugs=1&cseverity=1&ctags=1&caffected=1#results
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
