Bug#1067234: symfit: autopkgtest regression with NumPy 1.26
On Mon, 8 Apr 2024 17:09:33 + Graham Inggs wrote: > Control: tags -1 + patch > > Hi Maintainer > > While asserting that no warnings are raised is a useful test for the > upstream developers, I don't think it makes sense for downstreams. > > I propose to disable the assertion as follows: > > --- a/tests/test_minimizers.py > +++ b/tests/test_minimizers.py > @@ -117,7 +117,7 @@ > # Should no longer raise warnings, because internally we practice > # what we preach. > fit_custom = BFGS(chi_squared, [a, b]) > - assert len(recwarn) == 0 > +# assert len(recwarn) == 0 > > fit_custom_result = fit_custom.execute() > > Please let me know if you are happy with a team upload and I will proceed. > As a bonus, I attach a patch that fixes several SyntaxWarnings that > occur with Python 3.12. Hey Graham, A team upload is fine, thanks for the fixes; please go ahead and upload them. OpenPGP_signature.asc Description: OpenPGP digital signature
Bug#1067234: symfit: autopkgtest regression with NumPy 1.26
Control: tags -1 + patch
Hi Maintainer
While asserting that no warnings are raised is a useful test for the
upstream developers, I don't think it makes sense for downstreams.
I propose to disable the assertion as follows:
--- a/tests/test_minimizers.py
+++ b/tests/test_minimizers.py
@@ -117,7 +117,7 @@
# Should no longer raise warnings, because internally we practice
# what we preach.
fit_custom = BFGS(chi_squared, [a, b])
-assert len(recwarn) == 0
+#assert len(recwarn) == 0
fit_custom_result = fit_custom.execute()
Please let me know if you are happy with a team upload and I will proceed.
As a bonus, I attach a patch that fixes several SyntaxWarnings that
occur with Python 3.12.
Regards
Graham
Description: Fix several SyntaxWarnings
Use raw strings to avoid invalid escape sequence
Author: Graham Inggs
Last-Update: 2024-04-06
--- a/symfit/core/operators.py
+++ b/symfit/core/operators.py
@@ -45,7 +45,7 @@
# return orig_ne(self.__class__, other)
def call(self, *values, **named_values):
-"""
+r"""
Call an expression to evaluate it at the given point.
Future improvements: I would like if func and signature could be buffered after the
--- a/symfit/core/support.py
+++ b/symfit/core/support.py
@@ -293,7 +293,7 @@
return jac
def key2str(target):
-"""
+r"""
In ``symfit`` there are many dicts with symbol: value pairs.
These can not be used immediately as \*\*kwargs, even though this would make
a lot of sense from the context.
@@ -321,4 +321,4 @@
base_str += 'd{}{}'.format(var, count if count > 1 else '')
return base_str
-sympy.Derivative.name = property(name)
\ No newline at end of file
+sympy.Derivative.name = property(name)
--- a/symfit/core/fit.py
+++ b/symfit/core/fit.py
@@ -29,7 +29,7 @@
from the model.
"""
def __init__(self, model, *ordered_data, absolute_sigma=None, **named_data):
-"""
+r"""
:param model: (dict of) sympy expression or ``Model`` object.
:param bool absolute_sigma: True by default. If the sigma is only used
for relative weights in your problem, you could consider setting it to
--- a/symfit/core/minimizers.py
+++ b/symfit/core/minimizers.py
@@ -208,7 +208,7 @@
:class:`~symfit.core.minimizers.DifferentialEvolution`.
"""
def __init__(self, *args, minimizers=None, **kwargs):
-'''
+r'''
:param minimizers: a :class:`~collections.abc.Sequence` of
:class:`~symfit.core.minimizers.BaseMinimizer` objects, which need
to be run in order.
@@ -324,7 +324,7 @@
def execute(self, bounds=None, jacobian=None, hessian=None,
constraints=None, *, tol=1e-9, **minimize_options):
-"""
+r"""
Calls the wrapped algorithm.
:param bounds: The bounds for the parameters. Usually filled by
@@ -790,7 +790,7 @@
return lbounds, ubounds
def execute(self, jacobian=None, method='trf', **minpack_options):
-"""
+r"""
:param \*\*minpack_options: Any named arguments to be passed to
:func:`scipy.optimize.least_squares`
"""
--- a/symfit/core/fit_results.py
+++ b/symfit/core/fit_results.py
@@ -26,7 +26,7 @@
:class:`~symfit.core.models.Model`'s.
"""
def __init__(self, model, popt, covariance_matrix, minimizer, objective, message, *, constraints=None, **minimizer_output):
-"""
+r"""
:param model: :class:`~symfit.core.models.Model` that was fit to.
:param popt: best fit parameters, same ordering as in model.params.
:param covariance_matrix: covariance matrix.
@@ -276,4 +276,4 @@
f_is = [f_is[var] for var in model.dependent_vars]
SS_res = np.sum([np.sum((y_i - f_i)**2) for y_i, f_i in zip(y_is, f_is) if y_i is not None])
SS_tot = np.sum([np.sum((y_i - y_bar)**2) for y_i, y_bar in zip(y_is, y_bars) if y_i is not None])
-return 1 - SS_res/SS_tot
\ No newline at end of file
+return 1 - SS_res/SS_tot
--- a/symfit/core/objectives.py
+++ b/symfit/core/objectives.py
@@ -386,7 +386,7 @@
class HessianObjectiveJacApprox(HessianObjective):
-"""
+r"""
This object should only be used as a Mixin for covariance matrix estimation.
Since the covariance matrix for the least-squares method is proportional to
the Hessian of :math:`S`, this function attempts to return the Hessian
@@ -552,4 +552,4 @@
)
return np.array(evaluated_hess[0])
else:
-return None
\ No newline at end of file
+return None
Bug#1067234: symfit: autopkgtest regression with NumPy 1.26
Source: symfit
Version: 0.5.6-2
Severity: serious
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512
Dear maintainer,
your package has an autopkgtest regression with NumPy 1.26.
Hopefully relevant excerpt from the test log:
130s # Should no longer raise warnings, because internally we practice
130s # what we preach.
130s fit_custom = BFGS(chi_squared, [a, b])
130s > assert len(recwarn) == 0
130s E assert 1 == 0
130s E+ where 1 = len(WarningsRecorder(record=True))
130s
130s tests/test_minimizers.py:120: AssertionError
130s === warnings summary
===
130s symfit/core/operators.py:48
130s
/tmp/autopkgtest-lxc.jjpx74xp/downtmp/build.gp1/src/symfit/core/operators.py:48:
SyntaxWarning: invalid escape sequence '\*'
130s """
130s
130s symfit/core/support.py:296
130s
/tmp/autopkgtest-lxc.jjpx74xp/downtmp/build.gp1/src/symfit/core/support.py:296:
SyntaxWarning: invalid escape sequence '\*'
130s """
130s
130s symfit/core/printing.py:13
130s
/tmp/autopkgtest-lxc.jjpx74xp/downtmp/build.gp1/src/symfit/core/printing.py:13:
DeprecationWarning: pkg_resources is deprecated as an API. See
https://setuptools.pypa.io/en/latest/pkg_resources.html
130s import pkg_resources
130s
130s
../../../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:2871
130s /usr/lib/python3/dist-packages/pkg_resources/__init__.py:2871:
DeprecationWarning: Deprecated call to
`pkg_resources.declare_namespace('mpl_toolkits')`.
130s 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
130s declare_namespace(pkg)
130s
130s symfit/core/fit.py:32
130s
/tmp/autopkgtest-lxc.jjpx74xp/downtmp/build.gp1/src/symfit/core/fit.py:32:
SyntaxWarning: invalid escape sequence '\_'
130s """
130s
130s symfit/core/minimizers.py:211
130s
/tmp/autopkgtest-lxc.jjpx74xp/downtmp/build.gp1/src/symfit/core/minimizers.py:211:
SyntaxWarning: invalid escape sequence '\*'
130s '''
130s
130s symfit/core/minimizers.py:327
130s
/tmp/autopkgtest-lxc.jjpx74xp/downtmp/build.gp1/src/symfit/core/minimizers.py:327:
SyntaxWarning: invalid escape sequence '\*'
130s """
130s
130s symfit/core/minimizers.py:793
130s
/tmp/autopkgtest-lxc.jjpx74xp/downtmp/build.gp1/src/symfit/core/minimizers.py:793:
SyntaxWarning: invalid escape sequence '\*'
130s """
130s
130s symfit/core/fit_results.py:29
130s
/tmp/autopkgtest-lxc.jjpx74xp/downtmp/build.gp1/src/symfit/core/fit_results.py:29:
SyntaxWarning: invalid escape sequence '\*'
130s """
130s
130s symfit/core/objectives.py:389
130s
/tmp/autopkgtest-lxc.jjpx74xp/downtmp/build.gp1/src/symfit/core/objectives.py:389:
SyntaxWarning: invalid escape sequence '\c'
130s """
130s
130s ../../../../../usr/lib/python3/dist-packages/dateutil/tz/tz.py:37
130s /usr/lib/python3/dist-packages/dateutil/tz/tz.py:37:
DeprecationWarning: datetime.datetime.utcfromtimestamp() is deprecated and
scheduled for removal in a future version. Use timezone-aware objects to
represent datetimes in UTC: datetime.datetime.fromtimestamp(timestamp,
datetime.UTC).
130s EPOCH = datetime.datetime.utcfromtimestamp(0)
130s
130s tests/test_auto_fit.py: 3 warnings
130s tests/test_constrained.py: 14 warnings
130s tests/test_finite_difference.py: 1 warning
130s tests/test_fit_result.py: 5 warnings
130s tests/test_general.py: 16 warnings
130s tests/test_minimizers.py: 2 warnings
130s tests/test_objectives.py: 1 warning
130s tests/test_ode.py: 1 warning
130s
/tmp/autopkgtest-lxc.jjpx74xp/downtmp/build.gp1/src/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.
130s cov_matrix = self._covariance_matrix(best_fit_params,
130s
130s tests/test_auto_fit.py: 2 warnings
130s tests/test_constrained.py: 13 warnings
130s tests/test_finite_difference.py: 2 warnings
130s tests/test_fit_result.py: 1 warning
130s tests/test_general.py: 12 warnings
130s tests/test_global_opt.py: 3 warnings
130s tests/test_ode.py: 7 warnings
130s
/tmp/autopkgtest-lxc.jjpx74xp/downtmp/build.gp1/src/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.
130s cov_matrix = self._covariance_matrix(best_fit_params,
130s
130s tests/test_general.py::test_likelihood_fitting_exponential
130s /usr/lib/python3/dist-packages/_pytest/python.py:194:
DeprecationWarning: `product` is deprecated as of NumPy 1.25.0, and will be
removed in NumPy 2.0. Please use `prod` instead.
130s result = testfunction(**testargs)
130s
130s --
