Your message dated Sun, 30 Jun 2024 19:19:13 +0000
with message-id <e1so04v-000q0a...@fasolo.debian.org>
and subject line Bug#1067282: fixed in symfit 0.5.6-3
has caused the Debian Bug report #1067282,
regarding symfit: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i
python{version} -p "3.12 3.11" returned exit code 13
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
1067282: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1067282
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: symfit
Version: 0.5.6-2
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lu...@debian.org
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;users=lu...@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240319&fusertaguser=lu...@debian.org&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.
--- End Message ---
--- Begin Message ---
Source: symfit
Source-Version: 0.5.6-3
Done: Alexandre Detiste <tc...@debian.org>
We believe that the bug you reported is fixed in the latest version of
symfit, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1067...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Alexandre Detiste <tc...@debian.org> (supplier of updated symfit package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sun, 30 Jun 2024 19:53:58 +0200
Source: symfit
Architecture: source
Version: 0.5.6-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Team
<debian-science-maintain...@lists.alioth.debian.org>
Changed-By: Alexandre Detiste <tc...@debian.org>
Closes: 1064601 1067234 1067282
Changes:
symfit (0.5.6-3) unstable; urgency=medium
.
* Team upload
* Import Ubuntu 24.04 patch (Closes: #1067234, #1067282)
.
[ Stephan Lachnit ]
* Remove python3-six dependency (Closes: #1064601)
Checksums-Sha1:
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56ddc68cbfe8850dbda95ff0241fe8e42296c7c0 5772 symfit_0.5.6-3.debian.tar.xz
15a271916cb38da451f460813ed8c3378c4323d6 13923 symfit_0.5.6-3_source.buildinfo
Checksums-Sha256:
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symfit_0.5.6-3.dsc
7aa188c58dc27831a33ddf9fd6497f6e317e337c03b9e6069262bd5a5555c212 5772
symfit_0.5.6-3.debian.tar.xz
239bea4d9c756746cbf5fe402a08f42734c7e83a70f45537692c9ca370dd1c05 13923
symfit_0.5.6-3_source.buildinfo
Files:
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6c6fc4fc8b81dc7cfc81139bf4524bda 5772 python optional
symfit_0.5.6-3.debian.tar.xz
2100c5f13dc6d1d6b4da2ee47322513b 13923 python optional
symfit_0.5.6-3_source.buildinfo
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