[Debichem-devel] Bug#1118427: python-symfc: FTBFS: FAILED tests/basis_sets/test_basis_sets_O2.py::test_fc_basis_set_o2

[Santiago Vila]

Package: src:python-symfc
Version: 1.5.4-1
Severity: serious
Tags: ftbfs forky sid

Dear maintainer:

During a rebuild of all packages in unstable, this package failed to build.

Below you will find the last part of the build log (probably the most
relevant part, but not necessarily). If required, the full build log
is available here:

https://people.debian.org/~sanvila/build-logs/202510/

About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.

If you cannot reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.

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

Thanks.

--------------------------------------------------------------------------------
[...]
 debian/rules clean
dh clean --buildsystem pybuild
   dh_auto_clean -O--buildsystem=pybuild
   dh_autoreconf_clean -O--buildsystem=pybuild
   dh_clean -O--buildsystem=pybuild
 debian/rules binary
dh binary --buildsystem pybuild
   dh_update_autotools_config -O--buildsystem=pybuild
   dh_autoreconf -O--buildsystem=pybuild
   dh_auto_configure -O--buildsystem=pybuild
   dh_auto_build -O--buildsystem=pybuild
I: pybuild plugin_pyproject:129: Building wheel for python3.13 with "build" module
I: pybuild base:311: python3.13 -m build --skip-dependency-check --no-isolation --wheel --outdir /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_python-symfc  
* Building wheel...
No `packages` or `py_modules` configuration, performing automatic discovery.
`src-layout` detected -- analysing ./src
discovered packages -- ['symfc', 'symfc.utils', 'symfc.solvers', 'symfc.basis_sets', 'symfc.spg_reps', 'symfc.utils.rotation_dev']
discovered py_modules -- []
/usr/lib/python3/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
!!

        ********************************************************************************
        Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0).

        By 2026-Feb-18, you need to update your project and remove deprecated calls
        or your builds will no longer be supported.

        See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
        ********************************************************************************

!!
  corresp(dist, value, root_dir)
running bdist_wheel
running build
running build_py
creating build/lib/symfc
copying src/symfc/__init__.py -> build/lib/symfc
copying src/symfc/version.py -> build/lib/symfc
copying src/symfc/api_symfc.py -> build/lib/symfc
creating build/lib/symfc/utils
copying src/symfc/utils/__init__.py -> build/lib/symfc/utils
copying src/symfc/utils/rotation_tools_O2.py -> build/lib/symfc/utils
copying src/symfc/utils/translation_tools_O4.py -> build/lib/symfc/utils
copying src/symfc/utils/translation_tools_O2.py -> build/lib/symfc/utils
copying src/symfc/utils/permutation_tools_O2.py -> build/lib/symfc/utils
copying src/symfc/utils/permutation_tools_O4.py -> build/lib/symfc/utils
copying src/symfc/utils/cutoff_tools.py -> build/lib/symfc/utils
copying src/symfc/utils/matrix.py -> build/lib/symfc/utils
copying src/symfc/utils/eig_tools.py -> build/lib/symfc/utils
copying src/symfc/utils/utils_O3.py -> build/lib/symfc/utils
copying src/symfc/utils/graph.py -> build/lib/symfc/utils
copying src/symfc/utils/translation_tools_O3.py -> build/lib/symfc/utils
copying src/symfc/utils/utils_O2.py -> build/lib/symfc/utils
copying src/symfc/utils/translation_tools_O1.py -> build/lib/symfc/utils
copying src/symfc/utils/solver_funcs.py -> build/lib/symfc/utils
copying src/symfc/utils/utils_O1.py -> build/lib/symfc/utils
copying src/symfc/utils/utils_O4.py -> build/lib/symfc/utils
copying src/symfc/utils/utils.py -> build/lib/symfc/utils
copying src/symfc/utils/permutation_tools_O3.py -> build/lib/symfc/utils
copying src/symfc/utils/permutation_tools.py -> build/lib/symfc/utils
creating build/lib/symfc/solvers
copying src/symfc/solvers/solver_O3O4.py -> build/lib/symfc/solvers
copying src/symfc/solvers/solver_O2O3O4.py -> build/lib/symfc/solvers
copying src/symfc/solvers/solver_O4.py -> build/lib/symfc/solvers
copying src/symfc/solvers/__init__.py -> build/lib/symfc/solvers
copying src/symfc/solvers/solver_O2O3.py -> build/lib/symfc/solvers
copying src/symfc/solvers/solver_O2.py -> build/lib/symfc/solvers
copying src/symfc/solvers/solver_O3.py -> build/lib/symfc/solvers
copying src/symfc/solvers/solver_base.py -> build/lib/symfc/solvers
creating build/lib/symfc/basis_sets
copying src/symfc/basis_sets/__init__.py -> build/lib/symfc/basis_sets
copying src/symfc/basis_sets/basis_sets_O3.py -> build/lib/symfc/basis_sets
copying src/symfc/basis_sets/basis_sets_O4.py -> build/lib/symfc/basis_sets
copying src/symfc/basis_sets/basis_sets_base.py -> build/lib/symfc/basis_sets
copying src/symfc/basis_sets/basis_sets_O2.py -> build/lib/symfc/basis_sets
copying src/symfc/basis_sets/basis_sets_O1.py -> build/lib/symfc/basis_sets
creating build/lib/symfc/spg_reps
copying src/symfc/spg_reps/spg_reps_O4.py -> build/lib/symfc/spg_reps
copying src/symfc/spg_reps/__init__.py -> build/lib/symfc/spg_reps
copying src/symfc/spg_reps/spg_reps_base.py -> build/lib/symfc/spg_reps
copying src/symfc/spg_reps/spg_reps_O3.py -> build/lib/symfc/spg_reps
copying src/symfc/spg_reps/spg_reps_O2.py -> build/lib/symfc/spg_reps
copying src/symfc/spg_reps/spg_reps_O1.py -> build/lib/symfc/spg_reps
creating build/lib/symfc/utils/rotation_dev
copying src/symfc/utils/rotation_dev/run_rotation_tools_O2.py -> build/lib/symfc/utils/rotation_dev
copying src/symfc/utils/rotation_dev/__init__.py -> build/lib/symfc/utils/rotation_dev
copying src/symfc/utils/rotation_dev/run_rotation_tools_O3.py -> build/lib/symfc/utils/rotation_dev
copying src/symfc/utils/rotation_dev/run_test_O2.py -> build/lib/symfc/utils/rotation_dev
running egg_info
creating src/symfc.egg-info
writing src/symfc.egg-info/PKG-INFO
writing dependency_links to src/symfc.egg-info/dependency_links.txt
writing requirements to src/symfc.egg-info/requires.txt
writing top-level names to src/symfc.egg-info/top_level.txt
writing manifest file 'src/symfc.egg-info/SOURCES.txt'
reading manifest file 'src/symfc.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file 'src/symfc.egg-info/SOURCES.txt'
installing to build/bdist.linux-x86_64/wheel
running install
running install_lib
creating build/bdist.linux-x86_64/wheel
creating build/bdist.linux-x86_64/wheel/symfc
copying build/lib/symfc/__init__.py -> build/bdist.linux-x86_64/wheel/./symfc
copying build/lib/symfc/version.py -> build/bdist.linux-x86_64/wheel/./symfc
creating build/bdist.linux-x86_64/wheel/symfc/utils
copying build/lib/symfc/utils/__init__.py -> build/bdist.linux-x86_64/wheel/./symfc/utils
copying build/lib/symfc/utils/rotation_tools_O2.py -> build/bdist.linux-x86_64/wheel/./symfc/utils
copying build/lib/symfc/utils/translation_tools_O4.py -> build/bdist.linux-x86_64/wheel/./symfc/utils
copying build/lib/symfc/utils/translation_tools_O2.py -> build/bdist.linux-x86_64/wheel/./symfc/utils
creating build/bdist.linux-x86_64/wheel/symfc/utils/rotation_dev
copying build/lib/symfc/utils/rotation_dev/run_rotation_tools_O2.py -> build/bdist.linux-x86_64/wheel/./symfc/utils/rotation_dev
copying build/lib/symfc/utils/rotation_dev/__init__.py -> build/bdist.linux-x86_64/wheel/./symfc/utils/rotation_dev
copying build/lib/symfc/utils/rotation_dev/run_rotation_tools_O3.py -> build/bdist.linux-x86_64/wheel/./symfc/utils/rotation_dev
copying build/lib/symfc/utils/rotation_dev/run_test_O2.py -> build/bdist.linux-x86_64/wheel/./symfc/utils/rotation_dev
copying build/lib/symfc/utils/permutation_tools_O2.py -> build/bdist.linux-x86_64/wheel/./symfc/utils
copying build/lib/symfc/utils/permutation_tools_O4.py -> build/bdist.linux-x86_64/wheel/./symfc/utils
copying build/lib/symfc/utils/cutoff_tools.py -> build/bdist.linux-x86_64/wheel/./symfc/utils
copying build/lib/symfc/utils/matrix.py -> build/bdist.linux-x86_64/wheel/./symfc/utils
copying build/lib/symfc/utils/eig_tools.py -> build/bdist.linux-x86_64/wheel/./symfc/utils
copying build/lib/symfc/utils/utils_O3.py -> build/bdist.linux-x86_64/wheel/./symfc/utils
copying build/lib/symfc/utils/graph.py -> build/bdist.linux-x86_64/wheel/./symfc/utils
copying build/lib/symfc/utils/translation_tools_O3.py -> build/bdist.linux-x86_64/wheel/./symfc/utils
copying build/lib/symfc/utils/utils_O2.py -> build/bdist.linux-x86_64/wheel/./symfc/utils
copying build/lib/symfc/utils/translation_tools_O1.py -> build/bdist.linux-x86_64/wheel/./symfc/utils
copying build/lib/symfc/utils/solver_funcs.py -> build/bdist.linux-x86_64/wheel/./symfc/utils
copying build/lib/symfc/utils/utils_O1.py -> build/bdist.linux-x86_64/wheel/./symfc/utils
copying build/lib/symfc/utils/utils_O4.py -> build/bdist.linux-x86_64/wheel/./symfc/utils
copying build/lib/symfc/utils/utils.py -> build/bdist.linux-x86_64/wheel/./symfc/utils
copying build/lib/symfc/utils/permutation_tools_O3.py -> build/bdist.linux-x86_64/wheel/./symfc/utils
copying build/lib/symfc/utils/permutation_tools.py -> build/bdist.linux-x86_64/wheel/./symfc/utils
creating build/bdist.linux-x86_64/wheel/symfc/solvers
copying build/lib/symfc/solvers/solver_O3O4.py -> build/bdist.linux-x86_64/wheel/./symfc/solvers
copying build/lib/symfc/solvers/solver_O2O3O4.py -> build/bdist.linux-x86_64/wheel/./symfc/solvers
copying build/lib/symfc/solvers/solver_O4.py -> build/bdist.linux-x86_64/wheel/./symfc/solvers
copying build/lib/symfc/solvers/__init__.py -> build/bdist.linux-x86_64/wheel/./symfc/solvers
copying build/lib/symfc/solvers/solver_O2O3.py -> build/bdist.linux-x86_64/wheel/./symfc/solvers
copying build/lib/symfc/solvers/solver_O2.py -> build/bdist.linux-x86_64/wheel/./symfc/solvers
copying build/lib/symfc/solvers/solver_O3.py -> build/bdist.linux-x86_64/wheel/./symfc/solvers
copying build/lib/symfc/solvers/solver_base.py -> build/bdist.linux-x86_64/wheel/./symfc/solvers
creating build/bdist.linux-x86_64/wheel/symfc/basis_sets
copying build/lib/symfc/basis_sets/__init__.py -> build/bdist.linux-x86_64/wheel/./symfc/basis_sets
copying build/lib/symfc/basis_sets/basis_sets_O3.py -> build/bdist.linux-x86_64/wheel/./symfc/basis_sets
copying build/lib/symfc/basis_sets/basis_sets_O4.py -> build/bdist.linux-x86_64/wheel/./symfc/basis_sets
copying build/lib/symfc/basis_sets/basis_sets_base.py -> build/bdist.linux-x86_64/wheel/./symfc/basis_sets
copying build/lib/symfc/basis_sets/basis_sets_O2.py -> build/bdist.linux-x86_64/wheel/./symfc/basis_sets
copying build/lib/symfc/basis_sets/basis_sets_O1.py -> build/bdist.linux-x86_64/wheel/./symfc/basis_sets
creating build/bdist.linux-x86_64/wheel/symfc/spg_reps
copying build/lib/symfc/spg_reps/spg_reps_O4.py -> build/bdist.linux-x86_64/wheel/./symfc/spg_reps
copying build/lib/symfc/spg_reps/__init__.py -> build/bdist.linux-x86_64/wheel/./symfc/spg_reps
copying build/lib/symfc/spg_reps/spg_reps_base.py -> build/bdist.linux-x86_64/wheel/./symfc/spg_reps
copying build/lib/symfc/spg_reps/spg_reps_O3.py -> build/bdist.linux-x86_64/wheel/./symfc/spg_reps
copying build/lib/symfc/spg_reps/spg_reps_O2.py -> build/bdist.linux-x86_64/wheel/./symfc/spg_reps
copying build/lib/symfc/spg_reps/spg_reps_O1.py -> build/bdist.linux-x86_64/wheel/./symfc/spg_reps
copying build/lib/symfc/api_symfc.py -> build/bdist.linux-x86_64/wheel/./symfc
running install_egg_info
Copying src/symfc.egg-info to build/bdist.linux-x86_64/wheel/./symfc-1.5.4.egg-info
running install_scripts
creating build/bdist.linux-x86_64/wheel/symfc-1.5.4.dist-info/WHEEL
creating '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_python-symfc/.tmp-qq8oepc2/symfc-1.5.4-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it
adding 'symfc/__init__.py'
adding 'symfc/api_symfc.py'
adding 'symfc/version.py'
adding 'symfc/basis_sets/__init__.py'
adding 'symfc/basis_sets/basis_sets_O1.py'
adding 'symfc/basis_sets/basis_sets_O2.py'
adding 'symfc/basis_sets/basis_sets_O3.py'
adding 'symfc/basis_sets/basis_sets_O4.py'
adding 'symfc/basis_sets/basis_sets_base.py'
adding 'symfc/solvers/__init__.py'
adding 'symfc/solvers/solver_O2.py'
adding 'symfc/solvers/solver_O2O3.py'
adding 'symfc/solvers/solver_O2O3O4.py'
adding 'symfc/solvers/solver_O3.py'
adding 'symfc/solvers/solver_O3O4.py'
adding 'symfc/solvers/solver_O4.py'
adding 'symfc/solvers/solver_base.py'
adding 'symfc/spg_reps/__init__.py'
adding 'symfc/spg_reps/spg_reps_O1.py'
adding 'symfc/spg_reps/spg_reps_O2.py'
adding 'symfc/spg_reps/spg_reps_O3.py'
adding 'symfc/spg_reps/spg_reps_O4.py'
adding 'symfc/spg_reps/spg_reps_base.py'
adding 'symfc/utils/__init__.py'
adding 'symfc/utils/cutoff_tools.py'
adding 'symfc/utils/eig_tools.py'
adding 'symfc/utils/graph.py'
adding 'symfc/utils/matrix.py'
adding 'symfc/utils/permutation_tools.py'
adding 'symfc/utils/permutation_tools_O2.py'
adding 'symfc/utils/permutation_tools_O3.py'
adding 'symfc/utils/permutation_tools_O4.py'
adding 'symfc/utils/rotation_tools_O2.py'
adding 'symfc/utils/solver_funcs.py'
adding 'symfc/utils/translation_tools_O1.py'
adding 'symfc/utils/translation_tools_O2.py'
adding 'symfc/utils/translation_tools_O3.py'
adding 'symfc/utils/translation_tools_O4.py'
adding 'symfc/utils/utils.py'
adding 'symfc/utils/utils_O1.py'
adding 'symfc/utils/utils_O2.py'
adding 'symfc/utils/utils_O3.py'
adding 'symfc/utils/utils_O4.py'
adding 'symfc/utils/rotation_dev/__init__.py'
adding 'symfc/utils/rotation_dev/run_rotation_tools_O2.py'
adding 'symfc/utils/rotation_dev/run_rotation_tools_O3.py'
adding 'symfc/utils/rotation_dev/run_test_O2.py'
adding 'symfc-1.5.4.dist-info/licenses/LICENSE'
adding 'symfc-1.5.4.dist-info/METADATA'
adding 'symfc-1.5.4.dist-info/WHEEL'
adding 'symfc-1.5.4.dist-info/top_level.txt'
adding 'symfc-1.5.4.dist-info/RECORD'
removing build/bdist.linux-x86_64/wheel
Successfully built symfc-1.5.4-py3-none-any.whl
I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.13 with "installer" module
   dh_auto_test -O--buildsystem=pybuild
I: pybuild base:311: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_python-symfc/build; python3.13 -m pytest tests
============================= test session starts ==============================
platform linux -- Python 3.13.9, pytest-8.4.2, pluggy-1.6.0
rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_python-symfc/build
configfile: pyproject.toml
plugins: typeguard-4.4.4
collected 72 items

tests/basis_sets/test_basis_sets_O2.py F.........                        [ 13%]
tests/basis_sets/test_basis_sets_O3.py .....                             [ 20%]
tests/basis_sets/test_basis_sets_O4.py ...                               [ 25%]
tests/basis_sets/test_basis_sets_base.py .                               [ 26%]
tests/solvers/test_solver_utils.py ...                                   [ 30%]
tests/spg_reps/test_spg_reps_O1.py ..                                    [ 33%]
tests/spg_reps/test_spg_reps_O2.py .                                     [ 34%]
tests/spg_reps/test_spg_reps_O3.py .                                     [ 36%]
tests/spg_reps/test_spg_reps_O4.py .                                     [ 37%]
tests/spg_reps/test_spg_reps_base.py ..                                  [ 40%]
tests/test_api.py ..........                                             [ 54%]
tests/test_api_linalg.py .                                               [ 55%]
tests/utils/test_block_tree.py .                                         [ 56%]
tests/utils/test_cutoff_tools.py ..                                      [ 59%]
tests/utils/test_eig_tools.py ...                                        [ 63%]
tests/utils/test_graph.py .                                              [ 65%]
tests/utils/test_permutation_tools_O2.py ..                              [ 68%]
tests/utils/test_permutation_tools_O3.py ..                              [ 70%]
tests/utils/test_permutation_tools_O4.py .                               [ 72%]
tests/utils/test_solver_funcs.py ..                                      [ 75%]
tests/utils/test_translation_tools_O2.py .                               [ 76%]
tests/utils/test_translation_tools_O3.py .                               [ 77%]
tests/utils/test_utils.py ......                                         [ 86%]
tests/utils/test_utils_O1.py .                                           [ 87%]
tests/utils/test_utils_O2.py ....                                        [ 93%]
tests/utils/test_utils_O2_2.py ..                                        [ 95%]
tests/utils/test_utils_O3.py ..                                          [ 98%]
tests/utils/test_utils_O4.py .                                           [100%]

=================================== FAILURES ===================================
_____________________________ test_fc_basis_set_o2 _____________________________

    def test_fc_basis_set_o2():
        """Test symmetry adapted basis sets of FCBasisSetO2."""
        lattice = np.array([[2, 0, 0], [0, 2, 0], [0, 0, 2]])
        positions = np.array([[0, 0, 0], [0.5, 0.5, 0.5]])
        numbers = [1, 1]
        supercell = SymfcAtoms(cell=lattice, scaled_positions=positions, numbers=numbers)
        sbs = FCBasisSetO2(supercell, log_level=1).run()
    
        np.testing.assert_allclose(
            np.sort(sbs.basis_set), [[-np.sqrt(2) / 2], [np.sqrt(2) / 2]]
        )
    
        comp_mat = sbs.compression_matrix
>       np.testing.assert_allclose(comp_mat.data, [0.40824829046386313] * comp_mat.size)
E       AssertionError: 
E       Not equal to tolerance rtol=1e-07, atol=0
E       
E       Mismatched elements: 12 / 12 (100%)
E       Max absolute difference among violations: 0.81649658
E       Max relative difference among violations: 2.
E        ACTUAL: array([-0.408248, -0.408248, -0.408248, -0.408248, -0.408248, -0.408248,
E              -0.408248, -0.408248, -0.408248, -0.408248, -0.408248, -0.408248])
E        DESIRED: array([0.408248, 0.408248, 0.408248, 0.408248, 0.408248, 0.408248,
E              0.408248, 0.408248, 0.408248, 0.408248, 0.408248, 0.408248])

tests/basis_sets/test_basis_sets_O2.py:30: AssertionError
----------------------------- Captured stdout call -----------------------------
Permutation basis: 6/6
Permutation basis: 12/12
Construct permutation basis matrix.
Finding block diagonal structure in projector.
Using scipy connected_components.
Rank of projector: 2
Number of blocks in projector: 2
Finding block diagonal structure in projector.
Using scipy connected_components.
Number of blocks in projector (Sum rule): 1
--- Eigsh_solver_block: 1 / 1 ---
Block_size: 2
Use standard eigh solver.
Tree of FC basis block matrices:
- (2, 1), data: False
|-- (2, 1), data: True
=========================== short test summary info ============================
FAILED tests/basis_sets/test_basis_sets_O2.py::test_fc_basis_set_o2 - Asserti...
======================== 1 failed, 71 passed in 17.06s =========================
E: pybuild pybuild:389: test: plugin pyproject failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_python-symfc/build; python3.13 -m pytest tests
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.13 returned exit code 13
make: *** [debian/rules:6: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------