Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
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
I: pybuild base:311: python3.11 setup.py config
running config
dh_auto_build -O--buildsystem=pybuild
I: pybuild base:311: /usr/bin/python3 setup.py build
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/umap
copying umap/plot.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/umap
copying umap/sparse.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/umap
copying umap/aligned_umap.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/umap
copying umap/layouts.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/umap
copying umap/utils.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/umap
copying umap/umap_.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/umap
copying umap/parametric_umap.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/umap
copying umap/validation.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/umap
copying umap/spectral.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/umap
copying umap/distances.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/umap
copying umap/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/umap
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_test -- --system=custom --test-args="PYTHONPATH={build_dir} {interpreter} -m pytest"
I: pybuild base:311: PYTHONPATH=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build python3.11 -m pytest
============================= test session starts ==============================
platform linux -- Python 3.11.9, pytest-8.1.2, pluggy-1.5.0
rootdir: /<<PKGBUILDDIR>>
collected 209 items
umap/tests/test_aligned_umap.py ....s [ 2%]
umap/tests/test_chunked_parallel_spatial_metric.py sssssssssssssssssssss [ 12%]
sssssssssssssssssssss [ 22%]
umap/tests/test_composite_models.py .s.. [ 24%]
umap/tests/test_data_input.py . [ 24%]
umap/tests/test_densmap.py .s.. [ 26%]
umap/tests/test_parametric_umap.py sssssss [ 30%]
umap/tests/test_plot.py s [ 30%]
umap/tests/test_spectral.py .. [ 31%]
umap/tests/test_umap_get_feature_names_out.py .... [ 33%]
umap/tests/test_umap_metrics.py ............s.................s......... [ 52%]
.. [ 53%]
umap/tests/test_umap_nn.py ..sssssss.. [ 58%]
umap/tests/test_umap_on_iris.py ............ [ 64%]
umap/tests/test_umap_ops.py ...FFFFFFFF.....F.. [ 73%]
umap/tests/test_umap_repeated_data.py ......... [ 77%]
umap/tests/test_umap_trustworthiness.py .......... [ 82%]
umap/tests/test_umap_validation_params.py .............................. [ 97%]
...... [100%]
=================================== FAILURES ===================================
umap/tests/test_umap_ops.py:119:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = WarningsChecker(record=True), expected_warning = None, match_expr = None
def __init__(
self,
expected_warning: Union[Type[Warning], Tuple[Type[Warning], ...]] = Warning,
match_expr: Optional[Union[str, Pattern[str]]] = None,
*,
_ispytest: bool = False,
) -> None:
check_ispytest(_ispytest)
super().__init__(_ispytest=True)
msg = "exceptions must be derived from Warning, not %s"
if isinstance(expected_warning, tuple):
for exc in expected_warning:
if not issubclass(exc, Warning):
raise TypeError(msg % type(exc))
expected_warning_tup = expected_warning
elif isinstance(expected_warning, type) and issubclass(
expected_warning, Warning
):
expected_warning_tup = (expected_warning,)
else:
/usr/lib/python3/dist-packages/_pytest/recwarn.py:285: TypeError
umap/tests/test_umap_ops.py:119:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = WarningsChecker(record=True), expected_warning = None, match_expr = None
def __init__(
self,
expected_warning: Union[Type[Warning], Tuple[Type[Warning], ...]] = Warning,
match_expr: Optional[Union[str, Pattern[str]]] = None,
*,
_ispytest: bool = False,
) -> None:
check_ispytest(_ispytest)
super().__init__(_ispytest=True)
msg = "exceptions must be derived from Warning, not %s"
if isinstance(expected_warning, tuple):
for exc in expected_warning:
if not issubclass(exc, Warning):
raise TypeError(msg % type(exc))
expected_warning_tup = expected_warning
elif isinstance(expected_warning, type) and issubclass(
expected_warning, Warning
):
expected_warning_tup = (expected_warning,)
else:
/usr/lib/python3/dist-packages/_pytest/recwarn.py:285: TypeError
umap/tests/test_umap_ops.py:119:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = WarningsChecker(record=True), expected_warning = None, match_expr = None
def __init__(
self,
expected_warning: Union[Type[Warning], Tuple[Type[Warning], ...]] = Warning,
match_expr: Optional[Union[str, Pattern[str]]] = None,
*,
_ispytest: bool = False,
) -> None:
check_ispytest(_ispytest)
super().__init__(_ispytest=True)
msg = "exceptions must be derived from Warning, not %s"
if isinstance(expected_warning, tuple):
for exc in expected_warning:
if not issubclass(exc, Warning):
raise TypeError(msg % type(exc))
expected_warning_tup = expected_warning
elif isinstance(expected_warning, type) and issubclass(
expected_warning, Warning
):
expected_warning_tup = (expected_warning,)
else:
/usr/lib/python3/dist-packages/_pytest/recwarn.py:285: TypeError
umap/tests/test_umap_ops.py:119:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = WarningsChecker(record=True), expected_warning = None, match_expr = None
def __init__(
self,
expected_warning: Union[Type[Warning], Tuple[Type[Warning], ...]] = Warning,
match_expr: Optional[Union[str, Pattern[str]]] = None,
*,
_ispytest: bool = False,
) -> None:
check_ispytest(_ispytest)
super().__init__(_ispytest=True)
msg = "exceptions must be derived from Warning, not %s"
if isinstance(expected_warning, tuple):
for exc in expected_warning:
if not issubclass(exc, Warning):
raise TypeError(msg % type(exc))
expected_warning_tup = expected_warning
elif isinstance(expected_warning, type) and issubclass(
expected_warning, Warning
):
expected_warning_tup = (expected_warning,)
else:
/usr/lib/python3/dist-packages/_pytest/recwarn.py:285: TypeError
umap/tests/test_umap_ops.py:119:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = WarningsChecker(record=True), expected_warning = None, match_expr = None
def __init__(
self,
expected_warning: Union[Type[Warning], Tuple[Type[Warning], ...]] = Warning,
match_expr: Optional[Union[str, Pattern[str]]] = None,
*,
_ispytest: bool = False,
) -> None:
check_ispytest(_ispytest)
super().__init__(_ispytest=True)
msg = "exceptions must be derived from Warning, not %s"
if isinstance(expected_warning, tuple):
for exc in expected_warning:
if not issubclass(exc, Warning):
raise TypeError(msg % type(exc))
expected_warning_tup = expected_warning
elif isinstance(expected_warning, type) and issubclass(
expected_warning, Warning
):
expected_warning_tup = (expected_warning,)
else:
/usr/lib/python3/dist-packages/_pytest/recwarn.py:285: TypeError
umap/tests/test_umap_ops.py:119:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = WarningsChecker(record=True), expected_warning = None, match_expr = None
def __init__(
self,
expected_warning: Union[Type[Warning], Tuple[Type[Warning], ...]] = Warning,
match_expr: Optional[Union[str, Pattern[str]]] = None,
*,
_ispytest: bool = False,
) -> None:
check_ispytest(_ispytest)
super().__init__(_ispytest=True)
msg = "exceptions must be derived from Warning, not %s"
if isinstance(expected_warning, tuple):
for exc in expected_warning:
if not issubclass(exc, Warning):
raise TypeError(msg % type(exc))
expected_warning_tup = expected_warning
elif isinstance(expected_warning, type) and issubclass(
expected_warning, Warning
):
expected_warning_tup = (expected_warning,)
else:
/usr/lib/python3/dist-packages/_pytest/recwarn.py:285: TypeError
umap/tests/test_umap_ops.py:119:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = WarningsChecker(record=True), expected_warning = None, match_expr = None
def __init__(
self,
expected_warning: Union[Type[Warning], Tuple[Type[Warning], ...]] = Warning,
match_expr: Optional[Union[str, Pattern[str]]] = None,
*,
_ispytest: bool = False,
) -> None:
check_ispytest(_ispytest)
super().__init__(_ispytest=True)
msg = "exceptions must be derived from Warning, not %s"
if isinstance(expected_warning, tuple):
for exc in expected_warning:
if not issubclass(exc, Warning):
raise TypeError(msg % type(exc))
expected_warning_tup = expected_warning
elif isinstance(expected_warning, type) and issubclass(
expected_warning, Warning
):
expected_warning_tup = (expected_warning,)
else:
/usr/lib/python3/dist-packages/_pytest/recwarn.py:285: TypeError
umap/tests/test_umap_ops.py:119:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = WarningsChecker(record=True), expected_warning = None, match_expr = None
def __init__(
self,
expected_warning: Union[Type[Warning], Tuple[Type[Warning], ...]] = Warning,
match_expr: Optional[Union[str, Pattern[str]]] = None,
*,
_ispytest: bool = False,
) -> None:
check_ispytest(_ispytest)
super().__init__(_ispytest=True)
msg = "exceptions must be derived from Warning, not %s"
if isinstance(expected_warning, tuple):
for exc in expected_warning:
if not issubclass(exc, Warning):
raise TypeError(msg % type(exc))
expected_warning_tup = expected_warning
elif isinstance(expected_warning, type) and issubclass(
expected_warning, Warning
):
expected_warning_tup = (expected_warning,)
else:
/usr/lib/python3/dist-packages/_pytest/recwarn.py:285: TypeError
E assert 17.72839 < 3.0
umap/tests/test_umap_ops.py:262: AssertionError
=============================== warnings summary ===============================
umap/__init__.py:36
/<<PKGBUILDDIR>>/umap/__init__.py:36: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
import pkg_resources
umap/tests/test_chunked_parallel_spatial_metric.py:234
/<<PKGBUILDDIR>>/umap/tests/test_chunked_parallel_spatial_metric.py:234: PytestUnknownMarkWarning: Unknown pytest.mark.benchmark - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
@pytest.mark.benchmark(
umap/tests/test_chunked_parallel_spatial_metric.py:258
/<<PKGBUILDDIR>>/umap/tests/test_chunked_parallel_spatial_metric.py:258: PytestUnknownMarkWarning: Unknown pytest.mark.benchmark - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
@pytest.mark.benchmark(
umap/tests/test_chunked_parallel_spatial_metric.py:288
/<<PKGBUILDDIR>>/umap/tests/test_chunked_parallel_spatial_metric.py:288: PytestUnknownMarkWarning: Unknown pytest.mark.benchmark - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
@pytest.mark.benchmark(
umap/tests/test_chunked_parallel_spatial_metric.py:312
/<<PKGBUILDDIR>>/umap/tests/test_chunked_parallel_spatial_metric.py:312: PytestUnknownMarkWarning: Unknown pytest.mark.benchmark - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
@pytest.mark.benchmark(
umap/plot.py:20
/<<PKGBUILDDIR>>/umap/plot.py:20: UserWarning: The umap.plot package requires extra plotting libraries to be installed.
You can install these via pip using
pip install umap-learn[plot]
or via conda using
conda install pandas matplotlib datashader bokeh holoviews colorcet scikit-image
warn(
umap/tests/test_aligned_umap.py::test_aligned_update
/<<PKGBUILDDIR>>/umap/aligned_umap.py:195: NumbaTypeSafetyWarning: unsafe cast from int64 to int32. Precision may be lost.
if i in relation_dict:
umap/tests/test_composite_models.py: 7 warnings
umap/tests/test_densmap.py: 3 warnings
umap/tests/test_umap_on_iris.py: 8 warnings
umap/tests/test_umap_ops.py: 2 warnings
umap/tests/test_umap_trustworthiness.py: 9 warnings
/<<PKGBUILDDIR>>/umap/umap_.py:1943: UserWarning: n_jobs value -1 overridden to 1 by setting random_state. Use no seed for parallelism.
warn(f"n_jobs value {self.n_jobs} overridden to 1 by setting random_state. Use no seed for parallelism.")
umap/tests/test_umap_get_feature_names_out.py::test_get_feature_names_out_featureunion
umap/tests/test_umap_get_feature_names_out.py::test_get_feature_names_out_featureunion
umap/tests/test_umap_repeated_data.py::test_repeated_points_large_n
umap/tests/test_umap_validation_params.py::test_umap_too_many_neighbors_warns
umap/tests/test_umap_validation_params.py::test_umap_inverse_transform_fails_expectedly
/<<PKGBUILDDIR>>/umap/umap_.py:2433: UserWarning: n_neighbors is larger than the dataset size; truncating to X.shape[0] - 1
warn(
umap/tests/test_umap_metrics.py::test_hellinger
/<<PKGBUILDDIR>>/umap/tests/test_umap_metrics.py:413: RuntimeWarning: invalid value encountered in sqrt
dist_matrix = np.sqrt(dist_matrix)
umap/tests/test_umap_on_iris.py::test_precomputed_transform_on_iris
umap/tests/test_umap_on_iris.py::test_precomputed_sparse_transform_on_iris
umap/tests/test_umap_ops.py::test_multi_component_layout_precomputed
umap/tests/test_umap_ops.py::test_disconnected_data_precomputed[True-1]
umap/tests/test_umap_ops.py::test_disconnected_data_precomputed[False-1]
umap/tests/test_umap_trustworthiness.py::test_sparse_precomputed_metric_umap_trustworthiness
umap/tests/test_umap_validation_params.py::test_umap_update_bad_params
/<<PKGBUILDDIR>>/umap/umap_.py:1857: UserWarning: using precomputed metric; inverse_transform will be unavailable
warn("using precomputed metric; inverse_transform will be unavailable")
umap/tests/test_umap_on_iris.py::test_precomputed_transform_on_iris
umap/tests/test_umap_on_iris.py::test_precomputed_sparse_transform_on_iris
/<<PKGBUILDDIR>>/umap/umap_.py:2959: UserWarning: Transforming new data with precomputed metric. We are assuming the input data is a matrix of distances from the new points to the points in the training set. If the input matrix is sparse, it should contain distances from the new points to their nearest neighbours or approximate nearest neighbours in the training set.
warn(
umap/tests/test_umap_ops.py::test_multi_component_layout
umap/tests/test_umap_ops.py::test_multi_component_layout_precomputed
/usr/lib/python3/dist-packages/sklearn/manifold/_spectral_embedding.py:301: UserWarning: Graph is not fully connected, spectral embedding may not work as expected.
warnings.warn(
umap/tests/test_umap_ops.py::test_disconnected_data_precomputed[True-1]
/<<PKGBUILDDIR>>/umap/umap_.py:126: UserWarning: A few of your vertices were disconnected from the manifold. This shouldn't cause problems.
Disconnection_distance = 1 has removed 3 edges.
It has only fully disconnected 1 vertices.
Use umap.utils.disconnected_vertices() to identify them.
warn(
umap/tests/test_umap_ops.py::test_disconnected_data_precomputed[False-1]
/<<PKGBUILDDIR>>/umap/umap_.py:126: UserWarning: A few of your vertices were disconnected from the manifold. This shouldn't cause problems.
Disconnection_distance = 1 has removed 32 edges.
It has only fully disconnected 1 vertices.
Use umap.utils.disconnected_vertices() to identify them.
warn(
umap/tests/test_umap_validation_params.py::test_umap_inverse_transform_fails_expectedly
/<<PKGBUILDDIR>>/umap/umap_.py:1879: UserWarning: gradient function is not yet implemented for dice distance metric; inverse_transform will be unavailable
warn(