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test-failures.txt
nixpkgs on  samuela/scanpy
❯ nix-build -A python3Packages.anndata
this derivation will be built:
/nix/store/kgligwzymlzjy7wvlb9jc9wv0wl3i198-python3.12-anndata-0.11.4.drv
building '/nix/store/kgligwzymlzjy7wvlb9jc9wv0wl3i198-python3.12-anndata-0.11.4.drv'...
Sourcing python-remove-tests-dir-hook
Sourcing python-catch-conflicts-hook.sh
Sourcing python-remove-bin-bytecode-hook.sh
Sourcing pypa-build-hook
Using pypaBuildPhase
Sourcing python-runtime-deps-check-hook
Using pythonRuntimeDepsCheckHook
Sourcing pypa-install-hook
Using pypaInstallPhase
Sourcing python-imports-check-hook.sh
Using pythonImportsCheckPhase
Sourcing python-namespaces-hook
Sourcing python-catch-conflicts-hook.sh
Sourcing pytest-check-hook
Using pytestCheckPhase
Running phase: unpackPhase
unpacking source archive /nix/store/wdby4rb7pmhjlxp92j9w7al7p7l0cckh-source
source root is source
setting SOURCE_DATE_EPOCH to timestamp 315619200 of file "source/tests/test_x.py"
Running phase: patchPhase
Running phase: updateAutotoolsGnuConfigScriptsPhase
Running phase: configurePhase
no configure script, doing nothing
Running phase: buildPhase
Executing pypaBuildPhase
Setting SETUPTOOLS_SCM_PRETEND_VERSION to 0.11.4
Including all tracked files automatically
Creating a wheel...
pypa build flags: --no-isolation --outdir dist/ --wheel
* Getting build dependencies for wheel...
* Building wheel...
Successfully built anndata-0.11.4-py3-none-any.whl
Finished creating a wheel...
Finished executing pypaBuildPhase
Running phase: pythonRuntimeDepsCheckHook
Executing pythonRuntimeDepsCheck
Checking runtime dependencies for anndata-0.11.4-py3-none-any.whl
Finished executing pythonRuntimeDepsCheck
Running phase: installPhase
Executing pypaInstallPhase
Successfully installed anndata-0.11.4-py3-none-any.whl
Finished executing pypaInstallPhase
Running phase: pythonOutputDistPhase
Executing pythonOutputDistPhase
Finished executing pythonOutputDistPhase
Running phase: fixupPhase
shrinking RPATHs of ELF executables and libraries in /nix/store/lsjghdh2yhdzc8qjvylrgnll8vkax252-python3.12-anndata-0.11.4
checking for references to /build/ in /nix/store/lsjghdh2yhdzc8qjvylrgnll8vkax252-python3.12-anndata-0.11.4...
patching script interpreter paths in /nix/store/lsjghdh2yhdzc8qjvylrgnll8vkax252-python3.12-anndata-0.11.4
stripping (with command strip and flags -S -p) in /nix/store/lsjghdh2yhdzc8qjvylrgnll8vkax252-python3.12-anndata-0.11.4/lib
shrinking RPATHs of ELF executables and libraries in /nix/store/l091smj9gs60jy1qlrfgk9pababj7bqx-python3.12-anndata-0.11.4-dist
checking for references to /build/ in /nix/store/l091smj9gs60jy1qlrfgk9pababj7bqx-python3.12-anndata-0.11.4-dist...
patching script interpreter paths in /nix/store/l091smj9gs60jy1qlrfgk9pababj7bqx-python3.12-anndata-0.11.4-dist
Executing pythonRemoveTestsDir
Finished executing pythonRemoveTestsDir
Running phase: installCheckPhase
no Makefile or custom installCheckPhase, doing nothing
Running phase: pythonCatchConflictsPhase
Running phase: pythonRemoveBinBytecodePhase
Running phase: pythonImportsCheckPhase
Executing pythonImportsCheckPhase
Check whether the following modules can be imported: anndata
Running phase: pytestCheckPhase
Executing pytestCheckPhase
pytest flags: -m pytest --ignore-glob=src/anndata/_core/anndata.py --ignore-glob=src/anndata/_core/merge.py --ignore-glob=src/anndata/_core/sparse_dataset.py --ignore-glob=src/anndata/_io/specs/registry.py --ignore-glob=src/anndata/_io/utils.py --ignore-glob=src/anndata/_warnings.py --ignore-glob=src/anndata/experimental/merge.py --ignore-glob=src/anndata/experimental/multi_files/_anncollection.py --ignore-glob=src/anndata/utils.py -k not\ \(concatenation.rst\)\ and\ not\ \(test_adata_raw_gpu\)\ and\ not\ \(test_as_cupy_dask\)\ and\ not\ \(test_as_dask_functions\)\ and\ not\ \(test_concat_different_types_dask\)\ and\ not\ \(test_concatenate_layers\)\ and\ not\ \(test_concatenate_layers_misaligned\)\ and\ not\ \(test_concatenate_layers_outer\)\ and\ not\ \(test_concatenate_roundtrip\)\ and\ not\ \(test_concat_on_var_outer_join\)\ and\ not\ \(test_dask_to_memory_unbacked\)\ and\ not\ \(test_ellipsis_index\)\ and\ not\ \(test_error_on_mixed_device\)\ and\ not\ \(test_gpu\)\ and\ not\ \(test_io_spec_cupy\)\ and\ not\ \(test_modify_view_component\)\ and\ not\ \(test_nan_merge\)\ and\ not\ \(test_pairwise_concat\)\ and\ not\ \(test_raw_gpu\)\ and\ not\ \(test_set_scalar_subset_X\)\ and\ not\ \(test_transposed_concat\)\ and\ not\ \(test_view_different_type_indices\)\ and\ not\ \(test_view_of_view\) -o addopts=
============================= test session starts ==============================
platform linux -- Python 3.12.10, pytest-8.3.5, pluggy-1.5.0
rootdir: /build/source
configfile: pyproject.toml
testpaths: anndata, ./tests, ./ci/scripts, ./docs/concatenation.rst
collected 5063 items / 1697 deselected / 1 skipped / 3366 selected
tests/test_anncollection.py ..... [ 0%]
tests/test_annot.py ...... [ 0%]
tests/test_awkward.py .................................................. [ 1%]
...................... [ 2%]
tests/test_backed_dense.py .................. [ 3%]
tests/test_backed_hdf5.py ...........................x........x..x..x..x [ 4%]
..x..x..x..............................................................x [ 6%]
........x..x..x..x..x..x..x..x........x..x..x..x..x..x..x..x........x..x [ 8%]
..x..x..x..x..x..x........x..x..x..x..x..x..x..x........x..x..x..x..x..x [ 10%]
..x..x........x..x..x..x..x..x..x..x........x..x..x..x..x..x..x......... [ 12%]
. [ 12%]
tests/test_backed_sparse.py ............................................ [ 14%]
........................................................................ [ 16%]
........................................................................ [ 18%]
..............................EEEEEEEEEE................................ [ 20%]
........................................................................ [ 22%]
.................................ss [ 23%]
tests/test_base.py ..................................................... [ 25%]
......................... [ 26%]
tests/test_concatenate.py .............................................. [ 27%]
........................................................................ [ 29%]
........................................................................ [ 31%]
........................................................................ [ 33%]
...................................................................x.x.. [ 36%]
.x..................FFFFF [ 36%]
tests/test_concatenate_disk.py ......................................... [ 38%]
............................................................... [ 39%]
tests/test_dask.py ...........EEEEEEEEEE................................ [ 41%]
. [ 41%]
tests/test_deprecations.py ..................... [ 42%]
tests/test_get_vector.py . [ 42%]
tests/test_helpers.py ................................... [ 43%]
tests/test_inplace_subset.py ........................................... [ 44%]
........................................................................ [ 46%]
......................... [ 47%]
tests/test_io_backwards_compat.py .... [ 47%]
tests/test_io_conversion.py ................... [ 48%]
tests/test_io_dispatched.py ..... [ 48%]
tests/test_io_elementwise.py ........................................... [ 49%]
.......................................EE............................... [ 51%]
............FF....................................... [ 53%]
tests/test_io_partial.py ....ss [ 53%]
tests/test_io_utils.py ......... [ 53%]
tests/test_io_warnings.py s. [ 53%]
tests/test_layers.py .......s... [ 54%]
tests/test_obsmvarm.py ....... [ 54%]
tests/test_obspvarp.py ......... [ 54%]
tests/test_raw.py ......xx.... [ 54%]
tests/test_readwrite.py ..................FFFF....FFFF......FF.......... [ 56%]
............sssssssss........x............................sssssss....... [ 58%]
...... [ 58%]
tests/test_repr.py ......... [ 58%]
tests/test_settings.py ................... [ 59%]
tests/test_structured_arrays.py .... [ 59%]
tests/test_transpose.py .............. [ 59%]
tests/test_uns.py . [ 60%]
tests/test_utils.py .. [ 60%]
tests/test_views.py .................................................... [ 61%]
........................................................................ [ 63%]
........................................................................ [ 65%]
........................................................................ [ 68%]
........................................................................ [ 70%]
........................................................................ [ 72%]
........................................................................ [ 74%]
........................................................................ [ 76%]
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........................................................................ [ 87%]
........................................................................ [ 89%]
........................................................................ [ 91%]
........................................................................ [ 93%]
........................................................................ [ 95%]
....................... [ 96%]
tests/test_x.py ........................................................ [ 98%]
........................x....x....x....x..................... [100%]
==================================== ERRORS ====================================
___________ ERROR at setup of test_consecutive_bool[h5ad-randomized] ___________
file /build/source/tests/test_backed_sparse.py, line 180
@pytest.mark.parametrize(
("make_bool_mask", "should_trigger_optimization"),
[
(make_randomized_mask, None),
(make_alternating_mask_15, True),
(make_alternating_mask_5, False),
(make_one_group_mask, True),
(make_one_elem_mask, False),
],
ids=["randomized", "alternating_15", "alternating_5", "one_group", "one_elem"],
)
def test_consecutive_bool(
E fixture 'mocker' not found
> available fixtures: backing_h5ad, cache, capfd, capfdbinary, caplog, capsys, capsysbinary, diskfmt, doctest_namespace, ellipsis_index, ellipsis_index_with_equivalent, equivalent_ellipsis_index, local_cluster_addr, monkeypatch, ondisk_equivalent_adata, pytestconfig, record_property, record_testsuite_property, record_xml_attribute, recwarn, subset_func, subset_func2, tmp_path, tmp_path_factory, tmpdir, tmpdir_factory
> use 'pytest --fixtures [testpath]' for help on them.
/build/source/tests/test_backed_sparse.py:180
_________ ERROR at setup of test_consecutive_bool[h5ad-alternating_15] _________
file /build/source/tests/test_backed_sparse.py, line 180
@pytest.mark.parametrize(
("make_bool_mask", "should_trigger_optimization"),
[
(make_randomized_mask, None),
(make_alternating_mask_15, True),
(make_alternating_mask_5, False),
(make_one_group_mask, True),
(make_one_elem_mask, False),
],
ids=["randomized", "alternating_15", "alternating_5", "one_group", "one_elem"],
)
def test_consecutive_bool(
E fixture 'mocker' not found
> available fixtures: backing_h5ad, cache, capfd, capfdbinary, caplog, capsys, capsysbinary, diskfmt, doctest_namespace, ellipsis_index, ellipsis_index_with_equivalent, equivalent_ellipsis_index, local_cluster_addr, monkeypatch, ondisk_equivalent_adata, pytestconfig, record_property, record_testsuite_property, record_xml_attribute, recwarn, subset_func, subset_func2, tmp_path, tmp_path_factory, tmpdir, tmpdir_factory
> use 'pytest --fixtures [testpath]' for help on them.
/build/source/tests/test_backed_sparse.py:180
_________ ERROR at setup of test_consecutive_bool[h5ad-alternating_5] __________
file /build/source/tests/test_backed_sparse.py, line 180
@pytest.mark.parametrize(
("make_bool_mask", "should_trigger_optimization"),
[
(make_randomized_mask, None),
(make_alternating_mask_15, True),
(make_alternating_mask_5, False),
(make_one_group_mask, True),
(make_one_elem_mask, False),
],
ids=["randomized", "alternating_15", "alternating_5", "one_group", "one_elem"],
)
def test_consecutive_bool(
E fixture 'mocker' not found
> available fixtures: backing_h5ad, cache, capfd, capfdbinary, caplog, capsys, capsysbinary, diskfmt, doctest_namespace, ellipsis_index, ellipsis_index_with_equivalent, equivalent_ellipsis_index, local_cluster_addr, monkeypatch, ondisk_equivalent_adata, pytestconfig, record_property, record_testsuite_property, record_xml_attribute, recwarn, subset_func, subset_func2, tmp_path, tmp_path_factory, tmpdir, tmpdir_factory
> use 'pytest --fixtures [testpath]' for help on them.
/build/source/tests/test_backed_sparse.py:180
___________ ERROR at setup of test_consecutive_bool[h5ad-one_group] ____________
file /build/source/tests/test_backed_sparse.py, line 180
@pytest.mark.parametrize(
("make_bool_mask", "should_trigger_optimization"),
[
(make_randomized_mask, None),
(make_alternating_mask_15, True),
(make_alternating_mask_5, False),
(make_one_group_mask, True),
(make_one_elem_mask, False),
],
ids=["randomized", "alternating_15", "alternating_5", "one_group", "one_elem"],
)
def test_consecutive_bool(
E fixture 'mocker' not found
> available fixtures: backing_h5ad, cache, capfd, capfdbinary, caplog, capsys, capsysbinary, diskfmt, doctest_namespace, ellipsis_index, ellipsis_index_with_equivalent, equivalent_ellipsis_index, local_cluster_addr, monkeypatch, ondisk_equivalent_adata, pytestconfig, record_property, record_testsuite_property, record_xml_attribute, recwarn, subset_func, subset_func2, tmp_path, tmp_path_factory, tmpdir, tmpdir_factory
> use 'pytest --fixtures [testpath]' for help on them.
/build/source/tests/test_backed_sparse.py:180
____________ ERROR at setup of test_consecutive_bool[h5ad-one_elem] ____________
file /build/source/tests/test_backed_sparse.py, line 180
@pytest.mark.parametrize(
("make_bool_mask", "should_trigger_optimization"),
[
(make_randomized_mask, None),
(make_alternating_mask_15, True),
(make_alternating_mask_5, False),
(make_one_group_mask, True),
(make_one_elem_mask, False),
],
ids=["randomized", "alternating_15", "alternating_5", "one_group", "one_elem"],
)
def test_consecutive_bool(
E fixture 'mocker' not found
> available fixtures: backing_h5ad, cache, capfd, capfdbinary, caplog, capsys, capsysbinary, diskfmt, doctest_namespace, ellipsis_index, ellipsis_index_with_equivalent, equivalent_ellipsis_index, local_cluster_addr, monkeypatch, ondisk_equivalent_adata, pytestconfig, record_property, record_testsuite_property, record_xml_attribute, recwarn, subset_func, subset_func2, tmp_path, tmp_path_factory, tmpdir, tmpdir_factory
> use 'pytest --fixtures [testpath]' for help on them.
/build/source/tests/test_backed_sparse.py:180
___________ ERROR at setup of test_consecutive_bool[zarr-randomized] ___________
file /build/source/tests/test_backed_sparse.py, line 180
@pytest.mark.parametrize(
("make_bool_mask", "should_trigger_optimization"),
[
(make_randomized_mask, None),
(make_alternating_mask_15, True),
(make_alternating_mask_5, False),
(make_one_group_mask, True),
(make_one_elem_mask, False),
],
ids=["randomized", "alternating_15", "alternating_5", "one_group", "one_elem"],
)
def test_consecutive_bool(
E fixture 'mocker' not found
> available fixtures: backing_h5ad, cache, capfd, capfdbinary, caplog, capsys, capsysbinary, diskfmt, doctest_namespace, ellipsis_index, ellipsis_index_with_equivalent, equivalent_ellipsis_index, local_cluster_addr, monkeypatch, ondisk_equivalent_adata, pytestconfig, record_property, record_testsuite_property, record_xml_attribute, recwarn, subset_func, subset_func2, tmp_path, tmp_path_factory, tmpdir, tmpdir_factory
> use 'pytest --fixtures [testpath]' for help on them.
/build/source/tests/test_backed_sparse.py:180
_________ ERROR at setup of test_consecutive_bool[zarr-alternating_15] _________
file /build/source/tests/test_backed_sparse.py, line 180
@pytest.mark.parametrize(
("make_bool_mask", "should_trigger_optimization"),
[
(make_randomized_mask, None),
(make_alternating_mask_15, True),
(make_alternating_mask_5, False),
(make_one_group_mask, True),
(make_one_elem_mask, False),
],
ids=["randomized", "alternating_15", "alternating_5", "one_group", "one_elem"],
)
def test_consecutive_bool(
E fixture 'mocker' not found
> available fixtures: backing_h5ad, cache, capfd, capfdbinary, caplog, capsys, capsysbinary, diskfmt, doctest_namespace, ellipsis_index, ellipsis_index_with_equivalent, equivalent_ellipsis_index, local_cluster_addr, monkeypatch, ondisk_equivalent_adata, pytestconfig, record_property, record_testsuite_property, record_xml_attribute, recwarn, subset_func, subset_func2, tmp_path, tmp_path_factory, tmpdir, tmpdir_factory
> use 'pytest --fixtures [testpath]' for help on them.
/build/source/tests/test_backed_sparse.py:180
_________ ERROR at setup of test_consecutive_bool[zarr-alternating_5] __________
file /build/source/tests/test_backed_sparse.py, line 180
@pytest.mark.parametrize(
("make_bool_mask", "should_trigger_optimization"),
[
(make_randomized_mask, None),
(make_alternating_mask_15, True),
(make_alternating_mask_5, False),
(make_one_group_mask, True),
(make_one_elem_mask, False),
],
ids=["randomized", "alternating_15", "alternating_5", "one_group", "one_elem"],
)
def test_consecutive_bool(
E fixture 'mocker' not found
> available fixtures: backing_h5ad, cache, capfd, capfdbinary, caplog, capsys, capsysbinary, diskfmt, doctest_namespace, ellipsis_index, ellipsis_index_with_equivalent, equivalent_ellipsis_index, local_cluster_addr, monkeypatch, ondisk_equivalent_adata, pytestconfig, record_property, record_testsuite_property, record_xml_attribute, recwarn, subset_func, subset_func2, tmp_path, tmp_path_factory, tmpdir, tmpdir_factory
> use 'pytest --fixtures [testpath]' for help on them.
/build/source/tests/test_backed_sparse.py:180
___________ ERROR at setup of test_consecutive_bool[zarr-one_group] ____________
file /build/source/tests/test_backed_sparse.py, line 180
@pytest.mark.parametrize(
("make_bool_mask", "should_trigger_optimization"),
[
(make_randomized_mask, None),
(make_alternating_mask_15, True),
(make_alternating_mask_5, False),
(make_one_group_mask, True),
(make_one_elem_mask, False),
],
ids=["randomized", "alternating_15", "alternating_5", "one_group", "one_elem"],
)
def test_consecutive_bool(
E fixture 'mocker' not found
> available fixtures: backing_h5ad, cache, capfd, capfdbinary, caplog, capsys, capsysbinary, diskfmt, doctest_namespace, ellipsis_index, ellipsis_index_with_equivalent, equivalent_ellipsis_index, local_cluster_addr, monkeypatch, ondisk_equivalent_adata, pytestconfig, record_property, record_testsuite_property, record_xml_attribute, recwarn, subset_func, subset_func2, tmp_path, tmp_path_factory, tmpdir, tmpdir_factory
> use 'pytest --fixtures [testpath]' for help on them.
/build/source/tests/test_backed_sparse.py:180
____________ ERROR at setup of test_consecutive_bool[zarr-one_elem] ____________
file /build/source/tests/test_backed_sparse.py, line 180
@pytest.mark.parametrize(
("make_bool_mask", "should_trigger_optimization"),
[
(make_randomized_mask, None),
(make_alternating_mask_15, True),
(make_alternating_mask_5, False),
(make_one_group_mask, True),
(make_one_elem_mask, False),
],
ids=["randomized", "alternating_15", "alternating_5", "one_group", "one_elem"],
)
def test_consecutive_bool(
E fixture 'mocker' not found
> available fixtures: backing_h5ad, cache, capfd, capfdbinary, caplog, capsys, capsysbinary, diskfmt, doctest_namespace, ellipsis_index, ellipsis_index_with_equivalent, equivalent_ellipsis_index, local_cluster_addr, monkeypatch, ondisk_equivalent_adata, pytestconfig, record_property, record_testsuite_property, record_xml_attribute, recwarn, subset_func, subset_func2, tmp_path, tmp_path_factory, tmpdir, tmpdir_factory
> use 'pytest --fixtures [testpath]' for help on them.
/build/source/tests/test_backed_sparse.py:180
__________ ERROR at setup of test_dask_distributed_write[h5ad-sizes0] __________
file /build/source/tests/test_dask.py, line 113
@pytest.mark.xdist_group("dask")
def test_dask_distributed_write(
file /build/source/tests/conftest.py, line 81
@pytest.fixture(scope="session")
def local_cluster_addr(
E fixture 'worker_id' not found
> available fixtures: adata, backing_h5ad, cache, capfd, capfdbinary, caplog, capsys, capsysbinary, diskfmt, doctest_namespace, ellipsis_index, ellipsis_index_with_equivalent, equivalent_ellipsis_index, local_cluster_addr, monkeypatch, pytestconfig, record_property, record_testsuite_property, record_xml_attribute, recwarn, sizes, subset_func, tmp_path, tmp_path_factory, tmpdir, tmpdir_factory
> use 'pytest --fixtures [testpath]' for help on them.
/build/source/tests/conftest.py:81
__________ ERROR at setup of test_dask_distributed_write[h5ad-sizes1] __________
file /build/source/tests/test_dask.py, line 113
@pytest.mark.xdist_group("dask")
def test_dask_distributed_write(
file /build/source/tests/conftest.py, line 81
@pytest.fixture(scope="session")
def local_cluster_addr(
E fixture 'worker_id' not found
> available fixtures: adata, backing_h5ad, cache, capfd, capfdbinary, caplog, capsys, capsysbinary, diskfmt, doctest_namespace, ellipsis_index, ellipsis_index_with_equivalent, equivalent_ellipsis_index, local_cluster_addr, monkeypatch, pytestconfig, record_property, record_testsuite_property, record_xml_attribute, recwarn, sizes, subset_func, tmp_path, tmp_path_factory, tmpdir, tmpdir_factory
> use 'pytest --fixtures [testpath]' for help on them.
/build/source/tests/conftest.py:81
__________ ERROR at setup of test_dask_distributed_write[h5ad-sizes2] __________
file /build/source/tests/test_dask.py, line 113
@pytest.mark.xdist_group("dask")
def test_dask_distributed_write(
file /build/source/tests/conftest.py, line 81
@pytest.fixture(scope="session")
def local_cluster_addr(
E fixture 'worker_id' not found
> available fixtures: adata, backing_h5ad, cache, capfd, capfdbinary, caplog, capsys, capsysbinary, diskfmt, doctest_namespace, ellipsis_index, ellipsis_index_with_equivalent, equivalent_ellipsis_index, local_cluster_addr, monkeypatch, pytestconfig, record_property, record_testsuite_property, record_xml_attribute, recwarn, sizes, subset_func, tmp_path, tmp_path_factory, tmpdir, tmpdir_factory
> use 'pytest --fixtures [testpath]' for help on them.
/build/source/tests/conftest.py:81
__________ ERROR at setup of test_dask_distributed_write[h5ad-sizes3] __________
file /build/source/tests/test_dask.py, line 113
@pytest.mark.xdist_group("dask")
def test_dask_distributed_write(
file /build/source/tests/conftest.py, line 81
@pytest.fixture(scope="session")
def local_cluster_addr(
E fixture 'worker_id' not found
> available fixtures: adata, backing_h5ad, cache, capfd, capfdbinary, caplog, capsys, capsysbinary, diskfmt, doctest_namespace, ellipsis_index, ellipsis_index_with_equivalent, equivalent_ellipsis_index, local_cluster_addr, monkeypatch, pytestconfig, record_property, record_testsuite_property, record_xml_attribute, recwarn, sizes, subset_func, tmp_path, tmp_path_factory, tmpdir, tmpdir_factory
> use 'pytest --fixtures [testpath]' for help on them.
/build/source/tests/conftest.py:81
__________ ERROR at setup of test_dask_distributed_write[h5ad-sizes4] __________
file /build/source/tests/test_dask.py, line 113
@pytest.mark.xdist_group("dask")
def test_dask_distributed_write(
file /build/source/tests/conftest.py, line 81
@pytest.fixture(scope="session")
def local_cluster_addr(
E fixture 'worker_id' not found
> available fixtures: adata, backing_h5ad, cache, capfd, capfdbinary, caplog, capsys, capsysbinary, diskfmt, doctest_namespace, ellipsis_index, ellipsis_index_with_equivalent, equivalent_ellipsis_index, local_cluster_addr, monkeypatch, pytestconfig, record_property, record_testsuite_property, record_xml_attribute, recwarn, sizes, subset_func, tmp_path, tmp_path_factory, tmpdir, tmpdir_factory
> use 'pytest --fixtures [testpath]' for help on them.
/build/source/tests/conftest.py:81
__________ ERROR at setup of test_dask_distributed_write[zarr-sizes0] __________
file /build/source/tests/test_dask.py, line 113
@pytest.mark.xdist_group("dask")
def test_dask_distributed_write(
file /build/source/tests/conftest.py, line 81
@pytest.fixture(scope="session")
def local_cluster_addr(
E fixture 'worker_id' not found
> available fixtures: adata, backing_h5ad, cache, capfd, capfdbinary, caplog, capsys, capsysbinary, diskfmt, doctest_namespace, ellipsis_index, ellipsis_index_with_equivalent, equivalent_ellipsis_index, local_cluster_addr, monkeypatch, pytestconfig, record_property, record_testsuite_property, record_xml_attribute, recwarn, sizes, subset_func, tmp_path, tmp_path_factory, tmpdir, tmpdir_factory
> use 'pytest --fixtures [testpath]' for help on them.
/build/source/tests/conftest.py:81
__________ ERROR at setup of test_dask_distributed_write[zarr-sizes1] __________
file /build/source/tests/test_dask.py, line 113
@pytest.mark.xdist_group("dask")
def test_dask_distributed_write(
file /build/source/tests/conftest.py, line 81
@pytest.fixture(scope="session")
def local_cluster_addr(
E fixture 'worker_id' not found
> available fixtures: adata, backing_h5ad, cache, capfd, capfdbinary, caplog, capsys, capsysbinary, diskfmt, doctest_namespace, ellipsis_index, ellipsis_index_with_equivalent, equivalent_ellipsis_index, local_cluster_addr, monkeypatch, pytestconfig, record_property, record_testsuite_property, record_xml_attribute, recwarn, sizes, subset_func, tmp_path, tmp_path_factory, tmpdir, tmpdir_factory
> use 'pytest --fixtures [testpath]' for help on them.
/build/source/tests/conftest.py:81
__________ ERROR at setup of test_dask_distributed_write[zarr-sizes2] __________
file /build/source/tests/test_dask.py, line 113
@pytest.mark.xdist_group("dask")
def test_dask_distributed_write(
file /build/source/tests/conftest.py, line 81
@pytest.fixture(scope="session")
def local_cluster_addr(
E fixture 'worker_id' not found
> available fixtures: adata, backing_h5ad, cache, capfd, capfdbinary, caplog, capsys, capsysbinary, diskfmt, doctest_namespace, ellipsis_index, ellipsis_index_with_equivalent, equivalent_ellipsis_index, local_cluster_addr, monkeypatch, pytestconfig, record_property, record_testsuite_property, record_xml_attribute, recwarn, sizes, subset_func, tmp_path, tmp_path_factory, tmpdir, tmpdir_factory
> use 'pytest --fixtures [testpath]' for help on them.
/build/source/tests/conftest.py:81
__________ ERROR at setup of test_dask_distributed_write[zarr-sizes3] __________
file /build/source/tests/test_dask.py, line 113
@pytest.mark.xdist_group("dask")
def test_dask_distributed_write(
file /build/source/tests/conftest.py, line 81
@pytest.fixture(scope="session")
def local_cluster_addr(
E fixture 'worker_id' not found
> available fixtures: adata, backing_h5ad, cache, capfd, capfdbinary, caplog, capsys, capsysbinary, diskfmt, doctest_namespace, ellipsis_index, ellipsis_index_with_equivalent, equivalent_ellipsis_index, local_cluster_addr, monkeypatch, pytestconfig, record_property, record_testsuite_property, record_xml_attribute, recwarn, sizes, subset_func, tmp_path, tmp_path_factory, tmpdir, tmpdir_factory
> use 'pytest --fixtures [testpath]' for help on them.
/build/source/tests/conftest.py:81
__________ ERROR at setup of test_dask_distributed_write[zarr-sizes4] __________
file /build/source/tests/test_dask.py, line 113
@pytest.mark.xdist_group("dask")
def test_dask_distributed_write(
file /build/source/tests/conftest.py, line 81
@pytest.fixture(scope="session")
def local_cluster_addr(
E fixture 'worker_id' not found
> available fixtures: adata, backing_h5ad, cache, capfd, capfdbinary, caplog, capsys, capsysbinary, diskfmt, doctest_namespace, ellipsis_index, ellipsis_index_with_equivalent, equivalent_ellipsis_index, local_cluster_addr, monkeypatch, pytestconfig, record_property, record_testsuite_property, record_xml_attribute, recwarn, sizes, subset_func, tmp_path, tmp_path_factory, tmpdir, tmpdir_factory
> use 'pytest --fixtures [testpath]' for help on them.
/build/source/tests/conftest.py:81
_______________ ERROR at setup of test_read_lazy_h5_cluster[csr] _______________
file /build/source/tests/test_io_elementwise.py, line 348
@pytest.mark.xdist_group("dask")
def test_read_lazy_h5_cluster(
file /build/source/tests/conftest.py, line 81
@pytest.fixture(scope="session")
def local_cluster_addr(
E fixture 'worker_id' not found
> available fixtures: backing_h5ad, cache, capfd, capfdbinary, caplog, capsys, capsysbinary, diskfmt, doctest_namespace, ellipsis_index, ellipsis_index_with_equivalent, equivalent_ellipsis_index, local_cluster_addr, monkeypatch, pytestconfig, record_property, record_testsuite_property, record_xml_attribute, recwarn, sparse_format, store, subset_func, tmp_path, tmp_path_factory, tmpdir, tmpdir_factory
> use 'pytest --fixtures [testpath]' for help on them.
/build/source/tests/conftest.py:81
_______________ ERROR at setup of test_read_lazy_h5_cluster[csc] _______________
file /build/source/tests/test_io_elementwise.py, line 348
@pytest.mark.xdist_group("dask")
def test_read_lazy_h5_cluster(
file /build/source/tests/conftest.py, line 81
@pytest.fixture(scope="session")
def local_cluster_addr(
E fixture 'worker_id' not found
> available fixtures: backing_h5ad, cache, capfd, capfdbinary, caplog, capsys, capsysbinary, diskfmt, doctest_namespace, ellipsis_index, ellipsis_index_with_equivalent, equivalent_ellipsis_index, local_cluster_addr, monkeypatch, pytestconfig, record_property, record_testsuite_property, record_xml_attribute, recwarn, sparse_format, store, subset_func, tmp_path, tmp_path_factory, tmpdir, tmpdir_factory
> use 'pytest --fixtures [testpath]' for help on them.
/build/source/tests/conftest.py:81
=================================== FAILURES ===================================
______________ test_concat_dask_sparse_matches_memory[outer-None] ______________
join_type = 'outer', merge_strategy = None
def test_concat_dask_sparse_matches_memory(join_type, merge_strategy):
import dask.array as da
X = sparse.random(50, 20, density=0.5, format="csr")
X_dask = da.from_array(X, chunks=(5, 20))
var_names_1 = [f"gene_{i}" for i in range(20)]
var_names_2 = [f"gene_{i}{'_foo' if (i % 2) else ''}" for i in range(20, 40)]
ad1 = AnnData(X=X, var=pd.DataFrame(index=var_names_1))
ad2 = AnnData(X=X, var=pd.DataFrame(index=var_names_2))
ad1_dask = AnnData(X=X_dask, var=pd.DataFrame(index=var_names_1))
ad2_dask = AnnData(X=X_dask, var=pd.DataFrame(index=var_names_2))
res_in_memory = concat([ad1, ad2], join=join_type, merge=merge_strategy)
res_dask = concat([ad1_dask, ad2_dask], join=join_type, merge=merge_strategy)
> assert_equal(res_in_memory, res_dask)
tests/test_concatenate.py:1698:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/nix/store/8w718rm43x7z73xhw9d6vh8s4snrq67h-python3-3.12.10/lib/python3.12/functools.py:912: in wrapper
return dispatch(args[0].__class__)(*args, **kw)
/nix/store/lsjghdh2yhdzc8qjvylrgnll8vkax252-python3.12-anndata-0.11.4/lib/python3.12/site-packages/anndata/tests/helpers.py:763: in assert_adata_equal
assert_equal(
/nix/store/8w718rm43x7z73xhw9d6vh8s4snrq67h-python3-3.12.10/lib/python3.12/functools.py:912: in wrapper
return dispatch(args[0].__class__)(*args, **kw)
/nix/store/lsjghdh2yhdzc8qjvylrgnll8vkax252-python3.12-anndata-0.11.4/lib/python3.12/site-packages/anndata/tests/helpers.py:603: in assert_equal_sparse
assert_equal(b, a, exact, elem_name=elem_name)
/nix/store/8w718rm43x7z73xhw9d6vh8s4snrq67h-python3-3.12.10/lib/python3.12/functools.py:912: in wrapper
return dispatch(args[0].__class__)(*args, **kw)
/nix/store/lsjghdh2yhdzc8qjvylrgnll8vkax252-python3.12-anndata-0.11.4/lib/python3.12/site-packages/anndata/tests/helpers.py:626: in assert_equal_dask_array
assert_equal(b, a.compute(), exact, elem_name)
/nix/store/8w718rm43x7z73xhw9d6vh8s4snrq67h-python3-3.12.10/lib/python3.12/functools.py:912: in wrapper
return dispatch(args[0].__class__)(*args, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
a = array([[0. , 0.31147147, 0.07804689, ..., 0. , 0. ,
0.97761109],
[0. , 0. ... ],
[0. , 0. , 0. , ..., 0. , 0. ,
0. ]], shape=(100, 40))
b = array([[0. , 0.31147147, 0.07804689, ..., 0. , 0. ,
0.97761109],
[0. , 0. ...46234],
[0.14042709, 0.14042709, 0.14042709, ..., 0.14042709, 0.14042709,
0.14042709]], shape=(100, 40))
exact = False, elem_name = 'X'
@assert_equal.register(np.ndarray)
def assert_equal_ndarray(a, b, exact=False, elem_name=None):
b = asarray(b)
if not exact and is_numeric_dtype(a) and is_numeric_dtype(b):
assert a.shape == b.shape, format_msg(elem_name)
> np.testing.assert_allclose(a, b, equal_nan=True, err_msg=format_msg(elem_name))
E AssertionError:
E Not equal to tolerance rtol=1e-07, atol=0
E Error raised from element 'X'.
E Mismatched elements: 880 / 4000 (22%)
E Max absolute difference among violations: 0.95548829
E Max relative difference among violations: 1.
E ACTUAL: array([[0. , 0.311471, 0.078047, ..., 0. , 0. , 0.977611],
E [0. , 0. , 0.863563, ..., 0. , 0. , 0. ],
E [0.59661 , 0. , 0. , ..., 0. , 0. , 0.324186],...
E DESIRED: array([[0. , 0.311471, 0.078047, ..., 0. , 0. , 0.977611],
E [0. , 0. , 0.863563, ..., 0. , 0. , 0. ],
E [0.59661 , 0. , 0. , ..., 0. , 0. , 0.324186],...
/nix/store/lsjghdh2yhdzc8qjvylrgnll8vkax252-python3.12-anndata-0.11.4/lib/python3.12/site-packages/anndata/tests/helpers.py:577: AssertionError
______________ test_concat_dask_sparse_matches_memory[outer-same] ______________
join_type = 'outer', merge_strategy = 'same'
def test_concat_dask_sparse_matches_memory(join_type, merge_strategy):
import dask.array as da
X = sparse.random(50, 20, density=0.5, format="csr")
X_dask = da.from_array(X, chunks=(5, 20))
var_names_1 = [f"gene_{i}" for i in range(20)]
var_names_2 = [f"gene_{i}{'_foo' if (i % 2) else ''}" for i in range(20, 40)]
ad1 = AnnData(X=X, var=pd.DataFrame(index=var_names_1))
ad2 = AnnData(X=X, var=pd.DataFrame(index=var_names_2))
ad1_dask = AnnData(X=X_dask, var=pd.DataFrame(index=var_names_1))
ad2_dask = AnnData(X=X_dask, var=pd.DataFrame(index=var_names_2))
res_in_memory = concat([ad1, ad2], join=join_type, merge=merge_strategy)
res_dask = concat([ad1_dask, ad2_dask], join=join_type, merge=merge_strategy)
> assert_equal(res_in_memory, res_dask)
tests/test_concatenate.py:1698:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/nix/store/8w718rm43x7z73xhw9d6vh8s4snrq67h-python3-3.12.10/lib/python3.12/functools.py:912: in wrapper
return dispatch(args[0].__class__)(*args, **kw)
/nix/store/lsjghdh2yhdzc8qjvylrgnll8vkax252-python3.12-anndata-0.11.4/lib/python3.12/site-packages/anndata/tests/helpers.py:763: in assert_adata_equal
assert_equal(
/nix/store/8w718rm43x7z73xhw9d6vh8s4snrq67h-python3-3.12.10/lib/python3.12/functools.py:912: in wrapper
return dispatch(args[0].__class__)(*args, **kw)
/nix/store/lsjghdh2yhdzc8qjvylrgnll8vkax252-python3.12-anndata-0.11.4/lib/python3.12/site-packages/anndata/tests/helpers.py:603: in assert_equal_sparse
assert_equal(b, a, exact, elem_name=elem_name)
/nix/store/8w718rm43x7z73xhw9d6vh8s4snrq67h-python3-3.12.10/lib/python3.12/functools.py:912: in wrapper
return dispatch(args[0].__class__)(*args, **kw)
/nix/store/lsjghdh2yhdzc8qjvylrgnll8vkax252-python3.12-anndata-0.11.4/lib/python3.12/site-packages/anndata/tests/helpers.py:626: in assert_equal_dask_array
assert_equal(b, a.compute(), exact, elem_name)
/nix/store/8w718rm43x7z73xhw9d6vh8s4snrq67h-python3-3.12.10/lib/python3.12/functools.py:912: in wrapper
return dispatch(args[0].__class__)(*args, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
a = array([[0.70666451, 0.9810538 , 0.81099848, ..., 0. , 0. ,
0.39215538],
[0. , 0.80... ],
[0. , 0. , 0. , ..., 0. , 0. ,
0. ]], shape=(100, 40))
b = array([[0.70666451, 0.9810538 , 0.81099848, ..., 0. , 0. ,
0.39215538],
[0. , 0.80...70356],
[0.20455613, 0.20455613, 0.20455613, ..., 0.20455613, 0.20455613,
0.20455613]], shape=(100, 40))
exact = False, elem_name = 'X'
@assert_equal.register(np.ndarray)
def assert_equal_ndarray(a, b, exact=False, elem_name=None):
b = asarray(b)
if not exact and is_numeric_dtype(a) and is_numeric_dtype(b):
assert a.shape == b.shape, format_msg(elem_name)
> np.testing.assert_allclose(a, b, equal_nan=True, err_msg=format_msg(elem_name))
E AssertionError:
E Not equal to tolerance rtol=1e-07, atol=0
E Error raised from element 'X'.
E Mismatched elements: 920 / 4000 (23%)
E Max absolute difference among violations: 0.99341873
E Max relative difference among violations: 1.
E ACTUAL: array([[0.706665, 0.981054, 0.810998, ..., 0. , 0. , 0.392155],
E [0. , 0.800075, 0.320862, ..., 0.405274, 0.468094, 0. ],
E [0.720801, 0. , 0. , ..., 0. , 0.500157, 0. ],...
E DESIRED: array([[0.706665, 0.981054, 0.810998, ..., 0. , 0. , 0.392155],
E [0. , 0.800075, 0.320862, ..., 0.405274, 0.468094, 0. ],
E [0.720801, 0. , 0. , ..., 0. , 0.500157, 0. ],...
/nix/store/lsjghdh2yhdzc8qjvylrgnll8vkax252-python3.12-anndata-0.11.4/lib/python3.12/site-packages/anndata/tests/helpers.py:577: AssertionError
_____________ test_concat_dask_sparse_matches_memory[outer-unique] _____________
join_type = 'outer', merge_strategy = 'unique'
def test_concat_dask_sparse_matches_memory(join_type, merge_strategy):
import dask.array as da
X = sparse.random(50, 20, density=0.5, format="csr")
X_dask = da.from_array(X, chunks=(5, 20))
var_names_1 = [f"gene_{i}" for i in range(20)]
var_names_2 = [f"gene_{i}{'_foo' if (i % 2) else ''}" for i in range(20, 40)]
ad1 = AnnData(X=X, var=pd.DataFrame(index=var_names_1))
ad2 = AnnData(X=X, var=pd.DataFrame(index=var_names_2))
ad1_dask = AnnData(X=X_dask, var=pd.DataFrame(index=var_names_1))
ad2_dask = AnnData(X=X_dask, var=pd.DataFrame(index=var_names_2))
res_in_memory = concat([ad1, ad2], join=join_type, merge=merge_strategy)
res_dask = concat([ad1_dask, ad2_dask], join=join_type, merge=merge_strategy)
> assert_equal(res_in_memory, res_dask)
tests/test_concatenate.py:1698:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/nix/store/8w718rm43x7z73xhw9d6vh8s4snrq67h-python3-3.12.10/lib/python3.12/functools.py:912: in wrapper
return dispatch(args[0].__class__)(*args, **kw)
/nix/store/lsjghdh2yhdzc8qjvylrgnll8vkax252-python3.12-anndata-0.11.4/lib/python3.12/site-packages/anndata/tests/helpers.py:763: in assert_adata_equal
assert_equal(
/nix/store/8w718rm43x7z73xhw9d6vh8s4snrq67h-python3-3.12.10/lib/python3.12/functools.py:912: in wrapper
return dispatch(args[0].__class__)(*args, **kw)
/nix/store/lsjghdh2yhdzc8qjvylrgnll8vkax252-python3.12-anndata-0.11.4/lib/python3.12/site-packages/anndata/tests/helpers.py:603: in assert_equal_sparse
assert_equal(b, a, exact, elem_name=elem_name)
/nix/store/8w718rm43x7z73xhw9d6vh8s4snrq67h-python3-3.12.10/lib/python3.12/functools.py:912: in wrapper
return dispatch(args[0].__class__)(*args, **kw)
/nix/store/lsjghdh2yhdzc8qjvylrgnll8vkax252-python3.12-anndata-0.11.4/lib/python3.12/site-packages/anndata/tests/helpers.py:626: in assert_equal_dask_array
assert_equal(b, a.compute(), exact, elem_name)
/nix/store/8w718rm43x7z73xhw9d6vh8s4snrq67h-python3-3.12.10/lib/python3.12/functools.py:912: in wrapper
return dispatch(args[0].__class__)(*args, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
a = array([[0.41639268, 0. , 0.03259961, ..., 0. , 0. ,
0. ],
[0. , 0. ... ],
[0. , 0. , 0. , ..., 0. , 0. ,
0. ]], shape=(100, 40))
b = array([[0.41639268, 0. , 0.03259961, ..., 0. , 0. ,
0. ],
[0. , 0. ...20978],
[0. , 0. , 0. , ..., 0. , 0. ,
0. ]], shape=(100, 40))
exact = False, elem_name = 'X'
@assert_equal.register(np.ndarray)
def assert_equal_ndarray(a, b, exact=False, elem_name=None):
b = asarray(b)
if not exact and is_numeric_dtype(a) and is_numeric_dtype(b):
assert a.shape == b.shape, format_msg(elem_name)
> np.testing.assert_allclose(a, b, equal_nan=True, err_msg=format_msg(elem_name))
E AssertionError:
E Not equal to tolerance rtol=1e-07, atol=0
E Error raised from element 'X'.
E Mismatched elements: 1160 / 4000 (29%)
E Max absolute difference among violations: 0.99650923
E Max relative difference among violations: 1.
E ACTUAL: array([[0.416393, 0. , 0.0326 , ..., 0. , 0. , 0. ],
E [0. , 0. , 0. , ..., 0. , 0. , 0.991663],
E [0. , 0.394503, 0.99507 , ..., 0. , 0. , 0. ],...
E DESIRED: array([[0.416393, 0. , 0.0326 , ..., 0. , 0. , 0. ],
E [0. , 0. , 0. , ..., 0. , 0. , 0.991663],
E [0. , 0.394503, 0.99507 , ..., 0. , 0. , 0. ],...
/nix/store/lsjghdh2yhdzc8qjvylrgnll8vkax252-python3.12-anndata-0.11.4/lib/python3.12/site-packages/anndata/tests/helpers.py:577: AssertionError
_____________ test_concat_dask_sparse_matches_memory[outer-first] ______________
join_type = 'outer', merge_strategy = 'first'
def test_concat_dask_sparse_matches_memory(join_type, merge_strategy):
import dask.array as da
X = sparse.random(50, 20, density=0.5, format="csr")
X_dask = da.from_array(X, chunks=(5, 20))
var_names_1 = [f"gene_{i}" for i in range(20)]
var_names_2 = [f"gene_{i}{'_foo' if (i % 2) else ''}" for i in range(20, 40)]
ad1 = AnnData(X=X, var=pd.DataFrame(index=var_names_1))
ad2 = AnnData(X=X, var=pd.DataFrame(index=var_names_2))
ad1_dask = AnnData(X=X_dask, var=pd.DataFrame(index=var_names_1))
ad2_dask = AnnData(X=X_dask, var=pd.DataFrame(index=var_names_2))
res_in_memory = concat([ad1, ad2], join=join_type, merge=merge_strategy)
res_dask = concat([ad1_dask, ad2_dask], join=join_type, merge=merge_strategy)
> assert_equal(res_in_memory, res_dask)
tests/test_concatenate.py:1698:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/nix/store/8w718rm43x7z73xhw9d6vh8s4snrq67h-python3-3.12.10/lib/python3.12/functools.py:912: in wrapper
return dispatch(args[0].__class__)(*args, **kw)
/nix/store/lsjghdh2yhdzc8qjvylrgnll8vkax252-python3.12-anndata-0.11.4/lib/python3.12/site-packages/anndata/tests/helpers.py:763: in assert_adata_equal
assert_equal(
/nix/store/8w718rm43x7z73xhw9d6vh8s4snrq67h-python3-3.12.10/lib/python3.12/functools.py:912: in wrapper
return dispatch(args[0].__class__)(*args, **kw)
/nix/store/lsjghdh2yhdzc8qjvylrgnll8vkax252-python3.12-anndata-0.11.4/lib/python3.12/site-packages/anndata/tests/helpers.py:603: in assert_equal_sparse
assert_equal(b, a, exact, elem_name=elem_name)
/nix/store/8w718rm43x7z73xhw9d6vh8s4snrq67h-python3-3.12.10/lib/python3.12/functools.py:912: in wrapper
return dispatch(args[0].__class__)(*args, **kw)
/nix/store/lsjghdh2yhdzc8qjvylrgnll8vkax252-python3.12-anndata-0.11.4/lib/python3.12/site-packages/anndata/tests/helpers.py:626: in assert_equal_dask_array
assert_equal(b, a.compute(), exact, elem_name)
/nix/store/8w718rm43x7z73xhw9d6vh8s4snrq67h-python3-3.12.10/lib/python3.12/functools.py:912: in wrapper
return dispatch(args[0].__class__)(*args, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
a = array([[0. , 0. , 0. , ..., 0.18323909, 0. ,
0. ],
[0.23802404, 0. ... ],
[0. , 0. , 0. , ..., 0. , 0. ,
0. ]], shape=(100, 40))
b = array([[0. , 0. , 0. , ..., 0.18323909, 0. ,
0. ],
[0.23802404, 0. ...90483],
[0. , 0. , 0. , ..., 0. , 0. ,
0. ]], shape=(100, 40))
exact = False, elem_name = 'X'
@assert_equal.register(np.ndarray)
def assert_equal_ndarray(a, b, exact=False, elem_name=None):
b = asarray(b)
if not exact and is_numeric_dtype(a) and is_numeric_dtype(b):
assert a.shape == b.shape, format_msg(elem_name)
> np.testing.assert_allclose(a, b, equal_nan=True, err_msg=format_msg(elem_name))
E AssertionError:
E Not equal to tolerance rtol=1e-07, atol=0
E Error raised from element 'X'.
E Mismatched elements: 1240 / 4000 (31%)
E Max absolute difference among violations: 0.98815086
E Max relative difference among violations: 1.
E ACTUAL: array([[0. , 0. , 0. , ..., 0.183239, 0. , 0. ],
E [0.238024, 0. , 0. , ..., 0.529747, 0. , 0.761065],
E [0. , 0.205438, 0.723672, ..., 0. , 0. , 0. ],...
E DESIRED: array([[0. , 0. , 0. , ..., 0.183239, 0. , 0. ],
E [0.238024, 0. , 0. , ..., 0.529747, 0. , 0.761065],
E [0. , 0.205438, 0.723672, ..., 0. , 0. , 0. ],...
/nix/store/lsjghdh2yhdzc8qjvylrgnll8vkax252-python3.12-anndata-0.11.4/lib/python3.12/site-packages/anndata/tests/helpers.py:577: AssertionError
______________ test_concat_dask_sparse_matches_memory[outer-only] ______________
join_type = 'outer', merge_strategy = 'only'
def test_concat_dask_sparse_matches_memory(join_type, merge_strategy):
import dask.array as da
X = sparse.random(50, 20, density=0.5, format="csr")
X_dask = da.from_array(X, chunks=(5, 20))
var_names_1 = [f"gene_{i}" for i in range(20)]
var_names_2 = [f"gene_{i}{'_foo' if (i % 2) else ''}" for i in range(20, 40)]
ad1 = AnnData(X=X, var=pd.DataFrame(index=var_names_1))
ad2 = AnnData(X=X, var=pd.DataFrame(index=var_names_2))
ad1_dask = AnnData(X=X_dask, var=pd.DataFrame(index=var_names_1))
ad2_dask = AnnData(X=X_dask, var=pd.DataFrame(index=var_names_2))
res_in_memory = concat([ad1, ad2], join=join_type, merge=merge_strategy)
res_dask = concat([ad1_dask, ad2_dask], join=join_type, merge=merge_strategy)
> assert_equal(res_in_memory, res_dask)
tests/test_concatenate.py:1698:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/nix/store/8w718rm43x7z73xhw9d6vh8s4snrq67h-python3-3.12.10/lib/python3.12/functools.py:912: in wrapper
return dispatch(args[0].__class__)(*args, **kw)
/nix/store/lsjghdh2yhdzc8qjvylrgnll8vkax252-python3.12-anndata-0.11.4/lib/python3.12/site-packages/anndata/tests/helpers.py:763: in assert_adata_equal
assert_equal(
/nix/store/8w718rm43x7z73xhw9d6vh8s4snrq67h-python3-3.12.10/lib/python3.12/functools.py:912: in wrapper
return dispatch(args[0].__class__)(*args, **kw)
/nix/store/lsjghdh2yhdzc8qjvylrgnll8vkax252-python3.12-anndata-0.11.4/lib/python3.12/site-packages/anndata/tests/helpers.py:603: in assert_equal_sparse
assert_equal(b, a, exact, elem_name=elem_name)
/nix/store/8w718rm43x7z73xhw9d6vh8s4snrq67h-python3-3.12.10/lib/python3.12/functools.py:912: in wrapper
return dispatch(args[0].__class__)(*args, **kw)
/nix/store/lsjghdh2yhdzc8qjvylrgnll8vkax252-python3.12-anndata-0.11.4/lib/python3.12/site-packages/anndata/tests/helpers.py:626: in assert_equal_dask_array
assert_equal(b, a.compute(), exact, elem_name)
/nix/store/8w718rm43x7z73xhw9d6vh8s4snrq67h-python3-3.12.10/lib/python3.12/functools.py:912: in wrapper
return dispatch(args[0].__class__)(*args, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
a = array([[0.55364538, 0.41274351, 0. , ..., 0. , 0.72269803,
0. ],
[0.07384858, 0. ... ],
[0. , 0. , 0. , ..., 0. , 0. ,
0. ]], shape=(100, 40))
b = array([[0.55364538, 0.41274351, 0. , ..., 0. , 0.72269803,
0. ],
[0.07384858, 0. ...29171],
[0. , 0. , 0. , ..., 0. , 0. ,
0. ]], shape=(100, 40))
exact = False, elem_name = 'X'
@assert_equal.register(np.ndarray)
def assert_equal_ndarray(a, b, exact=False, elem_name=None):
b = asarray(b)
if not exact and is_numeric_dtype(a) and is_numeric_dtype(b):
assert a.shape == b.shape, format_msg(elem_name)
> np.testing.assert_allclose(a, b, equal_nan=True, err_msg=format_msg(elem_name))
E AssertionError:
E Not equal to tolerance rtol=1e-07, atol=0
E Error raised from element 'X'.
E Mismatched elements: 880 / 4000 (22%)
E Max absolute difference among violations: 0.88265018
E Max relative difference among violations: 1.
E ACTUAL: array([[0.553645, 0.412744, 0. , ..., 0. , 0.722698, 0. ],
E [0.073849, 0. , 0. , ..., 0. , 0.492596, 0.527854],
E [0. , 0. , 0. , ..., 0.822827, 0.68172 , 0. ],...
E DESIRED: array([[0.553645, 0.412744, 0. , ..., 0. , 0.722698, 0. ],
E [0.073849, 0. , 0. , ..., 0. , 0.492596, 0.527854],
E [0. , 0. , 0. , ..., 0.822827, 0.68172 , 0. ],...
/nix/store/lsjghdh2yhdzc8qjvylrgnll8vkax252-python3.12-anndata-0.11.4/lib/python3.12/site-packages/anndata/tests/helpers.py:577: AssertionError
_____________________ test_write_nullable_string_error[h5] _____________________
store = <HDF5 group "/" (1 members)>
def test_write_nullable_string_error(store):
> with pytest.raises(RuntimeError, match=r"allow_write_nullable_strings.*is False"):
E Failed: DID NOT RAISE <class 'RuntimeError'>
tests/test_io_elementwise.py:496: Failed
____________________ test_write_nullable_string_error[zarr] ____________________
store = <zarr.hierarchy.Group '/'>
def test_write_nullable_string_error(store):
> with pytest.raises(RuntimeError, match=r"allow_write_nullable_strings.*is False"):
E Failed: DID NOT RAISE <class 'RuntimeError'>
tests/test_io_elementwise.py:496: Failed
_________ test_readwrite_kitchensink[dataset_kwargs0-csr_matrix-h5ad] __________
tmp_path = PosixPath('/build/pytest-of-nixbld/pytest-0/test_readwrite_kitchensink_dat2')
storage = 'h5ad', typ = <class 'scipy.sparse._csr.csr_matrix'>
backing_h5ad = PosixPath('/build/pytest-of-nixbld/pytest-0/test_readwrite_kitchensink_dat2/test.h5ad')
dataset_kwargs = {}
@pytest.mark.parametrize("storage", ["h5ad", pytest.param("zarr", marks=[needs_zarr])])
@pytest.mark.parametrize("typ", [np.array, csr_matrix, csr_array, as_dense_dask_array])
def test_readwrite_kitchensink(tmp_path, storage, typ, backing_h5ad, dataset_kwargs):
X = typ(X_list)
adata_src = ad.AnnData(X, obs=obs_dict, var=var_dict, uns=uns_dict)
assert not isinstance(adata_src.obs["oanno1"].dtype, pd.CategoricalDtype)
adata_src.raw = adata_src.copy()
if storage == "h5ad":
adata_src.write(backing_h5ad, **dataset_kwargs)
adata_mid = ad.read_h5ad(backing_h5ad)
adata_mid.write(tmp_path / "mid.h5ad", **dataset_kwargs)
adata = ad.read_h5ad(tmp_path / "mid.h5ad")
else:
adata_src.write_zarr(tmp_path / "test_zarr_dir", chunks=True)
adata = ad.read_zarr(tmp_path / "test_zarr_dir")
assert isinstance(adata.obs["oanno1"].dtype, pd.CategoricalDtype)
assert not isinstance(adata.obs["oanno2"].dtype, pd.CategoricalDtype)
assert adata.obs.index.tolist() == ["name1", "name2", "name3"]
assert adata.obs["oanno1"].cat.categories.tolist() == ["cat1", "cat2"]
assert adata.obs["oanno1c"].cat.categories.tolist() == ["cat1"]
assert isinstance(adata.raw.var["vanno2"].dtype, pd.CategoricalDtype)
pd.testing.assert_frame_equal(adata.obs, adata_src.obs)
pd.testing.assert_frame_equal(adata.var, adata_src.var)
assert_equal(adata.var.index, adata_src.var.index)
assert adata.var.index.dtype == adata_src.var.index.dtype
# Dev. Note:
# either load as same type or load the convert DaskArray to array
# since we tested if assigned types and loaded types are DaskArray
# this would also work if they work
if isinstance(adata_src.raw.X, CSArray):
assert isinstance(adata.raw.X, CSMatrix)
else:
> assert isinstance(adata_src.raw.X, type(adata.raw.X) | DaskArray)
E AssertionError: assert False
E + where False = isinstance(<Compressed Sparse Row sparse matrix of dtype 'int64'\n with 4 stored elements and shape (3, 2)>, (<class 'scipy.sparse._csr.csr_array'> | DaskArray))
E + where <Compressed Sparse Row sparse matrix of dtype 'int64'\n with 4 stored elements and shape (3, 2)> = <anndata._core.raw.Raw object at 0x7ffee8d60d40>.X
E + where <anndata._core.raw.Raw object at 0x7ffee8d60d40> = AnnData object with n_obs × n_vars = 3 × 2\n obs: 'oanno1', 'oanno1b', 'oanno1c', 'oanno2', 'oanno3', 'oanno4'\n var: 'vanno1', 'vanno2', 'vanno3', 'vanno4'\n uns: 'oanno1_colors', 'uns2', 'uns3', 'uns4'.raw
E + and <class 'scipy.sparse._csr.csr_array'> = type(<Compressed Sparse Row sparse array of dtype 'int64'\n with 4 stored elements and shape (3, 2)>)
E + where <Compressed Sparse Row sparse array of dtype 'int64'\n with 4 stored elements and shape (3, 2)> = <anndata._core.raw.Raw object at 0x7ffee8d3f740>.X
E + where <anndata._core.raw.Raw object at 0x7ffee8d3f740> = AnnData object with n_obs × n_vars = 3 × 2\n obs: 'oanno1', 'oanno1b', 'oanno1c', 'oanno2', 'oanno3', 'oanno4'\n var: 'vanno1', 'vanno2', 'vanno3', 'vanno4'\n uns: 'oanno1_colors', 'uns2', 'uns3', 'uns4'.raw
tests/test_readwrite.py:163: AssertionError
_________ test_readwrite_kitchensink[dataset_kwargs0-csr_matrix-zarr] __________
tmp_path = PosixPath('/build/pytest-of-nixbld/pytest-0/test_readwrite_kitchensink_dat3')
storage = 'zarr', typ = <class 'scipy.sparse._csr.csr_matrix'>
backing_h5ad = PosixPath('/build/pytest-of-nixbld/pytest-0/test_readwrite_kitchensink_dat3/test.h5ad')
dataset_kwargs = {}
@pytest.mark.parametrize("storage", ["h5ad", pytest.param("zarr", marks=[needs_zarr])])
@pytest.mark.parametrize("typ", [np.array, csr_matrix, csr_array, as_dense_dask_array])
def test_readwrite_kitchensink(tmp_path, storage, typ, backing_h5ad, dataset_kwargs):
X = typ(X_list)
adata_src = ad.AnnData(X, obs=obs_dict, var=var_dict, uns=uns_dict)
assert not isinstance(adata_src.obs["oanno1"].dtype, pd.CategoricalDtype)
adata_src.raw = adata_src.copy()
if storage == "h5ad":
adata_src.write(backing_h5ad, **dataset_kwargs)
adata_mid = ad.read_h5ad(backing_h5ad)
adata_mid.write(tmp_path / "mid.h5ad", **dataset_kwargs)
adata = ad.read_h5ad(tmp_path / "mid.h5ad")
else:
adata_src.write_zarr(tmp_path / "test_zarr_dir", chunks=True)
adata = ad.read_zarr(tmp_path / "test_zarr_dir")
assert isinstance(adata.obs["oanno1"].dtype, pd.CategoricalDtype)
assert not isinstance(adata.obs["oanno2"].dtype, pd.CategoricalDtype)
assert adata.obs.index.tolist() == ["name1", "name2", "name3"]
assert adata.obs["oanno1"].cat.categories.tolist() == ["cat1", "cat2"]
assert adata.obs["oanno1c"].cat.categories.tolist() == ["cat1"]
assert isinstance(adata.raw.var["vanno2"].dtype, pd.CategoricalDtype)
pd.testing.assert_frame_equal(adata.obs, adata_src.obs)
pd.testing.assert_frame_equal(adata.var, adata_src.var)
assert_equal(adata.var.index, adata_src.var.index)
assert adata.var.index.dtype == adata_src.var.index.dtype
# Dev. Note:
# either load as same type or load the convert DaskArray to array
# since we tested if assigned types and loaded types are DaskArray
# this would also work if they work
if isinstance(adata_src.raw.X, CSArray):
assert isinstance(adata.raw.X, CSMatrix)
else:
> assert isinstance(adata_src.raw.X, type(adata.raw.X) | DaskArray)
E AssertionError: assert False
E + where False = isinstance(<Compressed Sparse Row sparse matrix of dtype 'int64'\n with 4 stored elements and shape (3, 2)>, (<class 'scipy.sparse._csr.csr_array'> | DaskArray))
E + where <Compressed Sparse Row sparse matrix of dtype 'int64'\n with 4 stored elements and shape (3, 2)> = <anndata._core.raw.Raw object at 0x7ffee932ef30>.X
E + where <anndata._core.raw.Raw object at 0x7ffee932ef30> = AnnData object with n_obs × n_vars = 3 × 2\n obs: 'oanno1', 'oanno1b', 'oanno1c', 'oanno2', 'oanno3', 'oanno4'\n var: 'vanno1', 'vanno2', 'vanno3', 'vanno4'\n uns: 'oanno1_colors', 'uns2', 'uns3', 'uns4'.raw
E + and <class 'scipy.sparse._csr.csr_array'> = type(<Compressed Sparse Row sparse array of dtype 'int64'\n with 4 stored elements and shape (3, 2)>)
E + where <Compressed Sparse Row sparse array of dtype 'int64'\n with 4 stored elements and shape (3, 2)> = <anndata._core.raw.Raw object at 0x7ffee8d62870>.X
E + where <anndata._core.raw.Raw object at 0x7ffee8d62870> = AnnData object with n_obs × n_vars = 3 × 2\n obs: 'oanno1', 'oanno1b', 'oanno1c', 'oanno2', 'oanno3', 'oanno4'\n var: 'vanno1', 'vanno2', 'vanno3', 'vanno4'\n uns: 'oanno1_colors', 'uns2', 'uns3', 'uns4'.raw
tests/test_readwrite.py:163: AssertionError
__________ test_readwrite_kitchensink[dataset_kwargs0-csr_array-h5ad] __________
tmp_path = PosixPath('/build/pytest-of-nixbld/pytest-0/test_readwrite_kitchensink_dat4')
storage = 'h5ad', typ = <class 'scipy.sparse._csr.csr_array'>
backing_h5ad = PosixPath('/build/pytest-of-nixbld/pytest-0/test_readwrite_kitchensink_dat4/test.h5ad')
dataset_kwargs = {}
@pytest.mark.parametrize("storage", ["h5ad", pytest.param("zarr", marks=[needs_zarr])])
@pytest.mark.parametrize("typ", [np.array, csr_matrix, csr_array, as_dense_dask_array])
def test_readwrite_kitchensink(tmp_path, storage, typ, backing_h5ad, dataset_kwargs):
X = typ(X_list)
adata_src = ad.AnnData(X, obs=obs_dict, var=var_dict, uns=uns_dict)
assert not isinstance(adata_src.obs["oanno1"].dtype, pd.CategoricalDtype)
adata_src.raw = adata_src.copy()
if storage == "h5ad":
adata_src.write(backing_h5ad, **dataset_kwargs)
adata_mid = ad.read_h5ad(backing_h5ad)
adata_mid.write(tmp_path / "mid.h5ad", **dataset_kwargs)
adata = ad.read_h5ad(tmp_path / "mid.h5ad")
else:
adata_src.write_zarr(tmp_path / "test_zarr_dir", chunks=True)
adata = ad.read_zarr(tmp_path / "test_zarr_dir")
assert isinstance(adata.obs["oanno1"].dtype, pd.CategoricalDtype)
assert not isinstance(adata.obs["oanno2"].dtype, pd.CategoricalDtype)
assert adata.obs.index.tolist() == ["name1", "name2", "name3"]
assert adata.obs["oanno1"].cat.categories.tolist() == ["cat1", "cat2"]
assert adata.obs["oanno1c"].cat.categories.tolist() == ["cat1"]
assert isinstance(adata.raw.var["vanno2"].dtype, pd.CategoricalDtype)
pd.testing.assert_frame_equal(adata.obs, adata_src.obs)
pd.testing.assert_frame_equal(adata.var, adata_src.var)
assert_equal(adata.var.index, adata_src.var.index)
assert adata.var.index.dtype == adata_src.var.index.dtype
# Dev. Note:
# either load as same type or load the convert DaskArray to array
# since we tested if assigned types and loaded types are DaskArray
# this would also work if they work
if isinstance(adata_src.raw.X, CSArray):
> assert isinstance(adata.raw.X, CSMatrix)
E AssertionError: assert False
E + where False = isinstance(<Compressed Sparse Row sparse array of dtype 'int64'\n with 4 stored elements and shape (3, 2)>, scipy.sparse._csr.csr_matrix | scipy.sparse._csc.csc_matrix)
E + where <Compressed Sparse Row sparse array of dtype 'int64'\n with 4 stored elements and shape (3, 2)> = <anndata._core.raw.Raw object at 0x7ffee8cddf10>.X
E + where <anndata._core.raw.Raw object at 0x7ffee8cddf10> = AnnData object with n_obs × n_vars = 3 × 2\n obs: 'oanno1', 'oanno1b', 'oanno1c', 'oanno2', 'oanno3', 'oanno4'\n var: 'vanno1', 'vanno2', 'vanno3', 'vanno4'\n uns: 'oanno1_colors', 'uns2', 'uns3', 'uns4'.raw
tests/test_readwrite.py:161: AssertionError
__________ test_readwrite_kitchensink[dataset_kwargs0-csr_array-zarr] __________
tmp_path = PosixPath('/build/pytest-of-nixbld/pytest-0/test_readwrite_kitchensink_dat5')
storage = 'zarr', typ = <class 'scipy.sparse._csr.csr_array'>
backing_h5ad = PosixPath('/build/pytest-of-nixbld/pytest-0/test_readwrite_kitchensink_dat5/test.h5ad')
dataset_kwargs = {}
@pytest.mark.parametrize("storage", ["h5ad", pytest.param("zarr", marks=[needs_zarr])])
@pytest.mark.parametrize("typ", [np.array, csr_matrix, csr_array, as_dense_dask_array])
def test_readwrite_kitchensink(tmp_path, storage, typ, backing_h5ad, dataset_kwargs):
X = typ(X_list)
adata_src = ad.AnnData(X, obs=obs_dict, var=var_dict, uns=uns_dict)
assert not isinstance(adata_src.obs["oanno1"].dtype, pd.CategoricalDtype)
adata_src.raw = adata_src.copy()
if storage == "h5ad":
adata_src.write(backing_h5ad, **dataset_kwargs)
adata_mid = ad.read_h5ad(backing_h5ad)
adata_mid.write(tmp_path / "mid.h5ad", **dataset_kwargs)
adata = ad.read_h5ad(tmp_path / "mid.h5ad")
else:
adata_src.write_zarr(tmp_path / "test_zarr_dir", chunks=True)
adata = ad.read_zarr(tmp_path / "test_zarr_dir")
assert isinstance(adata.obs["oanno1"].dtype, pd.CategoricalDtype)
assert not isinstance(adata.obs["oanno2"].dtype, pd.CategoricalDtype)
assert adata.obs.index.tolist() == ["name1", "name2", "name3"]
assert adata.obs["oanno1"].cat.categories.tolist() == ["cat1", "cat2"]
assert adata.obs["oanno1c"].cat.categories.tolist() == ["cat1"]
assert isinstance(adata.raw.var["vanno2"].dtype, pd.CategoricalDtype)
pd.testing.assert_frame_equal(adata.obs, adata_src.obs)
pd.testing.assert_frame_equal(adata.var, adata_src.var)
assert_equal(adata.var.index, adata_src.var.index)
assert adata.var.index.dtype == adata_src.var.index.dtype
# Dev. Note:
# either load as same type or load the convert DaskArray to array
# since we tested if assigned types and loaded types are DaskArray
# this would also work if they work
if isinstance(adata_src.raw.X, CSArray):
> assert isinstance(adata.raw.X, CSMatrix)
E AssertionError: assert False
E + where False = isinstance(<Compressed Sparse Row sparse array of dtype 'int64'\n with 4 stored elements and shape (3, 2)>, scipy.sparse._csr.csr_matrix | scipy.sparse._csc.csc_matrix)
E + where <Compressed Sparse Row sparse array of dtype 'int64'\n with 4 stored elements and shape (3, 2)> = <anndata._core.raw.Raw object at 0x7ffee8cde090>.X
E + where <anndata._core.raw.Raw object at 0x7ffee8cde090> = AnnData object with n_obs × n_vars = 3 × 2\n obs: 'oanno1', 'oanno1b', 'oanno1c', 'oanno2', 'oanno3', 'oanno4'\n var: 'vanno1', 'vanno2', 'vanno3', 'vanno4'\n uns: 'oanno1_colors', 'uns2', 'uns3', 'uns4'.raw
tests/test_readwrite.py:161: AssertionError
_________ test_readwrite_kitchensink[dataset_kwargs1-csr_matrix-h5ad] __________
tmp_path = PosixPath('/build/pytest-of-nixbld/pytest-0/test_readwrite_kitchensink_dat10')
storage = 'h5ad', typ = <class 'scipy.sparse._csr.csr_matrix'>
backing_h5ad = PosixPath('/build/pytest-of-nixbld/pytest-0/test_readwrite_kitchensink_dat10/test.h5ad')
dataset_kwargs = {'compression': 'gzip'}
@pytest.mark.parametrize("storage", ["h5ad", pytest.param("zarr", marks=[needs_zarr])])
@pytest.mark.parametrize("typ", [np.array, csr_matrix, csr_array, as_dense_dask_array])
def test_readwrite_kitchensink(tmp_path, storage, typ, backing_h5ad, dataset_kwargs):
X = typ(X_list)
adata_src = ad.AnnData(X, obs=obs_dict, var=var_dict, uns=uns_dict)
assert not isinstance(adata_src.obs["oanno1"].dtype, pd.CategoricalDtype)
adata_src.raw = adata_src.copy()
if storage == "h5ad":
adata_src.write(backing_h5ad, **dataset_kwargs)
adata_mid = ad.read_h5ad(backing_h5ad)
adata_mid.write(tmp_path / "mid.h5ad", **dataset_kwargs)
adata = ad.read_h5ad(tmp_path / "mid.h5ad")
else:
adata_src.write_zarr(tmp_path / "test_zarr_dir", chunks=True)
adata = ad.read_zarr(tmp_path / "test_zarr_dir")
assert isinstance(adata.obs["oanno1"].dtype, pd.CategoricalDtype)
assert not isinstance(adata.obs["oanno2"].dtype, pd.CategoricalDtype)
assert adata.obs.index.tolist() == ["name1", "name2", "name3"]
assert adata.obs["oanno1"].cat.categories.tolist() == ["cat1", "cat2"]
assert adata.obs["oanno1c"].cat.categories.tolist() == ["cat1"]
assert isinstance(adata.raw.var["vanno2"].dtype, pd.CategoricalDtype)
pd.testing.assert_frame_equal(adata.obs, adata_src.obs)
pd.testing.assert_frame_equal(adata.var, adata_src.var)
assert_equal(adata.var.index, adata_src.var.index)
assert adata.var.index.dtype == adata_src.var.index.dtype
# Dev. Note:
# either load as same type or load the convert DaskArray to array
# since we tested if assigned types and loaded types are DaskArray
# this would also work if they work
if isinstance(adata_src.raw.X, CSArray):
assert isinstance(adata.raw.X, CSMatrix)
else:
> assert isinstance(adata_src.raw.X, type(adata.raw.X) | DaskArray)
E AssertionError: assert False
E + where False = isinstance(<Compressed Sparse Row sparse matrix of dtype 'int64'\n with 4 stored elements and shape (3, 2)>, (<class 'scipy.sparse._csr.csr_array'> | DaskArray))
E + where <Compressed Sparse Row sparse matrix of dtype 'int64'\n with 4 stored elements and shape (3, 2)> = <anndata._core.raw.Raw object at 0x7ffee8d17800>.X
E + where <anndata._core.raw.Raw object at 0x7ffee8d17800> = AnnData object with n_obs × n_vars = 3 × 2\n obs: 'oanno1', 'oanno1b', 'oanno1c', 'oanno2', 'oanno3', 'oanno4'\n var: 'vanno1', 'vanno2', 'vanno3', 'vanno4'\n uns: 'oanno1_colors', 'uns2', 'uns3', 'uns4'.raw
E + and <class 'scipy.sparse._csr.csr_array'> = type(<Compressed Sparse Row sparse array of dtype 'int64'\n with 4 stored elements and shape (3, 2)>)
E + where <Compressed Sparse Row sparse array of dtype 'int64'\n with 4 stored elements and shape (3, 2)> = <anndata._core.raw.Raw object at 0x7ffee8d039e0>.X
E + where <anndata._core.raw.Raw object at 0x7ffee8d039e0> = AnnData object with n_obs × n_vars = 3 × 2\n obs: 'oanno1', 'oanno1b', 'oanno1c', 'oanno2', 'oanno3', 'oanno4'\n var: 'vanno1', 'vanno2', 'vanno3', 'vanno4'\n uns: 'oanno1_colors', 'uns2', 'uns3', 'uns4'.raw
tests/test_readwrite.py:163: AssertionError
_________ test_readwrite_kitchensink[dataset_kwargs1-csr_matrix-zarr] __________
tmp_path = PosixPath('/build/pytest-of-nixbld/pytest-0/test_readwrite_kitchensink_dat11')
storage = 'zarr', typ = <class 'scipy.sparse._csr.csr_matrix'>
backing_h5ad = PosixPath('/build/pytest-of-nixbld/pytest-0/test_readwrite_kitchensink_dat11/test.h5ad')
dataset_kwargs = {'compression': 'gzip'}
@pytest.mark.parametrize("storage", ["h5ad", pytest.param("zarr", marks=[needs_zarr])])
@pytest.mark.parametrize("typ", [np.array, csr_matrix, csr_array, as_dense_dask_array])
def test_readwrite_kitchensink(tmp_path, storage, typ, backing_h5ad, dataset_kwargs):
X = typ(X_list)
adata_src = ad.AnnData(X, obs=obs_dict, var=var_dict, uns=uns_dict)
assert not isinstance(adata_src.obs["oanno1"].dtype, pd.CategoricalDtype)
adata_src.raw = adata_src.copy()
if storage == "h5ad":
adata_src.write(backing_h5ad, **dataset_kwargs)
adata_mid = ad.read_h5ad(backing_h5ad)
adata_mid.write(tmp_path / "mid.h5ad", **dataset_kwargs)
adata = ad.read_h5ad(tmp_path / "mid.h5ad")
else:
adata_src.write_zarr(tmp_path / "test_zarr_dir", chunks=True)
adata = ad.read_zarr(tmp_path / "test_zarr_dir")
assert isinstance(adata.obs["oanno1"].dtype, pd.CategoricalDtype)
assert not isinstance(adata.obs["oanno2"].dtype, pd.CategoricalDtype)
assert adata.obs.index.tolist() == ["name1", "name2", "name3"]
assert adata.obs["oanno1"].cat.categories.tolist() == ["cat1", "cat2"]
assert adata.obs["oanno1c"].cat.categories.tolist() == ["cat1"]
assert isinstance(adata.raw.var["vanno2"].dtype, pd.CategoricalDtype)
pd.testing.assert_frame_equal(adata.obs, adata_src.obs)
pd.testing.assert_frame_equal(adata.var, adata_src.var)
assert_equal(adata.var.index, adata_src.var.index)
assert adata.var.index.dtype == adata_src.var.index.dtype
# Dev. Note:
# either load as same type or load the convert DaskArray to array
# since we tested if assigned types and loaded types are DaskArray
# this would also work if they work
if isinstance(adata_src.raw.X, CSArray):
assert isinstance(adata.raw.X, CSMatrix)
else:
> assert isinstance(adata_src.raw.X, type(adata.raw.X) | DaskArray)
E AssertionError: assert False
E + where False = isinstance(<Compressed Sparse Row sparse matrix of dtype 'int64'\n with 4 stored elements and shape (3, 2)>, (<class 'scipy.sparse._csr.csr_array'> | DaskArray))
E + where <Compressed Sparse Row sparse matrix of dtype 'int64'\n with 4 stored elements and shape (3, 2)> = <anndata._core.raw.Raw object at 0x7ffee8dc6390>.X
E + where <anndata._core.raw.Raw object at 0x7ffee8dc6390> = AnnData object with n_obs × n_vars = 3 × 2\n obs: 'oanno1', 'oanno1b', 'oanno1c', 'oanno2', 'oanno3', 'oanno4'\n var: 'vanno1', 'vanno2', 'vanno3', 'vanno4'\n uns: 'oanno1_colors', 'uns2', 'uns3', 'uns4'.raw
E + and <class 'scipy.sparse._csr.csr_array'> = type(<Compressed Sparse Row sparse array of dtype 'int64'\n with 4 stored elements and shape (3, 2)>)
E + where <Compressed Sparse Row sparse array of dtype 'int64'\n with 4 stored elements and shape (3, 2)> = <anndata._core.raw.Raw object at 0x7ffee8d62cc0>.X
E + where <anndata._core.raw.Raw object at 0x7ffee8d62cc0> = AnnData object with n_obs × n_vars = 3 × 2\n obs: 'oanno1', 'oanno1b', 'oanno1c', 'oanno2', 'oanno3', 'oanno4'\n var: 'vanno1', 'vanno2', 'vanno3', 'vanno4'\n uns: 'oanno1_colors', 'uns2', 'uns3', 'uns4'.raw
tests/test_readwrite.py:163: AssertionError
__________ test_readwrite_kitchensink[dataset_kwargs1-csr_array-h5ad] __________
tmp_path = PosixPath('/build/pytest-of-nixbld/pytest-0/test_readwrite_kitchensink_dat12')
storage = 'h5ad', typ = <class 'scipy.sparse._csr.csr_array'>
backing_h5ad = PosixPath('/build/pytest-of-nixbld/pytest-0/test_readwrite_kitchensink_dat12/test.h5ad')
dataset_kwargs = {'compression': 'gzip'}
@pytest.mark.parametrize("storage", ["h5ad", pytest.param("zarr", marks=[needs_zarr])])
@pytest.mark.parametrize("typ", [np.array, csr_matrix, csr_array, as_dense_dask_array])
def test_readwrite_kitchensink(tmp_path, storage, typ, backing_h5ad, dataset_kwargs):
X = typ(X_list)
adata_src = ad.AnnData(X, obs=obs_dict, var=var_dict, uns=uns_dict)
assert not isinstance(adata_src.obs["oanno1"].dtype, pd.CategoricalDtype)
adata_src.raw = adata_src.copy()
if storage == "h5ad":
adata_src.write(backing_h5ad, **dataset_kwargs)
adata_mid = ad.read_h5ad(backing_h5ad)
adata_mid.write(tmp_path / "mid.h5ad", **dataset_kwargs)
adata = ad.read_h5ad(tmp_path / "mid.h5ad")
else:
adata_src.write_zarr(tmp_path / "test_zarr_dir", chunks=True)
adata = ad.read_zarr(tmp_path / "test_zarr_dir")
assert isinstance(adata.obs["oanno1"].dtype, pd.CategoricalDtype)
assert not isinstance(adata.obs["oanno2"].dtype, pd.CategoricalDtype)
assert adata.obs.index.tolist() == ["name1", "name2", "name3"]
assert adata.obs["oanno1"].cat.categories.tolist() == ["cat1", "cat2"]
assert adata.obs["oanno1c"].cat.categories.tolist() == ["cat1"]
assert isinstance(adata.raw.var["vanno2"].dtype, pd.CategoricalDtype)
pd.testing.assert_frame_equal(adata.obs, adata_src.obs)
pd.testing.assert_frame_equal(adata.var, adata_src.var)
assert_equal(adata.var.index, adata_src.var.index)
assert adata.var.index.dtype == adata_src.var.index.dtype
# Dev. Note:
# either load as same type or load the convert DaskArray to array
# since we tested if assigned types and loaded types are DaskArray
# this would also work if they work
if isinstance(adata_src.raw.X, CSArray):
> assert isinstance(adata.raw.X, CSMatrix)
E AssertionError: assert False
E + where False = isinstance(<Compressed Sparse Row sparse array of dtype 'int64'\n with 4 stored elements and shape (3, 2)>, scipy.sparse._csr.csr_matrix | scipy.sparse._csc.csc_matrix)
E + where <Compressed Sparse Row sparse array of dtype 'int64'\n with 4 stored elements and shape (3, 2)> = <anndata._core.raw.Raw object at 0x7ffee93eb500>.X
E + where <anndata._core.raw.Raw object at 0x7ffee93eb500> = AnnData object with n_obs × n_vars = 3 × 2\n obs: 'oanno1', 'oanno1b', 'oanno1c', 'oanno2', 'oanno3', 'oanno4'\n var: 'vanno1', 'vanno2', 'vanno3', 'vanno4'\n uns: 'oanno1_colors', 'uns2', 'uns3', 'uns4'.raw
tests/test_readwrite.py:161: AssertionError
__________ test_readwrite_kitchensink[dataset_kwargs1-csr_array-zarr] __________
tmp_path = PosixPath('/build/pytest-of-nixbld/pytest-0/test_readwrite_kitchensink_dat13')
storage = 'zarr', typ = <class 'scipy.sparse._csr.csr_array'>
backing_h5ad = PosixPath('/build/pytest-of-nixbld/pytest-0/test_readwrite_kitchensink_dat13/test.h5ad')
dataset_kwargs = {'compression': 'gzip'}
@pytest.mark.parametrize("storage", ["h5ad", pytest.param("zarr", marks=[needs_zarr])])
@pytest.mark.parametrize("typ", [np.array, csr_matrix, csr_array, as_dense_dask_array])
def test_readwrite_kitchensink(tmp_path, storage, typ, backing_h5ad, dataset_kwargs):
X = typ(X_list)
adata_src = ad.AnnData(X, obs=obs_dict, var=var_dict, uns=uns_dict)
assert not isinstance(adata_src.obs["oanno1"].dtype, pd.CategoricalDtype)
adata_src.raw = adata_src.copy()
if storage == "h5ad":
adata_src.write(backing_h5ad, **dataset_kwargs)
adata_mid = ad.read_h5ad(backing_h5ad)
adata_mid.write(tmp_path / "mid.h5ad", **dataset_kwargs)
adata = ad.read_h5ad(tmp_path / "mid.h5ad")
else:
adata_src.write_zarr(tmp_path / "test_zarr_dir", chunks=True)
adata = ad.read_zarr(tmp_path / "test_zarr_dir")
assert isinstance(adata.obs["oanno1"].dtype, pd.CategoricalDtype)
assert not isinstance(adata.obs["oanno2"].dtype, pd.CategoricalDtype)
assert adata.obs.index.tolist() == ["name1", "name2", "name3"]
assert adata.obs["oanno1"].cat.categories.tolist() == ["cat1", "cat2"]
assert adata.obs["oanno1c"].cat.categories.tolist() == ["cat1"]
assert isinstance(adata.raw.var["vanno2"].dtype, pd.CategoricalDtype)
pd.testing.assert_frame_equal(adata.obs, adata_src.obs)
pd.testing.assert_frame_equal(adata.var, adata_src.var)
assert_equal(adata.var.index, adata_src.var.index)
assert adata.var.index.dtype == adata_src.var.index.dtype
# Dev. Note:
# either load as same type or load the convert DaskArray to array
# since we tested if assigned types and loaded types are DaskArray
# this would also work if they work
if isinstance(adata_src.raw.X, CSArray):
> assert isinstance(adata.raw.X, CSMatrix)
E AssertionError: assert False
E + where False = isinstance(<Compressed Sparse Row sparse array of dtype 'int64'\n with 4 stored elements and shape (3, 2)>, scipy.sparse._csr.csr_matrix | scipy.sparse._csc.csc_matrix)
E + where <Compressed Sparse Row sparse array of dtype 'int64'\n with 4 stored elements and shape (3, 2)> = <anndata._core.raw.Raw object at 0x7ffee8d75a90>.X
E + where <anndata._core.raw.Raw object at 0x7ffee8d75a90> = AnnData object with n_obs × n_vars = 3 × 2\n obs: 'oanno1', 'oanno1b', 'oanno1c', 'oanno2', 'oanno3', 'oanno4'\n var: 'vanno1', 'vanno2', 'vanno3', 'vanno4'\n uns: 'oanno1_colors', 'uns2', 'uns3', 'uns4'.raw
tests/test_readwrite.py:161: AssertionError
___________________ test_read_write_maintain_obsmvarm_dtypes ___________________
rw = (AnnData object with n_obs × n_vars = 100 × 101
obs: 'cat_unordered', 'obs_cat', 'int64', 'float64', 'uint8', 'boo...ray', 'sparse', 'sparse_array'
obsp: 'array', 'sparse', 'sparse_array'
varp: 'array', 'sparse', 'sparse_array')
def test_read_write_maintain_obsmvarm_dtypes(rw):
curr, orig = rw
assert type(orig.obsm["array"]) is type(curr.obsm["array"])
assert np.all(orig.obsm["array"] == curr.obsm["array"])
assert np.all(orig.varm["array"] == curr.varm["array"])
> assert type(orig.obsm["sparse"]) is type(curr.obsm["sparse"])
E AssertionError: assert <class 'scipy.sparse._csr.csr_matrix'> is <class 'scipy.sparse._csr.csr_array'>
E + where <class 'scipy.sparse._csr.csr_matrix'> = type(<Compressed Sparse Row sparse matrix of dtype 'float64'\n with 100 stored elements and shape (100, 100)>)
E + and <class 'scipy.sparse._csr.csr_array'> = type(<Compressed Sparse Row sparse array of dtype 'float64'\n with 100 stored elements and shape (100, 100)>)
tests/test_readwrite.py:192: AssertionError
_____________________________ test_maintain_layers _____________________________
rw = (AnnData object with n_obs × n_vars = 100 × 101
obs: 'cat_unordered', 'obs_cat', 'int64', 'float64', 'uint8', 'boo...ray', 'sparse', 'sparse_array'
obsp: 'array', 'sparse', 'sparse_array'
varp: 'array', 'sparse', 'sparse_array')
def test_maintain_layers(rw):
curr, orig = rw
assert type(orig.layers["array"]) is type(curr.layers["array"])
assert np.all(orig.layers["array"] == curr.layers["array"])
> assert type(orig.layers["sparse"]) is type(curr.layers["sparse"])
E AssertionError: assert <class 'scipy.sparse._csr.csr_matrix'> is <class 'scipy.sparse._csr.csr_array'>
E + where <class 'scipy.sparse._csr.csr_matrix'> = type(<Compressed Sparse Row sparse matrix of dtype 'float64'\n with 101 stored elements and shape (100, 101)>)
E + and <class 'scipy.sparse._csr.csr_array'> = type(<Compressed Sparse Row sparse array of dtype 'float64'\n with 101 stored elements and shape (100, 101)>)
tests/test_readwrite.py:205: AssertionError
=============================== warnings summary ===============================
../../nix/store/flh9b1l4y7zmmrik73gcmksvp7win5q2-python3.12-pytest-8.3.5/lib/python3.12/site-packages/_pytest/config/__init__.py:1441
/nix/store/flh9b1l4y7zmmrik73gcmksvp7win5q2-python3.12-pytest-8.3.5/lib/python3.12/site-packages/_pytest/config/__init__.py:1441: PytestConfigWarning: Unknown config option: filterwarnings_when_strict
self._warn_or_fail_if_strict(f"Unknown config option: {key}\n")
tests/test_dask.py:113
/build/source/tests/test_dask.py:113: PytestUnknownMarkWarning: Unknown pytest.mark.xdist_group - 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.xdist_group("dask")
tests/test_io_elementwise.py:348
/build/source/tests/test_io_elementwise.py:348: PytestUnknownMarkWarning: Unknown pytest.mark.xdist_group - 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.xdist_group("dask")
tests/test_backed_dense.py::test_assign_x_subset[h5ad]
tests/test_backed_dense.py::test_assign_x_subset[zarr]
/build/source/tests/test_backed_dense.py:88: ImplicitModificationWarning: Modifying `X` on a view results in data being overridden
view.X = np.zeros((4, 2))
tests/test_base.py: 5 warnings
tests/test_readwrite.py: 12 warnings
tests/test_views.py: 1 warning
/nix/store/lsjghdh2yhdzc8qjvylrgnll8vkax252-python3.12-anndata-0.11.4/lib/python3.12/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
warnings.warn("Transforming to str index.", ImplicitModificationWarning)
tests/test_concatenate.py::test_concatenate_obsm_outer[nan]
tests/test_concatenate.py::test_concatenate_obsm_outer[3.141592653589793]
tests/test_concatenate.py::test_concatenate_fill_value[nan]
tests/test_concatenate.py::test_concatenate_fill_value[3.141592653589793]
/nix/store/8f9zfpbmybfl09aq4a9nzp8a9gwgqjbf-python3.12-scipy-1.15.3/lib/python3.12/site-packages/scipy/sparse/_index.py:210: SparseEfficiencyWarning: Changing the sparsity structure of a csc_matrix is expensive. lil and dok are more efficient.
self._set_arrayXarray(i, j, x)
tests/test_concatenate.py: 43 warnings
tests/test_concatenate_disk.py: 104 warnings
tests/test_utils.py: 1 warning
/nix/store/lsjghdh2yhdzc8qjvylrgnll8vkax252-python3.12-anndata-0.11.4/lib/python3.12/site-packages/anndata/_core/anndata.py:1756: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.
utils.warn_names_duplicates("obs")
tests/test_concatenate.py: 9 warnings
tests/test_concatenate_disk.py: 96 warnings
tests/test_utils.py: 1 warning
/nix/store/lsjghdh2yhdzc8qjvylrgnll8vkax252-python3.12-anndata-0.11.4/lib/python3.12/site-packages/anndata/_core/anndata.py:1758: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.
utils.warn_names_duplicates("var")
tests/test_concatenate.py::test_concatenate_fill_value[nan]
tests/test_concatenate.py::test_concatenate_fill_value[3.141592653589793]
/nix/store/8f9zfpbmybfl09aq4a9nzp8a9gwgqjbf-python3.12-scipy-1.15.3/lib/python3.12/site-packages/scipy/sparse/_index.py:210: SparseEfficiencyWarning: Changing the sparsity structure of a csc_array is expensive. lil and dok are more efficient.
self._set_arrayXarray(i, j, x)
tests/test_views.py::test_views
/build/source/tests/test_views.py:114: ImplicitModificationWarning: Modifying `X` on a view results in data being overridden
adata[:2, 0].X = [0, 0]
tests/test_x.py::test_repeat_indices_view
/build/source/tests/test_x.py:53: ImplicitModificationWarning: Modifying `X` on a view results in data being overridden
subset.X = mat
tests/test_x.py: 21 warnings
/build/source/tests/test_x.py:66: ImplicitModificationWarning: Modifying `X` on a view results in data being overridden
view.X = to_assign
tests/test_x.py::test_setter_view[csr-csr]
tests/test_x.py::test_setter_view[csc-csr]
tests/test_x.py::test_setter_view[csr_array-csr]
tests/test_x.py::test_setter_view[csc_array-csr]
tests/test_x.py::test_setter_view[ndarray-csr]
/nix/store/8f9zfpbmybfl09aq4a9nzp8a9gwgqjbf-python3.12-scipy-1.15.3/lib/python3.12/site-packages/scipy/sparse/_index.py:201: SparseEfficiencyWarning: Changing the sparsity structure of a csr_matrix is expensive. lil and dok are more efficient.
self._set_arrayXarray_sparse(i, j, x)
tests/test_x.py::test_setter_view[csr-csc]
tests/test_x.py::test_setter_view[csc-csc]
tests/test_x.py::test_setter_view[csr_array-csc]
tests/test_x.py::test_setter_view[csc_array-csc]
tests/test_x.py::test_setter_view[ndarray-csc]
/nix/store/8f9zfpbmybfl09aq4a9nzp8a9gwgqjbf-python3.12-scipy-1.15.3/lib/python3.12/site-packages/scipy/sparse/_index.py:201: SparseEfficiencyWarning: Changing the sparsity structure of a csc_matrix is expensive. lil and dok are more efficient.
self._set_arrayXarray_sparse(i, j, x)
tests/test_x.py::test_setter_view[csr-csr_array]
tests/test_x.py::test_setter_view[csc-csr_array]
tests/test_x.py::test_setter_view[csr_array-csr_array]
tests/test_x.py::test_setter_view[csc_array-csr_array]
tests/test_x.py::test_setter_view[ndarray-csr_array]
/nix/store/8f9zfpbmybfl09aq4a9nzp8a9gwgqjbf-python3.12-scipy-1.15.3/lib/python3.12/site-packages/scipy/sparse/_index.py:201: SparseEfficiencyWarning: Changing the sparsity structure of a csr_array is expensive. lil and dok are more efficient.
self._set_arrayXarray_sparse(i, j, x)
tests/test_x.py::test_setter_view[csr-csc_array]
tests/test_x.py::test_setter_view[csc-csc_array]
tests/test_x.py::test_setter_view[csr_array-csc_array]
tests/test_x.py::test_setter_view[csc_array-csc_array]
tests/test_x.py::test_setter_view[ndarray-csc_array]
/nix/store/8f9zfpbmybfl09aq4a9nzp8a9gwgqjbf-python3.12-scipy-1.15.3/lib/python3.12/site-packages/scipy/sparse/_index.py:201: SparseEfficiencyWarning: Changing the sparsity structure of a csc_array is expensive. lil and dok are more efficient.
self._set_arrayXarray_sparse(i, j, x)
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED tests/test_concatenate.py::test_concat_dask_sparse_matches_memory[outer-None] - AssertionError:
FAILED tests/test_concatenate.py::test_concat_dask_sparse_matches_memory[outer-same] - AssertionError:
FAILED tests/test_concatenate.py::test_concat_dask_sparse_matches_memory[outer-unique] - AssertionError:
FAILED tests/test_concatenate.py::test_concat_dask_sparse_matches_memory[outer-first] - AssertionError:
FAILED tests/test_concatenate.py::test_concat_dask_sparse_matches_memory[outer-only] - AssertionError:
FAILED tests/test_io_elementwise.py::test_write_nullable_string_error[h5] - Failed: DID NOT RAISE <class 'RuntimeError'>
FAILED tests/test_io_elementwise.py::test_write_nullable_string_error[zarr] - Failed: DID NOT RAISE <class 'RuntimeError'>
FAILED tests/test_readwrite.py::test_readwrite_kitchensink[dataset_kwargs0-csr_matrix-h5ad] - AssertionError: assert False
FAILED tests/test_readwrite.py::test_readwrite_kitchensink[dataset_kwargs0-csr_matrix-zarr] - AssertionError: assert False
FAILED tests/test_readwrite.py::test_readwrite_kitchensink[dataset_kwargs0-csr_array-h5ad] - AssertionError: assert False
FAILED tests/test_readwrite.py::test_readwrite_kitchensink[dataset_kwargs0-csr_array-zarr] - AssertionError: assert False
FAILED tests/test_readwrite.py::test_readwrite_kitchensink[dataset_kwargs1-csr_matrix-h5ad] - AssertionError: assert False
FAILED tests/test_readwrite.py::test_readwrite_kitchensink[dataset_kwargs1-csr_matrix-zarr] - AssertionError: assert False
FAILED tests/test_readwrite.py::test_readwrite_kitchensink[dataset_kwargs1-csr_array-h5ad] - AssertionError: assert False
FAILED tests/test_readwrite.py::test_readwrite_kitchensink[dataset_kwargs1-csr_array-zarr] - AssertionError: assert False
FAILED tests/test_readwrite.py::test_read_write_maintain_obsmvarm_dtypes - AssertionError: assert <class 'scipy.sparse._csr.csr_matrix'> is <class 'sc...
FAILED tests/test_readwrite.py::test_maintain_layers - AssertionError: assert <class 'scipy.sparse._csr.csr_matrix'> is <class 'sc...
ERROR tests/test_backed_sparse.py::test_consecutive_bool[h5ad-randomized]
ERROR tests/test_backed_sparse.py::test_consecutive_bool[h5ad-alternating_15]
ERROR tests/test_backed_sparse.py::test_consecutive_bool[h5ad-alternating_5]
ERROR tests/test_backed_sparse.py::test_consecutive_bool[h5ad-one_group]
ERROR tests/test_backed_sparse.py::test_consecutive_bool[h5ad-one_elem]
ERROR tests/test_backed_sparse.py::test_consecutive_bool[zarr-randomized]
ERROR tests/test_backed_sparse.py::test_consecutive_bool[zarr-alternating_15]
ERROR tests/test_backed_sparse.py::test_consecutive_bool[zarr-alternating_5]
ERROR tests/test_backed_sparse.py::test_consecutive_bool[zarr-one_group]
ERROR tests/test_backed_sparse.py::test_consecutive_bool[zarr-one_elem]
ERROR tests/test_dask.py::test_dask_distributed_write[h5ad-sizes0]
ERROR tests/test_dask.py::test_dask_distributed_write[h5ad-sizes1]
ERROR tests/test_dask.py::test_dask_distributed_write[h5ad-sizes2]
ERROR tests/test_dask.py::test_dask_distributed_write[h5ad-sizes3]
ERROR tests/test_dask.py::test_dask_distributed_write[h5ad-sizes4]
ERROR tests/test_dask.py::test_dask_distributed_write[zarr-sizes0]
ERROR tests/test_dask.py::test_dask_distributed_write[zarr-sizes1]
ERROR tests/test_dask.py::test_dask_distributed_write[zarr-sizes2]
ERROR tests/test_dask.py::test_dask_distributed_write[zarr-sizes3]
ERROR tests/test_dask.py::test_dask_distributed_write[zarr-sizes4]
ERROR tests/test_io_elementwise.py::test_read_lazy_h5_cluster[csr]
ERROR tests/test_io_elementwise.py::test_read_lazy_h5_cluster[csc]
= 17 failed, 3231 passed, 23 skipped, 1697 deselected, 74 xfailed, 326 warnings, 22 errors in 369.50s (0:06:09) =
error: builder for '/nix/store/kgligwzymlzjy7wvlb9jc9wv0wl3i198-python3.12-anndata-0.11.4.drv' failed with exit code 1;
last 25 log lines:
> FAILED tests/test_readwrite.py::test_read_write_maintain_obsmvarm_dtypes - AssertionError: assert <class 'scipy.sparse._csr.csr_matrix'> is <class 'sc...
> FAILED tests/test_readwrite.py::test_maintain_layers - AssertionError: assert <class 'scipy.sparse._csr.csr_matrix'> is <class 'sc...
> ERROR tests/test_backed_sparse.py::test_consecutive_bool[h5ad-randomized]
> ERROR tests/test_backed_sparse.py::test_consecutive_bool[h5ad-alternating_15]
> ERROR tests/test_backed_sparse.py::test_consecutive_bool[h5ad-alternating_5]
> ERROR tests/test_backed_sparse.py::test_consecutive_bool[h5ad-one_group]
> ERROR tests/test_backed_sparse.py::test_consecutive_bool[h5ad-one_elem]
> ERROR tests/test_backed_sparse.py::test_consecutive_bool[zarr-randomized]
> ERROR tests/test_backed_sparse.py::test_consecutive_bool[zarr-alternating_15]
> ERROR tests/test_backed_sparse.py::test_consecutive_bool[zarr-alternating_5]
> ERROR tests/test_backed_sparse.py::test_consecutive_bool[zarr-one_group]
> ERROR tests/test_backed_sparse.py::test_consecutive_bool[zarr-one_elem]
> ERROR tests/test_dask.py::test_dask_distributed_write[h5ad-sizes0]
> ERROR tests/test_dask.py::test_dask_distributed_write[h5ad-sizes1]
> ERROR tests/test_dask.py::test_dask_distributed_write[h5ad-sizes2]
> ERROR tests/test_dask.py::test_dask_distributed_write[h5ad-sizes3]
> ERROR tests/test_dask.py::test_dask_distributed_write[h5ad-sizes4]
> ERROR tests/test_dask.py::test_dask_distributed_write[zarr-sizes0]
> ERROR tests/test_dask.py::test_dask_distributed_write[zarr-sizes1]
> ERROR tests/test_dask.py::test_dask_distributed_write[zarr-sizes2]
> ERROR tests/test_dask.py::test_dask_distributed_write[zarr-sizes3]
> ERROR tests/test_dask.py::test_dask_distributed_write[zarr-sizes4]
> ERROR tests/test_io_elementwise.py::test_read_lazy_h5_cluster[csr]
> ERROR tests/test_io_elementwise.py::test_read_lazy_h5_cluster[csc]
> = 17 failed, 3231 passed, 23 skipped, 1697 deselected, 74 xfailed, 326 warnings, 22 errors in 369.50s (0:06:09) =
For full logs, run:
nix log /nix/store/kgligwzymlzjy7wvlb9jc9wv0wl3i198-python3.12-anndata-0.11.4.drv
nixpkgs on  samuela/scanpy [!?] took 6m27s
❯
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