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[pre-commit.ci] pre-commit autoupdate #2784

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merged 1 commit into from
Dec 19, 2023

[pre-commit.ci] pre-commit autoupdate

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Merged

[pre-commit.ci] pre-commit autoupdate #2784

[pre-commit.ci] pre-commit autoupdate
5df0cf9
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Azure Pipelines / scverse.scanpy succeeded Dec 18, 2023 in 14m 43s

Build #20231218.14 had test failures

0 errors / 0 warnings

Details

Tests

  • Failed: 9 (0.16%)
  • Passed: 5,336 (94.61%)
  • Other: 295 (5.23%)
  • Total: 5,640
Code coverage

  • 9027 of 12390 lines covered (72.86%)

Annotations

Check failure on line 1 in scanpy/tests/test_ingest.py::test_representation

See this annotation in the file changed.

@azure-pipelines azure-pipelines / scverse.scanpy

scanpy/tests/test_ingest.py::test_representation 

adatas = (AnnData object with n_obs × n_vars = 500 × 765
    obs: 'bulk_labels', 'n_genes', 'percent_mito', 'n_counts', 'S_scor...pca', 'X_umap'
    varm: 'PCs'
    obsp: 'distances', 'connectivities', AnnData object with n_obs × n_vars = 200 × 765)

    def test_representation(adatas):
        adata_ref = adatas[0].copy()
        adata_new = adatas[1].copy()
    
>       ing = sc.tl.Ingest(adata_ref)

scanpy/tests/test_ingest.py:46: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
scanpy/tools/_ingest.py:424: in __init__
    self._init_neighbors(adata, neighbors_key)
scanpy/tools/_ingest.py:388: in _init_neighbors
    self._init_pynndescent(neighbors["distances"])
scanpy/tools/_ingest.py:325: in _init_pynndescent
    self._nnd_idx = NNDescent(
/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pynndescent/pynndescent_.py:931: in __init__
    self._neighbor_graph = nn_descent(
/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/numba/core/dispatcher.py:468: in _compile_for_args
    error_rewrite(e, 'typing')
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

e = TypingError('Failed in nopython mode pipeline (step: nopython frontend)\nFailed in nopython mode pipeline (step: nopyt...f nn_descent(\n    <source elided>\n    if low_memory:\n        nn_descent_internal_low_memory_parallel(\n        ^\n')
issue_type = 'typing'

    def error_rewrite(e, issue_type):
        """
        Rewrite and raise Exception `e` with help supplied based on the
        specified issue_type.
        """
        if config.SHOW_HELP:
            help_msg = errors.error_extras[issue_type]
            e.patch_message('\n'.join((str(e).rstrip(), help_msg)))
        if config.FULL_TRACEBACKS:
            raise e
        else:
>           raise e.with_traceback(None)
E           numba.core.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend)
E           Failed in nopython mode pipeline (step: nopython frontend)
E           Failed in nopython mode pipeline (step: nopython frontend)
E           Internal error at <numba.core.typeinfer.CallConstraint object at 0x7f062f316bd0>.
E           Failed in nopython mode pipeline (step: parfor prelowering)
E           'NoneType' object has no attribute 'name'
E           During: resolving callee type: type(CPUDispatcher(<function apply_graph_updates_low_memory at 0x7f06458479c0>))
E           During: typing of call at /opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pynndescent/pynndescent_.py (228)
E           
E           Enable logging at debug level for details.
E           
E           File "../../../../../opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pynndescent/pynndescent_.py", line 228:
E           def process_candidates(
E               <source elided>
E           
E                   c += apply_graph_updates_low_memory(current_graph, updates, n_threads)
E                   ^
E           
E           During: resolving callee type: type(CPUDispatcher(<function process_candidates at 0x7f0645465300>))
E           During: typing of call at /opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pynndescent/pynndescent_.py (258)
E           
E           During: resolving callee type: type(CPUDispatcher(<function process_candidates at 0x7f0645465300>))
E           During: typing of call at /opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pynndescent/pynndescent_.py (258)
E           
E           
E           File "../../../../../opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pynndescent/pynndescent_.py", line 258:
E           def nn_descent_internal_low_memory_parallel(
E               <source elided>
E           
E                   c = process_candidates(
E                   ^
E           
E           During: resolving callee type: type(CPUDispatcher(<
Raw output 
/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/numba/core/dispatcher.py:409: numba.core.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend)

Check failure on line 1 in scanpy/tests/test_ingest.py::test_neighbors

See this annotation in the file changed.

@azure-pipelines azure-pipelines / scverse.scanpy

scanpy/tests/test_ingest.py::test_neighbors 

adatas = (AnnData object with n_obs × n_vars = 500 × 765
    obs: 'bulk_labels', 'n_genes', 'percent_mito', 'n_counts', 'S_scor...pca', 'X_umap'
    varm: 'PCs'
    obsp: 'distances', 'connectivities', AnnData object with n_obs × n_vars = 200 × 765)

    def test_neighbors(adatas):
        adata_ref = adatas[0].copy()
        adata_new = adatas[1].copy()
    
>       ing = sc.tl.Ingest(adata_ref)

scanpy/tests/test_ingest.py:76: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
scanpy/tools/_ingest.py:424: in __init__
    self._init_neighbors(adata, neighbors_key)
scanpy/tools/_ingest.py:388: in _init_neighbors
    self._init_pynndescent(neighbors["distances"])
scanpy/tools/_ingest.py:325: in _init_pynndescent
    self._nnd_idx = NNDescent(
/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pynndescent/pynndescent_.py:931: in __init__
    self._neighbor_graph = nn_descent(
/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/numba/core/dispatcher.py:468: in _compile_for_args
    error_rewrite(e, 'typing')
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

e = TypingError('Failed in nopython mode pipeline (step: nopython frontend)\nFailed in nopython mode pipeline (step: nopyt...f nn_descent(\n    <source elided>\n    if low_memory:\n        nn_descent_internal_low_memory_parallel(\n        ^\n')
issue_type = 'typing'

    def error_rewrite(e, issue_type):
        """
        Rewrite and raise Exception `e` with help supplied based on the
        specified issue_type.
        """
        if config.SHOW_HELP:
            help_msg = errors.error_extras[issue_type]
            e.patch_message('\n'.join((str(e).rstrip(), help_msg)))
        if config.FULL_TRACEBACKS:
            raise e
        else:
>           raise e.with_traceback(None)
E           numba.core.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend)
E           Failed in nopython mode pipeline (step: nopython frontend)
E           Failed in nopython mode pipeline (step: nopython frontend)
E           Internal error at <numba.core.typeinfer.CallConstraint object at 0x7f062f316bd0>.
E           Failed in nopython mode pipeline (step: parfor prelowering)
E           'NoneType' object has no attribute 'name'
E           During: resolving callee type: type(CPUDispatcher(<function apply_graph_updates_low_memory at 0x7f06458479c0>))
E           During: typing of call at /opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pynndescent/pynndescent_.py (228)
E           
E           Enable logging at debug level for details.
E           
E           File "../../../../../opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pynndescent/pynndescent_.py", line 228:
E           def process_candidates(
E               <source elided>
E           
E                   c += apply_graph_updates_low_memory(current_graph, updates, n_threads)
E                   ^
E           
E           During: resolving callee type: type(CPUDispatcher(<function process_candidates at 0x7f0645465300>))
E           During: typing of call at /opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pynndescent/pynndescent_.py (258)
E           
E           During: resolving callee type: type(CPUDispatcher(<function process_candidates at 0x7f0645465300>))
E           During: typing of call at /opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pynndescent/pynndescent_.py (258)
E           
E           
E           File "../../../../../opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pynndescent/pynndescent_.py", line 258:
E           def nn_descent_internal_low_memory_parallel(
E               <source elided>
E           
E                   c = process_candidates(
E                   ^
E           
E           During: resolving callee type: type(CPUDispatcher(<funct
Raw output 
/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/numba/core/dispatcher.py:409: numba.core.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend)

Check failure on line 1 in scanpy/tests/test_ingest.py::test_neighbors_defaults[3]

See this annotation in the file changed.

@azure-pipelines azure-pipelines / scverse.scanpy

scanpy/tests/test_ingest.py::test_neighbors_defaults[3] 

adatas = (AnnData object with n_obs × n_vars = 500 × 765
    obs: 'bulk_labels', 'n_genes', 'percent_mito', 'n_counts', 'S_scor...pca', 'X_umap'
    varm: 'PCs'
    obsp: 'distances', 'connectivities', AnnData object with n_obs × n_vars = 200 × 765)
n = 3

    @pytest.mark.parametrize("n", [3, 4])
    def test_neighbors_defaults(adatas, n):
        adata_ref = adatas[0].copy()
        adata_new = adatas[1].copy()
    
        sc.pp.neighbors(adata_ref, n_neighbors=n)
    
>       ing = sc.tl.Ingest(adata_ref)

scanpy/tests/test_ingest.py:99: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
scanpy/tools/_ingest.py:424: in __init__
    self._init_neighbors(adata, neighbors_key)
scanpy/tools/_ingest.py:388: in _init_neighbors
    self._init_pynndescent(neighbors["distances"])
scanpy/tools/_ingest.py:325: in _init_pynndescent
    self._nnd_idx = NNDescent(
/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pynndescent/pynndescent_.py:931: in __init__
    self._neighbor_graph = nn_descent(
/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/numba/core/dispatcher.py:468: in _compile_for_args
    error_rewrite(e, 'typing')
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

e = TypingError('Failed in nopython mode pipeline (step: nopython frontend)\nFailed in nopython mode pipeline (step: nopyt...f nn_descent(\n    <source elided>\n    if low_memory:\n        nn_descent_internal_low_memory_parallel(\n        ^\n')
issue_type = 'typing'

    def error_rewrite(e, issue_type):
        """
        Rewrite and raise Exception `e` with help supplied based on the
        specified issue_type.
        """
        if config.SHOW_HELP:
            help_msg = errors.error_extras[issue_type]
            e.patch_message('\n'.join((str(e).rstrip(), help_msg)))
        if config.FULL_TRACEBACKS:
            raise e
        else:
>           raise e.with_traceback(None)
E           numba.core.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend)
E           Failed in nopython mode pipeline (step: nopython frontend)
E           Failed in nopython mode pipeline (step: nopython frontend)
E           Internal error at <numba.core.typeinfer.CallConstraint object at 0x7f062f316bd0>.
E           Failed in nopython mode pipeline (step: parfor prelowering)
E           'NoneType' object has no attribute 'name'
E           During: resolving callee type: type(CPUDispatcher(<function apply_graph_updates_low_memory at 0x7f06458479c0>))
E           During: typing of call at /opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pynndescent/pynndescent_.py (228)
E           
E           Enable logging at debug level for details.
E           
E           File "../../../../../opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pynndescent/pynndescent_.py", line 228:
E           def process_candidates(
E               <source elided>
E           
E                   c += apply_graph_updates_low_memory(current_graph, updates, n_threads)
E                   ^
E           
E           During: resolving callee type: type(CPUDispatcher(<function process_candidates at 0x7f0645465300>))
E           During: typing of call at /opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pynndescent/pynndescent_.py (258)
E           
E           During: resolving callee type: type(CPUDispatcher(<function process_candidates at 0x7f0645465300>))
E           During: typing of call at /opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pynndescent/pynndescent_.py (258)
E           
E           
E           File "../../../../../opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pynndescent/pynndescent_.py", line 258:
E           def nn_descent_internal_low_memory_parallel(
E               <source elided>
E           
E                   c = process_can
Raw output 
/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/numba/core/dispatcher.py:409: numba.core.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend)

Check failure on line 1 in scanpy/tests/test_ingest.py::test_neighbors_defaults[4]

See this annotation in the file changed.

@azure-pipelines azure-pipelines / scverse.scanpy

scanpy/tests/test_ingest.py::test_neighbors_defaults[4] 

adatas = (AnnData object with n_obs × n_vars = 500 × 765
    obs: 'bulk_labels', 'n_genes', 'percent_mito', 'n_counts', 'S_scor...pca', 'X_umap'
    varm: 'PCs'
    obsp: 'distances', 'connectivities', AnnData object with n_obs × n_vars = 200 × 765)
n = 4

    @pytest.mark.parametrize("n", [3, 4])
    def test_neighbors_defaults(adatas, n):
        adata_ref = adatas[0].copy()
        adata_new = adatas[1].copy()
    
        sc.pp.neighbors(adata_ref, n_neighbors=n)
    
>       ing = sc.tl.Ingest(adata_ref)

scanpy/tests/test_ingest.py:99: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
scanpy/tools/_ingest.py:424: in __init__
    self._init_neighbors(adata, neighbors_key)
scanpy/tools/_ingest.py:388: in _init_neighbors
    self._init_pynndescent(neighbors["distances"])
scanpy/tools/_ingest.py:325: in _init_pynndescent
    self._nnd_idx = NNDescent(
/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pynndescent/pynndescent_.py:931: in __init__
    self._neighbor_graph = nn_descent(
/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/numba/core/dispatcher.py:468: in _compile_for_args
    error_rewrite(e, 'typing')
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

e = TypingError('Failed in nopython mode pipeline (step: nopython frontend)\nFailed in nopython mode pipeline (step: nopyt...f nn_descent(\n    <source elided>\n    if low_memory:\n        nn_descent_internal_low_memory_parallel(\n        ^\n')
issue_type = 'typing'

    def error_rewrite(e, issue_type):
        """
        Rewrite and raise Exception `e` with help supplied based on the
        specified issue_type.
        """
        if config.SHOW_HELP:
            help_msg = errors.error_extras[issue_type]
            e.patch_message('\n'.join((str(e).rstrip(), help_msg)))
        if config.FULL_TRACEBACKS:
            raise e
        else:
>           raise e.with_traceback(None)
E           numba.core.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend)
E           Failed in nopython mode pipeline (step: nopython frontend)
E           Failed in nopython mode pipeline (step: nopython frontend)
E           Internal error at <numba.core.typeinfer.CallConstraint object at 0x7f062f316bd0>.
E           Failed in nopython mode pipeline (step: parfor prelowering)
E           'NoneType' object has no attribute 'name'
E           During: resolving callee type: type(CPUDispatcher(<function apply_graph_updates_low_memory at 0x7f06458479c0>))
E           During: typing of call at /opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pynndescent/pynndescent_.py (228)
E           
E           Enable logging at debug level for details.
E           
E           File "../../../../../opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pynndescent/pynndescent_.py", line 228:
E           def process_candidates(
E               <source elided>
E           
E                   c += apply_graph_updates_low_memory(current_graph, updates, n_threads)
E                   ^
E           
E           During: resolving callee type: type(CPUDispatcher(<function process_candidates at 0x7f0645465300>))
E           During: typing of call at /opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pynndescent/pynndescent_.py (258)
E           
E           During: resolving callee type: type(CPUDispatcher(<function process_candidates at 0x7f0645465300>))
E           During: typing of call at /opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pynndescent/pynndescent_.py (258)
E           
E           
E           File "../../../../../opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pynndescent/pynndescent_.py", line 258:
E           def nn_descent_internal_low_memory_parallel(
E               <source elided>
E           
E                   c = process_can
Raw output 
/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/numba/core/dispatcher.py:409: numba.core.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend)
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