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Backport PR #2801: Fix scanpy.read_10x_mtx’s gex_only=True mode #2812

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merged 2 commits into from
Jan 16, 2024

fix syntax

99d3acd
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Merged

Backport PR #2801: Fix scanpy.read_10x_mtx’s gex_only=True mode #2812

fix syntax
99d3acd
Select commit
Loading
Failed to load commit list.
Azure Pipelines / scverse.scanpy succeeded Jan 16, 2024 in 12m 1s

Build #20240116.2 had test failures

0 errors / 0 warnings

Details

Tests

  • Failed: 7 (0.17%)
  • Passed: 3,910 (96.21%)
  • Other: 147 (3.62%)
  • Total: 4,064
Code coverage

  • 8299 of 11643 lines covered (71.28%)

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:386: in __init__
    self._init_neighbors(adata, neighbors_key)
scanpy/tools/_ingest.py:352: in _init_neighbors
    self._init_pynndescent(neighbors['distances'])
scanpy/tools/_ingest.py:289: in _init_pynndescent
    self._nnd_idx = NNDescent(
/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/pynndescent/pynndescent_.py:931: in __init__
    self._neighbor_graph = nn_descent(
/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/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 0x7f8bfb80c400>.
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 0x7f8c0d614d30>))
E           During: typing of call at /opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/pynndescent/pynndescent_.py (228)
E           
E           Enable logging at debug level for details.
E           
E           File "../../../../../opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/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 0x7f8c0c8d11f0>))
E           During: typing of call at /opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/pynndescent/pynndescent_.py (258)
E           
E           During: resolving callee type: type(CPUDispatcher(<function process_candidates at 0x7f8c0c8d11f0>))
E           During: typing of call at /opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/pynndescent/pynndescent_.py (258)
E           
E           
E           File "../../../../../opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/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(<functio
Raw output 
/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/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:386: in __init__
    self._init_neighbors(adata, neighbors_key)
scanpy/tools/_ingest.py:352: in _init_neighbors
    self._init_pynndescent(neighbors['distances'])
scanpy/tools/_ingest.py:289: in _init_pynndescent
    self._nnd_idx = NNDescent(
/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/pynndescent/pynndescent_.py:931: in __init__
    self._neighbor_graph = nn_descent(
/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/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 0x7f8bfb80c400>.
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 0x7f8c0d614d30>))
E           During: typing of call at /opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/pynndescent/pynndescent_.py (228)
E           
E           Enable logging at debug level for details.
E           
E           File "../../../../../opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/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 0x7f8c0c8d11f0>))
E           During: typing of call at /opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/pynndescent/pynndescent_.py (258)
E           
E           During: resolving callee type: type(CPUDispatcher(<function process_candidates at 0x7f8c0c8d11f0>))
E           During: typing of call at /opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/pynndescent/pynndescent_.py (258)
E           
E           
E           File "../../../../../opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/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(<function nn_
Raw output 
/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/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:386: in __init__
    self._init_neighbors(adata, neighbors_key)
scanpy/tools/_ingest.py:352: in _init_neighbors
    self._init_pynndescent(neighbors['distances'])
scanpy/tools/_ingest.py:289: in _init_pynndescent
    self._nnd_idx = NNDescent(
/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/pynndescent/pynndescent_.py:931: in __init__
    self._neighbor_graph = nn_descent(
/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/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 0x7f8bfb80c400>.
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 0x7f8c0d614d30>))
E           During: typing of call at /opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/pynndescent/pynndescent_.py (228)
E           
E           Enable logging at debug level for details.
E           
E           File "../../../../../opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/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 0x7f8c0c8d11f0>))
E           During: typing of call at /opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/pynndescent/pynndescent_.py (258)
E           
E           During: resolving callee type: type(CPUDispatcher(<function process_candidates at 0x7f8c0c8d11f0>))
E           During: typing of call at /opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/pynndescent/pynndescent_.py (258)
E           
E           
E           File "../../../../../opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/pynndescent/pynndescent_.py", line 258:
E           def nn_descent_internal_low_memory_parallel(
E               <source elided>
E           
E                   c = process_candidates
Raw output 
/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/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:386: in __init__
    self._init_neighbors(adata, neighbors_key)
scanpy/tools/_ingest.py:352: in _init_neighbors
    self._init_pynndescent(neighbors['distances'])
scanpy/tools/_ingest.py:289: in _init_pynndescent
    self._nnd_idx = NNDescent(
/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/pynndescent/pynndescent_.py:931: in __init__
    self._neighbor_graph = nn_descent(
/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/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 0x7f8bfb80c400>.
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 0x7f8c0d614d30>))
E           During: typing of call at /opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/pynndescent/pynndescent_.py (228)
E           
E           Enable logging at debug level for details.
E           
E           File "../../../../../opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/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 0x7f8c0c8d11f0>))
E           During: typing of call at /opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/pynndescent/pynndescent_.py (258)
E           
E           During: resolving callee type: type(CPUDispatcher(<function process_candidates at 0x7f8c0c8d11f0>))
E           During: typing of call at /opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/pynndescent/pynndescent_.py (258)
E           
E           
E           File "../../../../../opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/pynndescent/pynndescent_.py", line 258:
E           def nn_descent_internal_low_memory_parallel(
E               <source elided>
E           
E                   c = process_candidates
Raw output 
/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/numba/core/dispatcher.py:409: numba.core.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend)
View more details on Azure Pipelines