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[pre-commit.ci] pre-commit autoupdate #1120

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Sep 5, 2023

[pre-commit.ci] pre-commit autoupdate

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[pre-commit.ci] pre-commit autoupdate #1120

[pre-commit.ci] pre-commit autoupdate
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Azure Pipelines / scverse.anndata succeeded Sep 4, 2023 in 7m 22s

Build #20230904.4 had test failures

Details

Tests

  • Failed: 1 (0.01%)
  • Passed: 9,103 (82.04%)
  • Other: 1,992 (17.95%)
  • Total: 11,096
Code coverage

  • 4220 of 5133 lines covered (82.21%)

Annotations

Check failure on line 1 in anndata.experimental.multi_files._anncollection.AnnCollection

See this annotation in the file changed.

@azure-pipelines azure-pipelines / scverse.anndata

anndata.experimental.multi_files._anncollection.AnnCollection

634         If  `True`, arrays from the subset objects will always have the same order
635         of indices as in selection used to subset.
636         This parameter can be set to `False` if the order in the returned arrays
637         is not important, for example, when using them for stochastic gradient descent.
638         In this case the performance of subsetting can be a bit better.
639 
640     Examples
641     ----------
642     >>> from scanpy.datasets import pbmc68k_reduced, pbmc3k_processed
643     >>> adata1, adata2 = pbmc68k_reduced(), pbmc3k_processed()
UNEXPECTED EXCEPTION: ModuleNotFoundError("No module named 'certifi'")
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/site-packages/scanpy/readwrite.py", line 952, in _download
    open_url = urlopen(req)
               ^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/urllib/request.py", line 216, in urlopen
    return opener.open(url, data, timeout)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/urllib/request.py", line 525, in open
    response = meth(req, response)
               ^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/urllib/request.py", line 634, in http_response
    response = self.parent.error(
               ^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/urllib/request.py", line 563, in error
    return self._call_chain(*args)
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/urllib/request.py", line 496, in _call_chain
    result = func(*args)
             ^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/urllib/request.py", line 643, in http_error_default
    raise HTTPError(req.full_url, code, msg, hdrs, fp)
urllib.error.HTTPError: HTTP Error 503: first byte timeout
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/doctest.py", line 1351, in __run
    exec(compile(example.source, filename, "single",
  File "<doctest anndata.experimental.multi_files._anncollection.AnnCollection[1]>", line 1, in <module>
  File "/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/site-packages/scanpy/datasets/_utils.py", line 32, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/site-packages/scanpy/datasets/_utils.py", line 15, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/site-packages/scanpy/datasets/_datasets.py", line 305, in pbmc3k_processed
    return read(
           ^^^^^
  File "/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/site-packages/scanpy/readwrite.py", line 111, in read
    return _read(
           ^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/site-packages/scanpy/readwrite.py", line 715, in _read
    is_present = _check_datafile_present_and_download(filename, backup_url=backup_url)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/site-packages/scanpy/readwrite.py", line 1001, in _check_datafile_present_and_download
    _download(backup_url, path)
  File "/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/site-packages/scanpy/readwrite.py", line 958, in _download
    from certifi import where
ModuleNotFoundError: No module named 'certifi'
/home/vsts/work/1/s/anndata/experimental/multi_files/_anncollection.py:643: UnexpectedException
Raw output
634         If  `True`, arrays from the subset objects will always have the same order
635         of indices as in selection used to subset.
636         This parameter can be set to `False` if the order in the returned arrays
637         is not important, for example, when using them for stochastic gradient descent.
638         In this case the performance of subsetting can be a bit better.
639 
640     Examples
641     ----------
642     >>> from scanpy.datasets import pbmc68k_reduced, pbmc3k_processed
643     >>> adata1, adata2 = pbmc68k_reduced(), pbmc3k_processed()
UNEXPECTED EXCEPTION: ModuleNotFoundError("No module named 'certifi'")
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/site-packages/scanpy/readwrite.py", line 952, in _download
    open_url = urlopen(req)
               ^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/urllib/request.py", line 216, in urlopen
    return opener.open(url, data, timeout)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/urllib/request.py", line 525, in open
    response = meth(req, response)
               ^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/urllib/request.py", line 634, in http_response
    response = self.parent.error(
               ^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/urllib/request.py", line 563, in error
    return self._call_chain(*args)
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/urllib/request.py", line 496, in _call_chain
    result = func(*args)
             ^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/urllib/request.py", line 643, in http_error_default
    raise HTTPError(req.full_url, code, msg, hdrs, fp)
urllib.error.HTTPError: HTTP Error 503: first byte timeout
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/doctest.py", line 1351, in __run
    exec(compile(example.source, filename, "single",
  File "<doctest anndata.experimental.multi_files._anncollection.AnnCollection[1]>", line 1, in <module>
  File "/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/site-packages/scanpy/datasets/_utils.py", line 32, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/site-packages/scanpy/datasets/_utils.py", line 15, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/site-packages/scanpy/datasets/_datasets.py", line 305, in pbmc3k_processed
    return read(
           ^^^^^
  File "/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/site-packages/scanpy/readwrite.py", line 111, in read
    return _read(
           ^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/site-packages/scanpy/readwrite.py", line 715, in _read
    is_present = _check_datafile_present_and_download(filename, backup_url=backup_url)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/site-packages/scanpy/readwrite.py", line 1001, in _check_datafile_present_and_download
    _download(backup_url, path)
  File "/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/site-packages/scanpy/readwrite.py", line 958, in _download
    from certifi import where
ModuleNotFoundError: No module named 'certifi'
/home/vsts/work/1/s/anndata/experimental/multi_files/_anncollection.py:643: UnexpectedException