[pre-commit.ci] pre-commit autoupdate #1120
Merged
This check has been archived and is scheduled for deletion.
Learn more about checks retention
Azure Pipelines / scverse.anndata
succeeded
Sep 4, 2023 in 7m 22s
Build #20230904.4 had test failures
Details
- Failed: 1 (0.01%)
- Passed: 9,103 (82.04%)
- Other: 1,992 (17.95%)
- Total: 11,096
- 4220 of 5133 lines covered (82.21%)
Annotations
Check failure on line 1 in anndata.experimental.multi_files._anncollection.AnnCollection
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
Loading