Control: tags -1 help
Hi Diane and Steffen,
I fixed the Build-Depends in this package which leads to the
effect that
a) the Build-time test is run
b) shows the same errors as the autopkgtest
...
anndata/tests/test_deprecations.py::test_get_uns_neighbors_deprecated FAILED [
36%]
...
anndata/tests/test_readwrite.py::test_read_csv FAILED [ 51%]
anndata/tests/test_readwrite.py::test_read_tsv_strpath FAILED [ 51%]
anndata/tests/test_readwrite.py::test_read_tsv_iter FAILED [ 51%]
...
anndata/tests/test_readwrite.py::test_read_excel FAILED [ 51%]
...
=================================== FAILURES ===================================
______________________ test_get_uns_neighbors_deprecated _______________________
adata = AnnData object with n_obs × n_vars = 2 × 3
obs: 'anno1'
var: 'anno2'
uns: 'neighbors'
layers: 'x2'
obsp: 'connectivities'
def test_get_uns_neighbors_deprecated(adata):
n = adata.shape[0]
mtx = sparse.random(n, n, density=0.3, format="csr")
adata.obsp["connectivities"] = mtx
adata.uns["neighbors"] = {}
....
with pytest.warns(FutureWarning):
from_uns = adata.uns["neighbors"]["connectivities"]
....
assert_equal(from_uns, mtx)
....
with pytest.warns(None) as rec:
v = adata[: n // 2]
> assert not rec
E assert not WarningsChecker(record=True)
anndata/tests/test_deprecations.py:113: AssertionError
________________________________ test_read_csv _________________________________
def test_read_csv():
> adata = ad.read_csv(HERE / "adata.csv")
anndata/tests/test_readwrite.py:308:.
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _.
anndata/_io/read.py:48: in read_csv
return read_text(filename, delimiter, first_column_names, dtype)
anndata/_io/read.py:321: in read_text
with filename.open() as f:
/usr/lib/python3.9/pathlib.py:1241: in open
return io.open(self, mode, buffering, encoding, errors, newline,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _.
self =
PosixPath('/build/python-anndata-0.7.4+ds/.pybuild/cpython3_3.9_anndata/build/anndata/tests/adata.csv')
name =
'/build/python-anndata-0.7.4+ds/.pybuild/cpython3_3.9_anndata/build/anndata/tests/adata.csv'
flags = 524288, mode = 438
def _opener(self, name, flags, mode=0o666):
# A stub for the opener argument to built-in open()
> return self._accessor.open(self, flags, mode)
E FileNotFoundError: [Errno 2] No such file or directory:
'/build/python-anndata-0.7.4+ds/.pybuild/cpython3_3.9_anndata/build/anndata/tests/adata.csv'
/usr/lib/python3.9/pathlib.py:1109: FileNotFoundError
____________________________ test_read_tsv_strpath _____________________________
def test_read_tsv_strpath():
> adata = ad.read_text(str(HERE / "adata-comments.tsv"), "\t")
anndata/tests/test_readwrite.py:315:.
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _.
anndata/_io/read.py:321: in read_text
with filename.open() as f:
/usr/lib/python3.9/pathlib.py:1241: in open
return io.open(self, mode, buffering, encoding, errors, newline,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _.
self =
PosixPath('/build/python-anndata-0.7.4+ds/.pybuild/cpython3_3.9_anndata/build/anndata/tests/adata-comments.tsv')
name =
'/build/python-anndata-0.7.4+ds/.pybuild/cpython3_3.9_anndata/build/anndata/tests/adata-comments.tsv'
flags = 524288, mode = 438
def _opener(self, name, flags, mode=0o666):
# A stub for the opener argument to built-in open()
> return self._accessor.open(self, flags, mode)
E FileNotFoundError: [Errno 2] No such file or directory:
'/build/python-anndata-0.7.4+ds/.pybuild/cpython3_3.9_anndata/build/anndata/tests/adata-comments.tsv'
/usr/lib/python3.9/pathlib.py:1109: FileNotFoundError
______________________________ test_read_tsv_iter ______________________________
def test_read_tsv_iter():
> with (HERE / "adata-comments.tsv").open() as f:
anndata/tests/test_readwrite.py:322:.
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _.
/usr/lib/python3.9/pathlib.py:1241: in open
return io.open(self, mode, buffering, encoding, errors, newline,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _.
self =
PosixPath('/build/python-anndata-0.7.4+ds/.pybuild/cpython3_3.9_anndata/build/anndata/tests/adata-comments.tsv')
name =
'/build/python-anndata-0.7.4+ds/.pybuild/cpython3_3.9_anndata/build/anndata/tests/adata-comments.tsv'
flags = 524288, mode = 438
def _opener(self, name, flags, mode=0o666):
# A stub for the opener argument to built-in open()
> return self._accessor.open(self, flags, mode)
E FileNotFoundError: [Errno 2] No such file or directory:
'/build/python-anndata-0.7.4+ds/.pybuild/cpython3_3.9_anndata/build/anndata/tests/adata-comments.tsv'
/usr/lib/python3.9/pathlib.py:1109: FileNotFoundError
_______________________________ test_read_excel ________________________________
def test_read_excel():
> adata = ad.read_excel(HERE / "data/excel.xlsx", "Sheet1", dtype=int)
anndata/tests/test_readwrite.py:365:.
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _.
anndata/_io/read.py:70: in read_excel
df = read_excel(fspath(filename), sheet)
/usr/lib/python3/dist-packages/pandas/util/_decorators.py:296: in wrapper
return func(*args, **kwargs)
/usr/lib/python3/dist-packages/pandas/io/excel/_base.py:304: in read_excel
io = ExcelFile(io, engine=engine)
/usr/lib/python3/dist-packages/pandas/io/excel/_base.py:867: in __init__
self._reader = self._engines[engine](self._io)
/usr/lib/python3/dist-packages/pandas/io/excel/_xlrd.py:22: in __init__
super().__init__(filepath_or_buffer)
/usr/lib/python3/dist-packages/pandas/io/excel/_base.py:353: in __init__
self.book = self.load_workbook(filepath_or_buffer)
/usr/lib/python3/dist-packages/pandas/io/excel/_xlrd.py:37: in load_workbook
return open_workbook(filepath_or_buffer)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _.
filename =
'/build/python-anndata-0.7.4+ds/.pybuild/cpython3_3.9_anndata/build/anndata/tests/data/excel.xlsx'
logfile = <_pytest.capture.EncodedFile object at 0x7ff6a4c226a0>, verbosity = 0
use_mmap = 1, file_contents = None, encoding_override = None
formatting_info = False, on_demand = False, ragged_rows = False
def open_workbook(filename=None,
logfile=sys.stdout,
verbosity=0,
use_mmap=USE_MMAP,
file_contents=None,
encoding_override=None,
formatting_info=False,
on_demand=False,
ragged_rows=False,
):
"""
Open a spreadsheet file for data extraction.
:param filename: The path to the spreadsheet file to be opened.
:param logfile: An open file to which messages and diagnostics are
written.
:param verbosity: Increases the volume of trace material written to the
logfile.
:param use_mmap:
Whether to use the mmap module is determined heuristically.
Use this arg to override the result.
Current heuristic: mmap is used if it exists.
:param file_contents:
A string or an :class:`mmap.mmap` object or some other behave-alike
object. If ``file_contents`` is supplied, ``filename`` will not be
used,
except (possibly) in messages.
:param encoding_override:
Used to overcome missing or bad codepage information
in older-version files. See :doc:`unicode`.
...
E FileNotFoundError: [Errno 2] No such file or directory:
'/build/python-anndata-0.7.4+ds/.pybuild/cpython3_3.9_anndata/build/anndata/tests/data/excel.xlsx'
/usr/lib/python3/dist-packages/xlrd/__init__.py:116: FileNotFoundError
=============================== warnings summary ===============================
...
= 5 failed, 1442 passed, 18 skipped, 25 xfailed, 910 warnings in 67.22 seconds =
E: pybuild pybuild:353: test: plugin distutils failed with: exit code=1: cd
/build/python-anndata-0.7.4+ds/.pybuild/cpython3_3.9_anndata/build; python3.9
-m pytest -v
The very same errors occure for Python3.8 so it does not seem to be just
a Python3.9 issue.
Any hints are welcome
Andreas.
--
http://fam-tille.de
