Re: Help: Test suite failures (Was: ITP: anndata -- Annotated gene by sample numpy matrix)
Dear Diane,
would you mind pushing your patch to the Git repository? I mean its
your ITP and you are Uploader - so I hesitate to push your very own
patch on behalf of you. ;-)
Thanks a lot for your helpful hints and contacting upstream
Andreas.
On Thu, Nov 05, 2020 at 02:14:12PM -0800, Diane Trout wrote:
> It sure looks like at least some of those failures are from upstreams
> tests assuming they'd be run directly in the source tree.
>
> All but one of the test cases can be fixed by including some test files
> in the package, though it ends up in anndata/tests/
>
> It's about 9 kilobytes with a csv, tsv, and xlsx file included.
>
> This is probably the easiest solution, though I though I remember
> Debian policy discouraging putting data into the dist-packages
> directory.
>
> I'm not sure about the last test failure though
>
> --- setup.py 2020-03-02 16:10:44.668936082 -0800
> +++ /run/schroot/mount/unstable-amd64-sbuild-6f63c09f-36e0-4302-9409-
> 6689c5b05354/build/python-anndata-exfcES/python-anndata-
> 0.7.4+ds/setup.py 2020-11-05 13:51:59.763629317 -0800
> @@ -28,4 +28,5 @@
> packages=find_namespace_packages(include=["anndata",
> "anndata.*"]),
> include_package_data=True,
> + package_data={"": ["*.csv", "*.tsv", "*.xlsx"]},
> zip_safe=False,
> classifiers=[
>
> On Thu, 2020-11-05 at 21:08 +0100, Andreas Tille wrote:
> > 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
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