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