gistfile1.txt

ubuntu@ip-172-31-20-78[prod][kerl/lib-sdf][python]$ ttsv tests/test_soma_dataframe.py
============================================================= test session starts =============================================================
platform linux -- Python 3.10.4, pytest-7.1.3, pluggy-1.0.0 -- /usr/bin/python
cachedir: .pytest_cache
rootdir: /home/ubuntu/git/single-cell-data/TileDB-SOMA/apis/python
plugins: typeguard-2.13.3
collected 19 items

tests/test_soma_dataframe.py::test_soma_dataframe_non_indexed FAILED                                                                    [  5%]
tests/test_soma_dataframe.py::test_SOMADataFrame_read_column_names[col_names0-None] PASSED                                              [ 10%]
tests/test_soma_dataframe.py::test_SOMADataFrame_read_column_names[col_names0-ids1] PASSED                                              [ 15%]
tests/test_soma_dataframe.py::test_SOMADataFrame_read_column_names[col_names0-ids2] PASSED                                              [ 21%]
tests/test_soma_dataframe.py::test_SOMADataFrame_read_column_names[col_names1-None] PASSED                                              [ 26%]
tests/test_soma_dataframe.py::test_SOMADataFrame_read_column_names[col_names1-ids1] PASSED                                              [ 31%]
tests/test_soma_dataframe.py::test_SOMADataFrame_read_column_names[col_names1-ids2] PASSED                                              [ 36%]
tests/test_soma_dataframe.py::test_SOMADataFrame_read_column_names[col_names2-None] PASSED                                              [ 42%]
tests/test_soma_dataframe.py::test_SOMADataFrame_read_column_names[col_names2-ids1] PASSED                                              [ 47%]
tests/test_soma_dataframe.py::test_SOMADataFrame_read_column_names[col_names2-ids2] PASSED                                              [ 52%]
tests/test_soma_dataframe.py::test_SOMADataFrame_read_column_names[col_names3-None] PASSED                                              [ 57%]
tests/test_soma_dataframe.py::test_SOMADataFrame_read_column_names[col_names3-ids1] PASSED                                              [ 63%]
tests/test_soma_dataframe.py::test_SOMADataFrame_read_column_names[col_names3-ids2] PASSED                                              [ 68%]
tests/test_soma_dataframe.py::test_SOMADataFrame_read_column_names[col_names4-None] PASSED                                              [ 73%]
tests/test_soma_dataframe.py::test_SOMADataFrame_read_column_names[col_names4-ids1] PASSED                                              [ 78%]
tests/test_soma_dataframe.py::test_SOMADataFrame_read_column_names[col_names4-ids2] PASSED                                              [ 84%]
tests/test_soma_dataframe.py::test_SOMADataFrame_read_column_names[None-None] PASSED                                                    [ 89%]
tests/test_soma_dataframe.py::test_SOMADataFrame_read_column_names[None-ids1] PASSED                                                    [ 94%]
tests/test_soma_dataframe.py::test_SOMADataFrame_read_column_names[None-ids2] PASSED                                                    [100%]

================================================================== FAILURES ===================================================================
_______________________________________________________ test_soma_dataframe_non_indexed _______________________________________________________

tmp_path = PosixPath('/tmp/pytest-of-ubuntu/pytest-48/test_soma_dataframe_non_indexe0')

    def test_soma_dataframe_non_indexed(tmp_path):
        sdf = t.SOMADataFrame(uri=tmp_path.as_posix())

        # Create
        asch = pa.schema(
            [
                ("foo", pa.int32()),
                ("bar", pa.float64()),
                ("baz", pa.large_string()),
            ]
        )
        sdf.create(schema=asch)

        # ----------------------------------------------------------------
        # Write
        for _i in range(3):
            pydict = {}
            pydict["soma_rowid"] = [0, 1, 2, 3, 4]
            pydict["foo"] = [10, 20, 30, 40, 50]
            pydict["bar"] = [4.1, 5.2, 6.3, 7.4, 8.5]
            pydict["baz"] = ["apple", "ball", "cat", "dog", "egg"]
            rb = pa.Table.from_pydict(pydict)
            sdf.write(rb)

        # ----------------------------------------------------------------
        # Read all
        table = sdf.read_all()
        assert table.num_rows == 5

        # We should be getting back the soma_rowid column as well
        # If sparse dataframe:
        assert table.num_columns == 4
        # If dense dataframe:
        # assert table.num_columns == 3

        # TODO assert [e.as_py() for e in list(table['soma_rowid'])] == [0,1,2,3,4]
        assert [e.as_py() for e in list(table["foo"])] == pydict["foo"]
        assert [e.as_py() for e in list(table["bar"])] == pydict["bar"]
        assert [e.as_py() for e in list(table["baz"])] == pydict["baz"]

        # ----------------------------------------------------------------
        # Read by ids
        table = sdf.read_all(ids=[1, 2])
        assert table.num_rows == 2

        # We should be getting back the soma_rowid column as well
        # If sparse dataframe:
        assert table.num_columns == 4
        # If dense dataframe:
        # assert table.num_columns == 3

        # TODO assert [e.as_py() for e in list(table['soma_rowid'])] == [0,1,2,3,4]
        assert sorted([e.as_py() for e in list(table["foo"])]) == [20, 30]
        assert sorted([e.as_py() for e in list(table["bar"])]) == [5.2, 6.3]
        assert sorted([e.as_py() for e in list(table["baz"])]) == ["ball", "cat"]

        # ----------------------------------------------------------------
        # Read by ids
        table = sdf.read_all(ids=slice(1, 2))
        assert table.num_rows == 2

        # We should be getting back the soma_rowid column as well
        # If sparse dataframe:
        assert table.num_columns == 4
        # If dense dataframe:
        # assert table.num_columns == 3

        # TODO assert [e.as_py() for e in list(table['soma_rowid'])] == [0,1,2,3,4]
        assert sorted([e.as_py() for e in list(table["foo"])]) == [20, 30]
        assert sorted([e.as_py() for e in list(table["bar"])]) == [5.2, 6.3]
        assert sorted([e.as_py() for e in list(table["baz"])]) == ["ball", "cat"]

        # ----------------------------------------------------------------
        # Read by value_filter
>       table = sdf.read_all(value_filter="foo == 40 or foo == 20")

tests/test_soma_dataframe.py:82:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/home/ubuntu/.local/lib/python3.10/site-packages/typeguard/__init__.py:1033: in wrapper
    retval = func(*args, **kwargs)
src/tiledbsoma/soma_dataframe.py:234: in read_all
    return pa.concat_tables(
pyarrow/table.pxi:5139: in pyarrow.lib.concat_tables
    ???
/home/ubuntu/.local/lib/python3.10/site-packages/typeguard/__init__.py:897: in __next__
    return self.send(None)
/home/ubuntu/.local/lib/python3.10/site-packages/typeguard/__init__.py:915: in send
    value = self.__wrapped.send(obj)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = SOMADataFrame(uri="/tmp/pytest-of-ubuntu/pytest-48/test_soma_dataframe_non_indexe0")

    def read(
        self,
        *,
        # TODO: find the right syntax to get the typechecker to accept args like ``ids=slice(0,10)``
        # ids: Optional[Union[Sequence[int], Slice]] = None,
        ids: Optional[Any] = None,
        value_filter: Optional[str] = None,
        column_names: Optional[Sequence[str]] = None,
        result_order: Optional[SOMAResultOrder] = None,
        # TODO: batch_size
        # TODO: partition,
        # TODO: platform_config,
    ) -> Iterator[pa.Table]:
        """
        Read a user-defined subset of data, addressed by the dataframe indexing column, optionally filtered, and return results as one or more ``Arrow.Table``.

        :param ids: Which rows to read. Defaults to ``None``, meaning no constraint -- all rows.

        :param column_names: the named columns to read and return. Defaults to ``None``, meaning no constraint -- all column names.

        :param partitions: an optional ``SOMAReadPartitions`` hint to indicate how results should be organized.

        :param result_order: order of read results.  This can be one of 'row-major', 'col-major', or 'unordered'.

        :param value_filter: an optional [value filter] to apply to the results. Defaults to no filter.

        **Indexing**: the ``ids`` parameter will support, per dimension: a row offset (uint), a row-offset range (slice), or a list of both.
        """
        with self._tiledb_open("r") as A:
            dim_names, attr_names = util_tiledb.split_column_names(
                A.schema, column_names
            )

            query_condition = None
            if value_filter is not None:
                # query_condition = tiledb.QueryCondition(value_filter)
                query_condition = QueryCondition(value_filter)

            # As an arg to this method, `column_names` is optional-None. For the pybind11
            # code it's optional-[].
            lib_column_names = [] if column_names is None else column_names

>           sr = clib.SOMAReader(
                self._uri,
                name=self.__class__.__name__,
                schema=A.schema,  # query_condition needs this
                column_names=lib_column_names,
                query_condition=query_condition,
            )
E           RuntimeError: TypeError: type of argument "node" must be a type; got ast.Compare instead
E
E           At:
E             /home/ubuntu/.local/lib/python3.10/site-packages/typeguard/__init__.py(875): check_argument_types
E             /home/ubuntu/.local/lib/python3.10/site-packages/typeguard/__init__.py(1032): wrapper
E             /usr/lib/python3.10/ast.py(410): visit
E             /home/ubuntu/git/single-cell-data/TileDB-SOMA/apis/python/src/tiledbsoma/query_condition.py(415): visit_BoolOp
E             /home/ubuntu/.local/lib/python3.10/site-packages/typeguard/__init__.py(1033): wrapper
E             /usr/lib/python3.10/ast.py(410): visit
E             /home/ubuntu/git/single-cell-data/TileDB-SOMA/apis/python/src/tiledbsoma/query_condition.py(135): init_query_condition
E             /home/ubuntu/.local/lib/python3.10/site-packages/typeguard/__init__.py(1033): wrapper
E             /home/ubuntu/git/single-cell-data/TileDB-SOMA/apis/python/src/tiledbsoma/soma_dataframe.py(193): read
E             /home/ubuntu/.local/lib/python3.10/site-packages/typeguard/__init__.py(915): send
E             /home/ubuntu/.local/lib/python3.10/site-packages/typeguard/__init__.py(897): __next__
E             /home/ubuntu/git/single-cell-data/TileDB-SOMA/apis/python/src/tiledbsoma/soma_dataframe.py(234): read_all
E             /home/ubuntu/.local/lib/python3.10/site-packages/typeguard/__init__.py(1033): wrapper
E             /home/ubuntu/git/single-cell-data/TileDB-SOMA/apis/python/tests/test_soma_dataframe.py(82): test_soma_dataframe_non_indexed
E             /home/ubuntu/.local/lib/python3.10/site-packages/_pytest/python.py(192): pytest_pyfunc_call
E             /home/ubuntu/.local/lib/python3.10/site-packages/pluggy/_callers.py(39): _multicall
E             /home/ubuntu/.local/lib/python3.10/site-packages/pluggy/_manager.py(80): _hookexec
E             /home/ubuntu/.local/lib/python3.10/site-packages/pluggy/_hooks.py(265): __call__
E             /home/ubuntu/.local/lib/python3.10/site-packages/_pytest/python.py(1761): runtest
E             /home/ubuntu/.local/lib/python3.10/site-packages/_pytest/runner.py(166): pytest_runtest_call
E             /home/ubuntu/.local/lib/python3.10/site-packages/pluggy/_callers.py(39): _multicall
E             /home/ubuntu/.local/lib/python3.10/site-packages/pluggy/_manager.py(80): _hookexec
E             /home/ubuntu/.local/lib/python3.10/site-packages/pluggy/_hooks.py(265): __call__
E             /home/ubuntu/.local/lib/python3.10/site-packages/_pytest/runner.py(259): <lambda>
E             /home/ubuntu/.local/lib/python3.10/site-packages/_pytest/runner.py(338): from_call
E             /home/ubuntu/.local/lib/python3.10/site-packages/_pytest/runner.py(258): call_runtest_hook
E             /home/ubuntu/.local/lib/python3.10/site-packages/_pytest/runner.py(219): call_and_report
E             /home/ubuntu/.local/lib/python3.10/site-packages/_pytest/runner.py(130): runtestprotocol
E             /home/ubuntu/.local/lib/python3.10/site-packages/_pytest/runner.py(111): pytest_runtest_protocol
E             /home/ubuntu/.local/lib/python3.10/site-packages/pluggy/_callers.py(39): _multicall
E             /home/ubuntu/.local/lib/python3.10/site-packages/pluggy/_manager.py(80): _hookexec
E             /home/ubuntu/.local/lib/python3.10/site-packages/pluggy/_hooks.py(265): __call__
E             /home/ubuntu/.local/lib/python3.10/site-packages/_pytest/main.py(347): pytest_runtestloop
E             /home/ubuntu/.local/lib/python3.10/site-packages/pluggy/_callers.py(39): _multicall
E             /home/ubuntu/.local/lib/python3.10/site-packages/pluggy/_manager.py(80): _hookexec
E             /home/ubuntu/.local/lib/python3.10/site-packages/pluggy/_hooks.py(265): __call__
E             /home/ubuntu/.local/lib/python3.10/site-packages/_pytest/main.py(322): _main
E             /home/ubuntu/.local/lib/python3.10/site-packages/_pytest/main.py(268): wrap_session
E             /home/ubuntu/.local/lib/python3.10/site-packages/_pytest/main.py(315): pytest_cmdline_main
E             /home/ubuntu/.local/lib/python3.10/site-packages/pluggy/_callers.py(39): _multicall
E             /home/ubuntu/.local/lib/python3.10/site-packages/pluggy/_manager.py(80): _hookexec
E             /home/ubuntu/.local/lib/python3.10/site-packages/pluggy/_hooks.py(265): __call__
E             /home/ubuntu/.local/lib/python3.10/site-packages/_pytest/config/__init__.py(164): main
E             /home/ubuntu/.local/lib/python3.10/site-packages/_pytest/config/__init__.py(187): console_main
E             /home/ubuntu/.local/lib/python3.10/site-packages/pytest/__main__.py(5): <module>
E             /usr/lib/python3.10/runpy.py(86): _run_code
E             /usr/lib/python3.10/runpy.py(196): _run_module_as_main

src/tiledbsoma/soma_dataframe.py:193: RuntimeError
=========================================================== short test summary info ===========================================================
FAILED tests/test_soma_dataframe.py::test_soma_dataframe_non_indexed - RuntimeError: TypeError: type of argument "node" must be a type; got ...
======================================================== 1 failed, 18 passed in 2.44s =========================================================
ubuntu@ip-172-31-20-78[prod][kerl/lib-sdf][python]$