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pytest failing on fastapi and pyspark tests on master
When I build a clean contributor environment as per Conda instructions https://github.com/pandera-dev/pandera/blob/main/.github/CONTRIBUTING.md, and run 'pytest tests' on the master branch, I get the following test failures. I didn't have this problem the last time I contributed in May/June timeframe. I also tried virtualenv to the same effect. Are there extra steps in environment setup that I'm missing?
======================================================================================================================================================================================= short test summary info =======================================================================================================================================================================================
FAILED tests/fastapi/test_app.py::test_items_endpoint - requests.exceptions.ConnectionError: HTTPConnectionPool(host='127.0.0.1', port=8000): Max retries exceeded with url: /items/ (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x156868f10>: Failed to establish a new connection: [Errno 61] Connection refused'))
FAILED tests/fastapi/test_app.py::test_transactions_endpoint - requests.exceptions.ConnectionError: HTTPConnectionPool(host='127.0.0.1', port=8000): Max retries exceeded with url: /transactions/ (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x1574ecee0>: Failed to establish a new connection: [Errno 61] Connection refused'))
FAILED tests/fastapi/test_app.py::test_upload_file_endpoint - requests.exceptions.ConnectionError: HTTPConnectionPool(host='127.0.0.1', port=8000): Max retries exceeded with url: /file/ (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x157bc21c0>: Failed to establish a new connection: [Errno 61] Connection refused'))
FAILED tests/pyspark/test_pyspark_check.py::TestCustomCheck::test_extension - AttributeError: '<class 'pandera.api.checks.Check'>' object has no attribute 'new_pyspark_check'. Make sure any custom checks have been registered using the extensions api.
FAILED tests/pyspark/test_pyspark_check.py::TestCustomCheck::test_extension_pydantic - pandera.errors.SchemaInitError: custom check 'new_pyspark_check' is not available. Make sure you use pandera.extensions.register_check_method decorator to register your custom check method.
FAILED tests/pyspark/test_schemas_on_pyspark_pandas.py::test_dataframe_schema_case[True] - py4j.protocol.Py4JJavaError: An error occurred while calling o15883.collectToPython.
FAILED tests/pyspark/test_schemas_on_pyspark_pandas.py::test_dataframe_schema_case[False] - py4j.protocol.Py4JJavaError: An error occurred while calling o16622.collectToPython.
FAILED tests/pyspark/test_schemas_on_pyspark_pandas.py::test_index_dtypes[Index-True-str] - py4j.protocol.Py4JJavaError: An error occurred while calling o31793.collectToPython.
FAILED tests/pyspark/test_schemas_on_pyspark_pandas.py::test_index_dtypes[Index-False-str] - py4j.protocol.Py4JJavaError: An error occurred while calling o36641.collectToPython.
FAILED tests/pyspark/test_schemas_on_pyspark_pandas.py::test_index_dtypes[MultiIndex-True-str] - py4j.protocol.Py4JJavaError: An error occurred while calling o43865.collectToPython.
FAILED tests/pyspark/test_schemas_on_pyspark_pandas.py::test_index_dtypes[MultiIndex-False-str] - py4j.protocol.Py4JJavaError: An error occurred while calling o51089.collectToPython.
FAILED tests/pyspark/test_schemas_on_pyspark_pandas.py::test_dtype_coercion[str-str] - py4j.protocol.Py4JJavaError: An error occurred while calling o74410.collectToPython.
FAILED tests/pyspark/test_schemas_on_pyspark_pandas.py::test_schema_model - py4j.protocol.Py4JJavaError: An error occurred while calling o77287.collectToPython.
FAILED tests/pyspark/test_schemas_on_pyspark_pandas.py::test_check_comparison_operators[check9-a-b] - py4j.protocol.Py4JJavaError: An error occurred while calling o79944.collectToPython.
FAILED tests/pyspark/test_schemas_on_pyspark_pandas.py::test_check_comparison_operators[check10-faa-foo] - py4j.protocol.Py4JJavaError: An error occurred while calling o80032.collectToPython.
FAILED tests/pyspark/test_schemas_on_pyspark_pandas.py::test_check_comparison_operators[check11-ab-ba] - py4j.protocol.Py4JJavaError: An error occurred while calling o80120.collectToPython.
FAILED tests/pyspark/test_schemas_on_pyspark_pandas.py::test_check_comparison_operators[check12-ba-ab] - py4j.protocol.Py4JJavaError: An error occurred while calling o80208.collectToPython.
========================================================================================================================================================= 17 failed, 2809 passed, 84 skipped, 8 xfailed, 123818 warnings in 581.28s (0:09:41) =========================================================================================================================================================
So far, looks like Fastapi release 0.100 introduced some incompatibility with Pandera tests. Downgrading to 0.99 resolved that issue for now. Still trying to figure out Pyspark.
It appears Pyspark is generally unhappy with string dtypes through Pandas? I don't have any experience with Pyspark so I don't think it would be wise for me to request changes. @cosmicBboy do you see this behavior at all?
Not sure if this is specific to my environment on Mac OS. One example where the 'test_dataframe_schema_case' tests fail.
https://github.com/unionai-oss/pandera/blob/57d826956b88f89c18e794c728b7f5547ab4ecf8/pandera/engines/pandas_engine.py#L707C1-L713C1
This test became happy when I modified like so:
def check(
self,
pandera_dtype: dtypes.DataType,
data_container: Optional[PandasObject] = None,
) -> Union[bool, Iterable[bool]]:
if data_container is None:
return isinstance(pandera_dtype, (numpy_engine.Object, type(self)))
is_na = pd.isna(data_container)
is_python_string = pd.api.types.is_string_dtype(data_container)
return is_na | is_python_string
Hi @derinwalters are you still seeing this issue with the latest release?
Heya @cosmicBboy most issues are gone now (thanks!). The first two below show up every time, and the third one shows up every once in a while.
=============================================================================================================================== short test summary info ================================================================================================================================
FAILED tests/pyspark/test_pyspark_check.py::TestCustomCheck::test_extension - AttributeError: '<class 'pandera.api.checks.Check'>' object has no attribute 'new_pyspark_check'. Make sure any custom checks have been registered using the extensions api.
FAILED tests/pyspark/test_pyspark_check.py::TestCustomCheck::test_extension_pydantic - pandera.errors.SchemaInitError: custom check 'new_pyspark_check' is not available. Make sure you use pandera.extensions.register_check_method decorator to register your custom check method.
FAILED tests/pyspark/test_schemas_on_pyspark_pandas.py::test_nullable[dtype10] - IndexError: tuple index out of range
================================================================================================= 3 failed, 2859 passed, 83 skipped, 13 xfailed, 109157 warnings in 516.28s (0:08:36) ==================================================================================================
Details for the third error are as follows
else:
try:
ks_null_sample: ps.DataFrame = ps.DataFrame(null_sample)
except TypeError as exc:
match = re.search(
> r"can not accept object (<NA>|NaT) in type", exc.args[0]
)
E IndexError: tuple index out of range
E Falsifying example: test_nullable(
E dtype=DataType(timedelta64[ns]),
E data=data(...),
E )
E Draw 1:
E field
E 0 NaT
E 1 0 days
E 2 0 days
E 3 0 days
E 4 0 days
E
E Draw 2:
E field
E 0 0 days
E 1 0 days
E 2 0 days
E 3 0 days
E 4 0 days
E
E Explanation:
E These lines were always and only run by failing examples:
E /Users/derinw/miniforge3/envs/pandera-dev/lib/python3.10/site-packages/pandas/core/arrays/_mixins.py:398
E /Users/derinw/miniforge3/envs/pandera-dev/lib/python3.10/site-packages/pandas/core/dtypes/missing.py:714
E /Users/derinw/miniforge3/envs/pandera-dev/lib/python3.10/site-packages/pandas/core/internals/blocks.py:1456
E /Users/derinw/miniforge3/envs/pandera-dev/lib/python3.10/site-packages/pandas/core/internals/blocks.py:246
E /Users/derinw/miniforge3/envs/pandera-dev/lib/python3.10/site-packages/pandas/core/internals/blocks.py:247
E (and 4 more with settings.verbosity >= verbose)
tests/pyspark/test_schemas_on_pyspark_pandas.py:344: IndexError
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From: Niels Bantilan @.> Date: Sunday, October 22, 2023 at 1:54 AM To: unionai-oss/pandera @.> Cc: Derin Walters @.>, Mention @.> Subject: Re: [unionai-oss/pandera] pytest failing on fastapi and pyspark tests on master (Issue #1279)
thanks @derinwaltershttps://github.com/derinwalters can you copy-paste your env's pip freeze here? just wanted to see if I can repro
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