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phofl opened this issue Jan 4, 2022 · 14 comments
Closed

CI: Numpy 1.22 caused CI to fail #45182

phofl opened this issue Jan 4, 2022 · 14 comments
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CI Continuous Integration Dependencies Required and optional dependencies numba numba-accelerated operations Typing type annotations, mypy/pyright type checking

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@phofl
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phofl commented Jan 4, 2022

The test

FAILED pandas/tests/frame/test_ufunc.py::test_alignment_deprecation_many_inputs

is failing.

Also we have some typing problems

Performing static analysis using mypy
pandas/core/internals/ops.py:130: error: Unused "type: ignore" comment
pandas/core/dtypes/common.py:539: error: Unused "type: ignore" comment
pandas/core/dtypes/cast.py:1127: error: Unused "type: ignore" comment
pandas/core/dtypes/cast.py:1149: error: Unused "type: ignore" comment
pandas/core/missing.py:337: error: Argument 1 to "apply_along_axis" has incompatible type "Callable[[ndarray[Any, Any]], None]"; expected "Callable[..., Union[_SupportsArray[dtype[<nothing>]], Sequence[_SupportsArray[dtype[<nothing>]]], Sequence[Sequence[_SupportsArray[dtype[<nothing>]]]], Sequence[Sequence[Sequence[_SupportsArray[dtype[<nothing>]]]]], Sequence[Sequence[Sequence[Sequence[_SupportsArray[dtype[<nothing>]]]]]]]]"  [arg-type]
pandas/core/missing.py:776: error: Argument 1 to "apply_along_axis" has incompatible type "partial[None]"; expected "Callable[..., Union[_SupportsArray[dtype[<nothing>]], Sequence[_SupportsArray[dtype[<nothing>]]], Sequence[Sequence[_SupportsArray[dtype[<nothing>]]]], Sequence[Sequence[Sequence[_SupportsArray[dtype[<nothing>]]]]], Sequence[Sequence[Sequence[Sequence[_SupportsArray[dtype[<nothing>]]]]]]]]"  [arg-type]
pandas/core/missing.py:776: note: "partial[None].__call__" has type "Callable[[VarArg(Any), KwArg(Any)], None]"
pandas/core/missing.py:782: error: Argument 2 to "apply_along_axis" has incompatible type "Union[str, int]"; expected "SupportsIndex"  [arg-type]
pandas/core/arraylike.py:271: error: Unused "type: ignore" comment
pandas/core/algorithms.py:772: error: Argument 2 to "append" has incompatible type "List[Union[str, float, Period, Timestamp, Timedelta, Any]]"; expected "Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]"  [arg-type]
pandas/core/algorithms.py:1071: error: Argument 1 to "__call__" of "_UFunc_Nin1_Nout1" has incompatible type "Optional[ndarray[Any, dtype[bool_]]]"; expected "Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]"  [arg-type]
pandas/core/strings/accessor.py:585: error: Incompatible types in assignment (expression has type "ndarray[Any, dtype[Any]]", variable has type "Series")  [assignment]
pandas/core/indexes/base.py:611: error: Unused "type: ignore" comment
pandas/core/indexes/base.py:4527: error: Argument 3 to "putmask" has incompatible type "Union[ExtensionArray, ndarray[Any, Any]]"; expected "Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]"  [arg-type]
pandas/core/indexes/base.py:5029: error: Item "ExtensionArray" of "Union[ExtensionArray, ndarray[Any, Any]]" has no attribute "_ndarray"  [union-attr]
pandas/core/indexes/base.py:5029: error: Item "ndarray[Any, Any]" of "Union[ExtensionArray, ndarray[Any, Any]]" has no attribute "_ndarray"  [union-attr]
pandas/core/indexes/base.py:6520: error: Incompatible types in assignment (expression has type "ExtensionArray", variable has type "ndarray[Any, dtype[Any]]")  [assignment]
pandas/core/indexes/base.py:6571: error: No overload variant of "insert" matches argument types "ndarray[Any, Any]", "int", "None"  [call-overload]
pandas/core/indexes/base.py:6571: note: Possible overload variants:
pandas/core/indexes/base.py:6571: note:     def [_SCT <: generic] insert(arr: Union[_SupportsArray[dtype[_SCT]], Sequence[_SupportsArray[dtype[_SCT]]], Sequence[Sequence[_SupportsArray[dtype[_SCT]]]], Sequence[Sequence[Sequence[_SupportsArray[dtype[_SCT]]]]], Sequence[Sequence[Sequence[Sequence[_SupportsArray[dtype[_SCT]]]]]]], obj: Union[slice, Union[_SupportsArray[dtype[Union[bool_, integer[Any]]]], _NestedSequence[_SupportsArray[dtype[Union[bool_, integer[Any]]]]], bool, int, _NestedSequence[Union[bool, int]]]], values: Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]], axis: Optional[SupportsIndex] = ...) -> ndarray[Any, dtype[_SCT]]
pandas/core/indexes/base.py:6571: note:     def insert(arr: Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]], obj: Union[slice, Union[_SupportsArray[dtype[Union[bool_, integer[Any]]]], _NestedSequence[_SupportsArray[dtype[Union[bool_, integer[Any]]]]], bool, int, _NestedSequence[Union[bool, int]]]], values: Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]], axis: Optional[SupportsIndex] = ...) -> ndarray[Any, dtype[Any]]
pandas/core/arrays/masked.py:770: error: Need type annotation for "npvalues"  [var-annotated]
pandas/core/arrays/masked.py:946: error: Argument 3 to "putmask" has incompatible type "object"; expected "Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]"  [arg-type]
pandas/core/arrays/masked.py:1022: error: Argument 3 to "putmask" has incompatible type "object"; expected "Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]"  [arg-type]
pandas/core/arrays/interval.py:1642: error: Argument 1 to "in1d" has incompatible type "Union[ExtensionArray, ndarray[Any, Any], ndarray[Any, dtype[Any]]]"; expected "Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]"  [arg-type]
pandas/core/arrays/sparse/array.py:775: error: Need type annotation for "new_values"  [var-annotated]
pandas/core/arrays/sparse/array.py:927: error: Invalid index type "Tuple[Union[int, ellipsis], ...]" for "ndarray[Any, Any]"; expected type "Union[SupportsIndex, _SupportsArray[dtype[Union[bool_, integer[Any]]]], _NestedSequence[_SupportsArray[dtype[Union[bool_, integer[Any]]]]], _NestedSequence[Union[bool, int]], Tuple[Union[SupportsIndex, _SupportsArray[dtype[Union[bool_, integer[Any]]]], _NestedSequence[_SupportsArray[dtype[Union[bool_, integer[Any]]]]], _NestedSequence[Union[bool, int]]], ...]]"  [index]
pandas/core/arrays/sparse/array.py:1167: error: Argument 2 to "IntIndex" has incompatible type "ndarray[Any, dtype[signedinteger[_32Bit]]]"; expected "Sequence[int]"  [arg-type]
pandas/core/arrays/sparse/array.py:1345: error: Need type annotation for "sparse_values"  [var-annotated]
pandas/core/indexes/multi.py:368: error: Incompatible types in assignment (expression has type "ndarray[Any, dtype[Any]]", variable has type "List[Any]")  [assignment]
pandas/core/indexes/multi.py:1091: error: Argument 1 to "concatenate" has incompatible type "List[object]"; expected "Union[_SupportsArray[dtype[<nothing>]], Sequence[_SupportsArray[dtype[<nothing>]]], Sequence[Sequence[_SupportsArray[dtype[<nothing>]]]], Sequence[Sequence[Sequence[_SupportsArray[dtype[<nothing>]]]]], Sequence[Sequence[Sequence[Sequence[_SupportsArray[dtype[<nothing>]]]]]]]"  [arg-type]
pandas/core/indexes/multi.py:1569: error: Argument 1 to "lexsort" has incompatible type "List[Union[ExtensionArray, ndarray[Any, Any]]]"; expected "Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]"  [arg-type]
pandas/core/indexing.py:2018: error: Incompatible types in assignment (expression has type "ndarray[Any, dtype[signedinteger[Any]]]", variable has type "List[Any]")  [assignment]
pandas/core/indexing.py:2080: error: Incompatible types in assignment (expression has type "ndarray[Any, dtype[Any]]", variable has type "Series")  [assignment]
pandas/io/stata.py:602: error: Value of type variable "_IntType" of "iinfo" cannot be "object"  [type-var]
pandas/io/stata.py:685: error: Need type annotation for "off"  [var-annotated]
pandas/io/stata.py:687: error: Need type annotation for "val"  [var-annotated]
pandas/io/stata.py:1698: error: Incompatible types in assignment (expression has type "DataFrame", variable has type "ndarray[Any, dtype[Any]]")  [assignment]
pandas/io/stata.py:1700: error: Incompatible types in assignment (expression has type "DataFrame", variable has type "ndarray[Any, dtype[Any]]")  [assignment]
pandas/io/stata.py:1701: error: "ndarray[Any, dtype[Any]]" has no attribute "columns"  [attr-defined]
pandas/io/stata.py:1707: error: "ndarray[Any, dtype[Any]]" has no attribute "index"  [attr-defined]
pandas/io/stata.py:1711: error: Incompatible types in assignment (expression has type "DataFrame", variable has type "ndarray[Any, dtype[Any]]")  [assignment]
pandas/io/stata.py:1711: error: Argument 1 to "_do_select_columns" of "StataReader" has incompatible type "ndarray[Any, dtype[Any]]"; expected "DataFrame"  [arg-type]
pandas/io/stata.py:1721: error: Incompatible types in assignment (expression has type "DataFrame", variable has type "ndarray[Any, dtype[Any]]")  [assignment]
pandas/io/stata.py:1721: error: Argument 1 to "_insert_strls" of "StataReader" has incompatible type "ndarray[Any, dtype[Any]]"; expected "DataFrame"  [arg-type]
pandas/io/stata.py:1725: error: "ndarray[Any, dtype[Any]]" has no attribute "index"  [attr-defined]
pandas/io/stata.py:1730: error: "ndarray[Any, dtype[Any]]" has no attribute "columns"  [attr-defined]
pandas/io/stata.py:1740: error: Incompatible types in assignment (expression has type "DataFrame", variable has type "ndarray[Any, dtype[Any]]")  [assignment]
pandas/io/stata.py:1743: error: Incompatible types in assignment (expression has type "DataFrame", variable has type "ndarray[Any, dtype[Any]]")  [assignment]
pandas/io/stata.py:1743: error: Argument 1 to "_do_convert_missing" of "StataReader" has incompatible type "ndarray[Any, dtype[Any]]"; expected "DataFrame"  [arg-type]
pandas/io/stata.py:1752: error: "ndarray[Any, dtype[Any]]" has no attribute "columns"  [attr-defined]
pandas/io/stata.py:1762: error: Incompatible types in assignment (expression has type "DataFrame", variable has type "ndarray[Any, dtype[Any]]")  [assignment]
pandas/io/stata.py:1763: error: Argument 1 to "_do_convert_categoricals" of "StataReader" has incompatible type "ndarray[Any, dtype[Any]]"; expected "DataFrame"  [arg-type]
pandas/io/stata.py:1783: error: Incompatible types in assignment (expression has type "DataFrame", variable has type "ndarray[Any, dtype[Any]]")  [assignment]
pandas/io/stata.py:1786: error: "ndarray[Any, dtype[Any]]" has no attribute "set_index"  [attr-defined]
pandas/io/stata.py:1786: error: "ndarray[Any, dtype[Any]]" has no attribute "pop"  [attr-defined]
pandas/io/stata.py:1788: error: Incompatible return value type (got "ndarray[Any, dtype[Any]]", expected "DataFrame")  [return-value]
pandas/io/parsers/c_parser_wrapper.py:385: error: Unused "type: ignore" comment
pandas/io/parsers/c_parser_wrapper.py:402: error: Argument 1 to "concatenate" has incompatible type "List[Union[ExtensionArray, ndarray[Any, Any]]]"; expected "Union[_SupportsArray[dtype[Any]], Sequence[_SupportsArray[dtype[Any]]], Sequence[Sequence[_SupportsArray[dtype[Any]]]], Sequence[Sequence[Sequence[_SupportsArray[dtype[Any]]]]], Sequence[Sequence[Sequence[Sequence[_SupportsArray[dtype[Any]]]]]]]"  [arg-type]
pandas/core/series.py:1983: error: Argument "minlength" to "bincount" has incompatible type "Optional[int]"; expected "SupportsIndex"  [arg-type]
pandas/core/generic.py:6983: error: Incompatible types in assignment (expression has type "Index", variable has type "ndarray[Any, dtype[signedinteger[Any]]]")  [assignment]
pandas/core/frame.py:2431: error: Argument 1 to "append" of "list" has incompatible type "Union[type, dtype[Any], str]"; expected "dtype[_SCT]"  [arg-type]
pandas/core/window/rolling.py:359: error: Unused "type: ignore" comment
pandas/core/reshape/reshape.py:1028: error: Incompatible types in assignment (expression has type "ndarray[Any, dtype[signedinteger[Any]]]", variable has type "Index")  [assignment]
pandas/core/reshape/reshape.py:1038: error: Incompatible types in assignment (expression has type "ndarray[Any, dtype[Any]]", variable has type "Index")  [assignment]
pandas/core/reshape/melt.py:136: error: Incompatible types in assignment (expression has type "ndarray[Any, dtype[Any]]", variable has type "Series")  [assignment]
pandas/core/internals/managers.py:1094: error: No overload variant of "__getitem__" of "tuple" matches argument type "ndarray[Any, dtype[signedinteger[Any]]]"  [call-overload]
pandas/core/internals/managers.py:1094: note: Possible overload variants:
pandas/core/internals/managers.py:1094: note:     def __getitem__(self, int) -> Block
pandas/core/internals/managers.py:1094: note:     def __getitem__(self, slice) -> Tuple[Block, ...]
pandas/core/internals/managers.py:1103: error: Argument "blkno" to "_iset_single" of "BlockManager" has incompatible type "ndarray[Any, dtype[signedinteger[Any]]]"; expected "int"  [arg-type]
pandas/core/internals/managers.py:1130: error: Incompatible types in assignment (expression has type "int", variable has type "ndarray[Any, dtype[signedinteger[Any]]]")  [assignment]
pandas/core/internals/managers.py:1131: error: No overload variant of "__getitem__" of "tuple" matches argument type "ndarray[Any, dtype[signedinteger[Any]]]"  [call-overload]
pandas/core/internals/managers.py:1131: note: Possible overload variants:
pandas/core/internals/managers.py:1131: note:     def __getitem__(self, int) -> Block
pandas/core/internals/managers.py:1131: note:     def __getitem__(self, slice) -> Tuple[Block, ...]
pandas/core/internals/managers.py:1156: error: Non-overlapping container check (element type: "int", container item type: "ndarray[Any, dtype[signedinteger[Any]]]")  [comparison-overlap]
pandas/core/internals/blocks.py:376: error: Argument 1 to "delete" has incompatible type "Union[ndarray[Any, Any], ExtensionArray]"; expected "Union[_SupportsArray[dtype[Any]], Sequence[_SupportsArray[dtype[Any]]], Sequence[Sequence[_SupportsArray[dtype[Any]]]], Sequence[Sequence[Sequence[_SupportsArray[dtype[Any]]]]], Sequence[Sequence[Sequence[Sequence[_SupportsArray[dtype[Any]]]]]]]"  [arg-type]
pandas/core/internals/array_manager.py:1206: error: Need type annotation for "array"  [var-annotated]
pandas/core/groupby/ops.py:163: error: Unused "type: ignore" comment
pandas/core/groupby/ops.py:813: error: Incompatible types in assignment (expression has type "List[<nothing>]", variable has type "ndarray[Any, dtype[signedinteger[Any]]]")  [assignment]
pandas/io/sas/sas7bdat.py:802: error: Incompatible types in assignment (expression has type "Series", target has type "ndarray[Any, dtype[Any]]")  [assignment]
pandas/io/sas/sas7bdat.py:805: error: Incompatible types in assignment (expression has type "Series", target has type "ndarray[Any, dtype[Any]]")  [assignment]
pandas/io/sas/sas7bdat.py:805: error: Argument 1 to "_convert_datetimes" has incompatible type "ndarray[Any, dtype[Any]]"; expected "Series"  [arg-type]
pandas/io/sas/sas7bdat.py:807: error: Incompatible types in assignment (expression has type "Series", target has type "ndarray[Any, dtype[Any]]")  [assignment]
pandas/io/sas/sas7bdat.py:807: error: Argument 1 to "_convert_datetimes" has incompatible type "ndarray[Any, dtype[Any]]"; expected "Series"  [arg-type]
pandas/io/sas/sas7bdat.py:810: error: Incompatible types in assignment (expression has type "Series", target has type "ndarray[Any, dtype[Any]]")  [assignment]
pandas/io/sas/sas7bdat.py:812: error: "ndarray[Any, dtype[Any]]" has no attribute "str"  [attr-defined]
pandas/io/sas/sas7bdat.py:816: error: "ndarray[Any, dtype[Any]]" has no attribute "str"  [attr-defined]
pandas/tests/extension/date/array.py:112: error: "object_" object is not iterable  [misc]
Found 80 errors in 27 files (checked 1340 source files)
@phofl phofl added CI Continuous Integration Dependencies Required and optional dependencies Typing type annotations, mypy/pyright type checking labels Jan 4, 2022
@lithomas1 lithomas1 added the numba numba-accelerated operations label Jan 4, 2022
@jreback jreback added this to the 1.4 milestone Jan 4, 2022
@jreback jreback added the Blocker Blocking issue or pull request for an upcoming release label Jan 4, 2022
@seberg
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seberg commented Jan 4, 2022

In the other PR/issue, this:

E numpy.core._exceptions._UFuncNoLoopError: ufunc 'my_ufunc' did not contain a loop with signature matching types (<class 'numpy.dtype[int64]'>, <class 'numpy.dtype[int64]'>, <class 'numpy.dtype[int64]'>) -> None

was said to be the only "real" issue (not typing related). I think this is a duplicate of numpy/numpy#20699 (comment) probably, I will look into it (I guess there may be non-nativ byte-order involved, although maybe not necessarily always)

@attack68
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attack68 commented Jan 4, 2022

fyi: dev-requirements.txt issues numba>=0.50.1, which resolves to the latest version: 0.54.1, which has the specific dependency of numpy<1.21.0, so any package resolver should yield numpy==1.20.3 for the dev environment, which doesn't run mypy without failures. I, at least, need numpy==1.21.0 to get mypy success on all files.

@padrepitufo
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not sure why but versions of numpy below 1.22 are causing whitesource security vulnerabilities triggers to go off per https://www.whitesourcesoftware.com/vulnerability-database/CVE-2021-41496 . It would seem that 1.21.5 would solve it as the fix (numpy/numpy@16f7824) shows it's present in 1.21.5

@seberg
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seberg commented Jan 5, 2022

@padrepitufo we have been getting nonsense CVEs for NumPy, this is one of them. I am pretty disappointed by these CVEs appearing out of no-where and being assigned ridiculous severity levels.

@phofl
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phofl commented Jan 6, 2022

I‘ll prepare a pr adressing the typing issues

@phofl phofl self-assigned this Jan 6, 2022
@rhshadrach
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rhshadrach commented Jan 15, 2022

For the NumPy issue, not sure if this will be fixed by numpy/numpy#20735

@seberg
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seberg commented Jan 15, 2022

@rhshadrach there was just a new numpy release that includes a fix for some reductions (reducelikes) failing with a weird type resolution error. I would hope that fixes the issue here.
The issue you linked to is very specific to numba's dynamic ufuncs, pandas should not care about it.

Please make sure to ping me if pandas still has any problems with the 1.22.1 release!

@rhshadrach
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Thanks @seberg - I am still seeing this with 1.22.1. Here is the test that's failing:

@vectorize([float64(float64, float64, float64)])
def my_ufunc(x, y, z):
return x + y + z
df1 = pd.DataFrame({"a": [1, 2, 3], "b": [4, 5, 6]})
df2 = pd.DataFrame({"b": [1, 2, 3], "c": [4, 5, 6]})
df3 = pd.DataFrame({"a": [1, 2, 3], "c": [4, 5, 6]})
with tm.assert_produces_warning(FutureWarning):
result = my_ufunc(df1, df2, df3)

and the error message I'm seeing is

numpy.core._exceptions.UFuncTypeError: ufunc 'my_ufunc' did not contain a loop with signature matching types (<class 'numpy.dtype[int64]'>, <class 'numpy.dtype[int64]'>, <class 'numpy.dtype[int64]'>) -> None

on

>>> import numpy as np; np.__version__
'1.22.1'

@rhshadrach
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I was previously running with numba 0.53.0; updating to 0.55.0 I'm no longer seeing a failure.

@seberg
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seberg commented Jan 15, 2022

Numba was broken for a long time for NumPy 1.21+ (they rely on the Python calling convention not changing, but Python optimized things by changing the calling convention, and I used that in NumPy 💥).

So I expect if you were on old numba, it is just a numba bug. If you use a dynamic numba vectorization (the types are not specified ahead of time), then there is still a problem on 1.22.1. I am planning to fix it soon, but do not feel like rushing it considering that Numba support for NumPy 1.21.x support took 3 months or so.

@simonjayhawkins
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moving to 1.4.1 and removing blocker label

@simonjayhawkins simonjayhawkins modified the milestones: 1.4, 1.4.1 Jan 21, 2022
@simonjayhawkins simonjayhawkins removed the Blocker Blocking issue or pull request for an upcoming release label Jan 21, 2022
@rhshadrach
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rhshadrach commented Jan 22, 2022

Not sure what the right course of action here is - would we want to bump the minimum version of Numba? It would need to be bumped to a recent version, which seems undesirable. We could always just document this somewhere - a warning in the whatsnew as well as in the Numba section of the docs.

@phofl phofl removed their assignment Jan 27, 2022
@simonjayhawkins simonjayhawkins modified the milestones: 1.4.1, 1.4.2 Feb 11, 2022
@simonjayhawkins simonjayhawkins removed this from the 1.4.2 milestone Apr 1, 2022
@simonjayhawkins simonjayhawkins added this to the 1.4.3 milestone Apr 1, 2022
@simonjayhawkins
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removing milestone.

@simonjayhawkins simonjayhawkins removed this from the 1.4.3 milestone Jun 22, 2022
@mroeschke
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Looks like these have been addressed so closing

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