Updated the python dependencies (targeted for Beam 2.63.0)

[liferoad]

Fixes #33639.

Following https://cwiki.apache.org/confluence/display/BEAM/Python+Tips#PythonTips-HowtoupdatedependenciesthatareinstalledinPythoncontainerimages:

./gradlew :sdks:python:container:generatePythonRequirementsAll

and https://cwiki.apache.org/confluence/display/BEAM/Python+Tips#PythonTips-InstallingPythoninterpreters, updated the base image deps.

Some notable package updates:

• numpy==2.0.2 and pandas==2.2.3 for Python 3.9 (note numpy >=2.1 does not support py39)
• numpy==2.2.1 and pandas==2.2.3 for Python 3.10, 3.11, and 3.12
• protobuf==5.29.3 for all Python versions

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[liferoad]

For :sdks:python:test-suites:tox:py312:testPython312:

apache_beam/dataframe/pandas_doctests_test.py:1073: AssertionError |  
  | ----------------------------- Captured stdout call ----------------------------- |  
  | ********************************************************************** |  
  | File "array", line 94, in array |  
  | Failed example: |  
  | pd.array(['a', 'b'], dtype=str) |  
  | Expected: |  
  | <NumpyExtensionArray> |  
  | ['a', 'b'] |  
  | Length: 2, dtype: str32 |  
  | Got: |  
  | <NumpyExtensionArray> |  
  | [np.str_('a'), np.str_('b')] |  
  | Length: 2, dtype: str32 |  
  | ********************************************************************** |  
  | File "array", line 103, in array |  
  | Failed example: |  
  | pd.array(['a', 'b'], dtype=np.dtype("<U1")) |  
  | Expected: |  
  | <NumpyExtensionArray> |  
  | ['a', 'b'] |  
  | Length: 2, dtype: str32 |  
  | Got: |  
  | <NumpyExtensionArray> |  
  | [np.str_('a'), np.str_('b')] |  
  | Length: 2, dtype: str32 |  
  | ********************************************************************** |  
  | File "array", line 182, in array |  
  | Failed example: |  
  | pd.array([1 + 1j, 3 + 2j]) |  
  | Expected: |  
  | <NumpyExtensionArray> |  
  | [(1+1j), (3+2j)] |  
  | Length: 2, dtype: complex128 |  
  | Got: |  
  | <NumpyExtensionArray> |  
  | [np.complex128(1+1j), np.complex128(3+2j)] |  
  | Length: 2, dtype: complex128 |  
  | ********************************************************************** |  
  | File "array", line 193, in array |  
  | Failed example: |  
  | pd.array([1, 2], dtype=np.dtype("int32")) |  
  | Expected: |  
  | <NumpyExtensionArray> |  
  | [1, 2] |  
  | Length: 2, dtype: int32 |  
  | Got: |  
  | <NumpyExtensionArray> |  
  | [np.int32(1), np.int32(2)] |  
  | Length: 2, dtype: int32 |  
  | ********************************************************************** |  
  | 1 items had failures: |  
  | 4 of  16 in array |  
  | ***Test Failed*** 4 failures. |  
 

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[tvalentyn]

For :sdks:python:test-suites:tox:py312:testPython312:

I see that all tests are passing - is it still an issue?

I might be risky to make this change in 2.63.0 given that we won't have much time to test the changes before the release train starts, hence, higher risk of upgrade issues in 2.63.0; i would target this for 2.64.0

[liferoad]

For :sdks:python:test-suites:tox:py312:testPython312:

I see that all tests are passing - is it still an issue?

I might be risky to make this change in 2.63.0 given that we won't have much time to test the changes before the release train starts, hence, higher risk of upgrade issues in 2.63.0; i would target this for 2.64.0

:sdks:python:test-suites:tox:py312:testPython312: flaky for some dataframe tests. Fine for now

I think it is not risky since we do not directly depend on pandas and numpy and the critical probuf version is already upgraded to 5.x with 813ef7c 3 weeks ago.

[tvalentyn]

LGTM

[liferoad]

#33697 is opened to track the flaky doctest issue.

[jrmccluskey]

LGTM, as discussed offline hopefully we'll find a better way to keep these in sync with dependabot PRs moving forward

[Abacn]

numpy 2 still fails a test, see #33774 (comment)