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Update to Python 3.12.x (#5736) #5951

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Commits on Nov 7, 2024

  1. Configuration menu
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  2. Disable FIPS mode in Docker container during apt-get update

    Resolves error with libgcrypt on bookworm:
    Fatal error in libgcrypt, requested algo not in md context
    dsotirho-ucsc committed Nov 7, 2024
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  3. Add FIXME (#6675)

    dsotirho-ucsc committed Nov 7, 2024
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  5. [R] Add setuptools as a requirement

    Fulfills transitive requirement of distutils, which Python 3.12 removed from the standard library
    dsotirho-ucsc committed Nov 7, 2024
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  6. [R] Update azul-chalice to 1.31.2+13

    For Python 3.12 support
    dsotirho-ucsc committed Nov 7, 2024
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  7. [R] Update jq package

    Resolves error during `make requirements`:
    
      × Building wheel for jq (pyproject.toml) did not run successfully.
      │ exit code: 1
      ╰─> [1390 lines of output]
          running bdist_wheel
          running build
          running build_ext
    ...
          jq.c:12124:55: error: no member named 'ob_digit' in 'struct _longobject'
                      const digit* digits = ((PyLongObject*)x)->ob_digit;
                                            ~~~~~~~~~~~~~~~~~~  ^
          jq.c:13608:47: error: no member named 'ob_digit' in 'struct _longobject'
              const digit* digits = ((PyLongObject*)b)->ob_digit;
                                    ~~~~~~~~~~~~~~~~~~  ^
          41 warnings and 7 errors generated.
          error: command '/usr/bin/clang' failed with exit code 1
          [end of output]
    
      note: This error originates from a subprocess, and is likely not a problem with pip.
      ERROR: Failed building wheel for jq
    dsotirho-ucsc committed Nov 7, 2024
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  8. [R] Update flake8 package

    Resolves errors originating from flake8 failing to parse f-strings under Python 3.12
    
    E122 continuation line missing indentation or outdented
    E131 continuation line unaligned for hanging indent
    E202 whitespace before ')'
    E202 whitespace before ']'
    E202 whitespace before '}'
    E203 whitespace before ':'
    E221 multiple spaces before operator
    E222 multiple spaces after operator
    E225 missing whitespace around operator
    E231 missing whitespace after ','
    E231 missing whitespace after ':'
    E231 missing whitespace after ';'
    E271 multiple spaces after keyword
    E272 multiple spaces before keyword
    E702 multiple statements on one line (semicolon)
    E713 test for membership should be 'not in'
    W604 backticks are deprecated, use 'repr()'
    dsotirho-ucsc committed Nov 7, 2024
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  9. [R] Update fastavro package

    Resolves error during `make requirements_update`:
    
    19.11 Building wheels for collected packages: fastavro
    19.11   Building wheel for fastavro (pyproject.toml): started
    36.96   Building wheel for fastavro (pyproject.toml): finished with status 'error'
    36.97   error: subprocess-exited-with-error
    36.97
    36.97   × Building wheel for fastavro (pyproject.toml) did not run successfully.
    36.97   │ exit code: 1
    36.97   ╰─> [73 lines of output]
    36.97       <string>:31: SyntaxWarning: invalid escape sequence '\('
    36.97       running bdist_wheel
    36.97       running build
    …
    36.97       gcc: internal compiler error: Illegal instruction signal terminated program as
    36.97       Please submit a full bug report,
    36.97       with preprocessed source if appropriate.
    36.97       See <file:///usr/share/doc/gcc-10/README.Bugs> for instructions.
    36.97       error: command '/usr/bin/gcc' failed with exit code 4
    36.97       [end of output]
    dsotirho-ucsc committed Nov 7, 2024
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  10. [R] Update openapi-spec-validator to 0.7.1

    Resolves error during test:
    
    ERROR: test_openapi (integration_test.OpenAPIIntegrationTest.test_openapi) (component='service')
    ----------------------------------------------------------------------
    Traceback (most recent call last):
      File "/Users/daniel/repo/azul1/test/integration_test.py", line 1856, in test_openapi
        validate_spec(spec)
      File "/Users/daniel/repo/azul1/.venv/lib/python3.12/site-packages/openapi_spec_validator/shortcuts.py", line 17, in validate_spec
        return validator.validate(spec, spec_url=spec_url)
    ...
    AttributeError: '_io.BufferedReader' object has no attribute 'decode'
    dsotirho-ucsc committed Nov 7, 2024
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  11. Implement referencing.Registry in JSON schema validation

    Resolves DeprecationWarning during schema validation:
    
    Traceback (most recent call last):
      File "/Users/daniel/.pyenv/versions/3.12.6/lib/python3.12/unittest/suite.py", line 306, in _tearDownPreviousClass
        tearDownClass()
    AssertionError: ["{message : DeprecationWarning('Automatically retrieving remote references can be a security vulnerability and is discouraged by the JSON Schema specifications. Relying on this behavior is deprecated and will shortly become an error. If you are sure you want to remotely retrieve your reference and that it is safe to do so, you can find instructions for doing so via referencing.Registry in the referencing documentation (https://referencing.readthedocs.org).'), category : 'DeprecationWarning', filename : '/Users/daniel/repo/azul1/.venv/lib/python3.12/site-packages/jsonschema/exceptions.py', lineno : 475, line : None}", ...]
    dsotirho-ucsc committed Nov 7, 2024
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  12. Remove unassigned type-hinted variable

    Resolves finding during `make pep8`:
    
    F842 local variable 'cs' is annotated but never used
    dsotirho-ucsc committed Nov 7, 2024
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  13. Reformat ternary operation

    Resolves finding during `make pep8`
    
    E122 continuation line missing indentation or outdented
    dsotirho-ucsc committed Nov 7, 2024
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  14. Fix broken assert of Mock object's not_called property

    Resolves error during test:
    
    AttributeError: 'not_called' is not a valid assertion. Use a spec for the mock if 'not_called' is meant to be an attribute.
    dsotirho-ucsc committed Nov 7, 2024
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