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bpo-22486 added math.gcd() and deprecated fractions.gcd() in Python 3.5: commit 48e47aaa28d6dfdae128142ffcbc4b0642422e90.
The function was deprecated during 4 cycles (3.5, 3.6, 3.7, 3.8): I propose attached PR to remove it.

New changeset 4691a2f2a2b8174a6c958ce6976ed5f3354c9504 by Victor Stinner in branch 'master':
bpo-39350: Remove deprecated fractions.gcd() (GH-18021)
https://github.com/python/cpython/commit/4691a2f2a2b8174a6c958ce6976ed5f3354c9504

I believe there is a regression here.
numpy fails to build with Python 3.9.0a3.
________________________ TestMatmul.test_matmul_object _________________________
self = <numpy.core.tests.test_multiarray.TestMatmul object at 0x7ff9bc008ca0>
 def test_matmul_object(self):
 import fractions
 
 f = np.vectorize(fractions.Fraction)
 def random_ints():
 return np.random.randint(1, 1000, size=(10, 3, 3))
> M1 = f(random_ints(), random_ints())
f = <numpy.vectorize object at 0x7ff9bc6751f0>
fractions = <module 'fractions' from '/usr/lib64/python3.9/fractions.py'>
random_ints = <function TestMatmul.test_matmul_object.<locals>.random_ints at 0x7ff9bcc2d700>
self = <numpy.core.tests.test_multiarray.TestMatmul object at 0x7ff9bc008ca0>
numpy/core/tests/test_multiarray.py:6259: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
numpy/lib/function_base.py:2091: in __call__
 return self._vectorize_call(func=func, args=vargs)
numpy/lib/function_base.py:2161: in _vectorize_call
 ufunc, otypes = self._get_ufunc_and_otypes(func=func, args=args)
numpy/lib/function_base.py:2121: in _get_ufunc_and_otypes
 outputs = func(*inputs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
cls = <class 'fractions.Fraction'>, numerator = 483, denominator = 809
 def __new__(cls, numerator=0, denominator=None, *, _normalize=True):
 """Constructs a Rational.
 
 Takes a string like '3/2' or '1.5', another Rational instance, a
 numerator/denominator pair, or a float.
 
 Examples
 --------
 
 >>> Fraction(10, -8)
 Fraction(-5, 4)
 >>> Fraction(Fraction(1, 7), 5)
 Fraction(1, 35)
 >>> Fraction(Fraction(1, 7), Fraction(2, 3))
 Fraction(3, 14)
 >>> Fraction('314')
 Fraction(314, 1)
 >>> Fraction('-35/4')
 Fraction(-35, 4)
 >>> Fraction('3.1415') # conversion from numeric string
 Fraction(6283, 2000)
 >>> Fraction('-47e-2') # string may include a decimal exponent
 Fraction(-47, 100)
 >>> Fraction(1.47) # direct construction from float (exact conversion)
 Fraction(6620291452234629, 4503599627370496)
 >>> Fraction(2.25)
 Fraction(9, 4)
 >>> Fraction(Decimal('1.47'))
 Fraction(147, 100)
 
 """
 self = super(Fraction, cls).__new__(cls)
 
 if denominator is None:
 if type(numerator) is int:
 self._numerator = numerator
 self._denominator = 1
 return self
 
 elif isinstance(numerator, numbers.Rational):
 self._numerator = numerator.numerator
 self._denominator = numerator.denominator
 return self
 
 elif isinstance(numerator, (float, Decimal)):
 # Exact conversion
 self._numerator, self._denominator = numerator.as_integer_ratio()
 return self
 
 elif isinstance(numerator, str):
 # Handle construction from strings.
 m = _RATIONAL_FORMAT.match(numerator)
 if m is None:
 raise ValueError('Invalid literal for Fraction: %r' %
 numerator)
 numerator = int(m.group('num') or '0')
 denom = m.group('denom')
 if denom:
 denominator = int(denom)
 else:
 denominator = 1
 decimal = m.group('decimal')
 if decimal:
 scale = 10**len(decimal)
 numerator = numerator * scale + int(decimal)
 denominator *= scale
 exp = m.group('exp')
 if exp:
 exp = int(exp)
 if exp >= 0:
 numerator *= 10**exp
 else:
 denominator *= 10**-exp
 if m.group('sign') == '-':
 numerator = -numerator
 
 else:
 raise TypeError("argument should be a string "
 "or a Rational instance")
 
 elif type(numerator) is int is type(denominator):
 pass # *very* normal case
 
 elif (isinstance(numerator, numbers.Rational) and
 isinstance(denominator, numbers.Rational)):
 numerator, denominator = (
 numerator.numerator * denominator.denominator,
 denominator.numerator * numerator.denominator
 )
 else:
 raise TypeError("both arguments should be "
 "Rational instances")
 
 if denominator == 0:
 raise ZeroDivisionError('Fraction(%s, 0)' % numerator)
 if _normalize:
 if type(numerator) is int is type(denominator):
 # *very* normal case
 g = math.gcd(numerator, denominator)
 if denominator < 0:
 g = -g
 else:
> g = _gcd(numerator, denominator)
E NameError: name '_gcd' is not defined
__class__ = <class 'fractions.Fraction'>
_normalize = True
cls = <class 'fractions.Fraction'>
denominator = 809
numerator = 483
self = <[AttributeError("_numerator") raised in repr()] Fraction object at 0x7ff9bc6753a0>
/usr/lib64/python3.9/fractions.py:164: NameError
This removed _gcd, but it is still called in:
https://github.com/python/cpython/blob/58a4054760bffbb20aff90290dd0f3554f7bea42/Lib/fractions.py#L164 

Reproducer:
class myint(int):
 def __mul__(self, other):
 return type(self)(int(self)*int(other))
 @property
 def numerator(self):
 return type(self)(super().numerator)
 @property
 def denominator(self):
 return type(self)(super().denominator)
Before:
>>> fractions.Fraction(myint(1), myint(2))
Fraction(1, 2)
After:
>>> fractions.Fraction(myint(1), myint(2))
Traceback (most recent call last):
 File "<stdin>", line 1, in <module>
 File "/usr/lib64/python3.9/fractions.py", line 164, in __new__
 g = _gcd(numerator, denominator)
NameError: name '_gcd' is not defined

The relevant piece of Python code from fractions.py looks like this:
 if type(numerator) is int is type(denominator):
 # *very* normal case
 g = math.gcd(numerator, denominator)
 if denominator < 0:
 g = -g
 else:
 g = _gcd(numerator, denominator)
I wonder whether we should simply drop the type check: math.gcd should accept anything that supports __index__ (and that includes NumPy integer types and anything that implements numbers.Integral).
OTOH, math.gcd will return a plain int, and if we have some subclass myint of int, we might want all the arithmetic to stay in the domain of myints (though I'm not really sure _why_ we'd want that). In that case we'll need to restore the pure Python _gcd implementation.

Naively implementing this code, I'd use isinstance(numerator, int) over type(numerator) is int. Is that strict type check really needed?
I could not find anywhere whether numerator and denominator of numbers.Rational need to be numbers.Integral. I would expect so, however this is not written in the documentation of numbers.Rational. If that's the case, I think checking it for being numbers.Integral and failing hard if not is a reasonable thing to do.

Apologies, I think I moved the discussion off-track. The first order of business should be to fix the regression. We can discuss behaviour changes after that.
I've opened GH-18309 as a quick fix for the regression.

I tried but failed to write a test to mimick numpy.int64 type. I tried to build a type which implements numbers.Rational but don't inherit from int, but there are way too many methods that I have to implement :-(
Morever, installing numpy on a Python 3.9 virtual environment is quite tricky. Lhe latest Cython release (0.29.14) isn't compatible with Python 3.9.
Miro gave me a command to install Cython on Python 3.9:
python -m pip install https://github.com/cython/cython/archive/master.tar.gz --install-option="--no-cython-compile"
But then "pip install numpy" tries to reinstall Cython which fails :-/

I managed to test my PR with numpy:
$ env/bin/python 
>>> import fractions
>>> import numpy
>>> f=fractions.Fraction(numpy.int64(1*3), numpy.int64(2*3))
>>> f
Fraction(1, 2)
>>> type(f.numerator)
<class 'numpy.int64'>
>>> type(f.denominator)
<class 'numpy.int64'>
So it works as expected: numerator and denominator have the expected type, and there is no exception ;-)
I used the following commands to get numpy in a Python 3.9 virtual environment:
./python -m venv env
env/bin/python -m pip install https://github.com/cython/cython/archive/master.tar.gz --install-option="--no-cython-compile"
curl -O https://files.pythonhosted.org/packages/40/de/0ea5092b8bfd2e3aa6fdbb2e499a9f9adf810992884d414defc1573dca3f/numpy-1.18.1.zip
unzip -d . numpy-1.18.1.zip
cd numpy-1.18.1/
../env/bin/python setup.py install

FYI the full numpy test suite pass with PR 18375:
(env) vstinner@apu$ python runtests.py -v
(...)
======================= 9879 passed, 443 skipped, 180 deselected, 17 xfailed, 3 xpassed in 305.17s (0:05:05) =======================

New changeset dc7a50d73a3d16918529669ff7b8783c08cff090 by Victor Stinner in branch 'master':
bpo-39350: Fix fractions for int subclasses (GH-18375)
https://github.com/python/cpython/commit/dc7a50d73a3d16918529669ff7b8783c08cff090

Thanks Miro for the bug report and thanks Mark for the great review and discussion! It should now be fixed. I tested manually that my change fix numpy test suite.