add a doctests tolerance

[cxzhong]

Fix #40980 (comment) , add a tolerance in this function.

📝 Checklist

• The title is concise and informative.
• The description explains in detail what this PR is about.
• I have linked a relevant issue or discussion.
• I have created tests covering the changes.
• I have updated the documentation and checked the documentation preview.

⌛ Dependencies

[cxzhong]

But I still do not understand why we have

**********************************************************************
File "src/sage/doctest/util.py", line 846, in sage.doctest.util.inaccuracy_tolerance
Failed example:
    with ensure_interruptible_after(2) as data: interruptible_sleep(1r)
Expected:
    Traceback (most recent call last):
    ...
    RuntimeError: Function terminates early after 1.00... < 2.0000 seconds
Got:
    <BLANKLINE>
    Traceback (most recent call last):
      File "/Users/buildbot-sage/worker/sage_git/build/src/sage/doctest/forker.py", line 734, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/Users/buildbot-sage/worker/sage_git/build/src/sage/doctest/forker.py", line 1158, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.doctest.util.inaccuracy_tolerance[9]>", line 1, in <module>
        with ensure_interruptible_after(Integer(2)) as data: interruptible_sleep(1)
      File "/Users/buildbot-sage/worker/sage_git/build/local/var/lib/sage/venv-python3.12.5/lib/python3.12/contextlib.py", line 144, in __exit__
        next(self.gen)
      File "/Users/buildbot-sage/worker/sage_git/build/src/sage/doctest/util.py", line 904, in ensure_interruptible_after
        raise RuntimeError(f"Function terminates early after {elapsed:.4f} < {seconds:.4f} seconds")
    RuntimeError: Function terminates early after 0.9982 < 2.0000 seconds
**********************************************************************

I am confuesd it is less than 1.

[vbraun]

That appears to be a headscratcher, indeed

My best guess is that there was a ntp time update during the run, which will skew clock_gettime(CLOCK_REALTIME, ...) but not alarm.

We should probably use clock_gettime(CLOCK_MONOTONIC, ...) for measuring time differences, this is (like sleep and alarm) independent of any changes to the clock by ntp or user actions.