test failures when using numpy==1.17.5

[jvesely]

pnl sets minimum numpy requirements as >=1.17.0, but the test suite fails with 18 errors:

FAILED tests/composition/test_composition.py::TestExecutionOrder::test_exact_time - TypeError: No loop matching the specified signature and casting was found for ufunc gcd
FAILED tests/scheduling/test_condition.py::TestAbsolute::test_TimeInterval_no_dependencies[conditions0-termination_conds0] - TypeError: No loop matching the specified signature and casting was found for ufunc gcd
FAILED tests/scheduling/test_condition.py::TestAbsolute::test_TimeInterval_linear_everynms[conditions4-termination_conds4] - TypeError: No loop matching the specified signature and casting was found for ufunc gcd
FAILED tests/scheduling/test_condition.py::TestAbsolute::test_TimeInterval_no_dependencies[conditions2-termination_conds2] - TypeError: No loop matching the specified signature and casting was found for ufunc gcd
FAILED tests/scheduling/test_condition.py::TestAbsolute::test_TimeInterval_linear_everynms[conditions1-termination_conds1] - TypeError: No loop matching the specified signature and casting was found for ufunc gcd
FAILED tests/scheduling/test_condition.py::TestAbsolute::test_TimeInterval_linear_everynms[conditions2-termination_conds2] - TypeError: No loop matching the specified signature and casting was found for ufunc gcd
FAILED tests/scheduling/test_condition.py::TestAbsolute::test_TimeInterval_linear_everynms[conditions0-termination_conds0] - TypeError: No loop matching the specified signature and casting was found for ufunc gcd
FAILED tests/scheduling/test_condition.py::TestAbsolute::test_TimeInterval_linear_everynms[conditions5-termination_conds5] - TypeError: No loop matching the specified signature and casting was found for ufunc gcd
FAILED tests/scheduling/test_condition.py::TestAbsolute::test_TimeInterval_linear_everynms[conditions3-termination_conds3] - TypeError: No loop matching the specified signature and casting was found for ufunc gcd
FAILED tests/scheduling/test_condition.py::TestAbsolute::test_TimeInterval_linear_everynms[conditions6-termination_conds6] - TypeError: No loop matching the specified signature and casting was found for ufunc gcd
FAILED tests/scheduling/test_scheduler.py::TestAbsoluteTime::test_absolute_interval_linear[conditions3-interval3] - TypeError: No loop matching the specified signature and casting was found for ufunc gcd
FAILED tests/scheduling/test_scheduler.py::TestAbsoluteTime::test_absolute_interval_linear[conditions1-interval1] - TypeError: No loop matching the specified signature and casting was found for ufunc gcd
FAILED tests/scheduling/test_scheduler.py::TestAbsoluteTime::test_absolute_interval_linear[conditions6-interval6] - TypeError: No loop matching the specified signature and casting was found for ufunc gcd
FAILED tests/scheduling/test_scheduler.py::TestAbsoluteTime::test_absolute_interval_linear[conditions0-interval0] - TypeError: No loop matching the specified signature and casting was found for ufunc gcd
FAILED tests/scheduling/test_scheduler.py::TestAbsoluteTime::test_absolute_interval_linear[conditions7-interval7] - TypeError: No loop matching the specified signature and casting was found for ufunc gcd
FAILED tests/scheduling/test_scheduler.py::TestAbsoluteTime::test_absolute_interval_linear[conditions5-interval5] - TypeError: No loop matching the specified signature and casting was found for ufunc gcd
FAILED tests/scheduling/test_scheduler.py::TestAbsoluteTime::test_absolute_interval_linear[conditions4-interval4] - TypeError: No loop matching the specified signature and casting was found for ufunc gcd
FAILED tests/scheduling/test_scheduler.py::TestAbsoluteTime::test_absolute_interval_linear[conditions2-interval2] - TypeError: No loop matching the specified signature and casting was found for ufunc gcd

the backtrace is similar:

_______________________ TestAbsoluteTime.test_absolute_interval_linear[conditions2-interval2] ________________________
[gw4] linux -- Python 3.8.10 /common/home/jv356/py38-venv/bin/python3

self = <test_scheduler.TestAbsoluteTime object at 0x7fd51e35f6a0>
three_node_linear_composition = ([(TransferMechanism A), (TransferMechanism B), (TransferMechanism C)], (Composition Composition-0))
conditions = {'A': <psyneulink.core.scheduling.condition.Any object at 0x7fd51e3cd820>}
interval = <Quantity(1/3, 'millisecond')>

    @pytest.mark.parametrize(
        'conditions, interval',
        [
            ({'A': TimeInterval(repeat=8), 'B': TimeInterval(repeat=4)}, fractions.Fraction(4, 3) * _unit_registry.ms),
            ({'A': TimeInterval(repeat=1), 'B': TimeInterval(repeat=3)}, fractions.Fraction(1, 3) * _unit_registry.ms),
            ({'A': Any(TimeInterval(repeat=2), TimeInterval(repeat=3))}, fractions.Fraction(1, 3) * _unit_registry.ms),
            ({'A': TimeInterval(repeat=6), 'B': TimeInterval(repeat=3)}, 1 * _unit_registry.ms),
            ({'A': TimeInterval(repeat=100 * _unit_registry.us), 'B': TimeInterval(repeat=2)}, fractions.Fraction(100, 3) * _unit_registry.us),
            ({'A': Any(TimeInterval(repeat=1000 * _unit_registry.us), TimeInterval(repeat=2))}, fractions.Fraction(1, 3) * _unit_registry.ms),
            ({'A': TimeInterval(repeat=1000 * _unit_registry.us), 'B': TimeInterval(repeat=2)}, fractions.Fraction(1, 3) * _unit_registry.ms),
            ({'A': Any(TimeInterval(repeat=1000), TimeInterval(repeat=1500)), 'B': TimeInterval(repeat=2000)}, fractions.Fraction(500, 3) * _unit_registry.ms),
        ]
    )
    def test_absolute_interval_linear(self, three_node_linear_composition, conditions, interval):
        [A, B, C], comp = three_node_linear_composition
    
        for node in conditions:
            comp.scheduler.add_condition(eval(node), conditions[node])
    
>       assert comp.scheduler._get_absolute_consideration_set_execution_unit() == interval

tests/scheduling/test_scheduler.py:1690: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <psyneulink.core.scheduling.scheduler.Scheduler object at 0x7fd51d08a100>
termination_conds = {<TimeScale.ENVIRONMENT_STATE_UPDATE: 2>: <psyneulink.core.scheduling.condition.AllHaveRun object at 0x7fd51d08a1c0>, <TimeScale.ENVIRONMENT_SEQUENCE: 3>: <psyneulink.core.scheduling.condition.Never object at 0x7fd51d08af40>}

    def _get_absolute_consideration_set_execution_unit(self, termination_conds=None):
        """Computes the time length of the gap between two consideration set executions
        """
        if termination_conds is None:
            termination_conds = self.termination_conds
    
        # all of the units of time that must occur on a consideration set execution
        intervals = []
        for c in self.get_absolute_conditions(termination_conds).values():
            intervals.extend(c.absolute_intervals)
            if self.mode is SchedulingMode.EXACT_TIME:
                intervals.extend(c.absolute_fixed_points)
    
        if len(intervals) == 0:
            return self.default_absolute_time_unit
        else:
            min_time_unit = min(intervals, key=lambda x: x.u).u
    
            # convert all intervals into the same unit
            for i, a in enumerate(intervals):
                unit_conversion = round(np.log10((1 * a.u).to(min_time_unit).m))
                intervals[i] = (int(a.m) * 10 ** unit_conversion) * min_time_unit
    
            # numerator is the largest possible length of a pass
            # denominator evenly divides this length by number of consideration set executions
>           numerator = np.gcd.reduce([interval.m for interval in intervals])
E           TypeError: No loop matching the specified signature and casting was found for ufunc gcd

../py38-venv/lib/python3.8/site-packages/graph_scheduler/scheduler.py:874: TypeError

[jvesely]

This is mostly for documentation purposes, I think we should bump minimum requirements until the tests pass.

[jvesely]

same failures with 1.18.5

[jvesely]

tests pass with numpy==1.19.5

[jvesely]

numpy==1.19.0 pass

[jvesely]

this was addressed in c1592c1