Improve performance and adapt existing bechmarks to SimPhoNy v4

[kysrpex]

• Introduced lru_cache_weak and lru_cache_timestamp decorators. Introduced the take method to take a limited number of items from an iterator.

• Applied such decorators to methods from OntologyEntity and OntologyClass in order to achieve faster performance while keeping the cache coherent when changes are done to a Session's graph.

Something similar was being done already on SimPhoNy v3, but this time the solution, even though it is quite similar, seems to be more effective.

• Adapt existing benchmarks to SimPhoNy v4.

• Fix performance on various other places so that it is on par with SimPhoNy v3.

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The performance was evaluated using the following code snippets.

SimPhoNy v4

from simphony_osp.namespaces import mechanical as mt
from simphony_osp.namespaces import math, metrology
from simphony_osp.namespaces import properties as prop
from time import time
from tqdm import tqdm

n = (333636 // 3)

start = time()
for i in tqdm(range(0, n)):
    bending_stiffness_average_value = 0.0312  # some numerical value
    cableSystem = mt.CableBundle()
    bendingStiffness_average = mt.BendingStiffness()
    realNumber = math.Real(hasNumericalData=bending_stiffness_average_value)
    bendingStiffness_average.connect(realNumber, rel=metrology.hasQuantityValue)
    cableSystem.connect(bendingStiffness_average, rel=prop.hasProperty)
end = time()
print("time %.2f" % (end - start))

SimPhoNy v3

from osp.core.namespaces import mechanical as mt
from osp.core.namespaces import math, metrology
from osp.core.namespaces import properties as prop
from time import time
from tqdm import tqdm

n = (333636 // 3)

start = time()
for i in tqdm(range(0, n)):
    bending_stiffness_average_value = 0.0312  # some numerical value
    cableSystem = mt.CableBundle()
    bendingStiffness_average = mt.BendingStiffness()
    realNumber = math.Real(hasNumericalData=bending_stiffness_average_value)
    bendingStiffness_average.add(realNumber, rel=metrology.hasQuantityValue)
    cableSystem.add(bendingStiffness_average, rel=prop.hasProperty)
end = time()
print("time %.2f" % (end - start))

Estimation given by tqdm for each case:

• SimPhoNy v4 without fix: 511/111212 [00:07<26:53, 68.62it/s]
• SimPhoNy v4 with fix: 5308/111212 [00:07<02:25, 728.48it/s]
• SimPhoNy v3: 2099/111212 [00:07<06:39, 272.89it/s]

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Edit: actually the performance increased due to other factors since the SimphoNy v3 test, so it is now just on the same range (see picture below from continuous benchmarking system).