Age base hint SFTs

[YeChen-IDM]

SFTs for AgeBasedHINT:

 demog.AddAgeDependentTransmission( 
            Age_Bin_Edges_In_Years = [0, 5, 20, 60, -1],
            TransmissionMatrix = [
                [2,1,0.5,0.1],
                [2,1,0.5,0.1],
                [2,1,0.5,0.1],
                [2,1,0.5,0.1]
            ]
        )

Here is a example configuration for AgeBasedHINT:

{"Age_Bin_Edges_In_Years":[0,5,20,60,-1],
"Property":"Age_Bin",
"TransmissionMatrix":{
  "contact":{
    "Matrix":[[2,1,0.5,0.1],[2,1,0.5,0.1],[2,1,0.5,0.1],[2,1,0.5,0.1]]},
    "environmental":{
      "Matrix":[[2,1,0.5,0.1],[2,1,0.5,0.1],[2,1,0.5,0.1],[2,1,0.5,0.1]]}}}

Some ad hoc testing:
https://comps2.idmod.org/#explore/Simulations?filters=Owner=yechen&offset=0&mode=chart&orderby=DateCreated+desc&count=100&selectedId=c00a0f28-5698-ee11-92fe-f0921c167864&resizer=492C842C0

Anther example of the AgeBasedHINT that targeting Younger individuals:

Compared to Baseline:

2 Sets of SFTs in this PR:

• TestAgeBaseHintTargetOneAgeBin: Which contains 4 tests each of them have AgeBasedHINT configured to target one age bin only, the purpose of the tests is to make sure the transmission matrix honors the Age_Bin_Edges_In_Years list. Existing issue: Test for AgeBaseHINT fails when targeting the first age bin #29.
• TestAgeBaseHintValues: This file contains 6 tests including a baseline which has no HINT. The other 5 tests have HINT matrix with different values. Please see the ad hoc testing section for how to use these simulations to verify the result. Existing issues: Simulation using TyphoidDemographics template should not have individuals that are over 125 years old #30 and Simulations crashes with OutOfRangeException when Age Base TransmissionMatrix set to higher value #31

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'->> Link to your documents from Dec 11-13:06.11'

[YeChen-IDM]

Jenkins pipeline: https://jenkins.apps.idmod.org/view/Emodpy/job/Emodpy-Typhoid-Pipelines/job/Emodpy-Typhoid-Pipeline-for-testing/
The multi branches pipeline does the same thing as the above pipeline: https://jenkins.apps.idmod.org/job/Emodpy-Typhoid%20Multibranch%20Pipeline/job/PR-32/.

Other open issues besides the 3 issues in the description of this PR: #33, #34 and #35.

[YeChen-IDM]

Here is the commands to install the dependencies:

pip3 install -r requirements_2018.txt --index-url=https://packages.idmod.org/api/pypi/pypi-production/simple
pip3 install -e .

If you want to run the SFT tests locally, you will need to install the idm_test package:
pip3 install idm-test>=0.1.2 --index-url=https://packages.idmod.org/api/pypi/pypi-production/simple

[jonathanhhb]

I will try to find time to run these locally and then merge. Thanks so much for getting this done. These tests look lovely.

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'->> Link to your documents from Dec 12-13:01.08'

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'->> Link to your documents from Jan 09-12:45.33'

[YeChen-IDM]

Fixed the test_vax_rollout_coverage SFT to have a dynamic tolerance for vaccine coverage check, this SFT passed is the latest build

[YeChen-IDM]

Age bin hint SFT failed with the latest Emod with this assertion:
Assertion failure, (contagionDecayRatesByRoute.size()), is false in file Eradication/MultiRouteTransmissionGroups.cpp at line 111
Intellectual Ventures(R)/EMOD Disease Transmission Kernel 2.11.4047.0
Built on Dec 8 2023 by luser from fix_ageased_hint_mr(9649109) checked in on 2023-12-08 11:42:17 -0800

https://comps2.idmod.org/#explore/Simulations?mode=list&orderby=DateCreated+desc&count=100&offset=0&resizer=392C282C0&selectedId=0d592f6d-35af-ee11-92ff-f0921c167860

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'->> Link to your documents from Jan 09-14:58.56'

[YeChen-IDM]

Age bin hint SFT failed with the latest Emod with this assertion: Assertion failure, (contagionDecayRatesByRoute.size()), is false in file Eradication/MultiRouteTransmissionGroups.cpp at line 111 Intellectual Ventures(R)/EMOD Disease Transmission Kernel 2.11.4047.0 Built on Dec 8 2023 by luser from fix_ageased_hint_mr(9649109) checked in on 2023-12-08 11:42:17 -0800

https://comps2.idmod.org/#explore/Simulations?mode=list&orderby=DateCreated+desc&count=100&offset=0&resizer=392C282C0&selectedId=0d592f6d-35af-ee11-92ff-f0921c167860

fixed with emod_api == 1.31.0.dev5

[YeChen-IDM]

@jonathanhhb , could you take a look at this PR and see if it's Okay to merge it? Thanks.

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'->> Link to your documents from Jan 22-16:36.45'

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'->> Link to your documents from Jan 22-17:31.19'

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