Releases: EMOD-Hub/EMOD
v2.32
What's Changed
- Adding GenomeCrossoverLocations to the ReportFPGNewInfections by @stitova-idm in #156
Full Changelog: v2.31...v2.32
Contributors
Assets 2
v2.31.16.dev 1
This is the New Pyrogenic Threshold and MSP1 Antibody Fix with changes from v2.31 release merged in.
v2.31
Hightlight
New serlialization format allows smaller for memory footprint when loading serialized files.
- New parameter: Serialization_Max_Humans_Per_Collection - The maximum number of human agents saved in a collection in the serialized file. Default is 1000. This can be used to balance spead of reading and writing a file (including in Python) with the amount of memory used. More people in a collection is faster, but uses more memory.
What's Changed
- SCons Build with no Git by @Bridenbecker in #151
- Remove NodeCount from demographics by @kfrey-idm in #150
- Gh 147 - Serialization Format V6 by @Bridenbecker in #154
- Gh152 blood capacity calculation fix by @stitova-idm in #153
Full Changelog: v2.30...v2.31
Contributors
Assets 3
New Pyrogenic Threshold and MSP1 Antibody Fix
InnateImmuneVariationType:
NONE
PYROGENIC_THRESHOLD
PYROGENIC_THRESHOLD_VS_AGE_CONCAVE <-- formerly PYROGENIC_THRESHOLD_VS_AGE
PYROGENIC_THRESHOLD_VS_AGE_INCREASING_AND_CYTOKINE_KILLING_INVERSE <-- new pyrogenic threshold logic
New parameters:
Pyrogenic_Threshold_Min - minimum below which person's pyrogenic threshold cannot be set. For example, if Pyrogenic_Threshold in configuration parameters is 1500, and person's innate immune variation coefficient is 0.01, but Pyrogenic_Threshold_Min is 1000 - that person's pyrogenic threshold will be set to 1000.
Pyrogenic_Threshold_Max - maximum above which person's pyrogenic threshold cannot be set. For example, if Pyrogenic_Threshold in configuration parameters is 1500, and person's innate immune variation coefficient is 10, but Pyrogenic_Threshold_Max is 2000 - that person's pyrogenic threshold will be set to 2000.
MSP1_Growth_Aligned - If true(1), the formula for calculating the MSP1 antibody capacity growth is aligned with the formula for calculating the PfEMP1 antibody capacity growth. If false(0), the original formula for calculating MSP1 antibody capacity growth is used. This is an optional parameter that gives us access to the fix for #140. You can run the code with or without the fix. The model needs to be re-calibrated for the fix as it changes the rate of growth.
For more info, please see emodpy-malaria documentaion
v2.30
What's Changed
- Update versioning and add build workflow by @kfrey-idm in #127
- Isolate workflows by @kfrey-idm in #135
- Update and simplify build workflows by @kfrey-idm in #137
- Align VS and Scons component tests by @kfrey-idm in #134
- Fix build workflow by @kfrey-idm in #138
- Node config corrections by @kfrey-idm in #141
- removed NodeSetPolygon - Schema improvements by @kfrey-idm in #144
- In Malaria Full Parasite Genetics coverting barcode_distance to float. by @stitova-idm in #136
- Remove intersphinx links by @kfrey-idm in #145
- Add malaria antibody long term decay functionality and ReportAntibodies report @stitova-idm in #146
- Fixed an issue with ReportAntibodies. by @stitova-idm in #148
- Update PyPI workflows by @kfrey-idm in #149
Full Changelog: v2.29...v2.30
Contributors
Assets 2
v2.29
What's Changed
- PurgeExisting fix by @stitova-idm in #121
- Adding IndoorIndividualEmanator and OutdoorNodeEmanator by @stitova-idm in #124
- Remove Enable_Demographics_Birth by @stitova-idm in #128
What it means:
General:
Default setting changes: Enable_Default_Reporting and Enable_Demographics_Reporting are now false (0) by default. This supports emodpy users as the system is better designed to turn on (or add) the reports, rather than turn them off.
Malaria:
Default behavior changes to receiving multiple of same intervention:
- Bednets - new bednet of any bednet class will replace any existing bednet. Individual will not be able to have multiple bednets.
- HousingModifications - new housing modifications are combined with already existing housing modifications of the same class.
- Larivices - new larvices are combined with already existing larvicides.
- Ivermectin - new Ivermectin is combined with already existing Ivermectin.
- Other node-level vector interventions - new intervention replaces existing intervention of the same class unless they have different Intervention_Name parameters.
Added OutdoorNodeEmanator intervention and IndoorIndividualEmanator interventions. See documentation for details.
Outdoor returning mortality:
- Added "outdoor returning mortality" (contributed to by OutdoorRestKill and OutdoorNodeEmanator) to indoor biting vectors as well. Vectors that have fed indoors and outdoors are now subject to those interventions.
- Fixed issue where "outdoor returning mortality" was applied after we calculated newly-infected-vector numbers, so you could get into a situation where even if your "outdoor returning mortality" is 100%, your vectors population would still get newly-infected vectors as if some of the vectors successfully survived feeding on an infected human.
Bloodmeal mortality:
- Fixed issue where bloodmeal mortality and Ivermectin mortality were applied to vectors that fed on a sugar trap instead of a human.
- Added bloodmeal mortality to animal feeding. Vectors that feed on animals are now also affected by bloodmeal mortality parameter.
Enable_Demographics_Birth parameter has been removed. If you have Enable_Demographics_Risk and/or Enable_Migration_Heterogeneity enabled (set to 1) and have births, the newborns in your simulation will now automatically receive parameters based on demographics risk and migration settings.
HIV:
- Fixed issue where newborns had higher rate of HIV at birth than they should have. The infection flag was not being reset for each new newborn and once a newborn was flagged to be infected, all the following newborns in that time step were flagged as infected as well.
Full Changelog: v2.28...v2.29
Contributors
Assets 4
v2.28
What's Changed
- Add logging parameters to schema by @kfrey-idm in #114
- Add demographics risk to InputEIR and MalariaChallenge interventions by @stitova-idm in #119
- MalariaSummaryReport HRP2 data fix by @stitova-idm in #126
Full Changelog: v2.27...v2.28
Contributors
Assets 3
v2.27 re-enabling Serialization_Mask_Node_Read/Write: 16
What's Changed
- Serialization Mask 16 Fix by @stitova-idm in #112
- fixed issues causing a crash when creating new simulations using serialized file with Serialization_Mask_Node_Read: 16 (overwriting larval habitats in serialized file with ones from vector configuration file).
Full Changelog: v2.26...v2.27
Contributors
Assets 3
v2.26
Contributors
Assets 3
v2.25
What's Changed
- added condomless sex acts event by @kaftand in #72
- GH-75 - AgeDistribution: Poor error message for Array of Arrays by @Bridenbecker in #76
- rtd yml sphinx config path by @RCarter-IDM in #78
- Assortivity Speed UP by @Bridenbecker in #95
- Use unique names for idmTypes with different configs by @kfrey-idm in #90
- Report fpg new infections by @Bridenbecker in #96
- Fix for the wrong period of data being collected issues in ReportHIVByAgeAndGender by @stitova-idm in #101
- Internal Schema Post-processing by @kfrey-idm in #98
New Contributors
- @kaftand made their first contribution in #72
- @RCarter-IDM made their first contribution in #78
Full Changelog: v2.24...v2.25
