vivarium-public-health 3.1.5__tar.gz → 3.2.0__tar.gz

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  1. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/CHANGELOG.rst +4 -0
  2. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/PKG-INFO +1 -1
  3. vivarium_public_health-3.2.0/src/vivarium_public_health/_version.py +1 -0
  4. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/risks/effect.py +2 -2
  5. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/risks/implementations/low_birth_weight_and_short_gestation.py +10 -13
  6. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health.egg-info/PKG-INFO +1 -1
  7. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health.egg-info/SOURCES.txt +1 -0
  8. vivarium_public_health-3.2.0/tests/data/rr_interpolator.csv +51 -0
  9. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tests/risks/conftest.py +8 -0
  10. vivarium_public_health-3.2.0/tests/risks/test_low_birth_weight_and_short_gestation.py +142 -0
  11. vivarium_public_health-3.1.5/src/vivarium_public_health/_version.py +0 -1
  12. vivarium_public_health-3.1.5/tests/risks/test_low_birth_weight_and_short_gestation.py +0 -34
  13. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/.bandit +0 -0
  14. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/.flake8 +0 -0
  15. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/.gitattributes +0 -0
  16. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/.github/CODEOWNERS +0 -0
  17. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/.github/pull_request_template.md +0 -0
  18. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/.github/workflows/build.yml +0 -0
  19. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/.github/workflows/deploy.yml +0 -0
  20. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/.gitignore +0 -0
  21. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/.pylintrc +0 -0
  22. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/.readthedocs.yml +0 -0
  23. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/.zenodo.json +0 -0
  24. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/CODE_OF_CONDUCT.rst +0 -0
  25. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/CONTRIBUTING.rst +0 -0
  26. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/Jenkinsfile +0 -0
  27. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/LICENSE.txt +0 -0
  28. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/MANIFEST.in +0 -0
  29. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/Makefile +0 -0
  30. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/README.rst +0 -0
  31. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/Makefile +0 -0
  32. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/nitpick-exceptions +0 -0
  33. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/_static/style.css +0 -0
  34. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/_templates/layout.html +0 -0
  35. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/disease/index.rst +0 -0
  36. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/disease/model.rst +0 -0
  37. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/disease/models.rst +0 -0
  38. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/disease/special_disease.rst +0 -0
  39. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/disease/state.rst +0 -0
  40. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/disease/transition.rst +0 -0
  41. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/index.rst +0 -0
  42. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/mslt/delay.rst +0 -0
  43. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/mslt/disease.rst +0 -0
  44. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/mslt/index.rst +0 -0
  45. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/mslt/intervention.rst +0 -0
  46. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/mslt/magic_wand_components.rst +0 -0
  47. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/mslt/observer.rst +0 -0
  48. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/mslt/population.rst +0 -0
  49. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/plugins/index.rst +0 -0
  50. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/plugins/parser.rst +0 -0
  51. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/population/add_new_birth_cohorts.rst +0 -0
  52. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/population/base_population.rst +0 -0
  53. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/population/data_transformations.rst +0 -0
  54. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/population/index.rst +0 -0
  55. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/population/mortality.rst +0 -0
  56. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/results/disability.rst +0 -0
  57. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/results/disease.rst +0 -0
  58. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/results/index.rst +0 -0
  59. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/results/mortality.rst +0 -0
  60. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/results/observer.rst +0 -0
  61. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/results/risk.rst +0 -0
  62. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/results/simple_cause.rst +0 -0
  63. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/results/stratification.rst +0 -0
  64. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/risks/base_risk.rst +0 -0
  65. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/risks/data_transformations.rst +0 -0
  66. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/risks/distributions.rst +0 -0
  67. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/risks/effect.rst +0 -0
  68. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/risks/implementations/index.rst +0 -0
  69. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/risks/implementations/low_birth_weight_and_short_gestation.rst +0 -0
  70. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/risks/index.rst +0 -0
  71. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/treatment/index.rst +0 -0
  72. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/treatment/magic_wand.rst +0 -0
  73. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/treatment/scale_up.rst +0 -0
  74. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/treatment/therapeutic_inertia.rst +0 -0
  75. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/api_reference/utilities.rst +0 -0
  76. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/conf.py +0 -0
  77. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/index.rst +0 -0
  78. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/tutorials/index.rst +0 -0
  79. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/docs/source/tutorials/risk_exposure.rst +0 -0
  80. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/pyproject.toml +0 -0
  81. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/setup.cfg +0 -0
  82. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/setup.py +0 -0
  83. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/__about__.py +0 -0
  84. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/__init__.py +0 -0
  85. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/disease/__init__.py +0 -0
  86. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/disease/exceptions.py +0 -0
  87. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/disease/model.py +0 -0
  88. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/disease/models.py +0 -0
  89. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/disease/special_disease.py +0 -0
  90. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/disease/state.py +0 -0
  91. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/disease/transition.py +0 -0
  92. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/mslt/__init__.py +0 -0
  93. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/mslt/delay.py +0 -0
  94. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/mslt/disease.py +0 -0
  95. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/mslt/intervention.py +0 -0
  96. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/mslt/magic_wand_components.py +0 -0
  97. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/mslt/observer.py +0 -0
  98. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/mslt/population.py +0 -0
  99. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/plugins/__init__.py +0 -0
  100. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/plugins/parser.py +0 -0
  101. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/population/__init__.py +0 -0
  102. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/population/add_new_birth_cohorts.py +0 -0
  103. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/population/base_population.py +0 -0
  104. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/population/data_transformations.py +0 -0
  105. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/population/mortality.py +0 -0
  106. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/results/__init__.py +0 -0
  107. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/results/columns.py +0 -0
  108. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/results/disability.py +0 -0
  109. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/results/disease.py +0 -0
  110. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/results/mortality.py +0 -0
  111. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/results/observer.py +0 -0
  112. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/results/risk.py +0 -0
  113. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/results/simple_cause.py +0 -0
  114. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/results/stratification.py +0 -0
  115. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/risks/__init__.py +0 -0
  116. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/risks/base_risk.py +0 -0
  117. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/risks/data_transformations.py +0 -0
  118. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/risks/distributions.py +0 -0
  119. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/risks/implementations/__init__.py +0 -0
  120. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/treatment/__init__.py +0 -0
  121. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/treatment/magic_wand.py +0 -0
  122. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/treatment/scale_up.py +0 -0
  123. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/treatment/therapeutic_inertia.py +0 -0
  124. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/utilities.py +0 -0
  125. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health.egg-info/dependency_links.txt +0 -0
  126. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health.egg-info/not-zip-safe +0 -0
  127. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health.egg-info/requires.txt +0 -0
  128. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health.egg-info/top_level.txt +0 -0
  129. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tests/__init__.py +0 -0
  130. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tests/conftest.py +0 -0
  131. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tests/disease/__init__.py +0 -0
  132. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tests/disease/test_disease.py +0 -0
  133. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tests/disease/test_special_disease.py +0 -0
  134. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tests/mock_artifact.py +0 -0
  135. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tests/plugins/__init__.py +0 -0
  136. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tests/plugins/test_parser.py +0 -0
  137. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tests/population/__init__.py +0 -0
  138. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tests/population/conftest.py +0 -0
  139. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tests/population/test_add_new_birth_cohort.py +0 -0
  140. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tests/population/test_base_population.py +0 -0
  141. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tests/population/test_data_transformations.py +0 -0
  142. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tests/population/test_mortality.py +0 -0
  143. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tests/results/__init__.py +0 -0
  144. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tests/results/test_categorical_risk_observer.py +0 -0
  145. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tests/results/test_disability.py +0 -0
  146. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tests/results/test_disability_observer.py +0 -0
  147. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tests/results/test_disease_observer.py +0 -0
  148. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tests/results/test_mortality_observer.py +0 -0
  149. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tests/results/test_stratification.py +0 -0
  150. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tests/risks/__init__.py +0 -0
  151. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tests/risks/test_base_risk.py +0 -0
  152. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tests/risks/test_data_transformations.py +0 -0
  153. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tests/risks/test_distributions.py +0 -0
  154. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tests/risks/test_effect.py +0 -0
  155. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tests/test_utilities.py +0 -0
  156. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tests/treatment/__init__.py +0 -0
  157. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tests/treatment/test_scale_up.py +0 -0
  158. {vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tox.ini +0 -0
{vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/CHANGELOG.rst RENAMED
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+ **3.2.0 - 1/15/25**
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+ - Bugfix: Fix bug in LBWSGRiskEffect where relative risk pipeline was not properly created
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  **3.1.5 - 01/14/25**
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  - Bugfix: Vivarium InteractiveContext no longer returns int
{vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/PKG-INFO RENAMED
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  Metadata-Version: 2.2
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  Name: vivarium_public_health
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- Version: 3.1.5
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+ Version: 3.2.0
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  Summary: Components for modelling diseases, risks, and interventions with ``vivarium``
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  Home-page: https://github.com/ihmeuw/vivarium_public_health
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  Author: The vivarium developers
vivarium_public_health-3.2.0/src/vivarium_public_health/_version.py ADDED
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+ __version__ = "3.2.0"
{vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/risks/effect.py RENAMED
@@ -114,7 +114,7 @@ class RiskEffect(Component):
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  self.exposure = self.get_risk_exposure(builder)
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  self._relative_risk_source = self.get_relative_risk_source(builder)
117
- self.relative_risk = self.get_relative_risk(builder)
117
+ self.relative_risk = self.get_relative_risk_pipeline(builder)
118
118
 
119
119
  self.register_target_modifier(builder)
120
120
  self.register_paf_modifier(builder)
@@ -297,7 +297,7 @@ class RiskEffect(Component):
297
297
 
298
298
  return generate_relative_risk
299
299
 
300
- def get_relative_risk(self, builder: Builder) -> Pipeline:
300
+ def get_relative_risk_pipeline(self, builder: Builder) -> Pipeline:
301
301
  return builder.value.register_value_producer(
302
302
  f"{self.risk.name}_on_{self.target.name}.relative_risk",
303
303
  self._relative_risk_source,
{vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health/risks/implementations/low_birth_weight_and_short_gestation.py RENAMED
@@ -361,18 +361,11 @@ class LBWSGRiskEffect(RiskEffect):
361
361
  paf_data = builder.data.load(paf_key)
362
362
  return paf_data, builder.data.value_columns()(paf_key)
363
363
 
364
- def get_target_modifier(
365
- self, builder: Builder
366
- ) -> Callable[[pd.Index, pd.Series], pd.Series]:
367
- def adjust_target(index: pd.Index, target: pd.Series) -> pd.Series:
368
- return target * self.relative_risk(index)
369
-
370
- return adjust_target
371
-
372
364
  def register_target_modifier(self, builder: Builder) -> None:
373
365
  builder.value.register_value_modifier(
374
366
  self.target_pipeline_name,
375
- modifier=self.target_modifier,
367
+ modifier=self.adjust_target,
368
+ component=self,
376
369
  requires_values=[self.relative_risk_pipeline_name],
377
370
  )
378
371
 
@@ -392,11 +385,12 @@ class LBWSGRiskEffect(RiskEffect):
392
385
  for age_start in exposed_age_group_starts
393
386
  }
394
387
 
395
- def get_relative_risk(self, builder: Builder) -> Pipeline:
388
+ def get_relative_risk_pipeline(self, builder: Builder) -> Pipeline:
396
389
  return builder.value.register_value_producer(
397
390
  self.relative_risk_pipeline_name,
398
- source=self.get_relative_risk_source,
399
- requires_columns=["age"] + self.rr_column_names,
391
+ source=self._relative_risk_source,
392
+ component=self,
393
+ required_resources=["age"] + self.rr_column_names,
400
394
  )
401
395
 
402
396
  def get_interpolator(self, builder: Builder) -> pd.Series:
@@ -469,7 +463,7 @@ class LBWSGRiskEffect(RiskEffect):
469
463
  # Pipeline sources and modifiers #
470
464
  ##################################
471
465
 
472
- def get_relative_risk_source(self, index: pd.Index) -> pd.Series:
466
+ def _get_relative_risk(self, index: pd.Index) -> pd.Series:
473
467
  pop = self.population_view.get(index)
474
468
  relative_risk = pd.Series(1.0, index=index, name=self.relative_risk_pipeline_name)
475
469
 
@@ -479,3 +473,6 @@ class LBWSGRiskEffect(RiskEffect):
479
473
  age_group_mask, self.relative_risk_column_name(age_group)
480
474
  ]
481
475
  return relative_risk
476
+
477
+ def get_relative_risk_source(self, builder: Builder) -> Callable[[pd.Index], pd.Series]:
478
+ return self._get_relative_risk
{vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.2
2
2
  Name: vivarium_public_health
3
- Version: 3.1.5
3
+ Version: 3.2.0
4
4
  Summary: Components for modelling diseases, risks, and interventions with ``vivarium``
5
5
  Home-page: https://github.com/ihmeuw/vivarium_public_health
6
6
  Author: The vivarium developers
{vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/src/vivarium_public_health.egg-info/SOURCES.txt RENAMED
@@ -124,6 +124,7 @@ tests/__init__.py
124
124
  tests/conftest.py
125
125
  tests/mock_artifact.py
126
126
  tests/test_utilities.py
127
+ tests/data/rr_interpolator.csv
127
128
  tests/disease/__init__.py
128
129
  tests/disease/test_disease.py
129
130
  tests/disease/test_special_disease.py
vivarium_public_health-3.2.0/tests/data/rr_interpolator.csv ADDED
@@ -0,0 +1,51 @@
1
+ ,sex,age_start,age_end,year_start,year_end,draw_0
2
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{vivarium_public_health-3.1.5 → vivarium_public_health-3.2.0}/tests/risks/conftest.py RENAMED
@@ -262,3 +262,11 @@ def coverage_gap():
262
262
  cg_data["affected_risk_factors"] = ["test_risk"]
263
263
  cg_data["distribution"] = "dichotomous"
264
264
  return Risk(f"coverage_gap.{cg}"), cg_data
265
+
266
+
267
+ @pytest.fixture
268
+ def mock_rr_interpolators() -> pd.DataFrame:
269
+ rr_interpolators = pd.read_csv("tests/data/rr_interpolator.csv")
270
+ idx_cols = [col for col in rr_interpolators.columns if "draw" not in col]
271
+ rr_interpolators = rr_interpolators.rename(columns={"draw_0": "value"})
272
+ return rr_interpolators