vivarium-public-health 1.0.1__tar.gz → 1.0.2__tar.gz

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Files changed (142) hide show
  1. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/.github/workflows/build.yml +10 -3
  2. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/CHANGELOG.rst +4 -0
  3. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/PKG-INFO +1 -1
  4. vivarium_public_health-1.0.2/src/vivarium_public_health/_version.py +1 -0
  5. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/metrics/disease.py +2 -1
  6. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health.egg-info/PKG-INFO +1 -1
  7. vivarium_public_health-1.0.1/src/vivarium_public_health/_version.py +0 -1
  8. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/.gitattributes +0 -0
  9. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/.github/CODEOWNERS +0 -0
  10. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/.github/pull_request_template.md +0 -0
  11. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/.github/workflows/deploy.yml +0 -0
  12. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/.gitignore +0 -0
  13. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/.pylintrc +0 -0
  14. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/.readthedocs.yml +0 -0
  15. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/.zenodo.json +0 -0
  16. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/CODE_OF_CONDUCT.rst +0 -0
  17. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/CONTRIBUTING.rst +0 -0
  18. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/LICENSE.txt +0 -0
  19. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/MANIFEST.in +0 -0
  20. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/README.rst +0 -0
  21. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/Makefile +0 -0
  22. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/nitpick-exceptions +0 -0
  23. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/_static/style.css +0 -0
  24. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/_templates/layout.html +0 -0
  25. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/disease/index.rst +0 -0
  26. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/disease/model.rst +0 -0
  27. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/disease/models.rst +0 -0
  28. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/disease/special_disease.rst +0 -0
  29. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/disease/state.rst +0 -0
  30. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/disease/transition.rst +0 -0
  31. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/index.rst +0 -0
  32. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/metrics/disability.rst +0 -0
  33. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/metrics/disease.rst +0 -0
  34. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/metrics/index.rst +0 -0
  35. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/metrics/mortality.rst +0 -0
  36. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/metrics/risk.rst +0 -0
  37. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/metrics/stratification.rst +0 -0
  38. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/mslt/delay.rst +0 -0
  39. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/mslt/disease.rst +0 -0
  40. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/mslt/index.rst +0 -0
  41. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/mslt/intervention.rst +0 -0
  42. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/mslt/magic_wand_components.rst +0 -0
  43. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/mslt/observer.rst +0 -0
  44. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/mslt/population.rst +0 -0
  45. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/population/add_new_birth_cohorts.rst +0 -0
  46. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/population/base_population.rst +0 -0
  47. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/population/data_transformations.rst +0 -0
  48. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/population/index.rst +0 -0
  49. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/population/mortality.rst +0 -0
  50. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/risks/base_risk.rst +0 -0
  51. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/risks/data_transformations.rst +0 -0
  52. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/risks/distributions.rst +0 -0
  53. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/risks/effect.rst +0 -0
  54. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/risks/implementations/index.rst +0 -0
  55. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/risks/implementations/low_birth_weight_and_short_gestation.rst +0 -0
  56. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/risks/index.rst +0 -0
  57. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/testing/index.rst +0 -0
  58. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/testing/mock_artifact.rst +0 -0
  59. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/testing/utils.rst +0 -0
  60. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/treatment/index.rst +0 -0
  61. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/treatment/magic_wand.rst +0 -0
  62. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/treatment/scale_up.rst +0 -0
  63. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/treatment/therapeutic_inertia.rst +0 -0
  64. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/api_reference/utilities.rst +0 -0
  65. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/conf.py +0 -0
  66. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/index.rst +0 -0
  67. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/tutorials/index.rst +0 -0
  68. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/docs/source/tutorials/risk_exposure.rst +0 -0
  69. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/pyproject.toml +0 -0
  70. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/setup.cfg +0 -0
  71. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/setup.py +0 -0
  72. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/__about__.py +0 -0
  73. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/__init__.py +0 -0
  74. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/disease/__init__.py +0 -0
  75. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/disease/model.py +0 -0
  76. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/disease/models.py +0 -0
  77. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/disease/special_disease.py +0 -0
  78. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/disease/state.py +0 -0
  79. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/disease/transition.py +0 -0
  80. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/metrics/__init__.py +0 -0
  81. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/metrics/disability.py +0 -0
  82. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/metrics/mortality.py +0 -0
  83. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/metrics/risk.py +0 -0
  84. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/metrics/stratification.py +0 -0
  85. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/mslt/__init__.py +0 -0
  86. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/mslt/delay.py +0 -0
  87. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/mslt/disease.py +0 -0
  88. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/mslt/intervention.py +0 -0
  89. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/mslt/magic_wand_components.py +0 -0
  90. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/mslt/observer.py +0 -0
  91. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/mslt/population.py +0 -0
  92. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/population/__init__.py +0 -0
  93. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/population/add_new_birth_cohorts.py +0 -0
  94. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/population/base_population.py +0 -0
  95. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/population/data_transformations.py +0 -0
  96. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/population/mortality.py +0 -0
  97. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/risks/__init__.py +0 -0
  98. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/risks/base_risk.py +0 -0
  99. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/risks/data_transformations.py +0 -0
  100. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/risks/distributions.py +0 -0
  101. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/risks/effect.py +0 -0
  102. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/risks/implementations/__init__.py +0 -0
  103. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/risks/implementations/low_birth_weight_and_short_gestation.py +0 -0
  104. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/testing/__init__.py +0 -0
  105. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/testing/mock_artifact.py +0 -0
  106. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/testing/utils.py +0 -0
  107. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/treatment/__init__.py +0 -0
  108. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/treatment/magic_wand.py +0 -0
  109. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/treatment/scale_up.py +0 -0
  110. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/treatment/therapeutic_inertia.py +0 -0
  111. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/utilities.py +0 -0
  112. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health.egg-info/SOURCES.txt +0 -0
  113. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health.egg-info/dependency_links.txt +0 -0
  114. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health.egg-info/not-zip-safe +0 -0
  115. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health.egg-info/requires.txt +0 -0
  116. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health.egg-info/top_level.txt +0 -0
  117. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/tests/__init__.py +0 -0
  118. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/tests/conftest.py +0 -0
  119. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/tests/disease/__init__.py +0 -0
  120. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/tests/disease/test_disease.py +0 -0
  121. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/tests/disease/test_special_disease.py +0 -0
  122. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/tests/metrics/__init__.py +0 -0
  123. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/tests/metrics/test_categorical_risk_observer.py +0 -0
  124. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/tests/metrics/test_disability.py +0 -0
  125. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/tests/metrics/test_disability_observer.py +0 -0
  126. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/tests/metrics/test_disease_observer.py +0 -0
  127. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/tests/metrics/test_mortality_observer.py +0 -0
  128. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/tests/metrics/test_stratification.py +0 -0
  129. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/tests/population/__init__.py +0 -0
  130. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/tests/population/conftest.py +0 -0
  131. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/tests/population/test_add_new_birth_cohort.py +0 -0
  132. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/tests/population/test_base_population.py +0 -0
  133. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/tests/population/test_data_transformations.py +0 -0
  134. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/tests/risks/__init__.py +0 -0
  135. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/tests/risks/conftest.py +0 -0
  136. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/tests/risks/test_base_risk.py +0 -0
  137. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/tests/risks/test_data_transformations.py +0 -0
  138. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/tests/risks/test_distributions.py +0 -0
  139. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/tests/risks/test_effect.py +0 -0
  140. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/tests/test_utilities.py +0 -0
  141. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/tests/treatment/__init__.py +0 -0
  142. {vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/tox.ini +0 -0
{vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/.github/workflows/build.yml RENAMED
@@ -20,9 +20,16 @@ jobs:
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  uses: actions/setup-python@v4
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  with:
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  python-version: ${{ matrix.python-version }}
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+ - name: get upstream branch name
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+ run: |
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+ if "${{ github.event_name == 'pull_request' }}" ; then
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+ echo "branch_name=${GITHUB_HEAD_REF}" >> $GITHUB_ENV
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+ else
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+ echo "branch_name=${GITHUB_REF_NAME}" >> $GITHUB_ENV
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+ fi
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  - name: check for upstream branch
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  run: |
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- if git ls-remote --exit-code --heads https://github.com/ihmeuw/vivarium.git ${GITHUB_HEAD_REF} == "0"; then
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+ if git ls-remote --exit-code --heads https://github.com/ihmeuw/vivarium.git ${branch_name} == "0"; then
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  echo "upstream_exist=true" >> $GITHUB_ENV
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  else
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  echo "upstream_exist=false" >> $GITHUB_ENV
@@ -36,8 +43,8 @@ jobs:
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  - name: Retrieve upstream branch if exists
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  if: env.upstream_exist == 'true'
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  run: |
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- echo "Cloning upstream branch: ${GITHUB_HEAD_REF}"
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- git clone --branch=${GITHUB_HEAD_REF} https://github.com/ihmeuw/vivarium.git
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+ echo "Cloning upstream branch: ${branch_name}"
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+ git clone --branch=${branch_name} https://github.com/ihmeuw/vivarium.git
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  pushd vivarium
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  pip install .
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  popd
{vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/CHANGELOG.rst RENAMED
@@ -1,3 +1,7 @@
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+ **1.0.2 - 08/10/23**
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+
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+ - Minor bugfix to ensure dead simulants do not get observed transitions
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+
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  **1.0.1 - 08/07/23**
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  - Minor bugfix to improve handling of excess mortality rate data
{vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: vivarium_public_health
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- Version: 1.0.1
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+ Version: 1.0.2
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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-1.0.2/src/vivarium_public_health/_version.py ADDED
@@ -0,0 +1 @@
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+ __version__ = "1.0.2"
{vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health/metrics/disease.py RENAMED
@@ -91,7 +91,8 @@ class DiseaseObserver:
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  filter_string = (
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  f'{self.previous_state_column_name} == "{transition.from_state}" '
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  f'and {self.disease} == "{transition.to_state}" '
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- f"and tracked==True"
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+ f"and tracked==True "
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+ f'and alive == "alive"'
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  )
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  builder.results.register_observation(
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  name=f"{transition}_event_count",
{vivarium_public_health-1.0.1 → vivarium_public_health-1.0.2}/src/vivarium_public_health.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: vivarium-public-health
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- Version: 1.0.1
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+ Version: 1.0.2
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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-1.0.1/src/vivarium_public_health/_version.py DELETED
@@ -1 +0,0 @@
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- __version__ = "1.0.1"