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base repository: DLab/covid19geomodeller
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base: v0.0.1
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head repository: DLab/covid19geomodeller
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compare: master
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Showing with 73,249 additions and 8,911 deletions.
  1. +8 −1 .gitignore
  2. +34 −0 .readthedocs.yaml
  3. +0 −18 Dockerfile
  4. +0 −13 Dockerfile.lite
  5. +0 −4,305 Examples/CV19GMData.ipynb
  6. +738 −0 Examples/CV19MULTISIM.ipynb
  7. +535 −0 Examples/CV19Mobility.ipynb
  8. +92 −1,361 Examples/CV19SIM.ipynb
  9. +5 −0 Examples/Examples.md
  10. +835 −310 Examples/SEIR.ipynb
  11. +1,330 −447 Examples/SEIRHVD.ipynb
  12. +1,009 −0 Examples/SEIRHVD_ABM.ipynb
  13. +16 −156 Examples/SEIRHVD_CFR.ipynb
  14. +928 −0 Examples/SEIRHVD_advancedstudies.ipynb
  15. +1,597 −0 Examples/SEIRMETA.ipynb
  16. +622 −0 Examples/SEIRTQ.ipynb
  17. +618 −0 Examples/SEIR_ABM.ipynb
  18. +951 −0 Examples/SIR.ipynb
  19. +563 −0 Examples/SIR_ABM.ipynb
  20. +24 −24 Examples/cfg/SEIRHVD.toml
  21. +103 −0 Examples/cfg/SEIRHVD_ABM.toml
  22. +31 −29 Examples/cfg/SEIRHVD_SEIR.toml
  23. +11 −10 Examples/cfg/SEIRHVD_v2.toml
  24. +11 −10 Examples/cfg/SEIRHVD_vac.toml
  25. +72 −0 Examples/cfg/SEIRMETA.toml
  26. +99 −0 Examples/cfg/SEIRTQ.toml
  27. +68 −0 Examples/cfg/SEIR_ABM.toml
  28. +36 −34 Examples/cfg/SEIR_data.toml
  29. 0 Examples/cfg/{SEIR_metasim.toml → SEIR_multisim.toml}
  30. +4 −4 Examples/cfg/SEIR_v2.toml
  31. +5 −17 config_files/SEIR.toml → Examples/cfg/SIR.toml
  32. +62 −0 Examples/cfg/SIR_ABM.toml
  33. +7 −19 config_files/SEIR_metasim.toml → Examples/cfg/SIR_dynamic.toml
  34. +0 −32 Examples/cfg/cv19.toml
  35. +12 −34 config_files/SEIRDynamic.toml → Examples/cfg/test.toml
  36. +326 −70 Examples/cv19functions.ipynb
  37. +1 −0 Examples/metaseir.json
  38. +2 −0 MANIFEST.in
  39. +8 −11 README.md
  40. +0 −624 cv19gm/backend/epic_backend.py
  41. +173 −0 cv19gm/cv19multisim.py
  42. +36 −155 cv19gm/cv19sim.py
  43. +377 −81 cv19gm/data/cv19data.py
  44. +865 −0 cv19gm/data/cv19data_national.py
  45. +22 −31 config_files/SEIRData.toml → cv19gm/default_config_files/SEIR.toml
  46. +31 −28 {config_files → cv19gm/default_config_files}/SEIRHVD.toml
  47. +99 −0 cv19gm/default_config_files/SEIRHVD_ABM.toml
  48. +95 −0 cv19gm/default_config_files/SEIRTQ.toml
  49. +72 −0 cv19gm/default_config_files/SEIR_ABM.toml
  50. +75 −0 cv19gm/default_config_files/SEIR_Metapopulation.toml
  51. +74 −0 cv19gm/default_config_files/SIR.toml
  52. +59 −0 cv19gm/default_config_files/SIR_ABM.toml
  53. 0 cv19gm/{backend → default_config_files}/__init__.py
  54. +93 −0 cv19gm/default_config_files/optionalparams.toml
  55. +124 −151 cv19gm/models/seir.py
  56. +80 −0 cv19gm/models/seir_ABM.py
  57. +276 −0 cv19gm/models/seir_meta.py
  58. +401 −0 cv19gm/models/seir_nb.py
  59. +200 −230 cv19gm/models/seirhvd.py
  60. +141 −0 cv19gm/models/seirhvd_ABM.py
  61. +291 −0 cv19gm/models/seirtq.py
  62. +0 −429 cv19gm/models/seirtqm.py
  63. +194 −113 cv19gm/models/sir.py
  64. +47 −0 cv19gm/models/sir_ABM.py
  65. +115 −0 cv19gm/utils/cv19errors.py
  66. +79 −78 cv19gm/utils/cv19files.py
  67. +175 −43 cv19gm/utils/cv19functions.py
  68. +396 −0 cv19gm/utils/cv19mobility.py
  69. +795 −0 cv19gm/utils/cv19paramfit.py
  70. +0 −41 cv19gm/utils/reproduction_number.py
  71. +1 −0 docs/.nojekyll
  72. +20 −0 docs/Makefile
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  80. +4 −0 docs/build/html/.buildinfo
  81. 0 docs/build/html/.nojekyll
  82. +295 −0 docs/build/html/_modules/cv19gm/cv19sim.html
  83. +2,675 −0 docs/build/html/_modules/cv19gm/data/cv19data.html
  84. +963 −0 docs/build/html/_modules/cv19gm/data/cv19data_national.html
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  94. +205 −0 docs/build/html/_modules/cv19gm/utils/cv19mobility.html
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  139. +6 −0 docs/build/html/_static/underscore.js
  140. +1,086 −0 docs/build/html/cv19gm.data.html
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  142. +562 −0 docs/build/html/cv19gm.models.html
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  144. +910 −0 docs/build/html/genindex.html
  145. +120 −0 docs/build/html/index.html
  146. +166 −0 docs/build/html/modules.html
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  149. +117 −0 docs/build/html/search.html
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  151. +45 −0 docs/conf.py
  152. +29 −0 docs/cv19gm.data.rst
  153. +77 −0 docs/cv19gm.models.rst
  154. +31 −0 docs/cv19gm.rst
  155. +69 −0 docs/cv19gm.utils.rst
  156. +1 −0 docs/index.html
  157. +20 −0 docs/index.rst
  158. +35 −0 docs/make.bat
  159. +7 −0 docs/modules.rst
  160. +8 −0 docs/rtd_requirements.txt
  161. +13 −0 julia/AbstractSpace.jl
  162. +16 −0 julia/GraphSpace.jl
  163. +548 −0 julia/Manifest.toml
  164. +9 −0 julia/Project.toml
  165. +128 −0 julia/SEIR.jl
  166. +310 −0 julia/SEIRHVD.jl
  167. +90 −0 julia/SEIRHVDModel.jl
  168. +50 −0 julia/SEIRModel.jl
  169. +117 −0 julia/SIR.jl
  170. +43 −0 julia/SIRModel.jl
  171. +78 −0 julia/collect_SEIR.jl
  172. +89 −0 julia/collect_SEIRHVD.jl
  173. +83 −0 julia/collect_SIR.jl
  174. +42 −0 julia/modules.jl
  175. +262 −0 julia/run.jl
  176. +9,150 −0 julia/test.ipynb
  177. +77 −0 julia/test.jl
  178. +3 −0 pyproject.toml
  179. +1 −0 requirements.txt
  180. +29 −0 setup.cfg
  181. +2 −2 setup.py
  182. +1,967 −0 tests/CV19Mobility_old.ipynb
  183. +538 −0 tests/CV19SIM_tests.ipynb
  184. +472 −0 tests/SEIRMETA_timetest.ipynb
9 changes: 8 additions & 1 deletion .gitignore
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@@ -1,5 +1,9 @@
# Images
*.png
*.pdf
*.jpg
*.jpeg

# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
@@ -71,7 +75,7 @@ instance/
.scrapy

# Sphinx documentation
docs/_build/
# docs/_build/

# PyBuilder
target/
@@ -129,3 +133,6 @@ dmypy.json

# Pyre type checker
.pyre/

# MacOs
.DS_Store
34 changes: 34 additions & 0 deletions .readthedocs.yaml
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# .readthedocs.yaml
# Read the Docs configuration file
# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details

# Required
version: 2

# Set the version of Python and other tools you might need
build:
os: ubuntu-22.04
tools:
python: "3.10"
# You can also specify other tool versions:
# nodejs: "19"
# rust: "1.64"
# golang: "1.19"

# Build documentation in the docs/ directory with Sphinx
sphinx:
configuration: docs/conf.py

# If using Sphinx, optionally build your docs in additional formats such as PDF
# formats:
# - pdf

# Optionally declare the Python requirements required to build your docs
python:
install:
- requirements: docs/rtd_requirements.txt
- method: pip
path: .

# - requirements: docs/requirements.tx
# path: .
18 changes: 0 additions & 18 deletions Dockerfile

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13 changes: 0 additions & 13 deletions Dockerfile.lite

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