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codebase_structure.md

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codebase_structure.md

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Folder Strucure

.
├── configs/
│   ├── seir/
│   ├── ihme/
│   ├── exper/
│   ├── simulated_data/
├── data/
│   ├── dataloader/
│   ├── processing/
├── docs/
│   ├── sphinx/
│   ├── *.md
├── main/
│   ├── ihme/
│   ├── seir/
│   ├───├─── optimisers/
│   ├───├─── uncertainty/
│   ├───├─── main.py/
├── models/
│   ├── ihme/
│   ├── seir/
├── notebooks/
│   ├── seir/
├── scripts/
│   ├── ihme/
│   ├── seir/
├── utils/
│   ├── fitting/
│   ├── generic/
├── viz/

configs

Contains all configs. Refer to config.md for more details.

├── configs/
│   ├── seir/
│   ├── ihme/
│   ├── exper/
│   ├── simulated_data/
  • seir : all SEIR configs
  • ihme : all IHME configs
  • exper : all experimentation configs. Generated N configs from 1 config, for experimentation
  • simulated_data : all simulated data configs.

data

Contains all dataloading and processing code. Refer to data.md for more details.

├── data/
│   ├── dataloader/
│   ├── processing/
  • dataloader : contains all dataloaders. If the user wishes to add more dataloaders, they will be children of the BaseLoader class
  • processing : contains code for processing all data post loading it. We wished to add a generic data transformations class and have all processing code be children of the base transformation class, but we were unable to do that.

docs

Contains all documentation.

├── docs/
│   ├── sphinx/
│   ├── *.md
  • sphinx : contains autodocs generated from docstrings of functions and classes
  • *.md : Markdown documentation of different aspects of the project

main

Contains the code for fitting the params of the model to data, and estimating uncertainty.

├── main/
│   ├── ihme/
│   ├── seir/
│   ├───├─── optimisers/
│   ├───├─── uncertainty/
│   ├───├─── main.py/
  • ihme : functions for fitting IHME models
  • seir : functions for fitting general models. Initially developed to fit only SEIR models, but then abstracted more with time to work with general models

models

Contains the code for fitting the params of the model to data, and estimating uncertainty.

├── models/
│   ├── ihme/
│   ├── seir/
  • ihme : the IHME model
  • seir : All SEIR models. If the user wishes to create a new SEIR model, it must be a child of the base epi-model class

If the user wishes to add a new model class, they can create a folder for it, implement a base class for that model class, and then create models as children of that base class.

notebooks and scripts

Contains all runnable code. Most important is notebooks/seir/[STABLE] generate_report.ipynb.

├── notebooks/
│   ├── seir/
├── scripts/
│   ├── ihme/
│   ├── seir/

utils

Fitting specific utils in fitting. Rest all in generic.

├── utils/
│   ├── fitting/
│   ├── generic/

viz

All visualisation code

├── viz/

Additionally,

  • All local logging is typically done in misc/reports, but can be changed.
  • All local data caching is done in misc/cache, but can be changed.
  • Pyathena credentials are stored in misc/pyathena, but can be changed.

None of this is stored on git.