Long-term forecasts for pathogen populations
Project description
popcast: Long-term forecasts for pathogen populations
See the methods of Huddleston et al. 2020 for more details or to cite this tool.
Install
python3 -m pip install popcast
Usage
Download seasonal influenza A/H3N2 data for model fitting.
curl -LO "https://github.com/blab/flu-forecasting/raw/master/results/builds/natural/natural_sample_1_with_90_vpm_sliding/tip_attributes_with_weighted_distances.tsv"
Fit a model using default 6 year training windows and 12-month forecasts.
popcast fit \
--tip-attributes tip_attributes_with_weighted_distances.tsv \
--output lbi_model.json \
--predictors lbi
Development
Install locally
python3 -m pip install ".[test]"
Lint and run tests
Lint code.
flake8 . --count --show-source --statistics
Run tests.
cram --shell=/bin/bash tests/
Publish
Install or upgrade publishing tools.
python3 -m pip install --upgrade build twine
Build the distribution packages.
python3 -m build
Upload the distribution packages.
python3 -m twine upload dist/*
Project details
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