1. 05 Oct, 2020 1 commit
    • Chris Jewell's avatar
      Major new pipelining structure · bfcaf904
      Chris Jewell authored
      enqueue_pipeline.sh --> covid_pipeline.sge --> prepare_config.py --> inference.py --> summary.py
      enqueue_pipeline.sh identifies the dataset and analysis period, launching 4 SGE jobs [P1, P1+2]\times[specimen_date, report_date]
      Each SGE job runs the inference and summary scripts, using information contained in a config.yaml file.
      The config.yaml file, together with results outputs, are stored in a results directory specified the config file
      and over-ridden in the top-level enqueue_pipeline.sh script.
  2. 01 Oct, 2020 1 commit
    • Chris Jewell's avatar
      Added inference summary metrics · 8eb0ab69
      Chris Jewell authored
      1. Added `data/example_cases.py`, `data/uk_clip.py`, `covid/summary.py`, `summary.py`
      2. `summary.py` computes summary values required by reports to SAGE
      3. Small changes to `inference.py` and `simulate.py` to reflect baked-in `nu` parameter in `model_spec.py`.