Milestones
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Work to systematically improve the runtime and resource consumption of `flepiMoP`.
No due date•0/1 issues closed- No due date•15/22 issues closed
Issues that enable module inference and comparison of different inference methodologies/improvements. Includes: The implementation of new inference algorithms & methodologies (hierarchical models, EMCEE, etc.), New features to decouple simulation and output storage from inference in gempyor, and Bugs encountered in inference algorithms that produce incorrect results. Issues that enable modular simulators/models. Includes: * The implementation of new simulators/models (Rt based nowcasts, machine learning models, etc.), * Extracting `gempyor`'s compartmental model into a structured format independent of inference/output storage, * Configuration changes required to enable modular simulators/models, and * Bugs encountered in developing simulators/models.
No due date•0/7 issues closedGeneral improvements to the software quality of flepiMoP including - Docstring documentation, - Unit tests, - Linting/styling, and - Removal of unused code. Issues under this milestone should not have any user facing changes beyond API changes. Any API changes should be considered carefully.
No due date•30/63 issues closed- No due date•0/7 issues closed
Creating and improving tools for post-processing and scenario analysis. Includes objectives like: * Updating post-processing tools designed for the R inference to work with EMCEE and other methodologies, * Creating new post-processing/scenario analysis tools, * Adding new features to post-processing to facilitate new SMH and other submissions, and * Making these tools easily accessible in batch runs to automate post-inference steps.
No due date•4/10 issues closedIssues that enable modular inference and comparison of different inference methodologies/improvements. Includes: * The implementation of new inference algorithms & methodologies (hierarchical models, EMCEE, etc.), * New features to decouple simulation and output storage from inference in `gempyor`, and * Bugs encountered in inference algorithms that produce incorrect results.
No due date•2/18 issues closedImprove the process of doing incremental calibrations and projections to meet tight timeline forecasting objectives like FluSight with an emphasis on operational user experience. Includes: * Improvements to CLI tooling used for incremental calibration and projections, * Additional features to ease the process of doing incremental work from a baseline well fitted model, * Addressing bugs that arise in the process of working with updated data and configurations for projections.
No due date•2/6 issues closedImprovements to documentation and `flepiMoP` itself to simplify installation and usage. Previously known as "Under 1Hr New Users!", which this milestone encompasses and more.
No due date•29/41 issues closedProject aims are to compare the effect of punctuated novel variant emergence vs our continuous immune ladder evolution structure on projections
Overdue by 2 year(s)•Due by December 22, 2023•1/1 issues closedStabilize the configuration file and supplementary input (seeding, parameters, etc.) file formats. Includes objectives like: * Creating a configuration/supplementary file format that is stable and tested, * Moving external inputs into the configuration, namely environment variables, * Writing documentation that clearly describes said file formats, * New features and additions to the configuration files, and * Improvements in catching input errors as early as possible for quick feedback.
No due date•27/61 issues closed