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Make pipeline inference tests more focused #475
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seabbs
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404-upgrade-the-testmode-pipeline-script-to-just-pipeline-script
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Make pipeline inference tests more focused #475
seabbs
merged 2 commits into
404-upgrade-the-testmode-pipeline-script-to-just-pipeline-script
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fix-pipeline-test
Oct 4, 2024
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Try this Pull Request!Open Julia and type: import Pkg
Pkg.activate(temp=true)
Pkg.add(url="https://github.com/CDCgov/Rt-without-renewal", rev="fix-pipeline-test", subdir="EpiAware")
using EpiAware |
Codecov ReportAll modified and coverable lines are covered by tests ✅
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## 404-upgrade-the-testmode-pipeline-script-to-just-pipeline-script #475 +/- ##
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Coverage 90.02% 90.02%
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Files 57 57
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Misses 74 74 ☔ View full report in Codecov by Sentry. |
seabbs
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seabbs
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…dictive + full (#445) * remove most compat from pipeline * Update test_pipelinefunctions.jl * Fix the truthdata output to be missing or Int * change to daily increments in latent processes * Change default AD mode to ReverseDiff{true} * Create changelog.md * reformat * change filename * Update simulate.jl * add a testmode to pipelinetypes * tighten typing * fix constructor * fix constructor * pipeline helper functions * unit tests and end-to-end tests * remove old scripts * Fix y_t type * bring inference prefixing into line with truthdata prefixing * reformat * interim commit * rename and collect plot functions * tidy up tests * basic plots to Makie * new plot tests and test reorganisation * Update runtests.jl * reformat * 455 plotting methods of prior predictive (#462) * add priorpredictive method to make_inference * Add pipeline priorpredictive boolean * reformat * remove inference_method kwarg because can be dispatched on * remove specialisation on forecast results add missing handling as well * move inference step into own function and give fail cover with error report * remove passing inference_method * add a latent model name to InferenceConfig * Util for setting up PI levels * prior pred plot * export prior_predictive_plot * remove dead end-to-end test in favour of direct test of prior_predictive_plot * Make pipeline inference tests more focused (#475) * fix tests and capture forecasting failures * delete stale end-to-end test * Full priorpred check pipeline script (#476) * Hotfix: Doc link to main * create xexpy function with x = 1 typestable (#473) * rename data folder * catch bug where objects were getting saved to root dir * fix bug where being saved to root * add priorpredictive mode to the inference config struct * do_truthdata behaviour modifed by prior predictive * send priorpredictive mode in generate_inference * update tests * prior predictive pipeline * reformat --------- Co-authored-by: Sam Abbott <[email protected]> * Add oneexpy to pipeline (#480) * Changed saved prior predictive data (#478) * change to pipeline being part of InferenceConfig This also splits figure saving from data saving * fix passed var * change serialisation target dir * update tests and config usage to pass pipeline object --------- Co-authored-by: Sam Abbott <[email protected]> * Update run_priorpred_pipeline.jl * Only save strings rather than Exception objects --------- Co-authored-by: Sam Abbott <[email protected]>
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This PR rationalises the tests in the pipeline to make it easier to identify the error in the forecast step.
Closes #474
From this branch
Which focuses the issue towards wild sampling (probably due to very badly specified priors).