Add oneexpy to pipeline #480
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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="add-oneexpy-to-pipeline", subdir="EpiAware")
using EpiAware |
SamuelBrand1
changed the base branch from
main
to
404-upgrade-the-testmode-pipeline-script-to-just-pipeline-script
seabbs
approved these changes
Oct 7, 2024
seabbs
merged commit ae8e3ca
into
404-upgrade-the-testmode-pipeline-script-to-just-pipeline-script
11 checks passed
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## 404-upgrade-the-testmode-pipeline-script-to-just-pipeline-script #480 +/- ##
=================================================================================================
Coverage 90.05% 90.05%
=================================================================================================
Files 57 57
Lines 744 744
=================================================================================================
Hits 670 670
Misses 74 74 ☔ View full report in Codecov by Sentry. |
Benchmark resultJudge resultBenchmark Report for /home/runner/work/Rt-without-renewal/Rt-without-renewalJob Properties
ResultsA ratio greater than
Benchmark Group ListHere's a list of all the benchmark groups executed by this job:
Julia versioninfoTargetBaselineTarget resultBenchmark Report for /home/runner/work/Rt-without-renewal/Rt-without-renewalJob Properties
ResultsBelow is a table of this job's results, obtained by running the benchmarks.
Benchmark Group ListHere's a list of all the benchmark groups executed by this job:
Julia versioninfoBaseline resultBenchmark Report for /home/runner/work/Rt-without-renewal/Rt-without-renewalJob Properties
ResultsBelow is a table of this job's results, obtained by running the benchmarks.
Benchmark Group ListHere's a list of all the benchmark groups executed by this job:
Julia versioninfoRuntime information
|
github-merge-queue bot
pushed a commit
that referenced
this pull request
Oct 7, 2024
…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 <azw1@cdc.gov> * 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 <azw1@cdc.gov> * Update run_priorpred_pipeline.jl * Only save strings rather than Exception objects --------- Co-authored-by: Sam Abbott <azw1@cdc.gov>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
A small PR which brings the
LogExpFunctionsbased use ofexptransform which has safety againstNaNetc fromEpiAwareinto the pipeline as the defaulttransformation.Closes #479