Upgrade the testmode pipeline script to pipeline scripts: prior predictive + full
#445
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
…dcasting-to-weekly-to-daily-increments-in-underlying-latent-processes
…just-pipeline-script
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="404-upgrade-the-testmode-pipeline-script-to-just-pipeline-script", subdir="EpiAware")
using EpiAware |
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #445 +/- ##
==========================================
+ Coverage 90.02% 90.05% +0.02%
==========================================
Files 57 57
Lines 742 744 +2
==========================================
+ Hits 668 670 +2
Misses 74 74 ☔ View full report in Codecov by Sentry. |
…just-pipeline-script
…ne-script' into 433-forecast-function-in-pipeline-is-broken-after-move-to-turing-033
…after-move-to-turing-033
…just-pipeline-script
…to-turing-033' into 404-upgrade-the-testmode-pipeline-script-to-just-pipeline-script
|
I've merged in removal of all basic plots in favour of |
|
Steps towards full PR:
|
* 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
…just-pipeline-script
…just-pipeline-script
* fix tests and capture forecasting failures * delete stale end-to-end test
* 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]>
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
|
* 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]>
…just-pipeline-script
|
This branch now runs both the prior predictive and the full pipelines, with in cases of numerical error in any of the steps it serialises the Since, it is no longer broken code, but rather improvable code I propose merging into |
SamuelBrand1
changed the title
testmode pipeline script to just pipeline script -- Do not mergetestmode pipeline script to pipeline scripts: prior predictive + full
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
|
seabbs
approved these changes
Oct 7, 2024
seabbs
deleted the
404-upgrade-the-testmode-pipeline-script-to-just-pipeline-script
branch
2 tasks
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.
This Draft PR has the improvements I'm making to the pipeline towards resolving #404. There were quite a number of improvements before I noticed that the forecast function was now broken:
pipelinetestmode boolean field which is useful for the test running.This is tested using the updated
EpiAwarehash 9c52763.Currently forecast function in pipeline is still broken, but this is a good place to fix from.