Patch fix: add Manifest.toml to benchmarking
#524
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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="patch-fix-benchmarkci-manifest", subdir="EpiAware")
using EpiAware |
seabbs
approved these changes
Nov 14, 2024
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #524 +/- ##
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Coverage 89.64% 89.64%
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Files 53 53
Lines 753 753
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Hits 675 675
Misses 78 78 ☔ View full report in Codecov by Sentry. |
seabbs
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Dec 5, 2024
* Patch: Switch to fork of benchmarkCI (#520) * patch to fork of benchmarkCI * put fork version of BenchmarkCI in [sources] * swap order * add EpiAware [source] * fix path * rm benchmarkCI from project * Patch fix: add `Manifest.toml` to benchmarking (#524) * trigger * Update benchmark.yaml * Update benchmark.yaml * commit benchmark Manifest * try alternate approach * Update benchmark.yaml * Update EpiMethod.jl * Update benchmark.yaml * change baseline to origin/main * remove trigger * rm other trigger * Issue 465: Add an infection generating model for ODE problems (#510) * CompatHelper: bump compat for Turing to 0.35 for package EpiAware, (drop existing compat) (#516) * CompatHelper: bump compat for Turing to 0.35 for package EpiAware, (drop existing compat) * Update Project.toml * fix Project.toml --------- Co-authored-by: CompatHelper Julia <[email protected]> Co-authored-by: Sam Abbott <[email protected]> Co-authored-by: Samuel Brand <[email protected]> Co-authored-by: Samuel Brand <[email protected]> * CompatHelper: bump compat for DynamicPPL to 0.30 for package EpiAware, (drop existing compat) (#528) Co-authored-by: CompatHelper Julia <[email protected]> * rename IDD -> IID * rename test file * Issue 529: Create null Latent model (#530) * Null Latent model * Null Latent model * fix doctest * fix generate_epiaware unit tests New usage of RW * fix turing method test underlying std of step size changed name * fix broadcast test Underlying std param changed name * fix HN unit test Default std prior had changed * fix AR unit tests --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: CompatHelper Julia <[email protected]> Co-authored-by: Sam Abbott <[email protected]>
seabbs
added a commit
that referenced
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Dec 12, 2024
* draft MA method * draft MA methd * use IDD for epsilon in all models * add MA benchmark * Add docs and tests for IDD * make episilon_t a arg of the latent model constructors * improve MA correctness * fully import EpiAwareUtils * add a test for IDD * add tests for MA.jl * add doc tests and unit tests + start on helper fn * more updatres to AR appraoc * chase down partial arg changes * clean up AR * clean up and add arma and arima helpers * Contributions towards Arma/Arima models (#531) * Patch: Switch to fork of benchmarkCI (#520) * patch to fork of benchmarkCI * put fork version of BenchmarkCI in [sources] * swap order * add EpiAware [source] * fix path * rm benchmarkCI from project * Patch fix: add `Manifest.toml` to benchmarking (#524) * trigger * Update benchmark.yaml * Update benchmark.yaml * commit benchmark Manifest * try alternate approach * Update benchmark.yaml * Update EpiMethod.jl * Update benchmark.yaml * change baseline to origin/main * remove trigger * rm other trigger * Issue 465: Add an infection generating model for ODE problems (#510) * CompatHelper: bump compat for Turing to 0.35 for package EpiAware, (drop existing compat) (#516) * CompatHelper: bump compat for Turing to 0.35 for package EpiAware, (drop existing compat) * Update Project.toml * fix Project.toml --------- Co-authored-by: CompatHelper Julia <[email protected]> Co-authored-by: Sam Abbott <[email protected]> Co-authored-by: Samuel Brand <[email protected]> Co-authored-by: Samuel Brand <[email protected]> * CompatHelper: bump compat for DynamicPPL to 0.30 for package EpiAware, (drop existing compat) (#528) Co-authored-by: CompatHelper Julia <[email protected]> * rename IDD -> IID * rename test file * Issue 529: Create null Latent model (#530) * Null Latent model * Null Latent model * fix doctest * fix generate_epiaware unit tests New usage of RW * fix turing method test underlying std of step size changed name * fix broadcast test Underlying std param changed name * fix HN unit test Default std prior had changed * fix AR unit tests --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: CompatHelper Julia <[email protected]> Co-authored-by: Sam Abbott <[email protected]> * revert define_ namming * clean out repeated utils from merge * fix MA tests * fix RW tests - feel made about RandomWalk vs AR naming * fix remaining unit tests that aren't doctests * update latent recovery test * try and fix doctests automatically * update all doctests to output nothing - this is awful * add doctests for arima and arma * fix doctest * clean up deps * update replication studies * add interface tests for combination functions and add benchmarks * add some basic theoretical properties tests * name change IDD -> IID benchmarks * moving all the constructors because this PR is too contained * catch missing using * update iid benchmark: * update extraction * remove old param namme from case study * get the dot * get the dot * fix initial guess point for MAP opt * Update index.jl * add a compile time branch for HN * add a compile time branch for HN * update test * add a new constructor to get old default behaviour * update docs * update docs - using the structs for priors is very brittle * reorder prior plots --------- Co-authored-by: Samuel Brand <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: CompatHelper Julia <[email protected]> Co-authored-by: Samuel Brand <[email protected]>
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After some problems with the benchmarking CI, I came to the conclusion that the failure was due to swapping to
Pkg.addin CI which was causing uncommitted changes to the branch in the CI run leading to a failure ("dirty commit").To stabilise the changes on the checked out branch in CI I've add a
Manifest.tomlfile for the benchmarking following https://github.com/tkf/BenchmarkCI.jl#setup-with-benchmarkmanifesttoml .BenchmarkCIwe are using is specified there.EpiAwaredep is specified there.This reduces the CI command to just
instantiateand stops an error occurring between running benchmarks for the target and the baseline commits.Evidence that this works is the test draft PR #523 which is aimed at benchmarking the test branch
trigger-bci-2against the test branchtrigger-bci: both of which have this approach to specifying thebenchmarkproject deps.