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SciML / JumpProcesses.jl

Build and simulate jump equations like Gillespie simulations and jump diffusions with constant and state-dependent rates and mix with differential equations and scientific machine learning (SciML)
https://docs.sciml.ai/JumpProcesses/stable/
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Juliacon2023 Revision #319

Closed gzagatti closed 1 year ago

gzagatti commented 1 year ago

This PR contains the revision on the latest draft of the paper. Changes that I have made throughout the paper are commented.

Please also find the PDF version for easy reference.

isaacsas commented 1 year ago

CI doesn't seem to have run on your most recent commits?

Happy to merge when you say it is done, and CI has run through ok.

gzagatti commented 1 year ago

@isaacsas I pushed the final version of the draft with the benchmark figures.

Unfortunately, the format check keeps failing. I did run JuliaFormatter multiple times, but no more formatting is performed. So I don't know why CI keeps failing on that. Can you help?

isaacsas commented 1 year ago

Formatting is failing on files in the paper subfolder. I'd suggest either excluding that folder, or running the formatter on them.

Also, why has CI stopped running with your recent commits? It was running before, but now seems to have stopped.

isaacsas commented 1 year ago

Also, the formatter failing is minor. The bigger issue is that the CI that runs tests is not running at all anymore. If you look back to the last green commit it stopped running sometime after that.

gzagatti commented 1 year ago

@isaacsas, all CI tests passed. The Invalidations job was skipped as it is only executed in the main branch.

isaacsas commented 1 year ago

CI that calls the test/*.jl still didn’t run.

gzagatti commented 1 year ago

Which test is this one? I can't find it.

gzagatti commented 1 year ago

Is it this workflow? https://github.com/SciML/JumpProcesses.jl/blob/master/.github/workflows/CI.yml

I think it's only supposed to run on the master branch:

name: CI
on:
  pull_request:
    branches:
      - master
  push:
    branches:
      - master
isaacsas commented 1 year ago

Huh, that’s weird. Wonder why it was running before. The PR was still set to merge to a branch at that point I thought.

Have you run tests locally to make sure there are no issues? It would suck to submit it and then have someone have code problems on this branch.

isaacsas commented 1 year ago

Or is this fully up to date with master now?

gzagatti commented 1 year ago

Yes, I merged with master. Doing a diff returns no difference from master:

git diff origin/master --name-only | grep -v '^paper'
isaacsas commented 1 year ago

Great, all merged. Thanks!