[REVIEW]: Extending JumpProcess.jl for fast point process simulation with time-varying intensities

whedon commented 10 months ago

Submitting author: !--author-handle-->@gzagatti@matbesancon@gdalle<!--end-reviewers-list-- Archive: 10.5281/zenodo.10786561

Status

Status badge code:

HTML: <a href="https://proceedings.juliacon.org/papers/886f7f58f837a2c2d7437254c024cb0e"><img src="https://proceedings.juliacon.org/papers/886f7f58f837a2c2d7437254c024cb0e/status.svg"></a>
Markdown: [![status](https://proceedings.juliacon.org/papers/886f7f58f837a2c2d7437254c024cb0e/status.svg)](https://proceedings.juliacon.org/papers/886f7f58f837a2c2d7437254c024cb0e)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@gdalle, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @matbesancon know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @gdalle

Conflict of interest

[ ] As the reviewer I confirm that I have read the JuliaCon conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

[ ] I confirm that I read and will adhere to the JuliaCon code of conduct.

General checks

[ ] Repository: Is the source code for this software available at the repository url?
[ ] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[ ] Authorship: Has the submitting author (@gzagatti) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[ ] Installation: Does installation proceed as outlined in the documentation?
[ ] Functionality: Have the functional claims of the software been confirmed?
[ ] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[ ] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[ ] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[ ] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[ ] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[ ] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
[ ] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Paper format

[ ] Authors: Does the paper.tex file include a list of authors with their affiliations?
[ ] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[ ] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
[ ] Page limit: Is the page limit for full papers respected by the submitted document?

Content

[ ] Context: is the scientific context motivating the work correctly presented?
[ ] Methodology: is the approach taken in the work justified, presented with enough details and reference to reproduce it?
[ ] Results: are the results presented and compared to approaches with similar goals?

gzagatti commented 2 months ago

That’s great news! Thanks everyone! Do you know when the paper shows up in the proceedings page?

matbesancon commented 2 months ago

that might be the last bit of the pipeline we have to investigate

gzagatti commented 2 months ago

I hope it gets fixed soon. I am looking forward to have the paper listed in the official proceedings page.

I noticed that the CI errored on the "Deposit with JCon" task. It looks like the link https://proceedings.juliacon.org/papers/api_deposit does not exist.

lucaferranti commented 2 months ago

@matbesancon now acceptance should be working!

matbesancon commented 2 months ago

@editorialbot accept

editorialbot commented 2 months ago

Doing it live! Attempting automated processing of paper acceptance...

editorialbot commented 2 months ago

:warning: Couldn't acccept/publish paper. An error happened.

lucaferranti commented 2 months ago

@editorialbot recommend-accept

editorialbot commented 2 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 months ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.48550/arXiv.1707.03003 is OK
- 10.1214/18-AOS1715 is OK
- 10.1017/9781009002127 is OK
- 10.1007/978-1-4612-0253-0_9 is OK
- 10.1007/b97277 is OK
- 10.5281/zenodo.10477603 is OK
- 10.1002/cpa.3160360204 is OK
- 10.1021/jp993732q is OK
- 10.1214/aoms/1177706098 is OK
- 10.1016/0021-9991(76)90041-3 is OK
- 10.1021/j100540a008 is OK
- 10.1063/1.1378322 is OK
- 10.1146/annurev.physchem.58.032806.104637 is OK
- 10.1086/225469 is OK
- 10.3390/computation6010009 is OK
- 10.18637/jss.v035.i08 is OK
- 10.5281/zenodo.3875233 is OK
- 10.1371/journal.pone.0246961 is OK
- 10.5281/zenodo.10786561 is OK
- 10.1007/978-3-030-84639-8 is OK
- 10.1080/03610926.2021.1921214 is OK
- 10.1007/s10915-017-0607-4 is OK
- 10.2307/2335727 is OK
- 10.1002/nav.3800260304 is OK
- 10.1007/978-3-319-63113-4 is OK
- 10.1007/978-3-642-36461-7_12 is OK
- 10.1142/q0033 is OK
- 10.1016/j.compbiolchem.2005.10.007 is OK
- 10.1137/1.9781611974645 is OK
- 10.1038/s41567-018-0076-1 is OK
- 10.1103/PhysRevE.98.062321 is OK
- 10.1109/TIT.1981.1056305 is OK
- 10.1016/c2013-0-08097-8 is OK
- 10.5334/jors.151 is OK
- 10.1101/2021.03.30.437703 is OK
- 10.1029/2006JB004536 is OK
- 10.1063/1.1835951 is OK
- 10.1063/1.4928635 is OK
- 10.5281/zenodo.3716127 is OK
- 10.1063/1.2919546 is OK
- 10.1103/PhysRevE.77.066109 is OK
- 10.1063/1.4896985 is OK
- 10.1109/TCBB.2016.2530066 is OK
- 10.48550/arXiv.1504.06873 is OK
- 10.1214/aos/1176346060 is OK
- 10.48550/arXiv.1810.10122 is OK

MISSING DOIs

- No DOI given, and none found for title: An Introduction to the Theory of Point Processes: ...
- No DOI given, and none found for title: On Random Graphs I
- No DOI given, and none found for title: On the Evolution of Random Graphs
- No DOI given, and none found for title: COEVOLVE: A Joint Point Process Model for Informat...
- 10.1007/978-3-319-16859-3_42 may be a valid DOI for title: On the Theory of Stochastic Processes, with Partic...
- No DOI given, and none found for title: Lectures on the Poisson Process

INVALID DOIs

- None

editorialbot commented 2 months ago

:warning: Error preparing paper acceptance.

gzagatti commented 2 months ago

@matbesancon @lucaferranti any chance the CLI issues around publishing the paper in the official proceedings page have already been resolved? Our paper is not yet listed in the proceedings page, but there is a new paper that has been published 4 days ago.

gzagatti commented 2 months ago

The main issue is that while the paper is not listed in the JuliaCon proceedings webpage it becomes harder to discover it. For instance, it is not listed in Google Scholar.

lucaferranti commented 2 months ago

@editorialbot recommend-accept

lucaferranti commented 2 months ago

@editorialbot recommend-accept

editorialbot commented 2 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 months ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.48550/arXiv.1707.03003 is OK
- 10.1214/18-AOS1715 is OK
- 10.1017/9781009002127 is OK
- 10.1007/978-1-4612-0253-0_9 is OK
- 10.1007/b97277 is OK
- 10.5281/zenodo.10477603 is OK
- 10.1002/cpa.3160360204 is OK
- 10.1021/jp993732q is OK
- 10.1214/aoms/1177706098 is OK
- 10.1016/0021-9991(76)90041-3 is OK
- 10.1021/j100540a008 is OK
- 10.1063/1.1378322 is OK
- 10.1146/annurev.physchem.58.032806.104637 is OK
- 10.1086/225469 is OK
- 10.3390/computation6010009 is OK
- 10.18637/jss.v035.i08 is OK
- 10.5281/zenodo.3875233 is OK
- 10.1371/journal.pone.0246961 is OK
- 10.5281/zenodo.10786561 is OK
- 10.1007/978-3-030-84639-8 is OK
- 10.1080/03610926.2021.1921214 is OK
- 10.1007/s10915-017-0607-4 is OK
- 10.2307/2335727 is OK
- 10.1002/nav.3800260304 is OK
- 10.1007/978-3-319-63113-4 is OK
- 10.1007/978-3-642-36461-7_12 is OK
- 10.1142/q0033 is OK
- 10.1016/j.compbiolchem.2005.10.007 is OK
- 10.1137/1.9781611974645 is OK
- 10.1038/s41567-018-0076-1 is OK
- 10.1103/PhysRevE.98.062321 is OK
- 10.1109/TIT.1981.1056305 is OK
- 10.1016/c2013-0-08097-8 is OK
- 10.5334/jors.151 is OK
- 10.1101/2021.03.30.437703 is OK
- 10.1029/2006JB004536 is OK
- 10.1063/1.1835951 is OK
- 10.1063/1.4928635 is OK
- 10.5281/zenodo.3716127 is OK
- 10.1063/1.2919546 is OK
- 10.1103/PhysRevE.77.066109 is OK
- 10.1063/1.4896985 is OK
- 10.1109/TCBB.2016.2530066 is OK
- 10.48550/arXiv.1504.06873 is OK
- 10.1214/aos/1176346060 is OK
- 10.48550/arXiv.1810.10122 is OK

MISSING DOIs

- No DOI given, and none found for title: An Introduction to the Theory of Point Processes: ...
- No DOI given, and none found for title: On Random Graphs I
- No DOI given, and none found for title: On the Evolution of Random Graphs
- No DOI given, and none found for title: COEVOLVE: A Joint Point Process Model for Informat...
- 10.1007/978-3-319-16859-3_42 may be a valid DOI for title: On the Theory of Stochastic Processes, with Partic...
- No DOI given, and none found for title: Lectures on the Poisson Process

INVALID DOIs

- None

editorialbot commented 2 months ago

:warning: Error preparing paper acceptance.

lucaferranti commented 2 months ago

@editorialbot recommend-accept

editorialbot commented 2 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 months ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.48550/arXiv.1707.03003 is OK
- 10.1214/18-AOS1715 is OK
- 10.1017/9781009002127 is OK
- 10.1007/978-1-4612-0253-0_9 is OK
- 10.1007/b97277 is OK
- 10.5281/zenodo.10477603 is OK
- 10.1002/cpa.3160360204 is OK
- 10.1021/jp993732q is OK
- 10.1214/aoms/1177706098 is OK
- 10.1016/0021-9991(76)90041-3 is OK
- 10.1021/j100540a008 is OK
- 10.1063/1.1378322 is OK
- 10.1146/annurev.physchem.58.032806.104637 is OK
- 10.1086/225469 is OK
- 10.3390/computation6010009 is OK
- 10.18637/jss.v035.i08 is OK
- 10.5281/zenodo.3875233 is OK
- 10.1371/journal.pone.0246961 is OK
- 10.5281/zenodo.10786561 is OK
- 10.1007/978-3-030-84639-8 is OK
- 10.1080/03610926.2021.1921214 is OK
- 10.1007/s10915-017-0607-4 is OK
- 10.2307/2335727 is OK
- 10.1002/nav.3800260304 is OK
- 10.1007/978-3-319-63113-4 is OK
- 10.1007/978-3-642-36461-7_12 is OK
- 10.1142/q0033 is OK
- 10.1016/j.compbiolchem.2005.10.007 is OK
- 10.1137/1.9781611974645 is OK
- 10.1038/s41567-018-0076-1 is OK
- 10.1103/PhysRevE.98.062321 is OK
- 10.1109/TIT.1981.1056305 is OK
- 10.1016/c2013-0-08097-8 is OK
- 10.5334/jors.151 is OK
- 10.1101/2021.03.30.437703 is OK
- 10.1029/2006JB004536 is OK
- 10.1063/1.1835951 is OK
- 10.1063/1.4928635 is OK
- 10.5281/zenodo.3716127 is OK
- 10.1063/1.2919546 is OK
- 10.1103/PhysRevE.77.066109 is OK
- 10.1063/1.4896985 is OK
- 10.1109/TCBB.2016.2530066 is OK
- 10.48550/arXiv.1504.06873 is OK
- 10.1214/aos/1176346060 is OK
- 10.48550/arXiv.1810.10122 is OK

MISSING DOIs

- No DOI given, and none found for title: An Introduction to the Theory of Point Processes: ...
- No DOI given, and none found for title: On Random Graphs I
- No DOI given, and none found for title: On the Evolution of Random Graphs
- No DOI given, and none found for title: COEVOLVE: A Joint Point Process Model for Informat...
- 10.1007/978-3-319-16859-3_42 may be a valid DOI for title: On the Theory of Stochastic Processes, with Partic...
- No DOI given, and none found for title: Lectures on the Poisson Process

INVALID DOIs

- None

editorialbot commented 2 months ago

:wave: @JuliaCon/jcon-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/JuliaCon/proceedings-papers/pull/88, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

lucaferranti commented 2 months ago

@gzagatti this is now fixed! Long story short, since accept failed in the first attempt, it had left the folder in the papers repository in a dirty state and needed some manual clean-up.

Now everything works! I'll let @matbesancon pull the final trigger to accept the paper, since he's the editor in charge here

matbesancon commented 2 months ago

Thanks a lot!

matbesancon commented 2 months ago

@editorialbot accept

editorialbot commented 2 months ago

Doing it live! Attempting automated processing of paper acceptance...

editorialbot commented 2 months ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JCON! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/JuliaCon/proceedings-papers/pull/89
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/jcon.00133
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

editorialbot commented 2 months ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://proceedings.juliacon.org/papers/10.21105/jcon.00133/status.svg)](https://doi.org/10.21105/jcon.00133)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/jcon.00133">
  <img src="https://proceedings.juliacon.org/papers/10.21105/jcon.00133/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://proceedings.juliacon.org/papers/10.21105/jcon.00133/status.svg
   :target: https://doi.org/10.21105/jcon.00133

This is how it will look in your documentation:

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matbesancon commented 2 months ago

congrats @gzagatti, and thanks to @gdalle too!

gzagatti commented 2 months ago

Awesome thanks for all involved in this thread! I am really happy to have the paper finally published!

One minor comment. The Perl keyword has been assigned to the published paper which is a bit odd. Otherwise everything else looks Ok. @matbesancon @lucaferranti.

JuliaCon / proceedings-review