[REVIEW]: Extending JumpProcess.jl for fast point process simulation with time-varying intensities #133

whedon · 2023-08-28T16:09:35Z

Submitting author: @gzagatti (Guilherme Augusto Zagatti)
Repository: https://github.com/SciML/JumpProcesses.jl
Branch with paper.md (empty if default branch): juliacon2023
Version: v9.9
Editor: @matbesancon
Reviewers: @gdalle
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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✨ 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?

The text was updated successfully, but these errors were encountered:

whedon · 2023-08-28T16:09:38Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @gdalle it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

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matbesancon · 2023-08-28T16:10:02Z

@whedon generate pdf from branch juliacon

whedon · 2023-08-28T16:10:05Z

Attempting PDF compilation from custom branch juliacon. Reticulating splines etc...

whedon · 2023-08-28T16:11:00Z

PDF failed to compile for issue #133 with the following error:

 Can't find any papers to compile :-(

whedon · 2023-08-28T16:11:01Z

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.17 s (554.4 files/s, 74814.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           68           1256            703           7287
Markdown                        13            601              0           2415
YAML                             8             12              8            183
TOML                             3              5              0             67
TeX                              1              0              0             13
-------------------------------------------------------------------------------
SUM:                            93           1874            711           9965
-------------------------------------------------------------------------------


Statistical information for the repository '0ca2f44339de62ccc342dbe0' was
gathered on 2023/08/28.
No commited files with the specified extensions were found.

matbesancon · 2023-08-28T16:11:18Z

@whedon generate pdf from branch juliacon2023

whedon · 2023-08-28T16:11:21Z

Attempting PDF compilation from custom branch juliacon2023. Reticulating splines etc...

whedon · 2023-08-28T16:11:38Z

PDF failed to compile for issue #133 with the following error:

 Can't find any papers to compile :-(

whedon · 2023-08-28T16:12:12Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

matbesancon · 2023-08-28T16:12:23Z

there we go

gdalle · 2023-08-28T16:17:48Z

thought we'd never get there 🤣

matbesancon · 2023-09-03T07:27:16Z

same 😬

matbesancon · 2023-09-06T08:15:27Z

@whedon add @mschauer as reviewer

whedon · 2023-09-06T08:15:33Z

OK, @mschauer is now a reviewer

mschauer · 2023-09-06T08:24:35Z

Disclaimer: I am collaborating with Chris on related topics, @matbesancon and I discussed shortly and decided that I will accept this review request.

matbesancon · 2023-09-08T10:23:44Z

@mschauer @gdalle thanks for agreeing to review, let us know if you need anything, indication, etc

whedon · 2023-09-11T16:09:47Z

👋 @gdalle, please update us on how your review is going (this is an automated reminder).

mschauer · 2023-09-11T16:50:19Z

Can you turn on line numbers?

gzagatti · 2023-09-12T03:31:41Z

Here is the paper with line numbers to facilitate your review: paper.pdf. Hope the review is going well. Thanks for doing it!

gzagatti · 2023-09-28T03:05:20Z

@gdalle @mschauer thanks for reviewing the paper. I was wondering if you had time to advance with the review. I'm looking forward to addressing your feedback to get the paper published as soon as possible.

gdalle · 2023-09-28T07:22:45Z

I'm sorry I was completely swamped lately. I'm gonna try to take a first look tomorrow

editorialbot · 2024-04-09T11:41:55Z

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

editorialbot · 2024-04-09T11:44:55Z

⚠️ Couldn't acccept/publish paper. An error happened.

lucaferranti · 2024-04-09T13:53:51Z

@editorialbot recommend-accept

editorialbot · 2024-04-09T13:53:54Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-04-09T13:54:20Z

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 · 2024-04-09T13:57:27Z

⚠️ Error preparing paper acceptance.

gzagatti · 2024-04-22T16:04:07Z

@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 · 2024-04-22T16:06:29Z

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 · 2024-04-23T08:50:02Z

@editorialbot recommend-accept

lucaferranti · 2024-04-23T08:53:17Z

@editorialbot recommend-accept

editorialbot · 2024-04-23T08:53:20Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-04-23T08:54:38Z

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 · 2024-04-23T08:56:24Z

⚠️ Error preparing paper acceptance.

lucaferranti · 2024-04-23T08:59:42Z

@editorialbot recommend-accept

editorialbot · 2024-04-23T08:59:45Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-04-23T09:01:23Z

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 · 2024-04-23T09:07:02Z

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

Check final proof 👉📄 Download article

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

lucaferranti · 2024-04-23T09:08:24Z

@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 · 2024-04-23T13:33:44Z

Thanks a lot!

matbesancon · 2024-04-23T13:34:02Z

@editorialbot accept

editorialbot · 2024-04-23T13:34:05Z

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

editorialbot · 2024-04-23T13:42:27Z

🚨🚨🚨 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 👉 Creating pull request for 10.21105.jcon.00133 proceedings-papers#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 · 2024-04-23T13:43:19Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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 · 2024-04-23T13:43:55Z

congrats @gzagatti, and thanks to @gdalle too!

gzagatti · 2024-04-23T14:40:15Z

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.

whedon added Julia review TeX labels Aug 28, 2023

whedon assigned matbesancon Aug 28, 2023

whedon mentioned this issue Aug 28, 2023

[PRE REVIEW]: Extending JumpProcess.jl for fast point process simulation with time-varying intensities #132

Closed

whedon assigned gdalle and matbesancon and unassigned matbesancon Sep 6, 2023

whedon assigned mschauer Sep 6, 2023

lucaferranti mentioned this issue Apr 23, 2024

remove dirty files JuliaCon/proceedings-papers#87

Merged

editorialbot added the recommend-accept label Apr 23, 2024

editorialbot added accepted published labels Apr 23, 2024

matbesancon closed this as completed Apr 23, 2024

[REVIEW]: Extending JumpProcess.jl for fast point process simulation with time-varying intensities #133

[REVIEW]: Extending JumpProcess.jl for fast point process simulation with time-varying intensities #133

Comments

whedon commented Aug 28, 2023 • edited by editorialbot

Status

Reviewer instructions & questions

Review checklist for @gdalle

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Paper format

Content

whedon commented Aug 28, 2023

matbesancon commented Aug 28, 2023

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gdalle commented Aug 28, 2023

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whedon commented Sep 6, 2023

mschauer commented Sep 6, 2023

matbesancon commented Sep 8, 2023

whedon commented Sep 11, 2023

mschauer commented Sep 11, 2023

gzagatti commented Sep 12, 2023

gzagatti commented Sep 28, 2023

gdalle commented Sep 28, 2023

editorialbot commented Apr 9, 2024

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gzagatti commented Apr 22, 2024

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whedon commented Aug 28, 2023 •

edited by editorialbot