[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:

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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?

matbesancon commented 4 months ago

@whedon remove @mschauer as reviewer

whedon commented 4 months ago

OK, @mschauer is no longer a reviewer

gdalle commented 4 months ago

I have kept this in mind, it is ominously hovering over my to-do list. Will try to get it over with this weekend

gdalle commented 4 months ago

About the docs, I didn't re-read all of it but I went through the home page and the first tutorial again, and they're much clearer. I liked the high level explanation of the concepts like jumps and aggregators. I ticked the last remaining box in this section

gdalle commented 4 months ago

@whedon commands

whedon commented 4 months ago

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

gdalle commented 4 months ago

@whedon check references

gdalle commented 4 months ago

@whedon check references

gdalle commented 4 months ago

Halfway through the paper. Sofar my remarks are mostly about the presentation rather than the scientific content, so nothing threatening :) see https://github.com/SciML/JumpProcesses.jl/issues/402

gdalle commented 4 months ago

@matbesancon do you know why @whedon doesn't wanna check the references?

matbesancon commented 4 months ago

@whedon check references

matbesancon commented 4 months ago

@whedon check references from branch juliacon2023

whedon commented 4 months ago

Attempting to check references... from custom branch juliacon2023

matbesancon commented 4 months ago

@gdalle there you go

whedon commented 4 months ago

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

OK DOIs

- 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
- 10.5281/zenodo.3875233 is OK
- 10.1371/journal.pone.0246961 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
- 10.5334/jors.151 is OK
- 10.1101/2021.03.30.437703 is OK
- 10.1029/2006JB004536 is OK
- 10.1063/1.1835951 is OK
- 10.5281/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

MISSING DOIs

- 10.1007/978-3-319-16859-3_42 may be a valid DOI for title: On the Theory of Stochastic Processes, with Particular Reference to Applications
- 10.1016/c2013-0-08097-8 may be a valid DOI for title: Foundations of General Topology

INVALID DOIs

- 10.5555/3122009.3122050 is INVALID

gdalle commented 4 months ago

Done here, I have checked all the items except the references, and put my last requests in another issue on the repo (https://github.com/SciML/JumpProcesses.jl/issues/402)

matbesancon commented 4 months ago

@gzagatti can you check the missing and invalid DOIs above?

gzagatti commented 4 months ago

Will do. I was planning to go over the review this week, but I will only have time next week. Thanks for the reminder.

gzagatti commented 3 months ago

@whedon generate pdf from branch juliacon2023

whedon commented 3 months ago

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

whedon commented 3 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

gzagatti commented 3 months ago

@whedon check references from branch juliacon2023

whedon commented 3 months ago

Attempting to check references... from custom branch juliacon2023

whedon commented 3 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
- 10.1007/978-3-030-84639-8 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

- 10.1007/978-3-319-16859-3_42 may be a valid DOI for title: On the Theory of Stochastic Processes, with Particular Reference to Applications

INVALID DOIs

- None

gzagatti commented 3 months ago

@gdalle We have completed our review. The latest version compiled and there were no DOI issues. The suggested missing DOI refers to a different document.

Please find the draft with changes highlighted in magenta here for easy reference.

gdalle commented 3 months ago

I have checked the remaining box and proofread the last version, which is fine by me! I spotted a few typos signalled in the issue (https://github.com/SciML/JumpProcesses.jl/issues/402) but otherwise the paper is good to go

gzagatti commented 3 months ago

@whedon generate pdf from branch juliacon2023

whedon commented 3 months ago

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

whedon commented 3 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

gzagatti commented 3 months ago

@whedon check references from branch juliacon2023

whedon commented 3 months ago

Attempting to check references... from custom branch juliacon2023

whedon commented 3 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
- 10.1007/978-3-030-84639-8 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

- 10.1007/978-3-319-16859-3_42 may be a valid DOI for title: On the Theory of Stochastic Processes, with Particular Reference to Applications

INVALID DOIs

- None

gzagatti commented 3 months ago

@gdalle Thanks very much for the time reviewing our paper. I'm glad that we finally reached the end of the review. Both the paper and the library documentation improved a great deal thanks to you!

@matbesancon I have fixed the typos and the latest version of the paper compiled without any issues. Please let us know about the next steps.

matbesancon commented 3 months ago

@whedon recomment-accept

whedon commented 3 months ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

matbesancon commented 3 months ago

@whedon recommend accept

whedon commented 3 months ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

matbesancon commented 3 months ago

@whedon recommend-accept

whedon commented 3 months ago

No archive DOI set. Exiting...

matbesancon commented 3 months ago

@gzagatti last two things to do:

give us the version of the package that corresponds to the submitted work
give us the DOI of the archive of the package as a Zenodo entry

gzagatti commented 3 months ago

I’m not familiar with Zenodo. Can you help me by pointing to some documentation that shows how to obtain the archive of the package as a Zenodo entry? Thanks.

matbesancon commented 3 months ago

Zenodo is an archiving system which produces a DOI from a given set of documents, files, datasets, etc. Once you connect on zenodo.org, there is an option in the menu to import a package from github

isaacsas commented 3 months ago

I turned on Zenodo for JumpProcesses, but it appears it only archives new releases going forward. @gzagatti you should probably just manually upload the version of record that was used in the paper benchmarking to Zenodo as a zip file to generate a custom DOI for it.

gzagatti commented 3 months ago

@whedon check references from branch juliacon2023

whedon commented 3 months ago

Attempting to check references... from custom branch juliacon2023

whedon commented 3 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

- 10.1007/978-3-319-16859-3_42 may be a valid DOI for title: On the Theory of Stochastic Processes, with Particular Reference to Applications

INVALID DOIs

- None

gzagatti commented 3 months ago

@whedon generate pdf from branch juliacon2023

whedon commented 3 months ago

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

whedon commented 3 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

gzagatti commented 3 months ago

@matbesancon, please see below the information you requested:

JumpProcesses.jl v9.9
Zenodo DOI: https://doi.org/10.5281/zenodo.10786561

FYI, we've made a minor update to the draft to include this information in the paper. See SciML/JumpProcesses.jl#407

JuliaCon / proceedings-review