[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

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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?

gzagatti commented 3 months ago

@matbesancon did you get all the information you needed? I was just wondering if you had a rough estimate when the paper should be published. Thanks.

isaacsas commented 3 months ago

@gzagatti @matbesancon is there anything left we on the JumpProcesses side need to do to finish this off now? Thanks!

gzagatti commented 3 months ago

On my side it's all completed. I'm waiting for @matbesancon for further steps.

matbesancon commented 3 months ago

@whedon set v9.9 as version

editorialbot commented 3 months ago

My name is now @editorialbot

matbesancon commented 3 months ago

@editorialbot set v9.9 as version

editorialbot commented 3 months ago

I'm sorry @matbesancon, I'm afraid I can't do that. That's something only editors are allowed to do.

matbesancon commented 3 months ago

@editorialbot help

editorialbot commented 3 months ago

Hello @matbesancon, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set juliacon-paper as branch

# Reject paper
@editorialbot reject

# Withdraw paper
@editorialbot withdraw

# Invite an editor to edit a submission (sending them an email)
@editorialbot invite @(.*) as editor

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Accept and publish the paper
@editorialbot accept

# Update data on an accepted/published paper
@editorialbot reaccept

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

matbesancon commented 3 months ago

@editorialbot list editors

editorialbot commented 3 months ago

List of JuliaCon editors

@arfon
@fcdimitr
@lucaferranti
@luraess
@matbesancon
@odow
@pitsianis

matbesancon commented 3 months ago

@editorialbot commands

editorialbot commented 3 months ago

Hello @matbesancon, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set juliacon-paper as branch

# Reject paper
@editorialbot reject

# Withdraw paper
@editorialbot withdraw

# Invite an editor to edit a submission (sending them an email)
@editorialbot invite @(.*) as editor

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Accept and publish the paper
@editorialbot accept

# Update data on an accepted/published paper
@editorialbot reaccept

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

matbesancon commented 3 months ago

@editorialbot set 10.5281/zenodo.10786561 as archive

editorialbot commented 3 months ago

I'm sorry @matbesancon, I'm afraid I can't do that. That's something only editors are allowed to do.

matbesancon commented 3 months ago

@editorialbot recommend-accept

editorialbot commented 3 months ago

I'm sorry @matbesancon, I'm afraid I can't do that. That's something only editors are allowed to do.

matbesancon commented 3 months ago

@editorialbot accept

editorialbot commented 3 months ago

Paper is not ready for acceptance yet, the archive is missing

matbesancon commented 3 months ago

@editorialbot accept

matbesancon commented 3 months ago

@editorialbot accept

editorialbot commented 3 months ago

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

matbesancon commented 3 months ago

we are still migrating to the new process, some things have to be worked out but we will be able to complete this soon :)

editorialbot commented 3 months ago

:warning: Couldn't acccept/publish paper. An error happened. Paper file not found.

matbesancon commented 3 months ago

@editorialbot set juliacon as branch

editorialbot commented 3 months ago

Done! branch is now juliacon

matbesancon commented 3 months ago

@editorialbot generate pdf

matbesancon commented 3 months ago

@editorialbot commands

editorialbot commented 3 months ago

Hello @matbesancon, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set juliacon-paper as branch

# Reject paper
@editorialbot reject

# Withdraw paper
@editorialbot withdraw

# Invite an editor to edit a submission (sending them an email)
@editorialbot invite @(.*) as editor

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Accept and publish the paper
@editorialbot accept

# Update data on an accepted/published paper
@editorialbot reaccept

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

matbesancon commented 3 months ago

@editorialbot generate pdf

matbesancon commented 3 months ago

@editorialbot generate pdf from branch juliacon

editorialbot commented 3 months ago

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

@editorialbot commands

editorialbot commented 3 months ago

:warning: An error happened when generating the pdf.

editorialbot commented 3 months ago

:warning: An error happened when generating the pdf.

matbesancon commented 3 months ago

@editorialbot set juliacon2023 as branch

editorialbot commented 3 months ago

Done! branch is now juliacon2023

matbesancon commented 3 months ago

@editorialbot generate pdf

editorialbot commented 3 months ago

:warning: An error happened when generating the pdf.

gdalle commented 3 months ago

well this looks fun

matbesancon commented 3 months ago

Sponsored by https://github.com/JuliaWTF/WatchJuliaBurn.jl

isaacsas commented 3 months ago

Hi, just to check. Can we at this point list the manuscript as accepted? (I realize there are still processing issues going on, but I'm wondering what the status should be listed as for grant reports and such.) Thanks!

gzagatti commented 2 months ago

@matbesancon any updates on the publication?

matbesancon commented 2 months ago

@editorialbot generate pdf

matbesancon commented 2 months ago

@gzagatti we finalized the migration to the new infrastructure.

Can we at this point list the manuscript as accepted?

yes absolutely :)

editorialbot commented 2 months ago

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

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. Could not deposit with Open Journals.

matbesancon commented 2 months ago

So it errored but still accepted it :tada:

matbesancon commented 2 months ago

https://github.com/JuliaCon/proceedings-papers/blob/master/jcon.00133/10.21105.jcon.00133.pdf

JuliaCon / proceedings-review