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[REVIEW]: Benchmarking Hierarchical Reasoning with HierarchyCraft #6468

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editorialbot opened this issue Mar 11, 2024 · 58 comments
Open

[REVIEW]: Benchmarking Hierarchical Reasoning with HierarchyCraft #6468

editorialbot opened this issue Mar 11, 2024 · 58 comments
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PowerShell Python review TeX Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning

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editorialbot commented Mar 11, 2024

Submitting author: @MathisFederico (Mathis Federico)
Repository: https://github.com/IRLL/HierarchyCraft
Branch with paper.md (empty if default branch):
Version: v1.2.4
Editor: @logological
Reviewers: @lwu9, @Christopher-Henry-UM, @inpefess
Archive: Pending

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/8cb63e5284d648614ab711bb52099988"><img src="https://joss.theoj.org/papers/8cb63e5284d648614ab711bb52099988/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/8cb63e5284d648614ab711bb52099988/status.svg)](https://joss.theoj.org/papers/8cb63e5284d648614ab711bb52099988)

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

@lwu9 & @Christopher-Henry-UM, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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

Checklists

📝 Checklist for @lwu9

📝 Checklist for @Christopher-Henry-UM

📝 Checklist for @inpefess

@editorialbot editorialbot added PowerShell Python review TeX Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning waitlisted Submissions in the JOSS backlog due to reduced service mode. labels Mar 11, 2024
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Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.12 s (1032.4 files/s, 205378.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          79           2128           1576           8445
SVG                              5              5              5           7817
HTML                            14            686             28           1470
Jinja Template                   5             27             39            527
CSS                              4            108             48            523
Markdown                         4            133              0            268
TeX                              1             22              0            225
YAML                             7             21             12            209
TOML                             1             19              7             89
JavaScript                       1              4              6             20
PowerShell                       2              0              0              2
-------------------------------------------------------------------------------
SUM:                           123           3153           1721          19595
-------------------------------------------------------------------------------

Commit count by author:

   856	Mathïs Fédérico
   134	MathisFederico
     3	SWang848
     2	metaylor

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Paper file info:

📄 Wordcount for paper.md is 1449

✅ The paper includes a Statement of need section

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License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

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

OK DOIs

- None

MISSING DOIs

- No DOI given, and none found for title: The Malmo Platform for Artificial Intelligence Exp...
- No DOI given, and none found for title: Unified Planning Framework
- No DOI given, and none found for title: Benchmarking the Spectrum of Agent Capabilities
- 10.1016/s0004-3702(99)00052-1 may be a valid DOI for title: Between MDPs and semi-MDPs: A framework for tempor...
- No DOI given, and none found for title: Minimalistic Gridworld Environment for Gymnasium
- 10.1613/jair.5699 may be a valid DOI for title: Revisiting the arcade learning environment: Evalua...
- No DOI given, and none found for title: The NetHack learning environment
- No DOI given, and none found for title: Retrospective Analysis of the 2019 MineRL Competit...
- No DOI given, and none found for title: The MineRL 2020 Competition on Sample Efficient Re...
- No DOI given, and none found for title: Mastering Diverse Domains through World Models
- No DOI given, and none found for title: Leveraging procedural generation to benchmark rein...
- 10.1613/jair.3912 may be a valid DOI for title: The arcade learning environment: An evaluation pla...
- No DOI given, and none found for title: DeepMind Lab
- No DOI given, and none found for title: OpenAI Gym
- No DOI given, and none found for title: PDDLGym: Gym Environments from PDDL Problems
- No DOI given, and none found for title: PDDL - The Planning Domain Definition Language
- No DOI given, and none found for title: Interval-based relaxation for general numeric plan...
- No DOI given, and none found for title: Stable-Baselines3: Reliable Reinforcement Learning...
- No DOI given, and none found for title: The ANML Language
- No DOI given, and none found for title: Insights From the NeurIPS 2021 NetHack Challenge

INVALID DOIs

- None

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

@logological logological removed the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Mar 12, 2024
@logological
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@lwu9 and @Christopher-Henry-UM, thanks for agreeing to review this submission. In case you didn't receive the notification from editorialbot, please visit this issue on GitHub and review the Reviewer Instructions at the top of the thread. Let me know if you have any questions about the review process.

@Christopher-Henry-UM
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Thanks for the reminder Tristan! I will get to the review this week.

@lwu9
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lwu9 commented Mar 19, 2024 via email

@logological
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I just heard from Chris Henry that he won't be able to start his review for a few more days yet. But don't let that stop you, @lwu9, from starting your review once you're ready.

@logological
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Hey there @lwu9 and @Christopher-Henry-UM! I just wanted to ping you to ask whether you'll be able to start your reviews of this submission soon.

@lwu9
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lwu9 commented Apr 9, 2024 via email

@Christopher-Henry-UM
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Thank you for bearing with me. I will get to it this week.

@Christopher-Henry-UM
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Christopher-Henry-UM commented Apr 15, 2024

Review checklist for @Christopher-Henry-UM

Conflict of interest

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the https://github.com/IRLL/HierarchyCraft?
  • License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@MathisFederico) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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 functionality 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

Software paper

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

@lwu9
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lwu9 commented Apr 15, 2024

Review checklist for @lwu9

Conflict of interest

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the https://github.com/IRLL/HierarchyCraft?
  • License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@MathisFederico) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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 functionality 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

Software paper

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

@lwu9
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lwu9 commented Apr 15, 2024

  1. There are two authors in the paper but there are three contributors in GitHub.
  2. I was able to install the package, but when I ran "action = get_human_action(env)", it got stuck.
  3. I didn't find clear community guidelines.

@logological
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@lwu9 Thanks for the review so far. Is your second issue blocking you from performing other steps in the review? @MathisFederico, perhaps you could comment on the three issues?

@Christopher-Henry-UM
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I have performed most of the review except I am not comfortable checking the Functionality or the Performance boxes. The software is used to create arbitrary hierarchical environments that are compatible with the OpenAI Gym Reinforcement Learning framework or the AIPlan4EU Unified Planning Framework. This library enables users to easily create complex hierarchical structures that can be used to test and develop various reinforcement learning or planning algorithms.

While I am familiar with the concept of reinforcement learning, I do not have the experience with the type of programming this library was created for. As a result, I have no way to test it other than to carry out the Quickstart steps listed in the documentation.

@logological
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Thanks, @Christopher-Henry-UM. @MathisFederico, are there any further reviewers you could nominate with the requisite knowledge of OpenAI Gym Reinforcement Learning or AIPlan4EU Unified Planning Framework to evaluate the functional claims of your submission? Also, could you please respond to my query upthread concerning the issues raised by @lwu9?

@MathisFederico
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MathisFederico commented May 1, 2024

Thanks for the reviews so far !

Sorry @logological for being long to answer, it has been two very busy weeks...

About @lwu9 issues:

  1. There are two authors in the paper but there are three contributors in GitHub.

I was not sure if I could add @SWang848 and @liyuxuan-academic because most of their contributions where non-code ones (testing, reviewing documentation, discussing ideas, ...) but re-reading JOSS authorship guidelines it seems that I could indeed ! I asked them if they want to be added as author (and not just being in acknowledgments as now) and will update according to their answers.

2. I was able to install the package, but when I ran "action = get_human_action(env)", it got stuck.

When using human actions, the program will pause and wait for the action of the human, meaning you !
A pygame window should pop (be sure to have gui optional requirements as indicated in the readme):

Initial pygame window for the readme example)

You can select action be either using arrows and pressing enter, or by just clicking on available actions.
Selecting wood block would result in this:

image

3. I didn't find clear community guidelines.

There was a CONTRIBUTING.md file but the readme didn't mention it indeed ! It is now added !

About @Christopher-Henry-UM issues:

There are tests that checks those facts automatically both for planning (see planning tests) and for gym API (see gym tests) also for the gym compatibility this library has been heavily used with stable-baselines3 that requires the gym API to be valid.

I still asked around in the planning community to know if someone would like to review, I will update here if I find someone !

@MathisFederico
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MathisFederico commented May 9, 2024

After their approval, I've added both non-code co-authors @logological

Need any help regarding issue 2 @lwu9 ?

@maltehelmert
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@maltehelmert @roeger Would you be willing and able to review this submission for the Journal of Open Source Software? We're particularly looking for a reviewer who has familiarity with the OpenAI Gym or AIPlan4EU platforms.

I'm sorry I'm currently overcommitted. :-( I think it's the same for @roeger. But perhaps you can recommend someone from the AIPlan4EU contributors, Gabi?

@logological
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@alvalentini @arbimo @mikand Would you be willing and able to review this submission for the Journal of Open Source Software? We're particularly looking for a reviewer who has familiarity with the OpenAI Gym or AIPlan4EU platforms.

@logological
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@hstairs Would you be willing and able to review this submission for the Journal of Open Source Software? We're particularly looking for a reviewer who has familiarity with the OpenAI Gym or AIPlan4EU platforms.

@logological
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@MathisFederico Thanks for your continued patience. I have been continuing to reach out to potential reviewers by e-mail, and will see if I can contact a few more today through GitHub. Hopefully we will get someone to accept soon.

@logological
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@inpefess @lutzhamel Would you be willing and able to review this submission for the Journal of Open Source Software? We're particularly looking for a reviewer who has familiarity with the OpenAI Gym or AIPlan4EU platforms.

@MathisFederico
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@MathisFederico Thanks for your continued patience. I have been continuing to reach out to potential reviewers by e-mail, and will see if I can contact a few more today through GitHub. Hopefully we will get someone to accept soon.

I'm not in a hurry no problem, Thanks for doing what you do.

I have to fix the AI4Plan compatibility with their last breaking changes anyway and adding the Hierarchical Task Network conversion is something that I have to finish up.

I guess software is always evolving anyway and I intend to maintain this repo as long as the question "How do we quantify the hierarchicality of a behavior, task and environment" remains open, and it is still wide open today.

@logological
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@madmage Would you be willing and able to review this submission for the Journal of Open Source Software? We're particularly looking for a reviewer who has familiarity with the OpenAI Gym or AIPlan4EU platforms.

@inpefess
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inpefess commented Aug 5, 2024

@inpefess @lutzhamel Would you be willing and able to review this submission for the Journal of Open Source Software? We're particularly looking for a reviewer who has familiarity with the OpenAI Gym or AIPlan4EU platforms.

Yes, it would be a pleasure for me to review this submission. I don't know anything about AIPlan4EU yet, but I have relveant experience in creating and using OpenAI Gym environments.

@madmage
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madmage commented Aug 5, 2024 via email

@logological
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@inpefess Thanks so much! We'd be delighted to have your review for this submission. I'll have our editorial bot prepare a review checklist for you and you can get to work on it at your convenience (though we'd ask that you try to submit your review in two to three weeks if possible.) You should receive a GitHub notification once the checklist is ready for you.

@logological
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@madmage It seems that another potential reviewer gave a positive response to my call a couple hours before you did, and so we wouldn't need your review after all. Nonetheless thanks for getting back to me, and I hope you might consider reviewing for JOSS in the future!

@logological
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@editorialbot add @inpefess as reviewer

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@inpefess added to the reviewers list!

@logological
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@inpefess I've added you as a reviewer, but it seems I may have been mistaken about being able to generate the review checklist for you. I think that you will need to do this yourself: please post a comment in this issue with the text @editorialbot generate my checklist.

@inpefess
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inpefess commented Aug 8, 2024

Review checklist for @inpefess

Conflict of interest

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the https://github.com/IRLL/HierarchyCraft?
  • License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@MathisFederico) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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 functionality 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

Software paper

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

@inpefess
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@MathisFederico Thank you for developing HierarchyCraft! It's really cool! I added several issues related to my check-list to your repository (linked to this one), please have a look at them when you have time.

@MathisFederico
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MathisFederico commented Aug 15, 2024

@inpefess Thank you for your review ! Lots of very good issues !

I'm currently in the process of making my research packages uploaded on nixpkgs for better reproducibility.
I'll take care of all the issues you mentioned right after that !

@MathisFederico
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@inpefess I've (hopefully) fixed the issues you raised code-wise, I'll get to the paper issue in the following week probably.
Could you please tell me for each issue if you confirm the fix ? Thanks !

@logological
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@MathisFederico I see that all the issues raised by @inpefess except for IRLL/HierarchyCraft#45 are now closed, and that a commit referencing the latter issue was applied a few days ago, though the commit message doesn't speak to every comment raised in that issue. Will you be continuing to revise the paper to address the remaining comments in that issue? (Not that I am trying to rush you—I'm just trying to keep track of the progress so that it doesn't stall.)

@MathisFederico
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Yes I will, sorry this past month has been filled with a lot of new things (new place, new job, ...)
But I do intend to finish it (the paper part is not my strong point)

@logological
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Hey there @MathisFederico – just wanted to check in with you once again to confirm that you still intend to complete the remaining revisions. If you haven't had the time to do any work so far, please let me know when I should ping you again for an update.

@MathisFederico
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MathisFederico commented Oct 26, 2024

Hey @logological ! Yeah crazy rush those past weeks, but this is still in my backlog !

I hope to do it by then end of november at best tbh ...

@logological
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@MathisFederico How are you coming along with the remaining revisions? Do you have an expected timeline for completion?

@logological
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Any update for me, @MathisFederico? I haven't heard from you since October 26—please let me know if you're still interested in seeing this submission through to publication.

@MathisFederico
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Hey @logological, sorry I missed your last message, we are currently working on the last issues and I will do a small code update then we will be good to go again !

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