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[REVIEW]: CM++ - A Meta-method for Well-Connected Community Detection #6073

Closed editorialbot closed 8 months ago

editorialbot commented 10 months ago

Submitting author: !--author-handle-->@chackoge<!--end-author-handle-- (George Chacko) Repository: https://github.com/illinois-or-research-analytics/cm_pipeline.git Branch with paper.md (empty if default branch): main Version: v4.0.0 Editor: !--editor-->@arfon<!--end-editor-- Reviewers: @LuisScoccola, @chryswoods Archive: 10.5281/zenodo.10501118

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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

@LuisScoccola & @chryswoods, 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 @arfon 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 @chryswoods

📝 Checklist for @LuisScoccola

editorialbot commented 10 months ago

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

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

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editorialbot commented 10 months ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (1166.6 files/s, 96696.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          43            723            400           2831
Markdown                         5            185              0            586
JSON                            16              0              0            547
TeX                              1             27              0            345
R                                5             62             76            117
YAML                             2              1              4             64
-------------------------------------------------------------------------------
SUM:                            72            998            480           4490
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 10 months ago

Wordcount for paper.md is 932

editorialbot commented 10 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1038/s41598-019-41695-z is OK
- 10.1162/qss_a_00184 is OK
- 10.1073/pnas.0706851105 is OK
- 10.1038/s41567-022-01716-7 is OK
- 10.1016/j.dam.2021.08.032 is OK
- 10.1126/sciadv.1602548 is OK
- 10.1002/asi.22990 is OK
- 10.1002/asi.22748 is OK
- 10.1093/molbev/mst228 is OK
- 10.1038/nature03288 is OK
- 10.1145/1134271.1134277 is OK
- 10.1371/journal.pcbi.1008239 is OK
- 10.1088/1742-5468/2008/10/P10008 is OK
- 10.1073/pnas.122653799 is OK
- 10.1002/sam.10133 is OK
- 10.1109/ibigdelft.2018.8625349 is OK
- 10.1002/wics.1566 is OK

MISSING DOIs

- 10.1101/gr.1239303 may be a valid DOI for title: Cytoscape: a software environment for integrated models of biomolecular interaction networks

INVALID DOIs

- None
editorialbot commented 10 months ago

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

arfon commented 10 months ago

@LuisScoccola, @chryswoods – This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above. Please create your checklist typing:

@editorialbot generate my checklist

As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/6073 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

(Noting here that @LuisScoccola mentioned in the pre-review thread that they won't be able to start for a couple of weeks).

chryswoods commented 10 months ago

Review checklist for @chryswoods

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

chryswoods commented 10 months ago

Hi - thanks for your submission. I've been going through the checklist above as part of the review. It's all going well, but I have a few questions / requests.

Traceback (most recent call last):

  File "/home/parallels/mambaforge/envs/review/lib/python3.10/runpy.py", line 196, in _run_module_as_main
    return _run_code(code, main_globals, None,

  File "/home/parallels/mambaforge/envs/review/lib/python3.10/runpy.py", line 86, in _run_code
    exec(code, run_globals)

  File "/home/parallels/review/cm_pipeline/hm01/cm.py", line 514, in <module>
    entry_point()

  File "/home/parallels/review/cm_pipeline/hm01/cm.py", line 510, in entry_point
    typer.run(main)

  File "/home/parallels/review/cm_pipeline/hm01/cm.py", line 422, in main
    assert resolution != -1, "Leiden requires resolution"

AssertionError: Leiden requires resolution

I recommend adding something like a "quick start" guide or similar, with complete input files for the examples, so that it is easier to get started straight away with the software. While you don't need as much, see here how in my software the user is taken on a journey from seeing if the software has the features they need, then a very simple install guide, then a quick start guide to quickly explore the software (before then more detailed guides and a tutorial). Something like this can really make a difference to a user's experience of the software.

Thanks :-)

chackoge commented 10 months ago

Thanks for these very helpful comments Christopher. We will respond ASAP. George Chacko

On Tue, Dec 5, 2023 at 10:56 AM Christopher Woods @.***> wrote:

Hi - thanks for your submission. I've been going through the checklist above as part of the review. It's all going well, but I have a few questions / requests.

-

I failed to get this installed on MacOS. I suspect I would also fail on Windows. I was able to follow the installation instructions on Linux/aarch64 in a VM, and all of the unit tests passed. Could you update the requirements to say this requires Linux, or could you do some testing to get this working on Mac and Windows?

Your requirements.txt file is very specific. Is there any way to relax the version requirements, e.g. to specify dependencies to only their minor version numbers rather than to their patch version numbers? I worry that this installation could be very brittle.

Could you include example usage in the paper? Or in the documentation? Could you structure the documentation in docs / README so that it is more clear where I should start to learn how to use this program? The examples directory just contains json files, while the command to run in the first documentation page (python -m hm01.cm -i network.tsv -e clustering.tsv -c leiden -t 1log10 -n 32 -o output.tsv) gives this error;

Traceback (most recent call last):

File "/home/parallels/mambaforge/envs/review/lib/python3.10/runpy.py", line 196, in _run_module_as_main return _run_code(code, main_globals, None,

File "/home/parallels/mambaforge/envs/review/lib/python3.10/runpy.py", line 86, in _run_code exec(code, run_globals)

File "/home/parallels/review/cm_pipeline/hm01/cm.py", line 514, in entry_point()

File "/home/parallels/review/cm_pipeline/hm01/cm.py", line 510, in entry_point typer.run(main)

File "/home/parallels/review/cm_pipeline/hm01/cm.py", line 422, in main assert resolution != -1, "Leiden requires resolution"

AssertionError: Leiden requires resolution

I recommend adding something like a "quick start" guide or similar, with complete input files for the examples, so that it is easier to get started straight away with the software. While you don't need as much, see here https://sire.openbiosim.org how in my software the user is taken on a journey from seeing if the software has the features they need, then a very simple install guide, then a quick start guide to quickly explore the software (before then more detailed guides and a tutorial). Something like this can really make a difference to a user's experience of the software.

-

Could you add some community guidelines as detailed in the checklist above? I am sorry if I missed them. Feel free to steal from How to ask for help https://sire.openbiosim.org/support.html and Contributing https://sire.openbiosim.org/contributing/index.html.

Could you provide the input files so that I can confirm the performance claims in figure 1? Also, could you change this into a scaling plot rather than a time to solve plot? (i.e. the speed relative to 1 core for each core count - ideally a 32-core job would be 32 times faster, but this would almost never be the case). This would give a better idea of how the code scales.

Thanks :-)

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6073#issuecomment-1841225737, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAVNKTIL5BWYBOBAYXYDWUDYH5G2HAVCNFSM6AAAAAA7UE4E6CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNBRGIZDKNZTG4 . You are receiving this because you were mentioned.Message ID: @.***>

chackoge commented 10 months ago

A quick update on this. We're making revisions based on your comments and will update this thread as soon as the guidelines and quick start are ready. Thank you again. George Chacko

On Tue, Dec 5, 2023 at 11:49 AM George Chacko @.***> wrote:

Thanks for these very helpful comments Christopher. We will respond ASAP. George Chacko

On Tue, Dec 5, 2023 at 10:56 AM Christopher Woods < @.***> wrote:

Hi - thanks for your submission. I've been going through the checklist above as part of the review. It's all going well, but I have a few questions / requests.

-

I failed to get this installed on MacOS. I suspect I would also fail on Windows. I was able to follow the installation instructions on Linux/aarch64 in a VM, and all of the unit tests passed. Could you update the requirements to say this requires Linux, or could you do some testing to get this working on Mac and Windows?

Your requirements.txt file is very specific. Is there any way to relax the version requirements, e.g. to specify dependencies to only their minor version numbers rather than to their patch version numbers? I worry that this installation could be very brittle.

Could you include example usage in the paper? Or in the documentation? Could you structure the documentation in docs / README so that it is more clear where I should start to learn how to use this program? The examples directory just contains json files, while the command to run in the first documentation page (python -m hm01.cm -i network.tsv -e clustering.tsv -c leiden -t 1log10 -n 32 -o output.tsv) gives this error;

Traceback (most recent call last):

File "/home/parallels/mambaforge/envs/review/lib/python3.10/runpy.py", line 196, in _run_module_as_main return _run_code(code, main_globals, None,

File "/home/parallels/mambaforge/envs/review/lib/python3.10/runpy.py", line 86, in _run_code exec(code, run_globals)

File "/home/parallels/review/cm_pipeline/hm01/cm.py", line 514, in entry_point()

File "/home/parallels/review/cm_pipeline/hm01/cm.py", line 510, in entry_point typer.run(main)

File "/home/parallels/review/cm_pipeline/hm01/cm.py", line 422, in main assert resolution != -1, "Leiden requires resolution"

AssertionError: Leiden requires resolution

I recommend adding something like a "quick start" guide or similar, with complete input files for the examples, so that it is easier to get started straight away with the software. While you don't need as much, see here https://sire.openbiosim.org how in my software the user is taken on a journey from seeing if the software has the features they need, then a very simple install guide, then a quick start guide to quickly explore the software (before then more detailed guides and a tutorial). Something like this can really make a difference to a user's experience of the software.

-

Could you add some community guidelines as detailed in the checklist above? I am sorry if I missed them. Feel free to steal from How to ask for help https://sire.openbiosim.org/support.html and Contributing https://sire.openbiosim.org/contributing/index.html.

Could you provide the input files so that I can confirm the performance claims in figure 1? Also, could you change this into a scaling plot rather than a time to solve plot? (i.e. the speed relative to 1 core for each core count - ideally a 32-core job would be 32 times faster, but this would almost never be the case). This would give a better idea of how the code scales.

Thanks :-)

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6073#issuecomment-1841225737, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAVNKTIL5BWYBOBAYXYDWUDYH5G2HAVCNFSM6AAAAAA7UE4E6CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNBRGIZDKNZTG4 . You are receiving this because you were mentioned.Message ID: @.***>

chryswoods commented 10 months ago

Thanks - and don't worry - there isn't a rush. I've got a lot of leave to use up before Christmas, so it may not be until January that I'll be able to look at the revision.

arfon commented 10 months ago

Thanks for the update @chackoge!

LuisScoccola commented 9 months ago

Review checklist for @LuisScoccola

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

chackoge commented 9 months ago

We have made revisions in response to the comments provided by Christopher Woods. The response is enclosed as a pdf. The changes are visible on the Github site. Thanks George Chacko

On Fri, Dec 15, 2023 at 5:24 AM LuisScoccola @.***> wrote:

Review checklist for @LuisScoccola https://github.com/LuisScoccola Conflict of interest

Code of Conduct

General checks

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 https://pandoc.org/MANUAL.html#extension-citations?

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LuisScoccola commented 9 months ago

Hi @chackoge! I just submitted an issue, probably related to the fact that I am running MacOS. Please let me know if you have any suggestions. I don't see the pdf response that you referred to in your last message, where can I find it?

chackoge commented 9 months ago

Dear @LuisScoccola https://github.com/LuisScoccola thanks very much for this feedback. We're working through your very helpful comments and hope to have a response back in less than one week. We don't think it's a MacOS issue- more about specifying dependencies but we'll report back. Happy New Year to all of you. George Chacko

On Thu, Dec 28, 2023 at 8:18 AM LuisScoccola @.***> wrote:

Hi @chackoge https://github.com/chackoge! I just submitted an issue, probably related to the fact that I am running MacOS. Please let me know if you have any suggestions. I don't see the pdf response that you referred to in your last message, where can I find it?

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chackoge commented 9 months ago

It looks like the pdf didn't transmit via email. I'm uploading it here. JOSS_Review_Comments_Ramavarapu.pdf JOSS_Review_Comments_Ramavarapu.pdf

chackoge commented 9 months ago

@LuisScoccola We looked into your issue. Vikram (the first author) has responded to it on Github. It turned out that std::binary_function is deprecated and this resulted in installation errors. python-mincut has been modified to use newer submodules and an alternate strategy (downgrading to gcc@13) is also described. I hope this addresses the problem.

chryswoods commented 9 months ago

Hi - Thanks for making the changes I requested. The website with quick start and user guide is very helpful, as are the examples. I am happy that this is ready for publication.

My only comment, which is minor, is that the example relies on running an R analysis script (one of the five R scripts that are in the scripts directory). I didn't have R installed in my test environment, so this exited with an error.

Could you add "R" and any required R packages to the list of dependencies? Or, if this is only needed for some jobs, mention on the examples page that R needs to be installed to be able to run the examples.

chackoge commented 9 months ago

Hi Chris- we're on it. Thanks for the comments. GC

On Thu, Jan 4, 2024 at 9:36 AM Christopher Woods @.***> wrote:

Hi - Thanks for making the changes I requested. The website with quick start and user guide is very helpful, as are the examples. I am happy that this is ready for publication.

My only comment, which is minor, is that the example relies on running an R analysis script (one of the five R scripts that are in the scripts directory). I didn't have R installed in my test environment, so this exited with an error.

Could you add "R" and any required R packages to the list of dependencies? Or, if this is only needed for some jobs, mention on the examples page that R needs to be installed to be able to run the examples.

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chackoge commented 9 months ago

@chryswoods We have added R as well as the data.table and feather packages as requirements in both the main readme and the documentation page. Please view the links to the updated requirements below: ReadMe: https://github.com/illinois-or-research-analytics/cm_pipeline/tree/main?tab=readme-ov-file#requirements Doc: https://illinois-or-research-analytics.github.io/cm_pipeline/installation/

chryswoods commented 9 months ago

Thanks - that's great. Those scripts worked when I have R and those packages installed. I'm happy that your manuscript is now ready. Thanks for being so quick and making all the changes I suggested.

LuisScoccola commented 9 months ago

@chackoge, here are my main comments about the manuscript. I am not asking for everything to be phrased as I suggest; but if you decide to not address one of the comments in the paper, please include an explanation in a response in this github issue.

chackoge commented 9 months ago

@LuisScoccola Thank you for these comments. I think we should be able to address them in a very short time.

chackoge commented 9 months ago

@LuisScoccola https://github.com/LuisScoccola Thank you for these helpful comments. We have modified the manuscript as follows.

Lines 14 and 29: Is there a precise definition of what it means for a community to be "well-connected"? Or are there many competing definitions, or is an informal notion? It would be good to add a few details about the notion of well-connectedness since it is a central motivation for your work.

The phrase “well-connected” as we and others have used (Traag, Bonchi,, Park cited in manuscript) has to do with the size of the minimum edge cut for the given cluster, and whether it is large enough to qualify for being “well connected”. The only variation in this definition has to do with the standard imposed for what is “large enough”. We allow this to be specified by the user, but explore (in our study) the requirement that the min cut size be at least log_10(n), a mild standard to impose. To us it seems that a lengthy discussion of what well-connected really means is out of scope and provides a level of detail that seems at variance with the purpose of the manuscript. Instead, we've added some clarifying text indicating that well-connectedness is defined by the mincut of a cluster/community and that the software allows users to set a discriminating value. Accordingly...

"A related expectation is that communities also should be well-connected (Bonchi et al., 2021; Traag et al., 2019), which is defined by the size of the minimum edge cut."

As mentioned, we've cited three papers in the manuscript; Bonchi et al. (2021), Traag et al. (2019), and Park et al. (2023), for anyone who really wants to delve into this issue. Given the lack of a definition that is universally accepted, the CM++ package was enginered to allow users to specify thresholds for well-connectedness.

Line 29: "several widely-used codes". Are these algorithms or software libraries, or both? It would be good to clarify this in any of these cases.

This has been addressed by specifying that they are software implementations of algorithms with citations.

Line 30: When you cite Park et al., it would be good to be more precise and cite a more specific section of the paper, or perhaps give a few more details regarding the how this is demonstrated in that paper

Yes, we have drawn the readers attention to Fig 2 of Park et al.

Lines 33 and 55: Rather than saying "Key features", it would be nicer to have full sentences. Even if at the end of the day the sentences don't add any new information, I think they would improve readability. I recommend this sentences to briefly recall what "CM++" and what "CM++ Pipeline" are (even if this has been done in the introduction), so that a reader that just jumps to those sections has enough information to read them without having to go back to the introduction.

We have changed the text in response.

Line 34: After "Flexibility" a colon is missing (for consistency).

Fixed

Line 50: Should "sets" be "set"?

Fixed, thanks for alerting us.

Line 69: I think the subsection "Parallel Strategy" is still part of the "Limitations" section. In that case (for consistency), it would be nice to either have each limitation in its own subsection, or perhaps even better, have limitations itemized in a bullet list (as the features in the previous sections), with a bold text serving as title, and then an explanation.

The header for that subsection has been removed and the text merged into the Limitations section.

Reply to this email directly, view it on GitHub, or unsubscribe.

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LuisScoccola commented 9 months ago

@chackoge thank you for the prompt response and for addressing my comments. I have checked the paper and it looks good to me. I have three more minor comments regarding the last set of changes.

chackoge commented 9 months ago

Hello @LuisScoccola:

Thanks for the quick turnaround on our revisions and the detailed comments. We'll fix Line 34 as suggested right away.

WIth respect to Line 15 (and this goes back to my earlier comment about scope and delving into the semantics of well connected). Mild is not used as a modifier for standard. We used a mild definition of well-connected defined by a slow growing function (as opposed to a stringent definition of well connected) when evaluating cluster quality from MCL, Infomap, Leiden (modularity or CPM), and IKC. Had a stringent definition been applied then very few clusters would have satisfied the condition imposed and our observation would have been artificially exaggerated. Hence we used 'mild' to illustrate the prevalence of poorly connected clusters and developed CM++ to remediate them. The function is plotted in Fig 9 of Park et al (arXiv).

Here are relevant extracts from the text of Park that may also help.

Extract 1. "We also observed that the number of clusters with small min cuts increases as the resolution parameter decreases. Intrigued by this observation, we performed a broader study to evaluate the extent to which clusters produced by algorithms of interest meet even a mild standard for a well connected cluster."

Extract 2. "While a large fraction of small min cuts intuitively signals “poorly-connected” clusters, there are different ways of formalizing this notion. Here we offer a formal definition for the purposes of this study. Briefly, we consider functions f(n) with the interpretation that if a cluster of size n has an edge cut of size at most f(n) then the cluster will be considered poorly connected. We want f(n) to grow very slowly so that it serves as a mild bound. We also want f(n) ≥ 1 for all n that are large enough for the cluster to be considered a potential community. From three examples of slowly growing functions (Materials and Methods), we choose f(n) = log10 n, the function that imposes the mildest constraint on large clusters and grows more slowly than the bound in (10)."

Regards

George Chacko

Line 15: Regarding "Applying a mild standard for well-connectedness". I think what is meant is clear, but I don't know if I have seen the word "mild" as a modifier for "standard". If this is usual, please disregard this comment. Otherwise, please consider replacing it with something like "Using a standard notion of well-connectedness".

Message ID: @.***>

LuisScoccola commented 9 months ago

@arfon I have finished the reviewing process and I'm happy with the submission.

Once @chackoge confirms that the last small changes are implemented in the paper, the submission is, from my side, ready.

I thank the authors for responding quickly and in detail to all of my comments.

chackoge commented 9 months ago

Thank you very much @chryswoodsand @LuisScoccola. Your comments have been extremely helpful to us and we appreciate the professional courtesy of reviewing our manuscript. I'l send out a confirmation later this morning in this thread adn we'll review the manuscript one last time before notfiying @arfon and everyone else in this thread.

GC

On Fri, Jan 12, 2024 at 7:03 AM LuisScoccola @.***> wrote:

@arfon I have finished the reviewing process and I'm happy with the submission.

Once @chackoge confirms that the last small changes are implemented in the paper, the submission is, from my side, ready.

I thank the authors for responding quickly and in detail to all of my comments.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.

Message ID: @.***>

chackoge commented 9 months ago

@chryswoodsand @LuisScoccola @arfon We have made all changes requested. Thanks again.

George Chacko

On Fri, Jan 12, 2024 at 7:11 AM George Chacko @.***> wrote:

Thank you very much @chryswoodsand @LuisScoccola. Your comments have been extremely helpful to us and we appreciate the professional courtesy of reviewing our manuscript. I'l send out a confirmation later this morning in this thread adn we'll review the manuscript one last time before notfiying @arfon and everyone else in this thread.

GC

On Fri, Jan 12, 2024 at 7:03 AM LuisScoccola @.***> wrote:

@arfon I have finished the reviewing process and I'm happy with the submission.

Once @chackoge confirms that the last small changes are implemented in the paper, the submission is, from my side, ready.

I thank the authors for responding quickly and in detail to all of my comments.

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arfon commented 9 months ago

@chackoge – looks like we're very close to being done here. I will circle back here next week, but in the meantime, please give your own paper a final read to check for any potential typos etc.

After that, could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

chackoge commented 9 months ago

We're on it. Thanks @arfon.

On Sat, Jan 13, 2024 at 7:27 AM Arfon Smith @.***> wrote:

@chackoge https://github.com/chackoge – looks like we're very close to being done here. I will circle back here next week, but in the meantime, please give your own paper a final read to check for any potential typos etc.

After that, could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

  • The title of the archive is the same as the JOSS paper title
  • That the authors of the archive are the same as the JOSS paper authors
  • I can then move forward with accepting the submission.

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vikramr2 commented 9 months ago

Hello @arfon,

I have updated the release to v4.0.1 and the Zenodo DOI is 10.5281/zenodo.10501118.

Thanks!

Vikram

chackoge commented 9 months ago

@arfon and we've reviewed the manuscript one last time.

Thanks

George Chacko

On Sat, Jan 13, 2024 at 2:01 PM Vikram Ramavarapu @.***> wrote:

Hello @arfon https://github.com/arfon,

I have updated the release to v4.0.1 and the Zenodo DOI is 10.5281/zenodo.10501118 https://doi.org/10.5281/zenodo.10501118.

Thanks!

Vikram

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arfon commented 8 months ago

@editorialbot set 10.5281/zenodo.10501118 as archive

editorialbot commented 8 months ago

Done! archive is now 10.5281/zenodo.10501118

arfon commented 8 months ago

@editorialbot recommend-accept

editorialbot commented 8 months ago 
Attempting dry run of processing paper acceptance...
editorialbot commented 8 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1038/s41598-019-41695-z is OK
- 10.1162/qss_a_00184 is OK
- 10.1073/pnas.0706851105 is OK
- 10.1038/s41567-022-01716-7 is OK
- 10.1016/j.dam.2021.08.032 is OK
- 10.1126/sciadv.1602548 is OK
- 10.1002/asi.22990 is OK
- 10.1002/asi.22748 is OK
- 10.1093/molbev/mst228 is OK
- 10.1038/nature03288 is OK
- 10.1145/1134271.1134277 is OK
- 10.1371/journal.pcbi.1008239 is OK
- 10.1088/1742-5468/2008/10/P10008 is OK
- 10.1073/pnas.122653799 is OK
- 10.1002/sam.10133 is OK
- 10.1109/ibigdelft.2018.8625349 is OK
- 10.1002/wics.1566 is OK
- 10.5281/zenodo.10501118 is OK
- 10.1137/040608635 is OK

MISSING DOIs

- 10.1101/gr.1239303 may be a valid DOI for title: Cytoscape: a software environment for integrated models of biomolecular interaction networks

INVALID DOIs

- None
editorialbot commented 8 months ago

:wave: @openjournals/csism-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/openjournals/joss-papers/pull/4925, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

arfon commented 8 months ago

@editorialbot accept

editorialbot commented 8 months ago 
Doing it live! Attempting automated processing of paper acceptance...
editorialbot commented 8 months ago

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

``` cff-version: "1.2.0" authors: - email: vikramr2@illinois.edu family-names: Ramavarapu given-names: Vikram orcid: "https://orcid.org/0009-0001-8875-7213" - family-names: Ayres given-names: Fábio Jose orcid: "https://orcid.org/0009-0000-6821-4687" - family-names: Park given-names: Minhyuk orcid: "https://orcid.org/0000-0002-8676-7565" - family-names: Pailodi given-names: Vidya Kamath orcid: "https://orcid.org/0009-0000-0987-5901" - family-names: Lamy given-names: João Alfredo Cardoso orcid: "https://orcid.org/0009-0005-4744-4754" - family-names: Warnow given-names: Tandy orcid: "https://orcid.org/0000-0001-7717-3514" - family-names: Chacko given-names: George orcid: "https://orcid.org/0000-0002-2127-1892" contact: - family-names: Chacko given-names: George orcid: "https://orcid.org/0000-0002-2127-1892" doi: 10.5281/zenodo.10501118 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - email: vikramr2@illinois.edu family-names: Ramavarapu given-names: Vikram orcid: "https://orcid.org/0009-0001-8875-7213" - family-names: Ayres given-names: Fábio Jose orcid: "https://orcid.org/0009-0000-6821-4687" - family-names: Park given-names: Minhyuk orcid: "https://orcid.org/0000-0002-8676-7565" - family-names: Pailodi given-names: Vidya Kamath orcid: "https://orcid.org/0009-0000-0987-5901" - family-names: Lamy given-names: João Alfredo Cardoso orcid: "https://orcid.org/0009-0005-4744-4754" - family-names: Warnow given-names: Tandy orcid: "https://orcid.org/0000-0001-7717-3514" - family-names: Chacko given-names: George orcid: "https://orcid.org/0000-0002-2127-1892" date-published: 2024-01-19 doi: 10.21105/joss.06073 issn: 2475-9066 issue: 93 journal: Journal of Open Source Software publisher: name: Open Journals start: 6073 title: CM++ - A Meta-method for Well-Connected Community Detection type: article url: "https://joss.theoj.org/papers/10.21105/joss.06073" volume: 9 title: CM++ - A Meta-method for Well-Connected Community Detection ```

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot commented 8 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 8 months ago

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/4927
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06073
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon commented 8 months ago

@LuisScoccola, @chryswoods – many thanks for your reviews here! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@chackoge – your paper is now accepted and published in JOSS :zap::rocket::boom:

editorialbot commented 8 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:
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HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06073">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06073/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06073/status.svg
   :target: https://doi.org/10.21105/joss.06073

This is how it will look in your documentation:

DOI

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chackoge commented 8 months ago

Well this is the best news I've had in 2024! Thank you very much @arfon @luisscoccola @chryswoods. The article was clearly improved by your input so we're very grateful. The journal review process was also quite refreshing in comparison with umm..another experience we had in 2023. Regards GC

On Fri, Jan 19, 2024 at 4:20 AM The Open Journals editorial robot < @.***> wrote:

🎉🎉🎉 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

HTML:

DOI badge

reStructuredText: .. image:: https://joss.theoj.org/papers/10.21105/joss.06073/status.svg :target: https://doi.org/10.21105/joss.06073

This is how it will look in your documentation:

[image: DOI] https://doi.org/10.21105/joss.06073

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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chackoge commented 8 months ago

Not sure how to make these @name things active.

@LuisScoccola https://github.com/LuisScoccola @chryswoods https://github.com/chryswoods

On Fri, Jan 19, 2024 at 12:28 PM George Chacko @.***> wrote:

Well this is the best news I've had in 2024! Thank you very much @arfon @luisscoccola @chryswoods. The article was clearly improved by your input so we're very grateful. The journal review process was also quite refreshing in comparison with umm..another experience we had in 2023. Regards GC

On Fri, Jan 19, 2024 at 4:20 AM The Open Journals editorial robot < @.***> wrote:

🎉🎉🎉 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

HTML:

DOI badge

reStructuredText: .. image:: https://joss.theoj.org/papers/10.21105/joss.06073/status.svg :target: https://doi.org/10.21105/joss.06073

This is how it will look in your documentation:

[image: DOI] https://doi.org/10.21105/joss.06073

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6073#issuecomment-1900040370, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAVNKTNDY6XCUZJ6ZXRVEG3YPI3E3AVCNFSM6AAAAAA7UE4E6CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMBQGA2DAMZXGA . You are receiving this because you were mentioned.Message ID: @.***>