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[REVIEW]: Phasik: a Python package to identify system states in partially temporal networks #5872

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editorialbot opened this issue Sep 25, 2023 · 57 comments
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accepted Jupyter Notebook published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials

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editorialbot commented Sep 25, 2023

Submitting author: @maximelucas (Maxime Lucas)
Repository: https://gitlab.com/habermann_lab/phasik
Branch with paper.md (empty if default branch): joss-paper
Version: v1.3.4
Editor: @csoneson
Reviewers: @GiulioRossetti, @alexbovet
Archive: 10.5281/zenodo.10113244

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/56260df85bde3a18d82a520180eb0fe4"><img src="https://joss.theoj.org/papers/56260df85bde3a18d82a520180eb0fe4/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/56260df85bde3a18d82a520180eb0fe4/status.svg)](https://joss.theoj.org/papers/56260df85bde3a18d82a520180eb0fe4)

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

@GiulioRossetti & @alexbovet, 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 @csoneson 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 @GiulioRossetti

📝 Checklist for @alexbovet

@editorialbot editorialbot added Jupyter Notebook Python review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Sep 25, 2023
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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 1.88  T=0.60 s (349.5 files/s, 282286.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                              3              2              2         104868
HTML                            65           8594            195          13636
JavaScript                      17           2438           2503           9412
Python                          37           1256           1696           4119
SVG                              4              0              0           3170
Jupyter Notebook                13              0          10868           2702
CSS                              6            202             54            822
Markdown                         6            182              0            317
reStructuredText                52            385            635            311
TeX                              1             36              0            244
YAML                             1              8              4             63
DOS Batch                        1              8              1             26
make                             1              4              7              9
TOML                             1              0              0              6
INI                              1              0              0              2
-------------------------------------------------------------------------------
SUM:                           209          13115          15965         139707
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 1491

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

OK DOIs

- 10.1140/epjst/e2013-01927-7 is OK
- 10.1126/sciadv.abj3063 is OK
- 10.5281/zenodo.3953119 is OK
- 10.1016/j.anbehav.2019.09.011 is OK
- 10.1016/j.physrep.2021.10.006 is OK
- 10.6084/m9.figshare.1164194 is OK
- 10.1371/journal.pone.0246961 is OK
- 10.1016/j.physrep.2012.03.001 is OK
- 10.1016/0955-0674(94)90039-6 is OK
- 10.48550/arXiv.2205.08820 is OK
- 10.1037/h0057431 is OK
- 10.1209/0295-5075/121/50008 is OK
- 10.1016/j.crmeth.2023.100397 is OK
- 10.1038/s41598-018-37534-2 is OK
- 10.1145/3442442.3452052 is OK
- 10.1162/netn_a_00142 is OK
- 10.48550/arXiv.2306.16309 is OK
- 10.1016/j.softx.2022.101301 is OK
- 10.5281/zenodo.3626827 is OK
- 10.1038/s41598-021-93128-5 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@csoneson
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👋🏼 @maximelucas, @GiulioRossetti, @alexbovet - this is the review thread for the submission. All of our communications will happen here from now on.

Please check the post at the top of the issue for instructions on how to generate your own review 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 directly in the software repository. If you do so, please mention this thread so that a link is created (and I can keep an eye on what is happening). Please also feel free to comment and ask questions in this thread. It is often easier to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

Please feel free to ping me (@csoneson) if you have any questions or concerns. Thanks!

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Five most similar historical JOSS papers:

pyscal: A python module for structural analysis of atomic environments
Reviewers: @lucydot, @bocklund
Similarity score: 0.7626

PyTeNet: A concise Python implementation of quantum tensor network algorithms
Reviewers: @mlxd, @jcmgray
Similarity score: 0.7618

Sinaps: A Python library to simulate voltage dynamics and ionic electrodiffusion in neurons
Reviewers: @martejulie, @meg-simula
Similarity score: 0.7610

Pycrostates: a Python library to study EEG microstates
Reviewers: @AJQuinn, @vahid-sb, @tuliofalmeida, @anshu-97
Similarity score: 0.7609

phasespace: n-body phase space generation in Python
Reviewers: @mdoucet, @stuartcampbell, @vyasr
Similarity score: 0.7600

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before before considering asking the reviewers of these papers to review again for JOSS.

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

@GiulioRossetti
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GiulioRossetti commented Sep 27, 2023

Review checklist for @GiulioRossetti

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://gitlab.com/habermann_lab/phasik?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@maximelucas) 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?

@alexbovet
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alexbovet commented Oct 12, 2023

Review checklist for @alexbovet

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://gitlab.com/habermann_lab/phasik?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@maximelucas) 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?

@maximelucas
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maximelucas commented Oct 20, 2023

Hi @csoneson, as you asked, just linking an issue raised by @alexbovet (thanks!). I have fixed it since then.

@csoneson
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👋🏻 Just wanted to check in on the reviews here.
@alexbovet - I see that you have checked all the boxes in the review checklist. Do you have additional comments for the authors, or are you happy with the current state of the submission?
@GiulioRossetti - I see that you have started filling your checklist, please let us know if you have questions or when you have comments for the authors.
Thanks all!

@alexbovet
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I'm happy with the current state of the submission. Everything looks good to me!

@csoneson
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csoneson commented Nov 1, 2023

👋🏻 @GiulioRossetti - could you provide a quick update on the status of your review here? Thanks!

@GiulioRossetti
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Sorry for the delay. A few deadlines have blocked me during the last two weeks. I'll complete the review by next Monday at the latest!

@GiulioRossetti
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@csoneson linking here an issue just raised concerning code examples in the API reference documentation.

@maximelucas
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Thank you for the suggestion @GiulioRossetti, good catch, I'll get right to it.

@maximelucas
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@csoneson I've now answered @GiulioRossetti's suggestions with two PRs. Once he is happy with the changes I'll make a new release of the library.

@GiulioRossetti
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@csoneson @maximelucas I checked the PRs: they are perfect! Everything looks good to me!

@maximelucas
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Thanks a lot @GiulioRossetti! I now released v1.3.4.
I believe everything is ready now @csoneson?

@csoneson
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Thanks @GiulioRossetti and @alexbovet for confirming that you are happy with the state of this submission. @maximelucas - I will take a quick look as well, and get back to you with the next steps.

@csoneson
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@editorialbot generate pdf

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@editorialbot check references

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

OK DOIs

- 10.1140/epjst/e2013-01927-7 is OK
- 10.1126/sciadv.abj3063 is OK
- 10.5281/zenodo.3953119 is OK
- 10.1016/j.anbehav.2019.09.011 is OK
- 10.1016/j.physrep.2021.10.006 is OK
- 10.6084/m9.figshare.1164194 is OK
- 10.1371/journal.pone.0246961 is OK
- 10.1016/j.physrep.2012.03.001 is OK
- 10.1016/0955-0674(94)90039-6 is OK
- 10.48550/arXiv.2205.08820 is OK
- 10.1037/h0057431 is OK
- 10.1209/0295-5075/121/50008 is OK
- 10.1016/j.crmeth.2023.100397 is OK
- 10.1038/s41598-018-37534-2 is OK
- 10.1145/3442442.3452052 is OK
- 10.1162/netn_a_00142 is OK
- 10.48550/arXiv.2306.16309 is OK
- 10.1016/j.softx.2022.101301 is OK
- 10.5281/zenodo.3626827 is OK
- 10.1038/s41598-021-93128-5 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@csoneson
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Thanks @maximelucas - only one abbreviated journal left (Masuda & Holme). Apart from that, looks good.

You don't need to bump the version again (also since the paper anyway is not in the main branch).

@maximelucas
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@editorialbot generate pdf

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

@maximelucas
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maximelucas commented Nov 11, 2023

Thank you, good catch!
Here is the Zenodo DOI: https://doi.org/10.5281/zenodo.10113244
I have done everything in your list (but I'm not able to tick the boxes myself).

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@editorialbot set 10.5281/zenodo.10113244 as archive

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Done! archive is now 10.5281/zenodo.10113244

@csoneson
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@editorialbot set v1.3.4 as version

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Done! version is now v1.3.4

@csoneson
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Thanks @maximelucas - one final thing: the license in your GitLab repo is 'GPL 3.0 or later', while the one in Zenodo is 'GPL v3.0 only'. Could you make these consistent please?

@maximelucas
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maximelucas commented Nov 12, 2023

Thank you @csoneson, I didn't know this difference existed. Done.

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Great! I think we're pretty much ready - I'll hand over to the track Associate EiC for the last steps. Thanks for submitting to JOSS!

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@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

OK DOIs

- 10.1140/epjst/e2013-01927-7 is OK
- 10.1126/sciadv.abj3063 is OK
- 10.5281/zenodo.3953119 is OK
- 10.1016/j.anbehav.2019.09.011 is OK
- 10.1016/j.physrep.2021.10.006 is OK
- 10.6084/m9.figshare.1164194 is OK
- 10.1371/journal.pone.0246961 is OK
- 10.1016/j.physrep.2012.03.001 is OK
- 10.1016/0955-0674(94)90039-6 is OK
- 10.48550/arXiv.2205.08820 is OK
- 10.1037/h0057431 is OK
- 10.1209/0295-5075/121/50008 is OK
- 10.1016/j.crmeth.2023.100397 is OK
- 10.1038/s41598-018-37534-2 is OK
- 10.1145/3442442.3452052 is OK
- 10.1162/netn_a_00142 is OK
- 10.48550/arXiv.2306.16309 is OK
- 10.1016/j.softx.2022.101301 is OK
- 10.5281/zenodo.3626827 is OK
- 10.1038/s41598-021-93128-5 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4776, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@editorialbot editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Nov 12, 2023
@Kevin-Mattheus-Moerman
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Kevin-Mattheus-Moerman commented Nov 14, 2023

@maximelucas as AEiC I will now help to process the final steps for this submission. I have checked this review, the software repository, the paper, and the archive link. Most looks in order, however, the below point needs your attention:

  • I did not see a tagged release on your repository. Please create one. The version tag should match the version tag we'll use here and on ZENODO, so let us know if it changes (and/or create a new ZENODO archive for it if needed).

@maximelucas
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maximelucas commented Nov 14, 2023

Thank you!
Should be okay now: https://gitlab.com/habermann_lab/phasik/-/releases
(Edit: just adding a tag @Kevin-Mattheus-Moerman in case it was needed, sorry if you were already notified)

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@maximelucas thanks. All looks good now so we'll proceed to process this for acceptance.

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@editorialbot accept

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

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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:
- family-names: Lucas
  given-names: Maxime
  orcid: "https://orcid.org/0000-0001-8087-2981"
- family-names: Townsend-Teague
  given-names: Alex
- family-names: Neri
  given-names: Matteo
  orcid: "https://orcid.org/0009-0007-0998-552X"
- family-names: Poetto
  given-names: Simone
- family-names: Morris
  given-names: Arthur
- family-names: Habermann
  given-names: Bianca
  orcid: "https://orcid.org/0000-0002-2457-7504"
- family-names: Tichit
  given-names: Laurent
  orcid: "https://orcid.org/0000-0002-8350-1446"
contact:
- family-names: Lucas
  given-names: Maxime
  orcid: "https://orcid.org/0000-0001-8087-2981"
doi: 10.5281/zenodo.10113244
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Lucas
    given-names: Maxime
    orcid: "https://orcid.org/0000-0001-8087-2981"
  - family-names: Townsend-Teague
    given-names: Alex
  - family-names: Neri
    given-names: Matteo
    orcid: "https://orcid.org/0009-0007-0998-552X"
  - family-names: Poetto
    given-names: Simone
  - family-names: Morris
    given-names: Arthur
  - family-names: Habermann
    given-names: Bianca
    orcid: "https://orcid.org/0000-0002-2457-7504"
  - family-names: Tichit
    given-names: Laurent
    orcid: "https://orcid.org/0000-0002-8350-1446"
  date-published: 2023-11-21
  doi: 10.21105/joss.05872
  issn: 2475-9066
  issue: 91
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5872
  title: "Phasik: a Python package to identify system states in
    partially temporal networks"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05872"
  volume: 8
title: "Phasik: a Python package to identify system states in partially
  temporal networks"

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.

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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

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🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.05872 joss-papers#4797
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05872
  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...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Nov 21, 2023
@Kevin-Mattheus-Moerman
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@maximelucas congratulations on this JOSS publication!

Thanks for editing @csoneson!

And a special thanks to the reviewers: @GiulioRossetti, @alexbovet !

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.05872/status.svg)](https://doi.org/10.21105/joss.05872)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05872">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05872/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05872/status.svg
   :target: https://doi.org/10.21105/joss.05872

This is how it will look in your documentation:

DOI

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:

@maximelucas
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Great, thank you @Kevin-Mattheus-Moerman, @csoneson, @GiulioRossetti, and @alexbovet for your time with this!

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