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

[editorialbot]

Submitting author: @maximelucas (Maxime Lucas)
Repository: https://gitlab.com/habermann_lab/phasik
Branch with paper.md (empty if default branch): joss-paper
Version: v1.3.2
Editor: @csoneson
Reviewers: @GiulioRossetti, @alexbovet
Managing EiC: George K. Thiruvathukal

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/56260df85bde3a18d82a520180eb0fe4/status.svg)](https://joss.theoj.org/papers/56260df85bde3a18d82a520180eb0fe4)

Author instructions

Thanks for submitting your paper to JOSS @maximelucas. Currently, there isn't a JOSS editor assigned to your paper.

@maximelucas if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

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[editorialbot]

Software report:

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gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1491

[editorialbot]

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

OK DOIs

- 10.1140/epjst/e2013-01927-7 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
- 10.1016/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
- 10.1016/j.softx.2022.101301 is OK
- 10.5281/zenodo.3626827 is OK
- 10.1038/s41598-021-93128-5 is OK

MISSING DOIs

- 10.1126/sciadv.abj3063 may be a valid DOI for title: Flow stability for dynamic community detection
- 10.1371/journal.pone.0246961 may be a valid DOI for title: Fast and principled simulations of the SIR model on temporal networks

INVALID DOIs

- 10.1162/netn5fa5f00142 is INVALID
- https://doi.org/10.48550/arXiv.2306.16309 is INVALID because of 'https://doi.org/' prefix

[editorialbot]

⚠️ An error happened when generating the pdf.

[maximelucas]

@editorialbot check references

[editorialbot]

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

[maximelucas]

@editorialbot generate pdf

[editorialbot]

⚠️ An error happened when generating the pdf.

[maximelucas]

@editorialbot generate pdf

[editorialbot]

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

[maximelucas]

Hi, here are a few reviewer suggestions:

• miratepuffin
• Haaroon
• ljeub-pometry
• pholme
• GiulioRossetti

Also, I've now released v1.3.3 that fixes a test bug from the previous version.

[Kevin-Mattheus-Moerman]

@editorialbot invite @csoneson as editor

[editorialbot]

Invitation to edit this submission sent!

[csoneson]

@editorialbot assign @csoneson as editor

[editorialbot]

Assigned! @csoneson is now the editor

[csoneson]

👋🏻 @maximelucas - I will be the editor for your submission, and will start by recruiting at least two reviewers (thanks for the suggestions!)

[csoneson]

👋🏻 @miratepuffin, @pholme, @GiulioRossetti - would you be interested in reviewing this submission for the Journal of Open Source Software (JOSS)?

Phasik: a Python package to identify system states in partially temporal networks
(#5799)

JOSS is a free, open-source, community-driven and developer-friendly online journal. The review process is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged.

JOSS reviews involve downloading and installing the software, and inspecting the repository and submitted paper for key elements. See https://joss.readthedocs.io/en/latest/review_criteria.html.

Thanks in advance!

[GiulioRossetti]

@csoneson Hi!

Sure, I'm happy to contribute. Do we have an expected deadline to meet for the review?

[csoneson]

@GiulioRossetti Brilliant, thanks!
Typically we ask reviewers to aim to provide an initial assessment within approximately 2 weeks after opening the review issue (which will happen once all reviewers have been assigned). However, in many cases it turns out to be easier to provide comments successively as one goes through the submission, rather than everything at once.

[GiulioRossetti]

That's perfect.
So, the review can be seen as a discussion focused on the key points listed in the page you shared (if I get it right). I assume all comments will be made in this thread, right?

[csoneson]

So, the review can be seen as a discussion focused on the key points listed in the page you shared (if I get it right).

Yes, exactly.

I assume all comments will be made in this thread, right?

Almost 🙂 As soon as I have secured one more reviewer, I will close this issue and we will move to the actual review issue. Once there, you will be able to generate a new post with your own review checklist (which will contain these points: https://joss.readthedocs.io/en/latest/review_checklist.html). The goal is then to work with the authors to help them meet these criteria. Reviewers are encouraged to open issues directly in the software repository, or to keep the discussion in the review issue if that seems more suitable.

So for now, you are of course very welcome to start looking at the submission, but to keep things simple and everything in one place, I would ask that you'd wait to provide your comments until both reviewers are secured and the actual review issue is opened.

Thanks, and don't hesitate to let me know if you have other questions!

[maximelucas]

Hi! Thank you @csoneson for editing this and @GiulioRossetti for agreeing to review.

[csoneson]

👋🏻 @Haaroon, @ljeub-pometry - would one of you be willing to review this submission for the Journal of Open Source Software?

Phasik: a Python package to identify system states in partially temporal networks
(#5799)

JOSS is a free, open-source, community-driven and developer-friendly online journal. The review process is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged.

JOSS reviews involve downloading and installing the software, and inspecting the repository and submitted paper for key elements. See https://joss.readthedocs.io/en/latest/review_criteria.html.

Thanks in advance!

[csoneson]

👋🏻 @benmaier - would you be willing to review this submission for the Journal of Open Source Software?

Phasik: a Python package to identify system states in partially temporal networks
(#5799)

JOSS is a free, open-source, community-driven and developer-friendly online journal. The review process is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged.

JOSS reviews involve downloading and installing the software, and inspecting the repository and submitted paper for key elements. See https://joss.readthedocs.io/en/latest/review_criteria.html.

Thanks in advance!

[csoneson]

👋🏻 @Viech - would you be interested in reviewing this submission for JOSS?

Phasik: a Python package to identify system states in partially temporal networks
(#5799)

[benmaier]

Hi @csoneson and @maximelucas ! Looks super interesting, but unfortunately I won't have the time to work on this as I'm currently transitioning out of academia. Apologies

[csoneson]

@benmaier Thanks for your response! If you can think of a suitable colleague who might be interested in reviewing, please feel free to let us know!

[maximelucas]

If needed, more potential reviewers:

• naokimas
• alexbovet
• wiheto

[mjstahlberg]

I would be available time-wise but I do not see a large enough intersection with my topic areas to feel comfortable reviewing.

[csoneson]

👋🏻 @naokimas, @alexbovet, @wiheto - would one of you be willing to review this submission for the Journal of Open Source Software?

Phasik: a Python package to identify system states in partially temporal networks
(#5799)

JOSS is a free, open-source, community-driven and developer-friendly online journal. The review process is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged.

JOSS reviews involve downloading and installing the software, and inspecting the repository and submitted paper for key elements. See https://joss.readthedocs.io/en/latest/review_criteria.html.

Thanks in advance!

[maximelucas]

I found some more on your list of reviewers that might be more active on Github:

• paulbrodersen
• dhimmel
• szhorvat
• dinacmistry

[wiheto]

Hey, thanks for inviting me and it’s something I definitely want to check out someday. I’m currently swamped with other commitments which means I am unable to give a sufficient review in a reasonable time period.

[alexbovet]

Hey, thanks for inviting me as well. What would be the deadline? I am also currently swamped...

[csoneson]

@alexbovet - usually we ask reviewers to give an initial assessment within 2-3 weeks. However, in many cases it turns out to be easier to provide comments successively as one goes through the submission and the checklist, rather than everything at once.

[csoneson]

👋🏻 @alexbovet - could you let us know if you would be willing to take on the review given the additional information above? Thanks!

[maximelucas]

No worries @wiheto. Thanks for considering it @alexbovet! If it helps deciding, the review is check-list driven, and you can see an example of the check-list here.

[alexbovet]

Yes, I'll do it. thanks

[csoneson]

Awesome, thanks @alexbovet! I'll assign both reviewers and start the review issue.

[csoneson]

@editorialbot add @GiulioRossetti as reviewer

[editorialbot]

@GiulioRossetti added to the reviewers list!

[csoneson]

@editorialbot add @alexbovet as reviewer

[editorialbot]

@alexbovet added to the reviewers list!

[csoneson]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #5872.