[PRE REVIEW]: PhenoFeatureFinder: a python package for linking developmental phenotypes to omics features

[editorialbot]

Submitting author: @petrableeker (Petra Bleeker)
Repository: https://github.com/BleekerLab/PhenoFeatureFinder
Branch with paper.md (empty if default branch):
Version: v0.1.1
Editor: @jromanowska
Reviewers: @AdmiralenOla, @lopeztarifa, @pierrepeterlongo
Managing EiC: Kevin M. Moerman

Status

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Markdown: [![status](https://joss.theoj.org/papers/74d0441a00a5c8d78f1842191edcf5eb/status.svg)](https://joss.theoj.org/papers/74d0441a00a5c8d78f1842191edcf5eb)

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.07 s (588.2 files/s, 389224.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
CSV                              8              0              0          18840
Python                           7            505           1201           1055
Markdown                        13            164              0            290
Jupyter Notebook                 6              0           3796            252
TeX                              1             14              0            227
TOML                             1              4              0             30
DOS Batch                        1              8              1             27
YAML                             2              3              7             27
make                             1              4              5             10
-------------------------------------------------------------------------------
SUM:                            40            702           5010          20758
-------------------------------------------------------------------------------

Commit count by author:

    79	LissyDenkers
    32	Marc Galland
    10	Lissy Denkers
     1	Petra Bleeker
     1	semantic-release

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1232

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: Other (Check here for OSI approval)

[editorialbot]

⚠️ An error happened when generating the pdf.

[LissyDenkers]

@editorialbot generate pdf

[editorialbot]

⚠️ An error happened when generating the pdf.

[LissyDenkers]

@editorialbot generate pdf

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@petrableeker thanks for this submission. I am the AEiC on this track and here to help with initial steps. I am currently reviewing if this work is in scope for JOSS. In particular given the relatively small size of the project I've just flagged this for scope review by our board, to see this conforms to our substantial scholarly effort criteria. This scope review should take about 2 weeks to complete.

[Kevin-Mattheus-Moerman]

@petrableeker I've just removed the query-scope label as I'm pleased to confirm that this submission has passed the initial scope review process. We will now be looking for a handling editor.

[Kevin-Mattheus-Moerman]

@petrableeker currently all editors in this space are busy handling other submission. I've hence assigned the waitlisted label. This will help ensure you will be next once an editor becomes available.

[Kevin-Mattheus-Moerman]

@editorialbot invite @jromanowska as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@petrableeker The editor I've just invited is actually unavailable for the moment. So we will have to leave this waitlisted for the moment. Apologies for the delay and thanks for your patience. I will continue to look for an editor or, once @jromanowska becomes available she may pick this up. I'll keep you up to date.

[Kevin-Mattheus-Moerman]

@editorialbot assign @jromanowska as editor

[editorialbot]

Assigned! @jromanowska is now the editor

[Kevin-Mattheus-Moerman]

@petrableeker I've just assigned Julia as she agreed to be editor. However, due to the summer holiday period it may take a while for her to be able to pick this up.

[jromanowska]

Hi everyone! I'm just back from holidays and will go on with this submission now. Thank you for your patience.

[jromanowska]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.07 s (589.5 files/s, 389841.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
CSV                              8              0              0          18840
Python                           7            505           1201           1055
Markdown                        13            165              0            292
Jupyter Notebook                 6              0           3776            252
TeX                              1             14              0            227
TOML                             1              4              0             30
DOS Batch                        1              8              1             27
YAML                             2              3              7             27
make                             1              4              5             10
-------------------------------------------------------------------------------
SUM:                            40            703           4990          20760
-------------------------------------------------------------------------------

Commit count by author:

    84	LissyDenkers
    32	Marc Galland
    10	Lissy Denkers
     1	Petra Bleeker
     1	semantic-release

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1235

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: Other (Check here for OSI approval)

[editorialbot]

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[jromanowska]

Hi, @petrableeker , I've just read the paper and have one comment: I find that the headers for "Summary" and "Statement of need" don't really match the content. I'd suggest headers like "Statement of need" and "Implementation" instead.

Also - do you have any suggestions for (or oppositions) reviewers? Above, our robot has suggested some names, so I'll probably choose some of them, but just wanted to know if you have any comments on this.

[jromanowska]

👋 @msabrysarhan, @adamyhe, @coughls, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[adamyhe]

Hi @jromanowska. I'm unfortunately rather swamped at the moment. I don't think I'll be able to review.

[jromanowska]

Hi @jromanowska. I'm unfortunately rather swamped at the moment. I don't think I'll be able to review.

@adamyhe OK, thanks, maybe next time! Do you have anyone you could recommend to be a reviewer on this one?

[jromanowska]

@petrableeker, @LissyDenkers - do you have any reviewer suggestions? I'm a bit stuck here.

[LissyDenkers]

Hi @jromanowska, So far, we could not yet find anyone. One of the authors suggested that Pablo Lopez-Tarifa (lopeztarifa on GitHub) might be able to help us. In the meantime, I'll continue searching.

[jromanowska]

@lopeztarifa 👋 - would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: joss.readthedocs.io/en/latest/review_criteria.html

[jromanowska]

@gbouras13 👋 - would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: joss.readthedocs.io/en/latest/review_criteria.html

[gbouras13]

Hi @jromanowska ,

I will have to decline to review this right now, apologies.

George

[jromanowska]

@gbouras13 , I understand, thank you for the message. Do you have any suggestions for reviewers?

[jromanowska]

@lopeztarifa 👋 - would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: joss.readthedocs.io/en/latest/review_criteria.html

[jromanowska]

Hi @jromanowska, So far, we could not yet find anyone. One of the authors suggested that Pablo Lopez-Tarifa (lopeztarifa on GitHub) might be able to help us. In the meantime, I'll continue searching.

@LissyDenkers - do you have maybe an email address to Pablo Lopez-Tarifa? Perhaps GitHub notifications did not reach him.

[LissyDenkers]

@jromanowska - I don't have an email address, but on the website where I found his GitHub name, there is also a LinkedIn profile: https://www.esciencecenter.nl/team/pablo-lopez-tarifa/

[jromanowska]

Thanks, yes, I've seen it too, but I don't have a LinkedIn paid account, so I cannot contact him through there either. And on the webpage of his employer, there is no email address.
I'll be searching and please, do keep on searching as well. You are more aware of relevant research groups in your field :)

[jromanowska]

@editorialbot add @AdmiralenOla as reviewer

[editorialbot]

@AdmiralenOla added to the reviewers list!

[jromanowska]

👋 @pierrepeterlongo, would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[pierrepeterlongo]

Hi,
Yes, I accept this review. However, I won't have time before 2 weeks. Is that acceptable?

[lopeztarifa]

Sorry for my late answer, I had notifications turned off. I can review it.

[jromanowska]

Thank you, @lopeztarifa and @pierrepeterlongo!
@pierrepeterlongo - I have also another reviewer who will need some time to start the review, so this suits us well. I'll create a new thread where the real review will start and each one of you can start when they're ready.

[jromanowska]

@editorialbot add @lopeztarifa as reviewer

[editorialbot]

@lopeztarifa added to the reviewers list!

[jromanowska]

@editorialbot add @pierrepeterlongo as reviewer

[editorialbot]

@pierrepeterlongo added to the reviewers list!

[jromanowska]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #7264.