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Reviews for the Journal of Open Source Software
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[REVIEW]: PhenoFeatureFinder: a python package for linking developmental phenotypes to omics features #7264

Open editorialbot opened 2 hours ago

editorialbot commented 2 hours ago

Submitting author: !--author-handle-->@petrableeker<!--end-author-handle-- (Petra Bleeker) Repository: https://github.com/BleekerLab/PhenoFeatureFinder Branch with paper.md (empty if default branch): Version: v0.1.1 Editor: !--editor-->@jromanowska<!--end-editor-- Reviewers: @admiralenola, @lopeztarifa, @pierrepeterlongo Archive: Pending

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/74d0441a00a5c8d78f1842191edcf5eb"><img src="https://joss.theoj.org/papers/74d0441a00a5c8d78f1842191edcf5eb/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/74d0441a00a5c8d78f1842191edcf5eb/status.svg)](https://joss.theoj.org/papers/74d0441a00a5c8d78f1842191edcf5eb)

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

@admiralenola & @lopeztarifa & @pierrepeterlongo, 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 @jromanowska 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

@admiralenola, please create your checklist typing: @editorialbot generate my checklist

@lopeztarifa, please create your checklist typing: @editorialbot generate my checklist

@pierrepeterlongo, please create your checklist typing: @editorialbot generate my checklist

editorialbot commented 2 hours ago

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
editorialbot commented 2 hours ago
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1007/978-3-030-80352-0_10 is OK
- 10.1104/pp.20.00433 is OK
- 10.1002/(SICI)1097-0282(1998)47:6<479::AID-BIP6>3.0.CO;2-K is OK
- 10.1186/s12870-021-03070-x is OK
- 10.1007/s00027-020-0698-0 is OK
- 10.3390/metabo10060243 is OK
- 10.1016/S2095-3119(21)63714-0 is OK
- 10.1007/s11829-018-9628-7 is OK
- 10.1186/s13071-016-1789-6 is OK
- 10.5539/ijsp.v10n3p93 is OK
- 10.1145/2908812.2908918 is OK
- 10.1371/journal.pone.0146021 is OK
- 10.1016/j.cj.2021.03.015 is OK
- 10.1007/978-94-007-5704-2 is OK
- 10.1007/s42690-022-00868-6 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- 10.1017/s0890037x00023253 may be a valid DOI for title: Log-logistic analysis of herbicide dose-response r...

❌ INVALID DOIs

- 10.5555/1953048.2078195 is INVALID - 10.5555 is a known broken prefix, replace with https://dl.acm.org/doi/{doi} in the {url} field
editorialbot commented 2 hours ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.08 s (527.7 files/s, 349002.0 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 commented 2 hours ago

Paper file info:

📄 Wordcount for paper.md is 1235

✅ The paper includes a Statement of need section

editorialbot commented 2 hours ago

License info:

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

editorialbot commented 2 hours ago

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

jromanowska commented 1 hour ago

👋🏼 @petrableeker, @LissyDenkers, @AdmiralenOla, @lopeztarifa, @pierrepeterlongo this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains 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 openjournals/joss-reviews#7264 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 reviews to be completed within about 2-4 weeks. (@AdmiralenOla, @pierrepeterlongo, I will wait couple of weeks before reminiding you to start the review, as agreed.) Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

I encourage you to over-communicate and let everyone know that you're on the task every now and then, instead of waiting several weeks to collect all your comments, questions, or suggestions.

Please feel free to ping me (@jromanowska) if you have any questions/concerns.