[REVIEW]: PyNM: a Lightweight Python implementation of Normative Modeling #4321

editorialbot · 2022-04-15T20:57:05Z

Submitting author: @harveyaa (Annabelle Harvey)
Repository: https://github.com/ppsp-team/PyNM
Branch with paper.md (empty if default branch): master
Version: v1.0.1
Editor: @dfm
Reviewers: @smkia, @saigerutherford
Archive: 10.5281/zenodo.7396721

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/f9a276711945e53109bddab19646c85f"><img src="https://joss.theoj.org/papers/f9a276711945e53109bddab19646c85f/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/f9a276711945e53109bddab19646c85f/status.svg)](https://joss.theoj.org/papers/f9a276711945e53109bddab19646c85f)

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

@smkia & @saigerutherford, 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 @dfm 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 @smkia

📝 Checklist for @saigerutherford

The text was updated successfully, but these errors were encountered:

editorialbot · 2022-04-15T20:57:07Z

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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editorialbot · 2022-04-15T20:57:21Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.11 s (191.3 files/s, 125593.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           9            334            720           1544
Jupyter Notebook                 7              0          10636            534
Markdown                         3             80              0            306
TeX                              1             11              0            240
YAML                             2              1              7             29
-------------------------------------------------------------------------------
SUM:                            22            426          11363           2653
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2022-04-15T20:57:22Z

Wordcount for paper.md is 863

editorialbot · 2022-04-15T20:57:22Z

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

OK DOIs

- 10.1038/s41380-019-0441-1 is OK
- 10.1016/j.biopsych.2015.12.023 is OK
- 10.1371/journal.pcbi.1009477 is OK
- 10.1371/journal.pone.0252108 is OK
- 10.1101/2021.08.08.455583 is OK
- 10.3389/fnins.2018.00662 is OK
- 10.3389/fpsyt.2019.00011 is OK
- 10.1038/s42003-020-01212-9 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1016/j.neuroimage.2021.118715 is INVALID because of 'https://doi.org/' prefix

editorialbot · 2022-04-15T20:58:22Z

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

dfm · 2022-04-15T20:59:21Z

@harveyaa, @smkia, @saigerutherford — This is the review thread for the paper. All of our communications will happen here from now on. Thanks again for agreeing to participate!

Please read the "Reviewer instructions & questions" in the first comment above, and generate your checklists by commenting @editorialbot generate my checklist on this issue ASAP. 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 openjournals/joss-reviews#4321 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 try to make a start 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.

dfm · 2022-04-15T21:00:37Z

@harveyaa — Can you take a look at fixing the DOI issue mentioned above by the bot?

smkia · 2022-04-16T04:38:34Z

Review checklist for @smkia

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

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/ppsp-team/PyNM?
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 (@harveyaa) 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

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 and who the target audience is?
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?

harveyaa · 2022-04-27T18:54:26Z

Hi,

I made a couple changes to the joss_submission branch to fix an import error a colleague caught - hopefully this doesn't confuse the review process too much - should I update pypi with the change or leave it in github for now?

Thank you,

Annabelle

dfm · 2022-05-03T14:21:50Z

@harveyaa — Sorry for the delayed response! We generally suggest minting a new release at the end of the review process, but you're also welcome to release new versions throughout the process and it shouldn't cause any problems.

saigerutherford · 2022-05-04T12:01:29Z

Review checklist for @saigerutherford

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

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/ppsp-team/PyNM?
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 (@harveyaa) 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

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 and who the target audience is?
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?

dfm · 2022-05-19T10:32:34Z

@smkia, @saigerutherford — This is just a little ping to make sure that this review stays on your radar. It's good to start chipping away at the checklists sooner rather than later!

smkia · 2022-06-04T10:41:59Z

Checking the functionality of the package, I am trying to run the first tutorial at https://github.com/ppsp-team/PyNM/blob/master/tutorials/1-getting_started.ipynb in Google Colab (see https://colab.research.google.com/drive/1LNEIT2T2omOr3iKa4qqUPz9VlwaxeuNG?usp=sharing). I receive the following error:

ModuleNotFoundError                       Traceback (most recent call last)
[<ipython-input-2-1a8dca4f882a>](https://localhost:8080/#) in <module>()
      1 import pandas as pd
      2 import numpy as np
----> 3 from pynm.pynm import PyNM
      4 import matplotlib.pyplot as plt
      5 import seaborn as sns

[/usr/local/lib/python3.7/dist-packages/pynm/pynm.py](https://localhost:8080/#) in <module>()
     36 
     37 from pynm.util import *
---> 38 from pynm.models.loess import *
     39 from pynm.models.centiles import *
     40 

ModuleNotFoundError: No module named 'pynm.models'

I suspect to the version difference between the package and the code in the tutorial. Would you please hint at that?

dfm · 2022-06-04T14:52:23Z

@smkia: Can you open this issue over on https://github.com/ppsp-team/PyNM/issues, referencing this thread instead? That tends to be a better workflow than putting issues in this thread. Thanks!

deep-introspection · 2022-06-16T23:29:20Z

Dear @smkia, it should be okay now.

dfm · 2022-06-21T14:16:32Z

@smkia, @saigerutherford — Just checking in here to see how your reviews are going and to keep this on your radar. Let me know if you have any questions or sticking points. Thanks!

(@smkia I see your most recent issue - thanks!)

saigerutherford · 2022-06-27T10:13:43Z

@dfm my sincere apologies for being so behind schedule with this review. Attending the first in-person conference of my Ph.D. plus a second round of being sick with COVID really put my schedule off track. Completing this review is my top priority this week!

dfm · 2022-06-27T10:59:29Z

@saigerutherford — thanks for the update and no stress - we all appreciate the time that you're able to volunteer! Let me know if there's anything comes up or if you have any questions!

deep-introspection · 2022-12-08T21:29:35Z

@dfm OK, great, thanks! I integrated your edits and made the title change on Zenodo.

dfm · 2022-12-08T21:39:29Z

@editorialbot generate pdf

dfm · 2022-12-08T21:40:03Z

@editorialbot set v1.0.1 as version

editorialbot · 2022-12-08T21:40:05Z

Done! version is now v1.0.1

dfm · 2022-12-08T21:40:24Z

@editorialbot set 10.5281/zenodo.7396721 as archive

editorialbot · 2022-12-08T21:40:26Z

Done! Archive is now 10.5281/zenodo.7396721

dfm · 2022-12-08T21:40:45Z

@editorialbot check references

editorialbot · 2022-12-08T21:41:16Z

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

editorialbot · 2022-12-08T21:41:27Z

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

OK DOIs

- 10.1038/s41380-019-0441-1 is OK
- 10.1016/j.biopsych.2015.12.023 is OK
- 10.1371/journal.pcbi.1009477 is OK
- 10.1371/journal.pone.0252108 is OK
- 10.5281/zenodo.5207839 is OK
- 10.1101/2021.05.28.446120 is OK
- 10.1101/2021.06.14.448106 is OK
- 10.1016/j.neuroimage.2021.118715 is OK
- 10.7554/eLife.72904 is OK
- 10.1038/s41596-022-00696-5 is OK
- 10.3389/fnins.2018.00662 is OK
- 10.3389/fpsyt.2019.00011 is OK
- 10.1038/s42003-020-01212-9 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1111/j.1467-9876.2005.00510.x is INVALID because of 'https://doi.org/' prefix

dfm · 2022-12-08T21:46:07Z

Thanks @deep-introspection!! With apologies I've opened one (last! I hope) PR fixing a syntax error that I introduced in an earlier PR. Very sorry about that!

dfm · 2022-12-08T21:46:35Z

@editorialbot check references

editorialbot · 2022-12-08T21:47:01Z

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

OK DOIs

- 10.1038/s41380-019-0441-1 is OK
- 10.1016/j.biopsych.2015.12.023 is OK
- 10.1371/journal.pcbi.1009477 is OK
- 10.1371/journal.pone.0252108 is OK
- 10.5281/zenodo.5207839 is OK
- 10.1101/2021.05.28.446120 is OK
- 10.1101/2021.06.14.448106 is OK
- 10.1016/j.neuroimage.2021.118715 is OK
- 10.7554/eLife.72904 is OK
- 10.1038/s41596-022-00696-5 is OK
- 10.1111/j.1467-9876.2005.00510.x is OK
- 10.3389/fnins.2018.00662 is OK
- 10.3389/fpsyt.2019.00011 is OK
- 10.1038/s42003-020-01212-9 is OK

MISSING DOIs

- None

INVALID DOIs

- None

dfm · 2022-12-08T21:48:25Z

@editorialbot recommend-accept

editorialbot · 2022-12-08T21:48:26Z

Attempting dry run of processing paper acceptance...

editorialbot · 2022-12-08T21:48:56Z

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

OK DOIs

- 10.1038/s41380-019-0441-1 is OK
- 10.1016/j.biopsych.2015.12.023 is OK
- 10.1371/journal.pcbi.1009477 is OK
- 10.1371/journal.pone.0252108 is OK
- 10.5281/zenodo.5207839 is OK
- 10.1101/2021.05.28.446120 is OK
- 10.1101/2021.06.14.448106 is OK
- 10.1016/j.neuroimage.2021.118715 is OK
- 10.7554/eLife.72904 is OK
- 10.1038/s41596-022-00696-5 is OK
- 10.1111/j.1467-9876.2005.00510.x is OK
- 10.3389/fnins.2018.00662 is OK
- 10.3389/fpsyt.2019.00011 is OK
- 10.1038/s42003-020-01212-9 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-12-08T21:50:17Z

👋 @openjournals/aass-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#3783, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

dfm · 2022-12-08T21:56:27Z

@editorialbot accept

editorialbot · 2022-12-08T21:56:29Z

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

deep-introspection · 2022-12-08T21:56:34Z

Thanks @dfm! I think this is good to go :) Congratulations @harveyaa for your first first-author paper!

editorialbot · 2022-12-08T21:58:34Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2022-12-08T21:58:35Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2022-12-08T21:58:36Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04321 joss-papers#3784
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04321
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

dfm · 2022-12-08T21:58:54Z

@smkia, @saigerutherford — 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!!

@harveyaa — Your paper is now accepted and published in JOSS! ⚡🚀💥

editorialbot · 2022-12-08T21:59:04Z

🎉🎉🎉 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.04321/status.svg)](https://doi.org/10.21105/joss.04321)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04321">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04321/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04321/status.svg
   :target: https://doi.org/10.21105/joss.04321

This is how it will look in your documentation:

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harveyaa · 2022-12-09T03:31:50Z

@dfm @deep-introspection @smkia @saigerutherford can't thank you all enough!!!! What a nice way to end the year!

editorialbot added Jupyter Notebook Python review TeX labels Apr 15, 2022

editorialbot assigned dfm Apr 15, 2022

editorialbot mentioned this issue Apr 15, 2022

[PRE REVIEW]: PyNM: a Lightweight Python implementation of Normative Modeling #4247

Closed

editorialbot added the Track: 1 (AASS) Astronomy, Astrophysics, and Space Sciences label Aug 12, 2022

dfm mentioned this issue Dec 8, 2022

Fixing broken DOI in JOSS bibliography ppsp-team/PyNM#34

Merged

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Dec 8, 2022

editorialbot added accepted published Papers published in JOSS labels Dec 8, 2022

dfm closed this as completed Dec 8, 2022

[REVIEW]: PyNM: a Lightweight Python implementation of Normative Modeling #4321

[REVIEW]: PyNM: a Lightweight Python implementation of Normative Modeling #4321

Comments

editorialbot commented Apr 15, 2022 • edited

Status

Reviewer instructions & questions

Checklists

editorialbot commented Apr 15, 2022

editorialbot commented Apr 15, 2022

editorialbot commented Apr 15, 2022

editorialbot commented Apr 15, 2022

editorialbot commented Apr 15, 2022

dfm commented Apr 15, 2022

dfm commented Apr 15, 2022

smkia commented Apr 16, 2022 • edited

Review checklist for @smkia

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

harveyaa commented Apr 27, 2022

dfm commented May 3, 2022

saigerutherford commented May 4, 2022 • edited

Review checklist for @saigerutherford

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

dfm commented May 19, 2022

smkia commented Jun 4, 2022 • edited

dfm commented Jun 4, 2022

deep-introspection commented Jun 16, 2022

dfm commented Jun 21, 2022

saigerutherford commented Jun 27, 2022

dfm commented Jun 27, 2022

deep-introspection commented Dec 8, 2022

dfm commented Dec 8, 2022

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dfm commented Dec 8, 2022

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harveyaa commented Dec 9, 2022

editorialbot commented Apr 15, 2022 •

edited

smkia commented Apr 16, 2022 •

edited

saigerutherford commented May 4, 2022 •

edited

smkia commented Jun 4, 2022 •

edited