[PRE REVIEW]: disksurf: Extracting the 3D Structure of Protoplanetary Disks

whedon commented 3 years ago

Submitting author: @richteague (Richard Teague) Repository: https://github.com/richteague/disksurf Version: v0.1.7 Editor: @christinahedges Reviewers: @emptymalei, @cpinte Managing EiC: Daniel S. Katz

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

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whedon commented 3 years ago

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

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

For a list of things I can do to help you, just type:

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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whedon commented 3 years ago

Wordcount for paper.md is 709

whedon commented 3 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.04 s (366.5 files/s, 75793.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           6            305            759           1102
TeX                              1             11              0            177
Markdown                         3             22              0             65
Jupyter Notebook                 1              0            485             55
reStructuredText                 2             19             15             33
DOS Batch                        1              8              1             26
make                             1              4              6              9
-------------------------------------------------------------------------------
SUM:                            15            369           1266           1467
-------------------------------------------------------------------------------

Statistical information for the repository '578941ac8d8dbf52135e0c23' was
gathered on 2021/09/29.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Jane Huang                       1             4              2            0.05
Richard Teague                  52          6863           4969           97.62
richteague                       3           276              6            2.33

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Richard Teague             2166           31.6          1.1               10.11

whedon commented 3 years ago

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

OK DOIs

- 10.1051/0004-6361/201629098 is OK
- 10.21105/joss.01632 is OK
- 10.1086/670067 is OK
- 10.1038/s41586-019-1642-0 is OK
- 10.3847/1538-4357/abf92e is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.5281/zenodo.4599319 is OK
- 10.1051/0004-6361/201731377 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 3 years ago

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

danielskatz commented 3 years ago

👋 @christinahedges - would you be able to edit this submission for JOSS?

danielskatz commented 3 years ago

@whedon invite @christinahedges as editor

whedon commented 3 years ago

@christinahedges has been invited to edit this submission.

christinahedges commented 3 years ago

@whedon assign me as editor

whedon commented 3 years ago

OK, the editor is @christinahedges

christinahedges commented 3 years ago

Hi @richteague, thanks for your submission to JOSS! I took a quick look at your submission and I have these comments:

Tests

I don't believe there are tests in your repo. One of the review checklist criteria for JOSS is:

Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?

You can see the checklist here. Before I find reviewers for this submission, do you want some time to address this checklist item?

Licensing

I see that you have used the detect_peaks.py module from this repo. I believe you need to make some changes to this file to be compliant with their license by adding their license and copyright notice at the top of the file, and stating any changes.

Reviewers

As I start to look for reviewers for this submission, I wanted to ask is there anyone you can identify you believe would be a good reviewer for this work? They would need to have no conflicts of interest.

richteague commented 3 years ago

Thanks @christinahedges!

I've updated the license for detect_peaks.py with the MIT version that it was originally written under.

Regarding the tests, we've developed a tutorial notebook which users can run that should act as a test that everything is installed correctly. It this sufficient for the "manual steps" described in the checklist criteria, or should we make a separate testing suite?

I will have a think about potential reviewers while we resolve the testing issue.

christinahedges commented 3 years ago

Hi @richteague! Thanks for updating to be compliant with the license.

Re tests, these are the instructions from JOSS:

Authors are strongly encouraged to include an automated test suite covering the core functionality of their software.

* Good: An automated test suite hooked up to continuous integration (GitHub Actions, Circle CI, or similar)
* OK: Documented manual steps that can be followed to objectively check the expected functionality of the software (e.g., a sample input file to assert behavior)
* Bad (not acceptable): No way for you, the reviewer, to objectively assess whether the software works

Based on this, I would say that having a tutorial notebook for testing comes under the "OK" bracket. I think because it meets this standard, I'm happy to let the compliance with testing (e.g. test coverage) be discussed with reviewers.

Let me know if you have any reviewer suggestions, I will also look to find appropriate reviewers.

christinahedges commented 3 years ago

Hi @richteague! I'm hunting down some reviewers for this submission, let me know if you have any suggestions of reviewers you think I should be considering. For example, I see this tool is based on the algorithm discussed here, would any of the authors make good reviewers of this tool? Otherwise I will keep searching for good reviewers.

christinahedges commented 3 years ago

@whedon assign @emptymalei as reviewer

@richteague I'll be looking for a reviewer who has more domain knowledge of disks too, let me know if you have good ideas, I'm chasing a few leads.

whedon commented 3 years ago

OK, @emptymalei is now a reviewer

richteague commented 3 years ago

Hi @christinahedges - apologies for the delay in getting back to you. I think some disk-related experts could be Christophe Pinte (lead author of the original paper) or perhaps Christian Rab, also a coauthor on that paper and someone that works a lot on these topics.

christinahedges commented 3 years ago

Hi @richteague, thanks that's great. I did ping Christophe Pinte, I'll give Christian Rab a shot too. Hopefully we'll get someone to review in the next few days and we can get started! I'll keep working on it.

cpinte commented 3 years ago

Hi @richteague ,

Happy to review the code. I'll try to do this asap.

christinahedges commented 3 years ago

@whedon add @cpinte as reviewer

whedon commented 3 years ago

OK, @cpinte is now a reviewer

christinahedges commented 3 years ago

@whedon start review

Ok everyone, looks like we can start this review! @emptymalei and @cpinte will be reviewing @richteague's submission. I'm going to start the review now, which will start a new GitHub issue with the instructions for review.

whedon commented 3 years ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/3827.

openjournals / joss-reviews