[REVIEW]: Wakeflow: A python package for semi-analytic models of planetary wakes

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@TomHilder@dfm<!--end-editor-- Reviewers: @richteague, @andizq Archive: 10.5281/zenodo.7679415

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/22d35f9b0bb35a8df4dab85b0b6f4eb7/status.svg)](https://joss.theoj.org/papers/22d35f9b0bb35a8df4dab85b0b6f4eb7)

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

@richteague & @andizq, 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 @andizq

📝 Checklist for @richteague

editorialbot commented 2 years 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 years ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.08 s (484.9 files/s, 90964.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          19            815           1227           2167
TeX                              1             21              0            285
Markdown                         2             91              0            215
reStructuredText                 4             72             69            167
Jupyter Notebook                 3              0           1588            126
YAML                             4             22             29             99
TOML                             1              6              1             49
DOS Batch                        1              8              1             26
INI                              1              3              0             19
make                             1              4              7              9
CSS                              1              0              0              3
-------------------------------------------------------------------------------
SUM:                            38           1042           2922           3165
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

Wordcount for paper.md is 522

editorialbot commented 2 years ago

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

OK DOIs

- 10.3847/2041-8213/ac64a7 is OK
- 10.1093/mnras/stab1145 is OK
- 10.1086/157448 is OK
- 10.1046/j.1365-8711.2002.05148.x is OK
- 10.1086/320572 is OK
- 10.1086/339399 is OK
- 10.1051/0004-6361:20053275 is OK
- 10.1051/0004-6361/200811555 is OK
- 10.1088/2041-8205/811/1/L5 is OK
- 10.3847/2041-8213/aac6dc is OK
- 10.1038/s41550-019-0852-6 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.3847/1538-4357/ac7c74 is OK

MISSING DOIs

- 10.3847/1538-4357/ac88ca may be a valid DOI for title: Mapping the Complex Kinematic Substructure in the TW Hya Disk

INVALID DOIs

- None

dfm commented 2 years ago

@richteague, @andizq — 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#4863 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.

editorialbot commented 2 years ago

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

dfm commented 2 years ago

@andizq — I know that you said that you're somewhat swamped for the next couple of weeks, but please comment @editorialbot generate my checklist on this thread to generate your checklist and at least take a look at the conflict of interest policy. I'll ping you in early November to get this back on your radar. Thanks!

andizq commented 2 years ago

Review checklist for @andizq

Conflict of interest

[x] 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

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

General checks

[x] Repository: Is the source code for this software available at the https://github.com/TomHilder/wakeflow?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@TomHilder) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 1 year ago

@richteague — This is a little reminder to keep this on your radar. Please try to get started ASAP!

richteague commented 1 year ago

Hi everyone, I'm really sorry but I must have turned off notification from GitHub as I haven't seen any of these before today after I specifically went looking for them. I'll get working on this ASAP and apologize for my tardiness.

richteague commented 1 year ago

Review checklist for @richteague

Conflict of interest

[x] 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

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

General checks

[x] Repository: Is the source code for this software available at the https://github.com/TomHilder/wakeflow?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@TomHilder) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

richteague commented 1 year ago

Hi @tomhilder! I've managed to successfully install and run Wakeflow. It's a very nice package! Just a few things which I've noticed as I've been working my way through the documentation:

The testing requires pytest-cov, which @andizq has already mentioned https://github.com/TomHilder/wakeflow/issues/10.
In the Quickstart Tutorial documentation, there's a few typos when talking about the results (just below cell 6). You've used delta_rho where I think you mean delta_vphi or similar. Further down in this document you also have a comment in cell 9 which describes a 1Mj example, but this is a 0.5Mj example.
In the Advanced Configuration section, I wonder whether the dict() syntax would be more useful than the {} format for writing the dictionary in cell 7 as this avoids having to explain the need to make the key a string.

richteague commented 1 year ago

To add to these comments, for the paper I'd recommend to expand the Summary section to be a bit more explicit about what properties about the wake you're able to extract (e.g., the velocity components and rho), and then say that this is how we can connect with observations as those are what are being observed.

dfm commented 1 year ago

@TomHilder — Happy new year! I'm checking in to see how things are going with the recommendations that @richteague and @andizq have made so far. Please let me know if there are any major stoppers or anything I can do to help things move along. Thanks!

TomHilder commented 1 year ago

Hi @dfm !

Thanks for checking in. I haven't made any progress yet as I submitted my Honours thesis in Nov 2022, and I've been on break since. I'll be commencing my PhD in Feb, so I can get straight onto this then. I'm not sure if there is a timeline restriction, so if I need to address this before then that is okay, I can do that :)

Cheers.

TomHilder commented 1 year ago

Hi @richteague , thank you for the feedback!

The documentation has been updated to include pytest-cov as a requirement for testing.
The mentioned typos in the quickstart tutorial have been fixed.
This is a good suggestion and I have changed the tutorial to use the dict() syntax.

I am hoping to address your comments in regards to the paper early next week. Thanks!

TomHilder commented 1 year ago

Hi @andizq , thank you also for the feedback! I have implemented all of your suggested changes, please see the issue threads for more details. I did stick with pcolormesh over contourf in the quickstart tutorial, and I have provided some justification in TomHilder/wakeflow#11 .

TomHilder commented 1 year ago

Hi @richteague , I have updated the paper based on your feedback to be a bit more specific about what wakeflow calculates and how these can be connected to observations.

The summary now reads:

Wakeflow is a Python package for generating semi-analytic models of the perturbations induced by planets embedded in gaseous circumstellar disks. These perturbations take the form of a spiral shock wave [@Ogilvie:2002], and are often called a "planet wake" in analogy with that produced by a boat in a lake. Using Wakeflow, users may calculate the perturbed density and velocity fields of the gas in the disk. These may be used with radiation transfer codes to generate synthetic observations that map both the gas distribution and the gas kinematics. Comparison with real observations, such as from molecular line emission taken with the Attacama Large Millimetre Array, allows researchers to infer the properties of potential planets as well as the disk itself.

Let me know if you think it needs to be updated further, I wasn't sure how specific to be when referring to observations.

I think that I have now addressed all the feedback that I received 😄

andizq commented 1 year ago

Hi @TomHilder, thank you for addressing the feedback and suggestions in such a positive way! I am happy with (and have tested) the new additions and therefore recommend your work for publication as long as @richteague is also happy with the modifications. It is a very nice, easy-to-use tool that will facilitate the analysis and prediction of kinematic observables resulting from planet-disc interaction!

richteague commented 1 year ago

Thanks, @TomHilder, I think all the changes are great and I'm happy to complete the review process. It's going to be a very useful code for the planet-formation community!

dfm commented 1 year ago

@editorialbot generate pdf

dfm commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.3847/2041-8213/ac64a7 is OK
- 10.1093/mnras/stab1145 is OK
- 10.1086/157448 is OK
- 10.1046/j.1365-8711.2002.05148.x is OK
- 10.1086/320572 is OK
- 10.1086/339399 is OK
- 10.1051/0004-6361:20053275 is OK
- 10.1051/0004-6361/200811555 is OK
- 10.1088/2041-8205/811/1/L5 is OK
- 10.3847/2041-8213/aac6dc is OK
- 10.1038/s41550-019-0852-6 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.3847/1538-4357/ac7c74 is OK

MISSING DOIs

- 10.3847/1538-4357/ac88ca may be a valid DOI for title: Mapping the Complex Kinematic Substructure in the TW Hya Disk

INVALID DOIs

- None

editorialbot commented 1 year ago

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

dfm commented 1 year ago

@richteague, @andizq — Thank you for your thorough and constructive reviews! I really appreciate the time you volunteered to this process!! 🎉 🎉

@TomHilder — I believe that @editorialbot is right about that suggested DOI above ☝️. Can you update the reference for Teague:2022 to the published version and then run the following steps:

Comment @editorialbot generate pdf, and take one last read through the manuscript to make sure that you're happy with it (it's harder to make changes later!), especially the author names and affiliations. I've taken a pass and it looks good to me!
Increment the version number of the software and report that version number back here.
Create an archived release of that version of the software (using Zenodo or something similar). Please make sure that the metadata (title and author list) exactly match the paper. Then report the DOI of the release back to this thread.

TomHilder commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

TomHilder commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.3847/2041-8213/ac64a7 is OK
- 10.1093/mnras/stab1145 is OK
- 10.1086/157448 is OK
- 10.1046/j.1365-8711.2002.05148.x is OK
- 10.1086/320572 is OK
- 10.1086/339399 is OK
- 10.1051/0004-6361:20053275 is OK
- 10.1051/0004-6361/200811555 is OK
- 10.3847/1538-4357/ac88ca is OK
- 10.1088/2041-8205/811/1/L5 is OK
- 10.3847/2041-8213/aac6dc is OK
- 10.1038/s41550-019-0852-6 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.3847/1538-4357/ac7c74 is OK

MISSING DOIs

- None

INVALID DOIs

- None

TomHilder commented 1 year ago

Hi @dfm! I have fixed the DOI and I am happy with the manuscript.

The version number is 1.3.1

The DOI for the Zenodo archive is 10.5281/zenodo.7679415

Thanks!

dfm commented 1 year ago

@editorialbot set 10.5281/zenodo.7679415 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7679415

dfm commented 1 year ago

@editorialbot set 1.3.1 as version

editorialbot commented 1 year ago

Done! version is now 1.3.1

dfm commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.3847/2041-8213/ac64a7 is OK
- 10.1093/mnras/stab1145 is OK
- 10.1086/157448 is OK
- 10.1046/j.1365-8711.2002.05148.x is OK
- 10.1086/320572 is OK
- 10.1086/339399 is OK
- 10.1051/0004-6361:20053275 is OK
- 10.1051/0004-6361/200811555 is OK
- 10.3847/1538-4357/ac88ca is OK
- 10.1088/2041-8205/811/1/L5 is OK
- 10.3847/2041-8213/aac6dc is OK
- 10.1038/s41550-019-0852-6 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.3847/1538-4357/ac7c74 is OK

MISSING DOIs

- None

INVALID DOIs

- None

dfm commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.3847/2041-8213/ac64a7 is OK
- 10.1093/mnras/stab1145 is OK
- 10.1086/157448 is OK
- 10.1046/j.1365-8711.2002.05148.x is OK
- 10.1086/320572 is OK
- 10.1086/339399 is OK
- 10.1051/0004-6361:20053275 is OK
- 10.1051/0004-6361/200811555 is OK
- 10.3847/1538-4357/ac88ca is OK
- 10.1088/2041-8205/811/1/L5 is OK
- 10.3847/2041-8213/aac6dc is OK
- 10.1038/s41550-019-0852-6 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.3847/1538-4357/ac7c74 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

:wave: @openjournals/aass-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3999, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

dfm commented 1 year ago

I opened a tiny PR. Once you've got that merged, we should be able to proceed with the final processing.

dfm commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.3847/2041-8213/ac64a7 is OK
- 10.1093/mnras/stab1145 is OK
- 10.1086/157448 is OK
- 10.1046/j.1365-8711.2002.05148.x is OK
- 10.1086/320572 is OK
- 10.1086/339399 is OK
- 10.1051/0004-6361:20053275 is OK
- 10.1051/0004-6361/200811555 is OK
- 10.3847/1538-4357/ac88ca is OK
- 10.1088/2041-8205/811/1/L5 is OK
- 10.3847/2041-8213/aac6dc is OK
- 10.1038/s41550-019-0852-6 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.3847/1538-4357/ac7c74 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

:wave: @openjournals/aass-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4002, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

dfm commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

:warning: Couldn't acccept/publish paper. An error happened.

dfm commented 1 year ago

@openjournals/dev — Any thoughts on this acceptance error?

dfm commented 1 year ago

@TomHilder — It doesn't look like this error has anything to do with your submission, so as soon as we get it debugged, we'll get this published!

openjournals / joss-reviews