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[REVIEW]: The ExoTETHyS package: Tools for Exoplanetary Transits around Host Stars #1834

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whedon opened this issue Oct 23, 2019 · 43 comments
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@whedon whedon commented Oct 23, 2019

Submitting author: @gmorello (Giuseppe Morello)
Repository: https://github.com/ucl-exoplanets/ExoTETHyS
Version: v1.0.1
Editor: @arfon
Reviewer: @steven-murray, @williamjameshandley
Archive: 10.5281/zenodo.3577740

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/4228224c360b4b32075cfe79475005d6"><img src="https://joss.theoj.org/papers/4228224c360b4b32075cfe79475005d6/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/4228224c360b4b32075cfe79475005d6/status.svg)](https://joss.theoj.org/papers/4228224c360b4b32075cfe79475005d6)

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

@steven-murray & @williamjameshandley, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @arfon know.

Please try and complete your review in the next two weeks

Review checklist for @steven-murray

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

General checks

  • Repository: Is the source code for this software available at the repository url?
  • 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 (@gmorello) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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?

Review checklist for @williamjameshandley

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

General checks

  • Repository: Is the source code for this software available at the repository url?
  • 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 (@gmorello) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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?
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@whedon whedon commented Oct 23, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @steven-murray, @williamjameshandley it looks like you're currently assigned to review this paper 🎉.

⭐️ Important ⭐️

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

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

@whedon commands

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

@whedon generate pdf
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@whedon whedon commented Oct 23, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Oct 23, 2019

@arfon arfon added the AAS label Oct 23, 2019
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@arfon arfon commented Oct 23, 2019

@steven-murray, @williamjameshandley - One thing I forgot to mention when inviting you both to review is that this JOSS submission/paper is a joint publication with AAS Journals, i.e. this JOSS paper will be published together with another paper in one of the AAS journals. As part of this collaboration, AAS publishing makes a small donation to the running costs of JOSS.

If this is unacceptable to you, please let me know and I can look for alternative reviewers.

Some related links:

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@steven-murray steven-murray commented Oct 23, 2019

@arfon it seems I am not able to check off the check-boxes in the original comment?

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@arfon arfon commented Oct 23, 2019

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@steven-murray steven-murray commented Oct 23, 2019

@arfon -- ahhh, OK now I have :-)

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@williamjameshandley williamjameshandley commented Oct 23, 2019

@arfon

(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.)

I would consider myself an aspiring completist, but am currently not enough of one in order to disambiguate the above instruction. Could you point me to an example of how to link between a JOSS review and a GitHub issue?

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@arfon arfon commented Oct 23, 2019

Well, this issue is the JOSS review (i.e. leave comments here), but if you were to open an issue on the repository being reviewed (https://github.com/ucl-exoplanets/ExoTETHyS), please link to this issue in issues opened on https://github.com/ucl-exoplanets/ExoTETHyS i.e. by saying something like:

This issue is related to this JOSS review: https://github.com/openjournals/joss-reviews/issues/1834

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@arfon arfon commented Oct 24, 2019

@whedon generate pdf

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@whedon whedon commented Oct 24, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Oct 24, 2019

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@steven-murray steven-murray commented Oct 29, 2019

Apart from the code issues, which I have opened in the repository itself, I have the following comments about the paper:

  1. While there is a statement of what the software's purpose is, there is no additional context in the opening sentences (i.e. is this an important task for the field? What motivates the construction of this code?)
  2. While there is a passing reference to the code being able to outperform other codes, there is no discussion of alternatives to this code, and what motivated the construction of this one, or whether this code is the only way (currently) to use the SAIL and TRIP algorithms/packages.
  3. Second sentence: "Now, " can be removed.
  4. The last section could be moved to its own paragraph, concerning "how the code is currently being used"
  5. It would be good to identify ways the code may be used outside of the current uses.
  6. "more details can be found in..." -- perhaps it should be "Scientific details of the algorithms can be found in <>, and technical usage details can be found on GitHub"
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@arfon arfon commented Nov 10, 2019

@williamjameshandley - how are you getting along with your review here?

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@arfon arfon commented Jan 6, 2020

👋 @gmorello - happy new year!

Could you give me an update on the status of your updates based on the reviewer feedback?

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@gmorello gmorello commented Jan 9, 2020

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@steven-murray steven-murray commented Jan 9, 2020

@gmorello is there an updated version of the paper I can read?

If you don't want to fully recapitulate the discussion concerning comparison to other codes in this paper, perhaps you could abbreviate it by saying something like "More details, and a comprehensive comparison to other relevant codes, can be found in ....".

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@labarba labarba commented Jan 26, 2020

@whedon generate pdf

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@whedon whedon commented Jan 26, 2020

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@labarba labarba commented Jan 26, 2020

👋 @steven-murray — you can find a new proof above

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@steven-murray steven-murray commented Jan 27, 2020

That looks good, thank you. I'm happy with this.

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@arfon arfon commented Jan 27, 2020

That looks good, thank you. I'm happy with this.

Thanks @steven-murray. There are a few checkboxes in the review unchecked still - could you give these a quick look again?

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@steven-murray steven-murray commented Jan 28, 2020

@arfon ah yes, re-checked them.

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@arfon arfon commented Jan 29, 2020

@gmorello - I've made a couple of minor updates to your paper for readability in ucl-exoplanets/ExoTETHyS#18

Also, do you know that the status of the AAS companion paper is here? Before we can publish this we should add the AAS paper DOI to the YAML header of the paper.md.

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@arfon arfon commented Jan 29, 2020

/ cc @crawfordsm for visibility on this submission that has now completed review and is accepted into JOSS.

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@arfon arfon commented Feb 11, 2020

@gmorello - could you please merge this PR too? ucl-exoplanets/ExoTETHyS#19 . It adds the AAS information to the JOSS paper.

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@arfon arfon commented Feb 11, 2020

@whedon accept

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@whedon whedon commented Feb 11, 2020

No archive DOI set. Exiting...

@arfon arfon removed the paused label Feb 11, 2020
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@arfon arfon commented Feb 11, 2020

@whedon set 10.5281/zenodo.3577740 as archive

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@whedon whedon commented Feb 11, 2020

OK. 10.5281/zenodo.3577740 is the archive.

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@arfon arfon commented Feb 11, 2020

@whedon accept

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@whedon whedon commented Feb 11, 2020

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Feb 11, 2020

Reference check summary:

OK DOIs

- 10.1111/j.1365-2966.2010.17094.x is OK
- 10.1093/mnras/stz2958 is OK
- 10.1038/s41550-019-0878-9 is OK

MISSING DOIs

- https://doi.org/10.3847/1538-3881/ab63dc may be missing for title: The ExoTETHyS package: Tools for Exoplanetary Transits around Host Stars

INVALID DOIs

- None
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@whedon whedon commented Feb 11, 2020

Check final proof 👉 openjournals/joss-papers#1297

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1297, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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@arfon arfon commented Feb 11, 2020

@whedon accept deposit=true

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@whedon whedon commented Feb 11, 2020

Doing it live! Attempting automated processing of paper acceptance...
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@whedon whedon commented Feb 11, 2020

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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@whedon whedon commented Feb 11, 2020

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#1298
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01834
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

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@arfon arfon commented Feb 11, 2020

@steven-murray, @williamjameshandley - many thanks for your reviews here

@gmorello - your paper is now published in JOSS ⚡️🚀💥

@arfon arfon closed this Feb 11, 2020
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@whedon whedon commented Feb 11, 2020

🎉🎉🎉 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.01834/status.svg)](https://doi.org/10.21105/joss.01834)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01834">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01834/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01834/status.svg
   :target: https://doi.org/10.21105/joss.01834

This is how it will look in your documentation:

DOI

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