Skip to content
Please note that GitHub no longer supports your web browser.

We recommend upgrading to the latest Google Chrome or Firefox.

Learn more

/joss-reviews

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

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

Open
whedon opened this issue Oct 23, 2019 · 17 comments
Assignees
@arfon @steven-murray @williamjameshandley
Labels
AAS review

Comments

@whedon
Copy link
Collaborator

@whedon whedon commented Oct 23, 2019 •
edited by williamjameshandley

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

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?
@whedon whedon added the review label Oct 23, 2019
@whedon whedon mentioned this issue Oct 23, 2019
Closed
@whedon

This comment has been minimized.

Sign in to view
Copy link
Collaborator Author

@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
@whedon

This comment has been minimized.

Sign in to view
Copy link
Collaborator Author

@whedon whedon commented Oct 23, 2019 

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Sign in to view
Copy link
Collaborator Author

@whedon whedon commented Oct 23, 2019

👉 Check article proof 📄 👈

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

This comment has been minimized.

Sign in to view
Copy link
Member

@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:
@steven-murray

This comment has been minimized.

Sign in to view
Copy link
Collaborator

@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?
@arfon

This comment has been minimized.

Sign in to view
Copy link
Member

@arfon arfon commented Oct 23, 2019

@steven-murray - did you accept the invite here? https://github.com/openjournals/joss-reviews/invitations
@steven-murray

This comment has been minimized.

Sign in to view
Copy link
Collaborator

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

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

This comment has been minimized.

Sign in to view
Copy link
Collaborator

@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?
@arfon

This comment has been minimized.

Sign in to view
Copy link
Member

@arfon arfon commented Oct 23, 2019 •
edited

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
@arfon

This comment has been minimized.

Sign in to view
Copy link
Member

@arfon arfon commented Oct 24, 2019

@whedon generate pdf
@whedon

This comment has been minimized.

Sign in to view
Copy link
Collaborator Author

@whedon whedon commented Oct 24, 2019 

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Sign in to view
Copy link
Collaborator Author

@whedon whedon commented Oct 24, 2019

👉 Check article proof 📄 👈

This was referenced Oct 29, 2019
Closed
Closed
Closed
Closed
Open
Closed
Open
Open
Open
Closed
@steven-murray

This comment has been minimized.

Sign in to view
Copy link
Collaborator

@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"
@arfon

This comment has been minimized.

Sign in to view
Copy link
Member

@arfon arfon commented Nov 10, 2019

@williamjameshandley - how are you getting along with your review here?
This was referenced Nov 18, 2019
Closed
Open
@williamjameshandley

This comment has been minimized.

Sign in to view
Copy link
Collaborator

@williamjameshandley williamjameshandley commented Nov 18, 2019

The repository installs fine on my machine (I'm using the recently released python 3.8, so that's a good sign given that I assume it hasn't necessarily been tested on this version).

  • [ ]The arXiv paper makes it pretty clear that the intention is to extend this system of package as time goes on, which I approve of. My main requirement for acceptance is that a template for continuous integration is set up which can also be extended as the codebase expands. I've added this as a GitHub issue, and we can discuss further there.

  • [ ]It would also be good to upload this to PyPi so that it can be installed without the need to clone the git repo. Also added as an issue

Other than this, more minor additions could be:

  1. SAIL (Stellar Atmosphere Intensity Limb), i.e., a calculator of stellar limb-darkening coeffi-
    cients that outperforms the existing software by one order of magnitude in terms of light-curve
    model accuracy, i.e., down to <10 parts per million (ppm);
  • This claim could be backed up by a specific example that the user can run
  1. TRIP (Transit Ring-Integrated Profile), which can compute an exact transit light-curve
    by direct integration of the occulted stellar flux from the model intensities, without using a
    parameterization (limb-darkening law) to approximate the stellar intensity profile.
  • There should be a clear example of this in the README, ideally with a plot to show it working.
@danielskatz

This comment has been minimized.

Sign in to view
Copy link

@danielskatz danielskatz commented Dec 5, 2019

👋 @arfon - How is this review going?
@steven-murray

This comment has been minimized.

Sign in to view
Copy link
Collaborator

@steven-murray steven-murray commented Dec 5, 2019

Currently the author is working on closing the issues that we have made in his repo -- most of them have now been addressed.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@arfon arfon

@steven-murray steven-murray

@williamjameshandley williamjameshandley

Labels
AAS review
Projects
None yet
Milestone
No milestone
5 participants
@whedon @arfon @steven-murray @williamjameshandley @danielskatz
You can’t perform that action at this time.