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[REVIEW]: Pippin: A pipeline for supernova cosmology #2122

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whedon opened this issue Feb 26, 2020 · 51 comments
Closed

[REVIEW]: Pippin: A pipeline for supernova cosmology #2122

whedon opened this issue Feb 26, 2020 · 51 comments

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@whedon whedon commented Feb 26, 2020

Submitting author: @Samreay (Samuel Hinton)
Repository: https://github.com/Samreay/Pippin
Version: 0.1.1
Editor: @arfon
Reviewer: @kboone, @temuller
Archive: 10.5281/zenodo.3716116

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/956143a352df07f181555e7d167ff20f"><img src="https://joss.theoj.org/papers/956143a352df07f181555e7d167ff20f/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/956143a352df07f181555e7d167ff20f/status.svg)](https://joss.theoj.org/papers/956143a352df07f181555e7d167ff20f)

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

@kboone & @temuller, 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 @kboone

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 (samreay) 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 @temuller

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 (samreay) 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 Feb 26, 2020

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

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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:

@whedon generate pdf
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@whedon whedon commented Feb 26, 2020

Reference check summary:

OK DOIs

- 10.1109/MCSE.2007.55 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.1086/605984 is OK
- 10.1103/PhysRevD.66.103511 is OK
- 10.21105/joss.00045 is OK
- 10.3847/2041-8213/ab04fa is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Feb 26, 2020

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@arfon arfon commented Feb 26, 2020

@kboone, @temuller - please carry out your review in this issue by updating the checklist above and giving feedback in this issue. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html and if possible I'd appreciate it if you could complete your review in the next 2-3 weeks.

Any questions/concerns please let me know!

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@temuller temuller commented Mar 10, 2020

See my review attached.
JOSS_Review_2122.pdf

The authors will need to make the suggested changes before accepting this for publication.

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@Samreay Samreay commented Mar 10, 2020

Hey Tomás! I've added a link to the SNANA report and made the purpose statement clearer in the main readme. As to reporting issues or seeking support, I've updated the contribution section to make it clear that it applies to seeking support and raising issues.

As to the functionality, this is definitely a hassle - because Pippin is a pipeline that stitches other software together, running it necessarily requires having those pieces installed (which is a big hassle for SNANA if you dont have a midway account). Even the data prep stages uses new code in SNANA to determine better starting conditions for the eventual light curve fitting of data.

I'd be happy to record a video showing the usage in action if that would help, just let me know.

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@temuller temuller commented Mar 10, 2020

Hi Sam, thanks for the prompt reply.

I know installing SNANA can be a hassle (I have installed it myself!), but as it is a core package used by Pippin, you should be able to provide a straight forward example (assuming the user has SNANA already installed). If you think recording a video can show the usage properly, there is no problem with that, but I am not sure if it is actually simpler that way.

By the way, the "Contributing to Pippin" hyperlink is broken.

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@Samreay Samreay commented Mar 10, 2020

Ah, thanks for the catch on the hyperlink I broke! And ah, if you have a working SNANA install, I am hoping that this config file would run without hassle for you: https://github.com/Samreay/Pippin/blob/master/configs/examples/example_sim.yml

If there are issues I'll record the video - Im conscious about not taking too much of your time installing deps and smacking paths around given how much work you've done already. Thanks for the comments so far too, appreciate it!

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@temuller temuller commented Mar 10, 2020

Pippin is complaining about the "group" keyword for SNANA in the cfg.yml file. It doesn't seem to find it anywhere. Is it meant to work with midway?

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@Samreay Samreay commented Mar 10, 2020

Ah, yes, it's trying to set the group ownership over newly created files to Rick Kessler's group by default (the one we use in DES) so that other members of the collaboration can use it. You should be able to set the group to your own name or whatever group you are part of

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@temuller temuller commented Mar 10, 2020

It doesn't find any group if I run it locally on my machine

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@Samreay Samreay commented Mar 10, 2020

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@temuller temuller commented Mar 10, 2020

Here is the output
pippin_output.txt

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@Samreay Samreay commented Mar 10, 2020

Ah, so yeah we need to find you a valid group - you can list groups in linux using groups $USER. The second error is then because Pippin needs python3.7+ as per the doco alas - text is a new kwarg. Let me make a quick video showing it in action so you dont have to dick around.

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@Samreay Samreay commented Mar 10, 2020

Heres a link to executing the sim example and showing the output log results of our preliminary 5yr DES analysis, let me know if youd like other examples: https://youtu.be/pCaPvzFCZ-Y

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@temuller temuller commented Mar 10, 2020

Thanks for the video Sam. I was able to correct the errors I had, but I encountered a new one (it has to do with subprocess.check_output). However, I think that after solving this one, the example should run fine. See below.

pippin_output2.txt

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@Samreay Samreay commented Mar 10, 2020

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@temuller temuller commented Mar 10, 2020

Ah, I see! I am not! I will see if I can do that tomorrow. I will just give it a try and see how that goes, but I guess I am quite happy with the changes. I will double-check everything tomorrow so I can finish the review. Thanks a lot!

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@temuller temuller commented Mar 11, 2020

Hi again Sam. I am finally happy with the changes you made. I would like you to add the description/example video to the documentation so users have access to it, but that is last thing I will ask you to do. Thanks!

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@Samreay Samreay commented Mar 11, 2020

Awesome, thanks for finally getting it working! I've added a link to the video in the description :)

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@arfon arfon commented Mar 14, 2020

Dear authors and reviewers

We wanted to notify you that in light of the current COVID-19 pandemic, JOSS has decided to suspend submission of new manuscripts and to handle existing manuscripts (such as this one) on a "best efforts basis". We understand that you may need to attend to more pressing issues than completing a review or updating a repository in response to a review. If this is the case, a quick note indicating that you need to put a "pause" on your involvement with a review would be appreciated but is not required.

Thanks in advance for your understanding.

Arfon Smith, Editor in Chief, on behalf of the JOSS editorial team.

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@kboone kboone commented Mar 18, 2020

I have attached my review. I have a couple of minor suggestions that should be fixed before accepting this paper for publication.

JOSS Review #2122.pdf

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@Samreay Samreay commented Mar 18, 2020

Hey Kyle! I've made the requested changes to improve the documentation and pushed them out. You can verify the changes here: Samreay/Pippin@7e4c108

Cheers!

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@kboone kboone commented Mar 18, 2020

The changes look good, and they address my concerns. I recommend this paper for acceptance.

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@Samreay Samreay commented Mar 19, 2020

Fantastic, thanks @kboone and @temuller. @arfon, both reviewers are now happy!

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@arfon arfon commented Mar 19, 2020

@whedon generate pdf

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@whedon whedon commented Mar 19, 2020

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@arfon arfon commented Mar 19, 2020

@Samreay - a few comments on your paper:

Do you want the title to be only 'Pippin'? Pippin: A pipeline for supernova cosmology seems more descriptive?

For the DES-3YR analysis (Abbott et al., 2019), we implemented a basic bash pipeline
to reduce manual labour. For the DES-5YR analysis, which greatly increases complexity, I
implement this pipeline to increase researcher productivity.

This ☝️ paragraph reads a little weirdly. You're using 'we' and then 'I' in the same sentence. Perhaps this could be rephrased as:

For the DES-3YR analysis (Abbott et al., 2019), we implemented a basic bash pipeline
to reduce manual labour. For the DES-5YR analysis, which greatly increases complexity, Pippin was developed as the pipeline to increase researcher productivity.

Should 'SALT2 supernova model' have a citation?

Last sentence change Github to GitHub. Also, consider linking the phrase 'development page' to to https://github.com/Samreay/Pippin/issues .

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@arfon arfon commented Mar 19, 2020

@whedon check references

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@whedon whedon commented Mar 19, 2020

Reference check summary:

OK DOIs

- 10.1109/MCSE.2007.55 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.1086/605984 is OK
- 10.1103/PhysRevD.66.103511 is OK
- 10.21105/joss.00045 is OK
- 10.3847/2041-8213/ab04fa is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@Samreay Samreay commented Mar 19, 2020

Hi @arfon, I've made the I/we consistent change in the latest commit. The SALT2 paper reference is still in draft and yet to be submitted. Github -> GitHub, and a link to the developer doco has been added.

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@Samreay Samreay commented Mar 19, 2020

@whedon generate pdf

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@whedon whedon commented Mar 19, 2020

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@arfon arfon commented Mar 19, 2020

@Samreay - At this point could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

  • The title of the archive is the same as the JOSS paper title
  • That the authors of the archive are the same as the JOSS paper authors

I can then move forward with accepting the submission.

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@Samreay Samreay commented Mar 19, 2020

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@arfon arfon commented Mar 19, 2020

@Samreay - last time I'll ask I promise 😸(as the title of the Zenodo release is Pippin: A pipeline for supernova cosmology. You definitely want the title of the JOSS paper to only be Pippin?

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@Samreay Samreay commented Mar 19, 2020

Oh I thought the title was the full "Pippin: A pipeline for supernova cosmology", as it is in this review. Definitely the full name makes more sense haha

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@arfon arfon commented Mar 19, 2020

Glad I checked :-) Samreay/Pippin#3 fixes this.

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@Samreay Samreay commented Mar 19, 2020

Ah right, the paper.md, of course! Thanks for the fix! :)

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@arfon arfon commented Mar 19, 2020

@whedon set 10.5281/zenodo.3716116 as archive

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@whedon whedon commented Mar 19, 2020

OK. 10.5281/zenodo.3716116 is the archive.

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@arfon arfon commented Mar 19, 2020

@whedon accept

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@whedon whedon commented Mar 19, 2020

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Mar 19, 2020

Reference check summary:

OK DOIs

- 10.1109/MCSE.2007.55 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.1086/605984 is OK
- 10.1103/PhysRevD.66.103511 is OK
- 10.21105/joss.00045 is OK
- 10.3847/2041-8213/ab04fa is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Mar 19, 2020

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#1379

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1379, 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 Mar 19, 2020

@whedon accept deposit=true

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@whedon whedon commented Mar 19, 2020

Doing it live! Attempting automated processing of paper acceptance...
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@whedon whedon commented Mar 19, 2020

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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@whedon whedon commented Mar 19, 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#1380
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02122
  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 Mar 19, 2020

@kboone, @temuller - many thanks for your reviews here

@Samreay - your paper is now accepted into JOSS ⚡️🚀💥

@arfon arfon closed this Mar 19, 2020
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@whedon whedon commented Mar 19, 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.02122/status.svg)](https://doi.org/10.21105/joss.02122)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02122">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02122/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02122/status.svg
   :target: https://doi.org/10.21105/joss.02122

This is how it will look in your documentation:

DOI

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