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

[REVIEW]: perfectns: perfect dynamic and standard nested sampling for spherically symmetric likelihoods and priors #985

Closed
whedon opened this Issue Sep 29, 2018 · 27 comments

Comments

Projects
None yet
4 participants
@whedon
Collaborator

whedon commented Sep 29, 2018

Submitting author: @ejhigson (Edward Higson)
Repository: https://github.com/ejhigson/perfectns
Version: v2.1.0
Editor: @arfon
Reviewer: @ziotom78
Archive: 10.5281/zenodo.1443509

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/364e6137dc43aeee3c244a3a8fde16ef"><img src="http://joss.theoj.org/papers/364e6137dc43aeee3c244a3a8fde16ef/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/364e6137dc43aeee3c244a3a8fde16ef/status.svg)](http://joss.theoj.org/papers/364e6137dc43aeee3c244a3a8fde16ef)

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) 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

@ziotom78, 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.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @arfon know.

Please try and complete your review in the next two weeks

Review checklist for @ziotom78

Conflict of interest

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?
  • Version: Does the release version given match the GitHub release (v2.1.0)?
  • Authorship: Has the submitting author (@ejhigson) 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 function 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

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
@whedon

This comment has been minimized.

Show comment
Hide comment
@whedon

whedon Sep 29, 2018

Collaborator

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @ziotom78 it looks like you're currently assigned as the reviewer for 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
Collaborator

whedon commented Sep 29, 2018

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @ziotom78 it looks like you're currently assigned as the reviewer for 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
@whedon

This comment has been minimized.

Show comment
Hide comment
@whedon

whedon Sep 29, 2018

Collaborator
Attempting PDF compilation. Reticulating splines etc...
Collaborator

whedon commented Sep 29, 2018

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

This comment has been minimized.

Show comment
Hide comment
@whedon
Collaborator

whedon commented Sep 29, 2018

@arfon

This comment has been minimized.

Show comment
Hide comment
@arfon

arfon Sep 29, 2018

Member

@ziotom78 - 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

Any questions/concerns please let me know.

Member

arfon commented Sep 29, 2018

@ziotom78 - 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

Any questions/concerns please let me know.

@ejhigson

This comment has been minimized.

Show comment
Hide comment
@ejhigson

ejhigson Sep 29, 2018

@ziotom78 thank you very much for taking the time to review my submission, I really appreciate it!

Unfortunately for personal reasons it looks like it will be very difficult for me to make changes from (next) Sunday 7th October onwards. I would therefore be extraordinarily grateful if you could do your review this coming week? I am aware the process is normally 2 weeks so please don't worry if this is inconvenient for you! And thank you again very much for your help

ejhigson commented Sep 29, 2018

@ziotom78 thank you very much for taking the time to review my submission, I really appreciate it!

Unfortunately for personal reasons it looks like it will be very difficult for me to make changes from (next) Sunday 7th October onwards. I would therefore be extraordinarily grateful if you could do your review this coming week? I am aware the process is normally 2 weeks so please don't worry if this is inconvenient for you! And thank you again very much for your help

@ziotom78

This comment has been minimized.

Show comment
Hide comment
@ziotom78

ziotom78 Oct 1, 2018

Collaborator

Hi @ejhigson, don't worry, I should be able to complete the review in a few days.

Collaborator

ziotom78 commented Oct 1, 2018

Hi @ejhigson, don't worry, I should be able to complete the review in a few days.

@ziotom78

This comment has been minimized.

Show comment
Hide comment
@ziotom78

ziotom78 Oct 1, 2018

Collaborator

I've read the paper; it looks ok, there are only one spelling error and one unclear sentence:

  • Third paragraph: "such problems provides" should be "such problems provide"
  • Same sentence: I do not fully understand the meaning of the clause "…and for use statistical research into nested sampling."
Collaborator

ziotom78 commented Oct 1, 2018

I've read the paper; it looks ok, there are only one spelling error and one unclear sentence:

  • Third paragraph: "such problems provides" should be "such problems provide"
  • Same sentence: I do not fully understand the meaning of the clause "…and for use statistical research into nested sampling."
@ejhigson

This comment has been minimized.

Show comment
Hide comment
@ejhigson

ejhigson commented Oct 1, 2018

@whedon generate pdf

@whedon

This comment has been minimized.

Show comment
Hide comment
@whedon

whedon Oct 1, 2018

Collaborator
Attempting PDF compilation. Reticulating splines etc...
Collaborator

whedon commented Oct 1, 2018

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

This comment has been minimized.

Show comment
Hide comment
@whedon
Collaborator

whedon commented Oct 1, 2018

@ejhigson

This comment has been minimized.

Show comment
Hide comment
@ejhigson

ejhigson Oct 1, 2018

Hi @ejhigson, don't worry, I should be able to complete the review in a few days.

Thank you so much for this! It is much appreciated.

I've read the paper; it looks ok, there are only one spelling error and one unclear sentence:

  • Third paragraph: "such problems provides" should be "such problems provide"
  • Same sentence: I do not fully understand the meaning of the clause "…and for use statistical research into nested sampling."

Thank you for pointing these out! They are both typos. The sentence now reads "Furthermore, such problems provide a rich source of test cases for assessing the capacity of other software implementations to perform the nested sampling algorithm accurately, and for use in statistical research into nested sampling."

ejhigson commented Oct 1, 2018

Hi @ejhigson, don't worry, I should be able to complete the review in a few days.

Thank you so much for this! It is much appreciated.

I've read the paper; it looks ok, there are only one spelling error and one unclear sentence:

  • Third paragraph: "such problems provides" should be "such problems provide"
  • Same sentence: I do not fully understand the meaning of the clause "…and for use statistical research into nested sampling."

Thank you for pointing these out! They are both typos. The sentence now reads "Furthermore, such problems provide a rich source of test cases for assessing the capacity of other software implementations to perform the nested sampling algorithm accurately, and for use in statistical research into nested sampling."

@ziotom78

This comment has been minimized.

Show comment
Hide comment
@ziotom78

ziotom78 Oct 1, 2018

Collaborator

@ejhigson , I noticed that some docstrings are not correct:

  • The docstring for priors.Uniform and priors.Gaussian are identical

  • In the docstrings of these two classes, it might be worth expliciting what is the meaning of the parameter prior_scale passed to __init__ (e.g., in the Gaussian prior it's just the sigma).

Collaborator

ziotom78 commented Oct 1, 2018

@ejhigson , I noticed that some docstrings are not correct:

  • The docstring for priors.Uniform and priors.Gaussian are identical

  • In the docstrings of these two classes, it might be worth expliciting what is the meaning of the parameter prior_scale passed to __init__ (e.g., in the Gaussian prior it's just the sigma).

@ejhigson

This comment has been minimized.

Show comment
Hide comment
@ejhigson

ejhigson Oct 2, 2018

@ejhigson , I noticed that some docstrings are not correct:

  • The docstring for priors.Uniform and priors.Gaussian are identical
  • In the docstrings of these two classes, it might be worth expliciting what is the meaning of the parameter prior_scale passed to __init__ (e.g., in the Gaussian prior it's just the sigma).

Well spotted! I have fixed this added more information about prior_scale as suggested in 2a68a7cea55f330733d028f3563b196915e1f14d

ejhigson commented Oct 2, 2018

@ejhigson , I noticed that some docstrings are not correct:

  • The docstring for priors.Uniform and priors.Gaussian are identical
  • In the docstrings of these two classes, it might be worth expliciting what is the meaning of the parameter prior_scale passed to __init__ (e.g., in the Gaussian prior it's just the sigma).

Well spotted! I have fixed this added more information about prior_scale as suggested in 2a68a7cea55f330733d028f3563b196915e1f14d

@ziotom78

This comment has been minimized.

Show comment
Hide comment
@ziotom78

ziotom78 Oct 3, 2018

Collaborator

Thanks @ejhigson, all looks ok from my side. @arfon, IMO the paper can be published as it is now.

Collaborator

ziotom78 commented Oct 3, 2018

Thanks @ejhigson, all looks ok from my side. @arfon, IMO the paper can be published as it is now.

@arfon arfon added the accepted label Oct 3, 2018

@arfon

This comment has been minimized.

Show comment
Hide comment
@arfon

arfon Oct 3, 2018

Member

@ejhigson - At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

Member

arfon commented Oct 3, 2018

@ejhigson - At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

@ejhigson

This comment has been minimized.

Show comment
Hide comment
@ejhigson

ejhigson commented Oct 3, 2018

@whedon generate pdf

@whedon

This comment has been minimized.

Show comment
Hide comment
@whedon

whedon Oct 3, 2018

Collaborator
Attempting PDF compilation. Reticulating splines etc...
Collaborator

whedon commented Oct 3, 2018

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

This comment has been minimized.

Show comment
Hide comment
@whedon
Collaborator

whedon commented Oct 3, 2018

@ejhigson

This comment has been minimized.

Show comment
Hide comment
@ejhigson

ejhigson commented Oct 3, 2018

@whedon generate pdf

@whedon

This comment has been minimized.

Show comment
Hide comment
@whedon

whedon Oct 3, 2018

Collaborator
Attempting PDF compilation. Reticulating splines etc...
Collaborator

whedon commented Oct 3, 2018

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

This comment has been minimized.

Show comment
Hide comment
@whedon
Collaborator

whedon commented Oct 3, 2018

@ejhigson

This comment has been minimized.

Show comment
Hide comment
@ejhigson

ejhigson Oct 3, 2018

@ziotom78 thank you so much for your very prompt review - it is much appreciated!

ejhigson commented Oct 3, 2018

@ziotom78 thank you so much for your very prompt review - it is much appreciated!

@ejhigson

This comment has been minimized.

Show comment
Hide comment
@ejhigson

ejhigson Oct 3, 2018

@arfon thank you very much for your help with this! I have archived the latest version at:

10.5281/zenodo.1443509

ejhigson commented Oct 3, 2018

@arfon thank you very much for your help with this! I have archived the latest version at:

10.5281/zenodo.1443509

@arfon

This comment has been minimized.

Show comment
Hide comment
@arfon

arfon Oct 3, 2018

Member

@whedon set 10.5281/zenodo.1443509 as archive

Member

arfon commented Oct 3, 2018

@whedon set 10.5281/zenodo.1443509 as archive

@whedon

This comment has been minimized.

Show comment
Hide comment
@whedon

whedon Oct 3, 2018

Collaborator

OK. 10.5281/zenodo.1443509 is the archive.

Collaborator

whedon commented Oct 3, 2018

OK. 10.5281/zenodo.1443509 is the archive.

@arfon

This comment has been minimized.

Show comment
Hide comment
@arfon

arfon Oct 3, 2018

Member

@ziotom78 - many thanks for your review here

@ejhigson - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00985 ⚡️ 🚀 💥

Member

arfon commented Oct 3, 2018

@ziotom78 - many thanks for your review here

@ejhigson - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00985 ⚡️ 🚀 💥

@arfon arfon closed this Oct 3, 2018

@whedon

This comment has been minimized.

Show comment
Hide comment
@whedon

whedon Oct 3, 2018

Collaborator

🎉🎉🎉 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](http://joss.theoj.org/papers/10.21105/joss.00985/status.svg)](https://doi.org/10.21105/joss.00985)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.00985">
  <img src="http://joss.theoj.org/papers/10.21105/joss.00985/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.00985/status.svg
   :target: https://doi.org/10.21105/joss.00985

This is how it will look in your documentation:

DOI

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

Collaborator

whedon commented Oct 3, 2018

🎉🎉🎉 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](http://joss.theoj.org/papers/10.21105/joss.00985/status.svg)](https://doi.org/10.21105/joss.00985)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.00985">
  <img src="http://joss.theoj.org/papers/10.21105/joss.00985/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.00985/status.svg
   :target: https://doi.org/10.21105/joss.00985

This is how it will look in your documentation:

DOI

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment