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[REVIEW]: pyuvsim: a comprehensive simulation package for radio interferometers in python. #1234

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whedon opened this Issue Feb 4, 2019 · 15 comments

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whedon commented Feb 4, 2019

Submitting author: @aelanman (Adam Lanman)
Repository: https://github.com/RadioAstronomySoftwareGroup/pyuvsim/
Version: v0.2.1
Editor: @arfon
Reviewer: @ygrange
Archive: Pending

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/cd19f6a8e807d57d3de8cde9f2abaeab"><img src="http://joss.theoj.org/papers/cd19f6a8e807d57d3de8cde9f2abaeab/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/cd19f6a8e807d57d3de8cde9f2abaeab/status.svg)](http://joss.theoj.org/papers/cd19f6a8e807d57d3de8cde9f2abaeab)

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

@ygrange, 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 @ygrange

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 (v0.2.1)?
  • Authorship: Has the submitting author (@aelanman) 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)?
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whedon commented Feb 4, 2019

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

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

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

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whedon commented Feb 4, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Feb 4, 2019

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arfon commented Feb 4, 2019

@ygrange - 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.

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ygrange commented Feb 6, 2019

Just going through the checkboxes I found two comments:

  • Please add doi to the Dalcin, Paz and Storti paper ( https://doi.org/10.1016/j.jpdc.2005.03.010 )
  • There seems to be no tag for version 0.2.1 (there is a 0.2.0). I don't referee often enough for JOSS to know what the exact policy here is: to have the version released after my comments or to have a release now and add a new one at publication time if the code needs to change because of sometning I said. Maybe the editor should comment on this.
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arfon commented Feb 6, 2019

I think it's OK to review what is in the repository now (i.e. master) and then for there to be a new release before publication.

Perhaps @aelanman could clarify what they're asking to be reviewed.

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aelanman commented Feb 6, 2019

Hello, @ygrange . We're asking for the contents of master to be reviewed. We've issued releases for every major version change (generation.major.minor) so far, but I assume we'll do another release after the review is finished.

I'll add the missing doi.

Thanks!

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aelanman commented Feb 6, 2019

@whedon generate pdf

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whedon commented Feb 6, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Feb 6, 2019

PDF failed to compile for issue #1234 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 16 0 16 0 0 179 0 --:--:-- --:--:-- --:--:-- 181
Error reading bibliography ./paper.bib (line 134, column 1):
unexpected "v"
expecting space, ",", white space or "}"
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

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aelanman commented Feb 6, 2019

@whedon generate pdf

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whedon commented Feb 6, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Feb 6, 2019

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aelanman commented Feb 8, 2019

I just noticed that some authors' first names were cut from citations. I'll have to fix this, but I'm going to wait for more feedback first.

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ygrange commented Feb 15, 2019

Just letting you know I got a bit delayed because I had some issues installing mpi4py on my centos test container. Now I have a running version and I can have a look at functionality.

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