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[REVIEW]: Retriever: Data Retrieval Tool #451

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whedon opened this Issue Nov 7, 2017 · 21 comments

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whedon commented Nov 7, 2017

Submitting author: @henrykironde (henry senyondo)
Repository: https://github.com/weecology/retriever
Version: v2.1.0
Editor: @leeper
Reviewer: @amoeba
Archive: 10.5281/zenodo.1038272

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/f76a72ab468973531f33b8a1449943a6"><img src="http://joss.theoj.org/papers/f76a72ab468973531f33b8a1449943a6/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/f76a72ab468973531f33b8a1449943a6/status.svg)](http://joss.theoj.org/papers/f76a72ab468973531f33b8a1449943a6)

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 questions

@amoeba, please carry out your review in this issue by updating the checklist below (please make sure you're logged in to GitHub). The reviewer guidelines are available here: http://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @leeper know.

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 (@henrykironde) 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 Nov 7, 2017

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Hello human, I'm @whedon. I'm here to help you with some common editorial tasks for JOSS. @amoeba 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 as reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all JOSS 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:

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whedon commented Nov 7, 2017

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks for JOSS. @amoeba 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 as reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all JOSS 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
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amoeba Nov 13, 2017

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Grade: 2) Minor revisions

I've had a chance to sit down and found this submission meets or exceeds the submission requirements on essentially every item on the reviewer checklist. It's clear to me what the software should do, it was easy for me to get the software installed and make use of it. On top of that, the documentation is abundant and well-written and it's clear a great deal of care has been put into many aspects of the project. I've checked all but one item off the list and am left with two outstanding issues:

  1. The paper.md does not appear to follow the BibTeX convention for in-text citations using the BibTeX @ identifiers and instead just hard-codes the reference. If my assessment is correct, I'd like to see a quick fix made for those.
  2. I'm not 100% confident this submission qualifies as research software. It's fundamental tooling for research so I would happily consider it research software. A quick 👍 from an editor or JOSS would suffice.

@leeper can you please take a look at my two remaining issues and let me know what you think?

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amoeba commented Nov 13, 2017

Grade: 2) Minor revisions

I've had a chance to sit down and found this submission meets or exceeds the submission requirements on essentially every item on the reviewer checklist. It's clear to me what the software should do, it was easy for me to get the software installed and make use of it. On top of that, the documentation is abundant and well-written and it's clear a great deal of care has been put into many aspects of the project. I've checked all but one item off the list and am left with two outstanding issues:

  1. The paper.md does not appear to follow the BibTeX convention for in-text citations using the BibTeX @ identifiers and instead just hard-codes the reference. If my assessment is correct, I'd like to see a quick fix made for those.
  2. I'm not 100% confident this submission qualifies as research software. It's fundamental tooling for research so I would happily consider it research software. A quick 👍 from an editor or JOSS would suffice.

@leeper can you please take a look at my two remaining issues and let me know what you think?

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henrykironde Nov 13, 2017

Updated to BibTeX citations

henrykironde commented Nov 13, 2017

Updated to BibTeX citations

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Great, thanks @henrykironde. Relevant checklist item is now checked.

Grade: 1) Accept

Last outstanding issue is just a quick 👍 from @leeper on fit. I have no outstanding issues.

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amoeba commented Nov 13, 2017

Great, thanks @henrykironde. Relevant checklist item is now checked.

Grade: 1) Accept

Last outstanding issue is just a quick 👍 from @leeper on fit. I have no outstanding issues.

@arfon arfon referenced this issue Nov 14, 2017

Closed

PeerJ R1C2 #7

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ethanwhite Nov 14, 2017

Regarding fit, this seems very much in line with other software published in JOSS. E.g.,

My group is a research lab and this software was built for our research and funded as research software by both NSF and the Moore Foundation.

ethanwhite commented Nov 14, 2017

Regarding fit, this seems very much in line with other software published in JOSS. E.g.,

My group is a research lab and this software was built for our research and funded as research software by both NSF and the Moore Foundation.

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amoeba Nov 14, 2017

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I totally agree, @ethanwhite, and imagine @leeper won't disagree either. Thanks for chiming in with those examples. Perhaps the fact that this submission is in the review phase is adequate confirmation of fit.

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amoeba commented Nov 14, 2017

I totally agree, @ethanwhite, and imagine @leeper won't disagree either. Thanks for chiming in with those examples. Perhaps the fact that this submission is in the review phase is adequate confirmation of fit.

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leeper Nov 15, 2017

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@whedon set 10.5281/zenodo.1038272 as archive

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leeper commented Nov 15, 2017

@whedon set 10.5281/zenodo.1038272 as archive

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whedon Nov 15, 2017

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OK. 10.5281/zenodo.1038272 is the archive.

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whedon commented Nov 15, 2017

OK. 10.5281/zenodo.1038272 is the archive.

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@amoeba Excellent. Thank you for your quick review! Very much appreciated.

@henrykironde This looks ready to me. Great submission and thanks for your quick response to the review.

@arfon Over to you.

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leeper commented Nov 15, 2017

@amoeba Excellent. Thank you for your quick review! Very much appreciated.

@henrykironde This looks ready to me. Great submission and thanks for your quick response to the review.

@arfon Over to you.

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@amoeba - many thanks for your review and to @leeper for your help editing this one

@henrykironde - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00451 ⚡️ 🚀 💥

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arfon commented Nov 15, 2017

@amoeba - many thanks for your review and to @leeper for your help editing this one

@henrykironde - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00451 ⚡️ 🚀 💥

@arfon arfon closed this Nov 15, 2017

@arfon arfon added the accepted label Nov 15, 2017

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henrykironde Nov 15, 2017

On behalf of the team @Data Retriever, we thank you for the time taken to review this paper.

henrykironde commented Nov 15, 2017

On behalf of the team @Data Retriever, we thank you for the time taken to review this paper.

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henrykironde Nov 15, 2017

@arfon, I have just noted that I made a mistake in importing the names of the authors. The main author's name has been corrected. Is there away we could update the paper?

henrykironde commented Nov 15, 2017

@arfon, I have just noted that I made a mistake in importing the names of the authors. The main author's name has been corrected. Is there away we could update the paper?

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Deborah-Digges Nov 16, 2017

@arfon I have been affiliated with the University of Florida. Could this affiliation be removed?

The submitted paper does not have this affiliation: https://raw.githubusercontent.com/weecology/retriever/master/paper/paper.md

Deborah-Digges commented Nov 16, 2017

@arfon I have been affiliated with the University of Florida. Could this affiliation be removed?

The submitted paper does not have this affiliation: https://raw.githubusercontent.com/weecology/retriever/master/paper/paper.md

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henrykironde Nov 16, 2017

@Deborah-Digges what is your affiliation? We provided default association (University of Florida) for you since you didn't not have affiliation at the time you worked on the Data Retriever.

henrykironde commented Nov 16, 2017

@Deborah-Digges what is your affiliation? We provided default association (University of Florida) for you since you didn't not have affiliation at the time you worked on the Data Retriever.

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Deborah-Digges Nov 16, 2017

You could mention "PES Institute of Technology".

Thank you!

Deborah-Digges commented Nov 16, 2017

You could mention "PES Institute of Technology".

Thank you!

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@henrykironde - please update the affiliations in paper.md in https://github.com/weecology/retriever and let me know when you're ready to have the paper re-generated.

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arfon commented Nov 16, 2017

@henrykironde - please update the affiliations in paper.md in https://github.com/weecology/retriever and let me know when you're ready to have the paper re-generated.

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henrykironde Nov 16, 2017

@arfon I have updated the paper.md

henrykironde commented Nov 16, 2017

@arfon I have updated the paper.md

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arfon commented Nov 17, 2017

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ethanwhite Dec 11, 2017

@arfon - it looks like maybe the regeneration didn't take care of something somewhere because I just noticed that the citation on the website is for the old (incorrect) name.

screenshot from 2017-12-11 12-40-18

ethanwhite commented Dec 11, 2017

@arfon - it looks like maybe the regeneration didn't take care of something somewhere because I just noticed that the citation on the website is for the old (incorrect) name.

screenshot from 2017-12-11 12-40-18

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@ethanwhite - good catch. That's fixed now.

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arfon commented Dec 11, 2017

@ethanwhite - good catch. That's fixed now.

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ethanwhite commented Dec 11, 2017

Thanks @arfon!

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