[REVIEW]: ENASearch: A Python library for interacting with ENA's API

[whedon]

Submitting author: @bebatut (Bérénice Batut)
Repository: https://github.com/bebatut/enasearch
Version: 0.2.0
Editor: @brainstorm
Reviewer: @vals
Archive: 10.5281/zenodo.1034619

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Reviewer questions

@vals, 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 @brainstorm know.

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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 (0.1.1)?
• Authorship: Has the submitting author (@bebatut) 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?
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• 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]

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks for JOSS. @vals it looks like you're currently assigned as the reviewer for this paper 🎉.

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[brainstorm]

@vals, hope all is clear with the instructions above? Let me know if you run into doubts/issues, happy to help!

[vals]

I have now reviewed the repository in accordance to the guidelines.

Due to the following issues, I would not accept it at the moment:

• No functional claims of the software: No functional claims of the software bebatut/enasearch#25
• No statement of need: No statement of need bebatut/enasearch#26
• No example usage: No example usage bebatut/enasearch#27
• The functionality documentation is not clear: The functionality documentation is not clear bebatut/enasearch#28
• No JOSS paper file: No JOSS paper file bebatut/enasearch#29

/Valentine

[brainstorm]

Thanks @vals for your thorough review 👍

Let's give a chance to @bebatut to address those issues and give some feedback ;)

[bebatut]

Thanks a lot @vals for the review! It helps us to improve a lot the documentation at http://bebatut.fr/enasearch/. So I hope I solved the issues you pointed:

• No functional claims of the software: it should be solved with PR#33 and PR#30
• No statement of need: it should be solved with PR#30
• No example usage: it should be solved with PR#33
• The functionality documentation is not clear
  • More documentation about the interaction with ENA has been added with PR#34. It should clarify the different type of data and commands
  • I will add more description about the outputs of the commands during the week
• No JOSS paper file: it is located in src/paper/paper.md
  Must it be at the root of the repo?

Please tell me if you think there is more missing or not clear

[vals]

Hi @bebatut

With these changes the software is more clear. It now satisfies the conditions for a JOSS publication.

/Valentine

[brainstorm]

Thanks much @vals for your review!

@bebatut 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.

[bebatut]

@brainstorm I will make an archive on Zenodo. But, because of the changes I made thanks to @vals, I was thinking about increasing the version. Is it possible?

[brainstorm]

Yeah, make sure you include the changes proposed by Valentine and bump up the version ;)

[bebatut]

The release is: 0.2.0
Its DOI: 10.5281/zenodo.1034619

[brainstorm]

@whedon set 10.5281/zenodo.1034619 as archive

[whedon]

OK. 10.5281/zenodo.1034619 is the archive.

[bebatut]

@whedon set 0.2.0 as version

[bebatut]

(I am trying... but not working).
@brainstorm How can we change the version?

[brainstorm]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the reviewer of this submission
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# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Open the review issue
@whedon start review

🚧 Important 🚧

This is all quite new. Please make sure you check the top of the issue after running a @whedon command (you might also need to refresh the page to see the issue update).

[brainstorm]

@arfon I guess that indicating a new version does require a new DOI? I don't know what's the status of that discussion I'm afraid :-S

[bebatut]

Which DOI? Because the DOI for the archive is currently for the new version.

[arfon]

Which DOI? Because the DOI for the archive is currently for the new version.

I think this should be fine.

[arfon]

@vals - many thanks for your review and to @brainstorm for editing this submission ✨

@bebatut - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00418 ⚡️ 🚀 💥

[bebatut]

Thanks @vals for the reviews, @brainstorm for editing and @arfon globally