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[REVIEW]: Mordecai: Full Text Geoparsing and Event Geocoding #91

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whedon opened this Issue Oct 12, 2016 · 21 comments

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whedon commented Oct 12, 2016

Submitting author: @ahalterman (Andrew Lee Halterman)
Repository: https://github.com/openeventdata/mordecai
Version: v1.1.0
Editor: @acabunoc
Reviewer: @riordan
Archive: 10.5281/zenodo.250879

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/20e4b21d74e3ba78d2fb2fde5403be96"><img src="http://joss.theoj.org/papers/20e4b21d74e3ba78d2fb2fde5403be96/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/20e4b21d74e3ba78d2fb2fde5403be96/status.svg)](http://joss.theoj.org/papers/20e4b21d74e3ba78d2fb2fde5403be96)

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

Conflict of interest

  • As the reviewer I confirm that there are no conflicts of interest for me to review this work (such as being a major contributor to the software).

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 (v1.1.0)?
  • Authorship: Has the submitting author (@ahalterman) made major contributions to the software?

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: Have any performance claims of the software been confirmed?

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

Paper PDF: 10.21105.joss.00091.pdf

  • 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 Oct 12, 2016

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Hello human, I'm @whedon. I'm here to help you with some common editorial tasks for JOSS.

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

@whedon commands
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whedon commented Oct 12, 2016

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks for JOSS.

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

@whedon commands
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acabunoc Oct 12, 2016

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@whedon commands

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acabunoc commented Oct 12, 2016

@whedon commands

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whedon Oct 12, 2016

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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
@whedon assign @username as reviewer

# List the GitHub usernames of the JOSS editors
@whedon list editors

# List of JOSS reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# 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).

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whedon commented Oct 12, 2016

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
@whedon assign @username as reviewer

# List the GitHub usernames of the JOSS editors
@whedon list editors

# List of JOSS reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# 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).

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ahalterman Nov 1, 2016

@riordan, let me know if you run into any trouble with the documentation/installation. The model's pretty big, unfortunately, so getting it stood up doesn't go smoothly depending on how much memory you have.

ahalterman commented Nov 1, 2016

@riordan, let me know if you run into any trouble with the documentation/installation. The model's pretty big, unfortunately, so getting it stood up doesn't go smoothly depending on how much memory you have.

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riordan Nov 14, 2016

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@whedon start review

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riordan commented Nov 14, 2016

@whedon start review

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whedon Nov 14, 2016

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I'm sorry @riordan, I'm afraid I can't do that. That's something only JOSS editors are allowed to do.

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whedon commented Nov 14, 2016

I'm sorry @riordan, I'm afraid I can't do that. That's something only JOSS editors are allowed to do.

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arfon Nov 14, 2016

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@riordan - need any help? Looks like the review is already happening (you're checking items off the list)

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arfon commented Nov 14, 2016

@riordan - need any help? Looks like the review is already happening (you're checking items off the list)

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ahalterman Dec 4, 2016

I merged a PR in that reorganizes how it deals with the data download, which is something you had changed, @riordan. This is sort of a general JOSS question, should I re-release the repo and change which version is being submitted? Or should we keep going with the existing version? The differences aren't too big so it shouldn't matter too much either way.

ahalterman commented Dec 4, 2016

I merged a PR in that reorganizes how it deals with the data download, which is something you had changed, @riordan. This is sort of a general JOSS question, should I re-release the repo and change which version is being submitted? Or should we keep going with the existing version? The differences aren't too big so it shouldn't matter too much either way.

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arfon Dec 4, 2016

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This is sort of a general JOSS question, should I re-release the repo and change which version is being submitted? Or should we keep going with the existing version? The differences aren't too big so it shouldn't matter too much either way.

@ahalterman - I would recommend making a new release once the review is complete and all of the changes (associated with the review) have been made.

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arfon commented Dec 4, 2016

This is sort of a general JOSS question, should I re-release the repo and change which version is being submitted? Or should we keep going with the existing version? The differences aren't too big so it shouldn't matter too much either way.

@ahalterman - I would recommend making a new release once the review is complete and all of the changes (associated with the review) have been made.

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ahalterman Jan 3, 2017

I wanted to check in and see if there's anything I can do to help along the review process. I really appreciate all the work you all have already put in.

ahalterman commented Jan 3, 2017

I wanted to check in and see if there's anything I can do to help along the review process. I really appreciate all the work you all have already put in.

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riordan Jan 3, 2017

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@ahalterman: Thank you for the prod! I finished my tests up 2 weeks ago and it's really impressive.

The installation ran according to documentation, which was really straightforward for installation. I'd suggest a clearer statement of need in the paper (something you do well in the README.md). Bringing in a bit more context, especially from your experience scanning news articles to find the places that are being written about, would be really useful here.

Other than that, I think it just needs an archival DOI (though I'd defer to @acabunoc or @arfon on that).

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riordan commented Jan 3, 2017

@ahalterman: Thank you for the prod! I finished my tests up 2 weeks ago and it's really impressive.

The installation ran according to documentation, which was really straightforward for installation. I'd suggest a clearer statement of need in the paper (something you do well in the README.md). Bringing in a bit more context, especially from your experience scanning news articles to find the places that are being written about, would be really useful here.

Other than that, I think it just needs an archival DOI (though I'd defer to @acabunoc or @arfon on that).

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ahalterman Jan 8, 2017

@riordan Thanks so much for doing this review! I'm glad you liked it and that things checked out. I just updated the paper to include more of the statement of need. If it looks good to you, it sounds like the paper ready to go. Thanks everyone!

ahalterman commented Jan 8, 2017

@riordan Thanks so much for doing this review! I'm glad you liked it and that things checked out. I just updated the paper to include more of the statement of need. If it looks good to you, it sounds like the paper ready to go. Thanks everyone!

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ahalterman Jan 18, 2017

I wanted to check in again and see if that commit addressed your last request, @riordan. If so, I think it should be ready for a DOI.

ahalterman commented Jan 18, 2017

I wanted to check in again and see if that commit addressed your last request, @riordan. If so, I think it should be ready for a DOI.

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riordan Jan 18, 2017

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Totally! 👍

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riordan commented Jan 18, 2017

Totally! 👍

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ahalterman Jan 18, 2017

Great! Thanks. I owe you a beer next time I'm in New York or you're in Cambridge. @acabunoc or @arfon, what happens now?

ahalterman commented Jan 18, 2017

Great! Thanks. I owe you a beer next time I'm in New York or you're in Cambridge. @acabunoc or @arfon, what happens now?

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acabunoc Jan 18, 2017

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Thanks for the great work here @riordan & @ahalterman 👏 🎉

@ahalterman, could you make sure there's an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? Thanks!

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acabunoc commented Jan 18, 2017

Thanks for the great work here @riordan & @ahalterman 👏 🎉

@ahalterman, could you make sure there's an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? Thanks!

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ahalterman Jan 18, 2017

Here it is! Thanks a lot.

DOI

ahalterman commented Jan 18, 2017

Here it is! Thanks a lot.

DOI

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@whedon set 10.5281/zenodo.250879 as archive

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acabunoc commented Jan 18, 2017

@whedon set 10.5281/zenodo.250879 as archive

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OK. 10.5281/zenodo.250879 is the archive.

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whedon commented Jan 18, 2017

OK. 10.5281/zenodo.250879 is the archive.

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acabunoc Jan 18, 2017

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flagging @arfon, I think we're good to go here! Thanks @riordan & @ahalterman

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acabunoc commented Jan 18, 2017

flagging @arfon, I think we're good to go here! Thanks @riordan & @ahalterman

@acabunoc acabunoc added accepted and removed review labels Jan 18, 2017

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arfon Jan 20, 2017

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@ahalterman your paper is now accepted into JOSS and your paper DOI is http://dx.doi.org/10.21105/joss.00091 ⚡️ 🚀 💥

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arfon commented Jan 20, 2017

@ahalterman your paper is now accepted into JOSS and your paper DOI is http://dx.doi.org/10.21105/joss.00091 ⚡️ 🚀 💥

@arfon arfon closed this Jan 20, 2017

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