Joss-reviews: [REVIEW]: MorphoMetriX: a photogrammetric measurement GUI for morphometric analysis of megafauna
Submitting author: @wingtorres (Walter Torres)
Repository: https://github.com/wingtorres/morphometrix
Version: v1.0.2
Editor: @Kevin-Mattheus-Moerman
Reviewer: @isaacvandor, @bw4sz
Archive: 10.5281/zenodo.3606865
Status
Status badge code:
HTML: <a href="https://joss.theoj.org/papers/716faddf06d43b06f4c8a5e890fb23d1"><img src="https://joss.theoj.org/papers/716faddf06d43b06f4c8a5e890fb23d1/status.svg"></a>
Markdown: [](https://joss.theoj.org/papers/716faddf06d43b06f4c8a5e890fb23d1)
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) by leaving comments 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
@isaacvandor & @bw4sz, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:
- Make sure you're logged in to your GitHub account
- Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @Kevin-Mattheus-Moerman know.
✨ Please try and complete your review in the next two weeks ✨
Review checklist for @isaacvandor
Conflict of interest
- [x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.
Code of Conduct
- [x] I confirm that I read and will adhere to the JOSS code of conduct.
General checks
- [x] Repository: Is the source code for this software available at the repository url?
- [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
- [x] Contribution and authorship: Has the submitting author (@wingtorres) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Functionality
- [x] Installation: Does installation proceed as outlined in the documentation?
- [x] Functionality: Have the functional claims of the software been confirmed?
- [x] 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
- [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
- [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
- [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
- [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
- [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
- [x] 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
- [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
- [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
- [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
- [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
- [x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?
Review checklist for @bw4sz
Conflict of interest
- [x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.
Code of Conduct
- [x] I confirm that I read and will adhere to the JOSS code of conduct.
General checks
- [x] Repository: Is the source code for this software available at the repository url?
- [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
- [x] Contribution and authorship: Has the submitting author (@wingtorres) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Functionality
- [x] Installation: Does installation proceed as outlined in the documentation?
- [x] Functionality: Have the functional claims of the software been confirmed?
- [x] 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
- [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
- [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
- [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
- [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
- [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
- [x] 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
- [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
- [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
- [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
- [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
- [x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?
whedon
All 82 comments
Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @isaacvandor, @bw4sz it looks like you're currently assigned to review this paper :tada:.
:star: Important :star:
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:
- Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:
- You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications
For a list of things I can do to help you, just type:
@whedon commands
For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
@whedon generate pdf
Attempting PDF compilation. Reticulating splines etc...
@Kevin-Mattheus-Moerman I've completed my review and there doesn't seem to be anything impeding acceptance. I did open an issue in the target repo with a feature enhancement I think could help, but that certainly shouldn't stop the rest of the review process.
Updating with link to issue filed in target repo: Issue #1: Allow user to change size of width lines/dots
isaacvandor
on 22 Oct 2019
@isaacvandor thanks. Can you mention/link to that issue here so we have a record of it? Thanks a lot for your help!
Kevin-Mattheus-Moerman
on 22 Oct 2019
@bw4sz this is where the review takes place. The check boxes at the top guide you through the process. Let me know if you have questions.
Kevin-Mattheus-Moerman
on 22 Oct 2019
@patrickcgray throw me some sample whale images to play with here?
bw4sz
on 22 Oct 2019
grabbing and testing with some data from https://github.com/patrickcgray/cetacean_photogram
bw4sz
on 22 Oct 2019
testing with this image looks good.
bw4sz
on 22 Oct 2019
added a small idea https://github.com/wingtorres/morphometrix/issues/2
bw4sz
on 22 Oct 2019
What a cool picture to get in my email from github notifications!
kthyng
on 22 Oct 2019
Hey Ben,
Late in replying but I'm happy to provide more imagery as needed, should be
plenty in that DataDryad repo as you likely saw!
Cheers,
Patrick
On Tue, Oct 22, 2019 at 5:47 PM Kristen Thyng notifications@github.com
wrote:
What a cool picture to get in my email from github notifications!
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You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
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--
Patrick Clifton Gray http://patrickgray.me/
PhD Student
Marine Robotics and Remote Sensing Lab http://sites.nicholas.duke.edu/uas/
Duke University, Nicholas School of the Environment
Computer Science '14, University of North Carolina
patrickcgray
on 25 Oct 2019
@wingtorres can you work on adding community guidelines?
Here is some more information on this:
https://help.github.com/en/github/site-policy/github-community-guidelines
Also here is a link to one of my projects. There I link to contributing guidelines in a CONTRIBUTING.md file in the README.md, which is an approach I recommend.
https://github.com/gibbonCode/GIBBON
If you imagine your contributors community will grow I also recommend adding a CODE_OF_CONDUCT.mdfile too (e.g. based on this template: https://www.contributor-covenant.org/).
Kevin-Mattheus-Moerman
on 1 Nov 2019
@wingtorres can you work on the issues raised by the reviewers? https://github.com/wingtorres/morphometrix/issues
Kevin-Mattheus-Moerman
on 1 Nov 2019
@Kevin-Mattheus-Moerman Sorry to be out of touch! I've been a bit swamped recently, but I have some time blocked out end of next week to incorporate the reviewers suggestions and add the community guidelines. Thanks!
wingtorres
on 15 Nov 2019
👋 @wingtorres - Have you made progress on this?
danielskatz
on 5 Dec 2019
@danielskatz Yes finally! I have updated the code to address @bw4sz 's suggestion and in regards to @isaacvandor 's thoughts I have at least pointed to where users can customize their version of the code in lieu of adding a preferences menu to modify the GUI cosmetics (although we may want to do this down the line, I believe the code will be useful to people without it for now). @Kevin-Mattheus-Moerman thank you for your suggestion to include the contribute and code of conduct files - I have added those as well. Thanks y'all! Let me know what else needs to be done.
wingtorres
on 15 Dec 2019
@whedon generate pdf
wingtorres
on 15 Dec 2019
Attempting PDF compilation. Reticulating splines etc...
@isaacvandor, @bw4sz are you happy with the changes implemented? I see all boxes are ticked. Are you happy to recommend acceptance for this work? Thanks!
Kevin-Mattheus-Moerman
on 16 Dec 2019
@wingtorres thanks for adding community guidelines. One note on your CONTRIBUTING.md file (https://github.com/wingtorres/morphometrix/blob/master/CONTRIBUTING.md). It appears it was copied from my own project's file I referred to. Please review the variable naming section since I changed that to suit my project (MATLAB syntax for mesh data handling). Perhaps yours should instead refer to some Python coding style (perhaps check what other major Python projects use there).
Kevin-Mattheus-Moerman
on 16 Dec 2019
You are totally right that's embarrassing :D, sorry I should have paid closer attention. I'm a bit new to Python, but I try to adhere to the PEP-008 standards so I'll post a link to that.
wingtorres
on 16 Dec 2019
@isaacvandor, @bw4sz are you happy with the changes implemented? I see all boxes are ticked. Are you happy to recommend acceptance for this work? Thanks!
@isaacvandor, @bw4sz :point_up: Thanks again for your help!
Kevin-Mattheus-Moerman
on 26 Dec 2019
@whedon generate pdf
Kevin-Mattheus-Moerman
on 26 Dec 2019
Attempting PDF compilation. Reticulating splines etc...
@whedon check references
Kevin-Mattheus-Moerman
on 26 Dec 2019
Attempting to check references...
hey @Kevin-Mattheus-Moerman thanks for checking in! KC and I had some time over the holidays to improve the GUI and add one feature (measure area), so we would like to make some minor updates to the paper figures and text before publication. Would it be alright if we had until Tuesday Dec. 31 to push these changes before closing review?
wingtorres
on 27 Dec 2019
@wingtorres Sure that is fine.
Kevin-Mattheus-Moerman
on 27 Dec 2019
@whedon generate pdf
wingtorres
on 31 Dec 2019
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
wingtorres
on 1 Jan 2020
Attempting PDF compilation. Reticulating splines etc...
@Kevin-Mattheus-Moerman okay it's good to go!
wingtorres
on 1 Jan 2020
@wingtorres I have one minor comment on the paper.
[x] The accepted version will have links to your repo so please remove the last sentence:
Source code and manual are available at https: //github.com/wingtorres/morphometrix/
Once you've made the above change please regenerate the pdf here.[ ] Also please archive the software on Zenodo and report back the DOI here. For the Zenodo archive please ensure the meta-data is set such that the author names and the title match that of the paper.
[x] Is the version tag v1.0.0 still accurate?
Kevin-Mattheus-Moerman
on 11 Jan 2020
@whedon generate pdf
wingtorres
on 13 Jan 2020
whedon
on 13 Jan 2020
@Kevin-Mattheus-Moerman
- [x] sentence removed
- [x] software archived. DOI is 10.5281/zenodo.3606865 URL to repository is https://zenodo.org/record/3606865#.XhzlQhdKiuU
- [x] released new version (v1.0.2) that is now archived on Zenodo
wingtorres
on 13 Jan 2020
@whedon generate pdf
wingtorres
on 14 Jan 2020
whedon
on 14 Jan 2020
@whedon set v1.0.2 as version
Kevin-Mattheus-Moerman
on 14 Jan 2020
OK. v1.0.2 is the version.
whedon
on 14 Jan 2020
@whedon set 10.5281/zenodo.3606865 as archive
Kevin-Mattheus-Moerman
on 14 Jan 2020
OK. 10.5281/zenodo.3606865 is the archive.
whedon
on 14 Jan 2020
@wingtorres
- [ ] Please update the Zenodo meta-data such that the author names and the title match that of the JOSS paper
Kevin-Mattheus-Moerman
on 14 Jan 2020
@Kevin-Mattheus-Moerman
- [x] edited the "basic information" section of the archive to include our names and paper title and published the updated archive on zenodo
wingtorres
on 14 Jan 2020
@openjournals/joss-eics this submission is ready to be processed for acceptance.
Kevin-Mattheus-Moerman
on 14 Jan 2020
Thanks for your review work @isaacvandor, @bw4sz !
Kevin-Mattheus-Moerman
on 14 Jan 2020
@whedon generate pdf
kyleniemeyer
on 15 Jan 2020
whedon
on 15 Jan 2020
@whedon check references
kyleniemeyer
on 15 Jan 2020
@whedon check references
arfon
on 15 Jan 2020
Reference check summary:
OK DOIs
- 10.1126/science.290.5497.1695b is OK
MISSING DOIs
- https://doi.org/10.2307/1374074 may be missing for title: Southern Blue and Fin Whales
INVALID DOIs
- https://doi.org/10.1007/BF00233083 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1038/s41559-018-0534-2 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1371/journal.pone.0017686 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1641/0006-3568(2003)053[0210:WAS]2.0.CO;2 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1139/z85-345 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1111/1365-2435.12200 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.3354/meps12522 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1139/z98-195 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.3354/meps09675 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1146/annurev-marine-010318-095323 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.3389/fmars.2017.00366 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1139/cjz-2014-0311 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/ajp.1350300207 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1111/j.1748-7692.2009.00288.x is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1111/mms.12527 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1038/nmeth.2089 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/ecs2.1468 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1139/juvs-2015-0020 is INVALID because of 'https://doi.org/' prefix
Reference check summary:
OK DOIs
- 10.1126/science.290.5497.1695b is OK
MISSING DOIs
- https://doi.org/10.2307/1374074 may be missing for title: Southern Blue and Fin Whales
INVALID DOIs
- https://doi.org/10.1007/BF00233083 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1038/s41559-018-0534-2 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1371/journal.pone.0017686 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1641/0006-3568(2003)053[0210:WAS]2.0.CO;2 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1139/z85-345 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1111/1365-2435.12200 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.3354/meps12522 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1139/z98-195 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.3354/meps09675 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1146/annurev-marine-010318-095323 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.3389/fmars.2017.00366 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1139/cjz-2014-0311 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/ajp.1350300207 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1111/j.1748-7692.2009.00288.x is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1111/mms.12527 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1038/nmeth.2089 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/ecs2.1468 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1139/juvs-2015-0020 is INVALID because of 'https://doi.org/' prefix
@whedon check references
wingtorres
on 15 Jan 2020
Reference check summary:
OK DOIs
- 10.1126/science.290.5497.1695b is OK
MISSING DOIs
- https://doi.org/10.2307/1374074 may be missing for title: Southern Blue and Fin Whales
INVALID DOIs
- https://doi.org/10.1007/BF00233083 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1038/s41559-018-0534-2 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1371/journal.pone.0017686 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1641/0006-3568(2003)053[0210:WAS]2.0.CO;2 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1139/z85-345 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1111/1365-2435.12200 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.3354/meps12522 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1139/z98-195 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.3354/meps09675 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1146/annurev-marine-010318-095323 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.3389/fmars.2017.00366 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1139/cjz-2014-0311 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/ajp.1350300207 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1111/j.1748-7692.2009.00288.x is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1111/mms.12527 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1038/nmeth.2089 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/ecs2.1468 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1139/juvs-2015-0020 is INVALID because of 'https://doi.org/' prefix
hey @arfon @kyleniemeyer , I edited the paper.bib doc and removed the 'https://doi.org/' prefixes, but am still getting invalid DOI's after checking references. Do y'all know how to sort this out?
edit: nevermind, just had to generate the pdf first!
wingtorres
on 15 Jan 2020
@whedon generate pdf
wingtorres
on 15 Jan 2020
whedon
on 15 Jan 2020
@whedon check references
wingtorres
on 15 Jan 2020
Reference check summary:
OK DOIs
- 10.1007/BF00233083 is OK
- 10.1038/s41559-018-0534-2 is OK
- 10.1371/journal.pone.0017686 is OK
- 10.1139/z85-345 is OK
- 10.1111/1365-2435.12200 is OK
- 10.3354/meps12522 is OK
- 10.1139/z98-195 is OK
- 10.3354/meps09675 is OK
- 10.1146/annurev-marine-010318-095323 is OK
- 10.3389/fmars.2017.00366 is OK
- 10.1139/cjz-2014-0311 is OK
- 10.1002/ajp.1350300207 is OK
- 10.1111/j.1748-7692.2009.00288.x is OK
- 10.1111/mms.12527 is OK
- 10.1038/nmeth.2089 is OK
- 10.1126/science.290.5497.1695b is OK
- 10.1002/ecs2.1468 is OK
- 10.1139/juvs-2015-0020 is OK
MISSING DOIs
- https://doi.org/10.2307/1374074 may be missing for title: Southern Blue and Fin Whales
INVALID DOIs
- 10.1641/0006-3568(2003)053[0210:WAS]2.0.CO;2 is INVALID
The missing DOI is for a paper that was published in 1929 so it does not have one as far as we can tell. I'm not sure what to do about the invalid DOI though...it should link to the article below. https://academic.oup.com/bioscience/article/53/3/210/251944
wingtorres
on 15 Jan 2020
I'm not sure what to do about the invalid DOI though...it should link to the article below. https://academic.oup.com/bioscience/article/53/3/210/251944
I think you can ignore this. The URL library we're using for Whedon doesn't like https://doi.org/10.1641/0006-3568(2003)053[0210:WAS]2.0.CO;2 (it's a pretty unusual URL) but it looks like it resolves.
arfon
on 15 Jan 2020
Reference check summary:
OK DOIs
- 10.1007/BF00233083 is OK
- 10.1038/s41559-018-0534-2 is OK
- 10.1371/journal.pone.0017686 is OK
- 10.1139/z85-345 is OK
- 10.1111/1365-2435.12200 is OK
- 10.3354/meps12522 is OK
- 10.1139/z98-195 is OK
- 10.3354/meps09675 is OK
- 10.1146/annurev-marine-010318-095323 is OK
- 10.3389/fmars.2017.00366 is OK
- 10.1139/cjz-2014-0311 is OK
- 10.1002/ajp.1350300207 is OK
- 10.1111/j.1748-7692.2009.00288.x is OK
- 10.1111/mms.12527 is OK
- 10.1038/nmeth.2089 is OK
- 10.1126/science.290.5497.1695b is OK
- 10.1002/ecs2.1468 is OK
- 10.1139/juvs-2015-0020 is OK
MISSING DOIs
- https://doi.org/10.2307/1374074 may be missing for title: Southern Blue and Fin Whales
INVALID DOIs
- 10.1641/0006-3568(2003)053[0210:WAS]2.0.CO;2 is INVALID
Hi @wingtorres, looks like the references are fine, but I have just a few typographic issues to resolve:
- Can you remove the period at the end of the title?
- in a number of places, you are missing commas after "i.e." and "e.g."
- in the 4th paragraph, there are some inconsistencies in some citation formatting; you can use these syntax options for in-text citations:
- `@author:2001` -> "Author et al. (2001)"
- `[@author:2001]` -> "(Author et al., 2001)"
- `[@author1:2001; @author2:2001]` -> "(Author1 et al., 2001; Author2 et al., 2002)"
Otherwise, it is well written, thanks!
kyleniemeyer
on 15 Jan 2020
@whedon generate pdf
wingtorres
on 15 Jan 2020
whedon
on 15 Jan 2020
@kyleniemeyer thank you for the typographic edits! Just made the changes you suggested and generated a new proof.
wingtorres
on 15 Jan 2020
@whedon accept
kyleniemeyer
on 16 Jan 2020
Attempting dry run of processing paper acceptance...
Reference check summary:
OK DOIs
- 10.1007/BF00233083 is OK
- 10.1038/s41559-018-0534-2 is OK
- 10.1371/journal.pone.0017686 is OK
- 10.1139/z85-345 is OK
- 10.1111/1365-2435.12200 is OK
- 10.3354/meps12522 is OK
- 10.1139/z98-195 is OK
- 10.3354/meps09675 is OK
- 10.1146/annurev-marine-010318-095323 is OK
- 10.3389/fmars.2017.00366 is OK
- 10.1139/cjz-2014-0311 is OK
- 10.1002/ajp.1350300207 is OK
- 10.1111/j.1748-7692.2009.00288.x is OK
- 10.1111/mms.12527 is OK
- 10.1038/nmeth.2089 is OK
- 10.1126/science.290.5497.1695b is OK
- 10.1002/ecs2.1468 is OK
- 10.1139/juvs-2015-0020 is OK
MISSING DOIs
- https://doi.org/10.2307/1374074 may be missing for title: Southern Blue and Fin Whales
INVALID DOIs
- 10.1641/0006-3568(2003)053[0210:WAS]2.0.CO;2 is INVALID
Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1222
If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1222, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true
whedon
on 16 Jan 2020
@whedon accept deposit=true
kyleniemeyer
on 16 Jan 2020
Doing it live! Attempting automated processing of paper acceptance...
🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦
whedon
on 16 Jan 2020
🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨
Here's what you must now do:
- Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1223
- Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01825
- If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘
Any issues? notify your editorial technical team...
whedon
on 16 Jan 2020
Congrats on your article's publication in JOSS @wingtorres!
Many thanks to @isaacvandor and @bw4sz for reviewing this submission, and @Kevin-Mattheus-Moerman for editing.
kyleniemeyer
on 16 Jan 2020
:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:
If you would like to include a link to your paper from your README use the following code snippets:
Markdown:
[](https://doi.org/10.21105/joss.01825)
HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01825">
<img src="https://joss.theoj.org/papers/10.21105/joss.01825/status.svg" alt="DOI badge" >
</a>
reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01825/status.svg
:target: https://doi.org/10.21105/joss.01825
This is how it will look in your documentation:
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:
- Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
- Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss
whedon
on 16 Jan 2020
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