[REVIEW]: Comet Time Series (CometTS) Visualizer

whedon commented 6 years ago

Submitting author: @jshermeyer (Jacob Shermeyer) Repository: https://github.com/CosmiQ/CometTS Version: <v1.2.0> Editor: @Kevin-Mattheus-Moerman Reviewers: @zhampel, @rmsare, @jjmcnelis Archive: 10.5281/zenodo.3418091

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/2e38056740935063b95551d23334a1c1"><img src="http://joss.theoj.org/papers/2e38056740935063b95551d23334a1c1/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/2e38056740935063b95551d23334a1c1/status.svg)](http://joss.theoj.org/papers/2e38056740935063b95551d23334a1c1)

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

@zhampel, and @rmsare 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.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @Kevin-Mattheus-Moerman know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @zhampel

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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] Version: <v1.2.0>
[x] Authorship: Has the submitting author (@jshermeyer) 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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
[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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @rmsare

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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] Version: <v1.2.0>
[x] Authorship: Has the submitting author (@jshermeyer) 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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
[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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @jjmcnelis

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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] Version: <v1.2.0>
[x] Authorship: Has the submitting author (@jshermeyer) 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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
[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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

jshermeyer commented 5 years ago

Hi Kevin,

@Kevin-Mattheus-Moerman https://github.com/Kevin-Mattheus-Moerman Updated the text to make it seem as if "Cloud and snow masking" were not new functionality. If there is any further specific changes required for the text let me know, otherwise I am satisfied with it.

-Jake

On Sat, Aug 24, 2019 at 5:30 AM Kevin Mattheus Moerman < notifications@github.com> wrote:

@jshermeyer https://github.com/jshermeyer can you give an update on progress in terms of replying/dealing with @rmsare https://github.com/rmsare comments? It looks like we are nearly there.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/1047?email_source=notifications&email_token=AGNX2AOT2JWN55T3PTTYNULQGD5TLA5CNFSM4F672LN2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5B4QTQ#issuecomment-524535886, or mute the thread https://github.com/notifications/unsubscribe-auth/AGNX2AI72FIL23AHRZAM5KDQGD5TLANCNFSM4F672LNQ .

rmsare commented 5 years ago

@jshermeyer, Thanks for making that change. It's nearly there, but some small edits are required for clarity and a typo.

I've noted the three changes to be made in a comment to this issue.

Kevin-Mattheus-Moerman commented 5 years ago

@jshermeyer :point_up: see above. It looks like we are close. Can you work on these minor sounding issues?

Kevin-Mattheus-Moerman commented 5 years ago

Thanks @zhampel for your contribution. I've just unticked the "conflict of interest" box for you since you indicated to me in an email that "Jake Shermeyer, is a member of a sister lab of [your] organization". I'm reiterating that here for the record.

rmsare commented 5 years ago

My last comments were addressed, and I am comfortable recommending the paper be accepted @Kevin-Mattheus-Moerman. Thanks for your patience, and congratulations @jshermeyer

zhampel commented 5 years ago

@Kevin-Mattheus-Moerman When I brought this up, I was informed that there was in fact no conflict of interest and thus not a problem during the first round of reviews, hence the box was checked.

danielskatz commented 5 years ago

Let's go back and have this box be checked - there is a conflict here, but we've recorded it and waived it for the purpose of this review. (We probably need to rephrase this criteria slightly, which I will bring up outside this review thread.)

Kevin-Mattheus-Moerman commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

Kevin-Mattheus-Moerman commented 5 years ago

@whedon check references

whedon commented 5 years ago

Attempting to check references...

whedon commented 5 years ago


OK DOIs

- 10.5281/zenodo.267110 is OK
- 10.5281/zenodo.1324419 is OK
- 10.1117/12.2325585 is OK
- 10.1016/j.cageo.2004.05.006 is OK
- 10.5281/zenodo.1974065 is OK

MISSING DOIs

- None

INVALID DOIs

- None

Kevin-Mattheus-Moerman commented 5 years ago

@jshermeyer looks good. We are ready for the next steps. Can you please:

[ ] Can you deposit the release (version) of the reviewed software in Zenodo? Once you have archived the software there please report the DOI of the archived version here. Please ensure the authors and title on the Zenodo archive match those of the paper.
[ ] Can you list the version number? (is it still v1.0 or has it changed)?

thanks

Kevin-Mattheus-Moerman commented 5 years ago

@jshermeyer :wave: let me know if you have questions about depositing and archived version on Zenodo. Thanks

jshermeyer commented 5 years ago

New version on Zenodo: https://zenodo.org/record/3418091 Version number is 1.2.0 which incorporates all the edits and comments from reviewer. This version has also been pushed to pypi.

Thanks!

kthyng commented 5 years ago

Hi @jshermeyer! I see that the title in this submission and the zenodo archive just barely don't match... can you update the Zenodo archive to match exactly?

jshermeyer commented 5 years ago

@kthyng Good catch, fixed.

kthyng commented 5 years ago

@whedon set v1.2.0 as version

whedon commented 5 years ago

OK. <v1.2.0> is the version.

kthyng commented 5 years ago

@whedon set 10.5281/zenodo.3418091 as archive

whedon commented 5 years ago

OK. 10.5281/zenodo.3418091 is the archive.

kthyng commented 5 years ago

@jshermeyer: Edits for paper:

[ ] Spacing issues throughout. Make sure there are spaces next to parentheses, this is coming up around references mostly but other times too.
[ ] ROI is used before being defined
[ ] obligatory spelled wrong first page 2nd paragraph
[ ] Figure 3 caption appears to be set up incorrectly.
[ ] The line above Figure 3: What is this? Is it trying to link to its own DOI? That is out of date and shouldn't be in the references anyway, it is on the left side of the page on the first page of the paper.

kthyng commented 5 years ago

Another edit, @jshermeyer: your citation e-sensing/sits:2018 is not formatted correctly. In particular at least the authors in the author list need to be separated by "and" as in your other entries. There may be other problems too, but you can see in your reference list and when you cite it inline that it is not working correctly.

jshermeyer commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

jshermeyer commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

jshermeyer commented 5 years ago

@kthyng I think I have fixed all of the issues you flagged (among a few others). Let me know if there's anything else you notice. Thanks!

kthyng commented 5 years ago

Another edit, @jshermeyer: your citation e-sensing/sits:2018 is not formatted correctly. In particular at least the authors in the author list need to be separated by "and" as in your other entries. There may be other problems too, but you can see in your reference list and when you cite it inline that it is not working correctly.

@jshermeyer This doesn't appear to have changed yet.

jshermeyer commented 5 years ago

Please send me the appropriate format exactly, I added an “and” between the second to last and final author. I’m not sure what you’re looking for.

On Sep 26, 2019, at 12:45 PM, Kristen Thyng notifications@github.com wrote:

Another edit, @jshermeyer: your citation e-sensing/sits:2018 is not formatted correctly. In particular at least the authors in the author list need to be separated by "and" as in your other entries. There may be other problems too, but you can see in your reference list and when you cite it inline that it is not working correctly.

@jshermeyer This doesn't appear to have changed yet.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

kthyng commented 5 years ago

Here under "example paper.bib", the first example paper shows how multiple authors (each author) should be separated by "and" instead of a semi-colon. You can check to make sure it worked properly and there aren't other errors by how it looks when cited (shouldn't take up a whole line in the paper) and how it looks in the references (some of the authors are being abbreviated to a single letter I think?).

jshermeyer commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

jshermeyer commented 5 years ago

@kthyng thanks, looks like that worked

kthyng commented 5 years ago

@whedon accept

whedon commented 5 years ago

Attempting dry run of processing paper acceptance...

whedon commented 5 years ago


OK DOIs

- 10.5281/zenodo.267110 is OK
- 10.1117/12.2325585 is OK
- 10.1016/j.cageo.2004.05.006 is OK
- 10.5281/zenodo.1974065 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 5 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/992

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/992, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

kthyng commented 5 years ago

@whedon accept deposit=true

whedon commented 5 years ago

Doing it live! Attempting automated processing of paper acceptance...

whedon commented 5 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 5 years ago

🚨🚨🚨 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/993
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01047
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

kthyng commented 5 years ago

Woohoo congratulations @jshermeyer!!! Thanks so much to @zhampel, @rmsare, @jjmcnelis for reviewing, and to @Kevin-Mattheus-Moerman for editing!

whedon commented 5 years ago

: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:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.01047/status.svg)](https://doi.org/10.21105/joss.01047)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01047">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01047/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01047/status.svg
   :target: https://doi.org/10.21105/joss.01047

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.salsalabs.org/donate-to-joss

jshermeyer commented 5 years ago

Thanks all @zhampel, @rmsare, @jjmcnelis, @Kevin-Mattheus-Moerman, @kthyng !

This is presently giving me a 404: https://joss.theoj.org/papers/10.21105/joss.01047

Assuming it will auto-update given a bit of time?

kthyng commented 5 years ago

Weird! It is not giving me a 404. Is it still?

openjournals / joss-reviews