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[REVIEW]: PYroMat: A Python package for thermodynamic properties #4757

Closed editorialbot closed 1 year ago

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@jranalli<!--end-author-handle-- (Joseph Ranalli) Repository: https://github.com/chmarti1/PYroMat Branch with paper.md (empty if default branch): joss2022 Version: 2.2.4 Editor: !--editor-->@jgostick<!--end-editor-- Reviewers: @espottesmith, @fwitte Archive: 10.5281/zenodo.7262173

Status

status

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HTML: <a href="https://joss.theoj.org/papers/42d6ea5759b5467dad54709db33ea03d"><img src="https://joss.theoj.org/papers/42d6ea5759b5467dad54709db33ea03d/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/42d6ea5759b5467dad54709db33ea03d/status.svg)](https://joss.theoj.org/papers/42d6ea5759b5467dad54709db33ea03d)

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

@espottesmith & @fwitte, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @jgostick know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @espottesmith

jranalli commented 1 year ago

10.18260/1-232083 is INVALID

This one appears to resolve correctly in the paper, and the link works. It seems like the -- is parsing incorrectly in editorialbot's tests? image

That will likely be a similar issue with the (now fixed) peer.asee.org paper, as it has the same string in its DOI.

For the REFPROP NIST reference, thanks for the link you suggested. For the second NIST ref though I found a DOI for the whole webbook, which is more appropriate for the Shomate equation.

I looked in depth for the NASA paper, but based on its age, I don't think a DOI exists. My understanding is that DOIs were only instituted around 2000.

So the only two things without DOIs right now are the Pyromat reference handbook and the NASA paper.

jranalli commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

jgostick commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1109/FIE.2016.7757589 is OK
- 10.1021/ie4033999 is OK
- 10.1021/acs.iecr.2c01427 is OK
- 10.1023/A:1022390430888 is OK
- 10.1023/A:1022310214958 is OK
- 10.1023/A:1022362231796 is OK
- 10.18434/T4D303 is OK
- 10.1038/s41586-020-2649-2 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.18260/1-228757 is INVALID
- 10.18260/1-232083 is INVALID
jgostick commented 1 year ago

Yes, there does seem to be a bug in joss's doi parser. I can confirm that the '--' are missing from the editorialbot output and if I put them back in, the doi resolves just fine. I'll figure how to report this to the team.

jgostick commented 1 year ago

I opened an issue here. I think for now we can proceed with the process.

danielskatz commented 1 year ago

@xuanxu - any thoughts here?

xuanxu commented 1 year ago

Two hyphens is a LaTeX command for a en-dash, so the parser creates an invalid DOI. I've opened a PR that should fix it.

jranalli commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

jranalli commented 1 year ago

@xuanxu I committed that change, but it messes up the printout in the paper, so I need to revert it: image

I think the problem is just with the bot's parsing when it does the tests for valid DOIs, rather than the document rendering. The document rendered fine before, the only issue was the output from the check references command.

jranalli commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

chmarti1 commented 1 year ago

Sorry about the issues with Zenodo. It looks like I had some confusion about the work flow with Zenodo. I think I've got it sorted now - my fault.

jgostick commented 1 year ago

Nice!

jgostick commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago 
Attempting dry run of processing paper acceptance...
editorialbot commented 1 year ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1109/FIE.2016.7757589 is OK
- 10.1021/ie4033999 is OK
- 10.1021/acs.iecr.2c01427 is OK
- 10.1023/A:1022390430888 is OK
- 10.1023/A:1022310214958 is OK
- 10.1023/A:1022362231796 is OK
- 10.18434/T4D303 is OK
- 10.1038/s41586-020-2649-2 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.18260/1-228757 is INVALID
- 10.18260/1-232083 is INVALID
editorialbot commented 1 year ago

:wave: @openjournals/pe-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3685, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

jgostick commented 1 year ago

Hi @openjournals/pe-eics, note that the two INVALID DOIs in the reference check are false alarms. The dois in the paper have 2 dashes, and this is breaking editorialbot when it attempts to check them.

kyleniemeyer commented 1 year ago

Hi @openjournals/pe-eics, note that the two INVALID DOIs in the reference check are false alarms. The dois in the paper have 2 dashes, and this is breaking editorialbot when it attempts to check them.

Thanks for the heads-up @jgostick—however, I did notice that some information was missing from those entries (notably the proceedings/book title).

@jranalli I made a few typo fixes and bibliography updates in https://github.com/chmarti1/PYroMat/pull/76, could you merge that?

jranalli commented 1 year ago

Done

PS I just wanted to say thanks to everyone who has been part of this process! I'm really impressed by how easily, efficiently this went and how easy it was to follow. I wish more journals would use this type of review.

kyleniemeyer commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

kyleniemeyer commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago 
Doing it live! Attempting automated processing of paper acceptance...
editorialbot commented 1 year ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 1 year ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/3686
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04757
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kyleniemeyer commented 1 year ago

@jranalli @chmarti1 congratulations on your article's publication in JOSS!

Many thanks to @espottesmith and @fwitte for reviewing this, and @jgostick for editing.

editorialbot commented 1 year 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.04757/status.svg)](https://doi.org/10.21105/joss.04757)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04757">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04757/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04757/status.svg
   :target: https://doi.org/10.21105/joss.04757

This is how it will look in your documentation:

DOI

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