[PRE REVIEW]: MatD3: A Database and Online Presentation Package for Research Data Supporting Materials Discovery, Design, and Dissemination #1919

whedon · 2019-11-28T21:20:50Z

Submitting author: @raullaasner (Raul Laasner)
Repository: https://github.com/HybriD3-database/MatD3
Version: 1.0.0
Editor: @majensen
Reviewers: @dgasmith, @mkhorton

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whedon · 2019-11-28T21:20:53Z

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whedon · 2019-11-28T21:20:54Z

Attempting to check references...

whedon · 2019-11-28T21:20:55Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-11-28T21:21:08Z

PDF failed to compile for issue #1919 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-df8b50fe58b8/lib/whedon/author.rb:68:in block in build_affiliation_string': Problem with affiliations for Xiaochen Du, perhaps the affiliations index need quoting? (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-df8b50fe58b8/lib/whedon/author.rb:67:in each'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-df8b50fe58b8/lib/whedon/author.rb:67:in build_affiliation_string' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-df8b50fe58b8/lib/whedon/author.rb:17:in initialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-df8b50fe58b8/lib/whedon.rb:201:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-df8b50fe58b8/lib/whedon.rb:201:in block in parse_authors'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-df8b50fe58b8/lib/whedon.rb:198:in each' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-df8b50fe58b8/lib/whedon.rb:198:in parse_authors'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-df8b50fe58b8/lib/whedon.rb:91:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-df8b50fe58b8/lib/whedon/processor.rb:36:in new'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-df8b50fe58b8/lib/whedon/processor.rb:36:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-df8b50fe58b8/bin/whedon:55:in prepare'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-df8b50fe58b8/bin/whedon:116:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

whedon · 2019-11-28T21:21:16Z


OK DOIs

- None

MISSING DOIs

- https://doi.org/10.1038/sdata.2019.2 may be missing for title: Qresp, a tool for curating, discovering and
 exploring reproducible scientific papers
- https://doi.org/10.1063/1.4812323 may be missing for title: Commentary: The Materials Project: A materials
 genome approach to accelerating materials
 innovation
- https://doi.org/10.1007/s11837-016-2001-3 may be missing for title: The Materials Data Facility: Data services to
 advance materials science research
- https://doi.org/10.1016/j.commatsci.2012.02.005 may be missing for title: AFLOW: An automatic framework for high-throughput
 materials discovery
- https://doi.org/10.1007/s11837-013-0755-4 may be missing for title: Materials Design and Discovery with High-Throughput
 Density Functional Theory: The Open Quantum
 Materials Database (OQMD)

INVALID DOIs

- None

Kevin-Mattheus-Moerman · 2019-11-28T21:27:35Z

@openjournals/dev can you see what is wrong here? The affiliation index does use quotes.

Kevin-Mattheus-Moerman · 2019-11-28T21:28:44Z

@raullaasner while trouble shooting this you can try compiling your paper here too: https://whedon.theoj.org/
If it is compiling you can run @whedon generate pdf here

xuanxu · 2019-11-30T10:56:52Z

@Kevin-Mattheus-Moerman, @raullaasner: There was an error with the indexing of the affiliations, this PR should fix the compiling error.

Kevin-Mattheus-Moerman · 2019-11-30T11:19:32Z

Thanks @xuanxu !

Kevin-Mattheus-Moerman · 2019-11-30T11:20:26Z

@raullaasner can you check the above fix by @xuanxu ?

raullaasner · 2019-11-30T18:08:32Z

@Kevin-Mattheus-Moerman Yes, sorry for the delay. This is fixed now.

Kevin-Mattheus-Moerman · 2019-11-30T19:45:57Z

@whedon generate pdf

whedon · 2019-11-30T19:46:00Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-11-30T19:46:34Z

👉 Check article proof 📄 👈

Kevin-Mattheus-Moerman · 2019-12-01T09:22:53Z

@raullaasner can you also work on those missing DOI's? You can run @whedon check references and @whedon generate pdf here too to check things.

Kevin-Mattheus-Moerman · 2019-12-01T09:26:34Z

@trallard @csoneson @majensen @akeshavan could one of you edit this submission? Thanks!

majensen · 2019-12-01T13:19:36Z

@whedon assign @majensen as editor

whedon · 2019-12-01T13:19:40Z

OK, the editor is @majensen

raullaasner · 2019-12-01T18:07:21Z

@Kevin-Mattheus-Moerman I added DOIs to the paper references except for the SpringerMaterials and Nomad citations, which are only web links. It seems there is no better way to cite these at this point.

raullaasner · 2019-12-01T18:13:16Z

Regarding the proof, would it possible have "3" as a superscript in MatD³? In the paper, I had written MatD<sup>3</sup> everywhere but this formatting seems not to be present in the proof.

Kevin-Mattheus-Moerman · 2019-12-01T19:47:15Z

@whedon generate pdf

whedon · 2019-12-01T19:47:18Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-12-01T19:47:47Z

👉 Check article proof 📄 👈

Kevin-Mattheus-Moerman · 2019-12-01T19:52:48Z

@openjournals/dev do you know how to use superscript in the text as the author requests?

Regarding the proof, would it possible have "3" as a superscript in MatD3? In the paper, I had written MatD<sup>3</sup> everywhere but this formatting seems not to be present in the proof.

pythonpanda2 · 2019-12-10T02:22:31Z

@majensen

I was reviewing the JOSS Conflict of Interest (COI) Policy. I regret to inform you that my current employment at ANL and an ongoing collaboration with submitter's research group might lead to COI.

I would like to nominate @aykol for review.

majensen · 2019-12-10T03:11:24Z

Thanks for your diligence on that issue @pythonpanda2 -- @aykol are you willing to review this submission?

pythonpanda2 · 2019-12-10T13:18:56Z

@majensen I would also nominate @dgasmith

majensen · 2019-12-10T15:25:52Z

Hi @dgasmith - would you be willing to review this submission to JOSS?

dgasmith · 2019-12-10T18:19:43Z

@majensen Yes, happy to review the submission.

majensen · 2019-12-10T21:53:32Z

@whedon assign @dgasmith as reviewer

whedon · 2019-12-10T21:53:37Z

OK, the reviewer is @dgasmith

computron · 2019-12-10T22:06:19Z

Hey @majensen , sorry but I am unable to perform this review

dgasmith · 2019-12-10T22:12:59Z

@computron /wave!

I could also suggest @mkhorton.

mkhorton · 2019-12-10T22:23:15Z

I'd be happy to take a look at this, I can't make a strong commitment on time however.

majensen · 2019-12-11T01:04:13Z

Thanks for your response @computron -
@mkhorton - thx - what would be a workable timeline for you?

mkhorton · 2019-12-11T01:49:34Z

Hopefully within the next two weeks but it's difficult to guarantee with the holidays.

…

On Tue, Dec 10, 2019 at 5:04 PM Mark Jensen ***@***.***> wrote: Thanks for your response @computron <https://github.com/computron> - @mkhorton <https://github.com/mkhorton> - thx - what would be a workable timeline for you? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1919?email_source=notifications&email_token=AAWWWREBOFAECAXCHM6JZCLQYA4A7A5CNFSM4JSYXEUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGRP63I#issuecomment-564330349>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAWWWRF73CZ3GD5X6UOGMALQYA4A7ANCNFSM4JSYXEUA> .

majensen · 2019-12-11T02:36:13Z

@mkhorton understood. I will start the review, but @raullaasner I expect we all will be off and on until 1 Jan - does this sound ok?

majensen · 2019-12-11T02:36:29Z

@whedon add @mkhorton as reviewer

whedon · 2019-12-11T02:36:35Z

OK, @mkhorton is now a reviewer

majensen · 2019-12-12T14:26:03Z

Applying the tacit approval principle, I will start this review. Thanks all.

majensen · 2019-12-12T14:26:23Z

@whedon start review

whedon · 2019-12-12T14:26:29Z

OK, I've started the review over in #1945. Feel free to close this issue now!

aykol · 2019-12-13T22:54:23Z

Sorry for the delayed response. I'm glad new reviewers were found, as I wasn't going to be able to review it.

majensen · 2019-12-14T00:32:24Z

Thanks for following up @aykol !

whedon added the pre-review label Nov 28, 2019

whedon added CSS HTML Python labels Nov 28, 2019

xuanxu mentioned this issue Nov 30, 2019

Fix indexing in affiliations HybriD3-database/MatD3#2

Merged

whedon assigned majensen Dec 1, 2019

whedon assigned dgasmith and majensen and unassigned majensen and pythonpanda2 Dec 10, 2019

whedon assigned dgasmith, majensen and mkhorton and unassigned majensen and dgasmith Dec 11, 2019

majensen closed this as completed Dec 12, 2019

[PRE REVIEW]: MatD3: A Database and Online Presentation Package for Research Data Supporting Materials Discovery, Design, and Dissemination #1919

[PRE REVIEW]: MatD3: A Database and Online Presentation Package for Research Data Supporting Materials Discovery, Design, and Dissemination #1919

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