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[REVIEW]: LobsterPy: A package to automatically analyze LOBSTER runs #6286

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editorialbot opened this issue Jan 26, 2024 · 81 comments
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accepted published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials

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editorialbot commented Jan 26, 2024

Submitting author: @JaGeo (Janine George)
Repository: https://github.com/JaGeo/LobsterPy
Branch with paper.md (empty if default branch):
Version: v0.3.8
Editor: @RMeli
Reviewers: @berquist, @srmnitc
Archive: 10.5281/zenodo.10713348

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/4e8524125e36486c65a4b435bbfe2df2"><img src="https://joss.theoj.org/papers/4e8524125e36486c65a4b435bbfe2df2/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/4e8524125e36486c65a4b435bbfe2df2/status.svg)](https://joss.theoj.org/papers/4e8524125e36486c65a4b435bbfe2df2)

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

@berquist & @srmnitc, 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 @RMeli 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 @berquist

📝 Checklist for @srmnitc

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Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

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Software report:

github.com/AlDanial/cloc v 1.88  T=6.64 s (12.1 files/s, 11022.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                            12              0              0          55254
Python                          25           1716           1395          11457
Markdown                        12            120              0            438
YAML                             6             36             46            254
reStructuredText                18            172            225            175
TOML                             1             20              1            159
TeX                              1             15              0            157
Jupyter Notebook                 2              0           1231            141
CSS                              1             21             44             63
HTML                             2              0              0             28
-------------------------------------------------------------------------------
SUM:                            80           2100           2942          68126
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 720

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Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1021/j100135a014 is OK
- 10.1515/9783111167213 is OK
- 10.1021/acsomega.3c00395 is OK
- 10.1038/s41597-023-02477-5 is OK
- 10.1021/jacs.2c11908 is OK
- 10.1021/acs.chemmater.1c03349 is OK
- 10.1002/anie.198708461 is OK
- 10.1016/j.apsusc.2022.156064 is OK
- 10.1021/ja00349a027 is OK
- 10.1021/acs.jpcc.1c00718 is OK
- 10.1002/cplu.202200123 is OK
- 10.1002/adfm.202314565 is OK
- 10.1063/1.4812323 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@berquist
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berquist commented Jan 26, 2024

Review checklist for @berquist

Conflict of interest

  • 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

General checks

  • Repository: Is the source code for this software available at the https://github.com/JaGeo/LobsterPy?
  • License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@JaGeo) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
    • I worked through the Jupyter Notebook tutorial which seems to cover most of what's claimed in the paper summary.
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)
    • No claims

Documentation

Software paper

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • 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?

@RMeli
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RMeli commented Feb 6, 2024

Hello @berquist and @srmnitc, how are you? How is the review coming along?

@srmnitc please generate your review checklist with

@editorialbot generate my checklist

when you have time, so that you can track progress.

@srmnitc
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srmnitc commented Feb 7, 2024

Review checklist for @srmnitc

Conflict of interest

  • 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

General checks

  • Repository: Is the source code for this software available at the https://github.com/JaGeo/LobsterPy?
  • License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@JaGeo) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

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

  • 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 functionality 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

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • 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?

@srmnitc
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srmnitc commented Feb 9, 2024

@RMeli I have now finished my review. Lobsterpy is a well-designed, and maintained package which I believe would be useful for the community. It has already been employed in a number of studies. The code and documentation are in very good shape, and it was really easy to get started with the tool. I had only some minor issues, which @JaGeo and team fixed very quickly. There are only minor corrections to the paper remaining. Overall, I recommend the publication of this package. Thanks @RMeli for inviting me to review, and @JaGeo for this nice software.

@JaGeo
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JaGeo commented Feb 9, 2024

Thank you very much, @srmnitc (I mixed up the handles first, sorry!)
We are, of course, happy to include corrections to our paper as well.

@RMeli
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RMeli commented Feb 9, 2024

Thank you @srmnitc for all the hard work!

I had only some minor issues, which @JaGeo and team fixed very quickly.

I've noticed it, thanks @JaGeo for the very prompt replies to the reviewer queries and comments.

There are only minor corrections to the paper remaining.

Did you suggest these minor corrections anywhere? I only see JaGeo/LobsterPy#225, are you referring just to those two suggestions?

@srmnitc
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srmnitc commented Feb 9, 2024

Thank you @srmnitc for all the hard work!

I had only some minor issues, which @JaGeo and team fixed very quickly.

I've noticed it, thanks @JaGeo for the very prompt replies to the reviewer queries and comments.

There are only minor corrections to the paper remaining.

Did you suggest these minor corrections anywhere? I only see JaGeo/LobsterPy#225, are you referring just to those two suggestions?

Yes, correct, just the two.

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srmnitc commented Feb 9, 2024

@editorialbot generate pdf

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

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srmnitc commented Feb 9, 2024

Thank you @srmnitc for all the hard work!

I had only some minor issues, which @JaGeo and team fixed very quickly.

I've noticed it, thanks @JaGeo for the very prompt replies to the reviewer queries and comments.

There are only minor corrections to the paper remaining.

Did you suggest these minor corrections anywhere? I only see JaGeo/LobsterPy#225, are you referring just to those two suggestions?

Once JaGeo/LobsterPy#226 is merged, all my comments would be addressed. All comments addressed :)

@JaGeo
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JaGeo commented Feb 9, 2024

We (@naik-aakash and I) have addressed the comments in JaGeo/LobsterPy#226, @RMeli .

@naik-aakash
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@editorialbot generate pdf

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@naik-aakash
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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@RMeli
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RMeli commented Feb 19, 2024

Hello @berquist, how are you? How is the review coming along? Please let me know if you have any questions or blockers.

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RMeli commented Feb 26, 2024

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Done! archive is now 10.5281/zenodo.10713348

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RMeli commented Feb 26, 2024

@editorialbot set v0.3.8 as version

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Done! version is now v0.3.8

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RMeli commented Feb 26, 2024

@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1021/jp202489s is OK
- 10.1002/jcc.23424 is OK
- 10.1002/jcc.24300 is OK
- 10.21105/joss.00717 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1021/j100135a014 is OK
- 10.1515/9783111167213 is OK
- 10.1021/acsomega.3c00395 is OK
- 10.1038/s41597-023-02477-5 is OK
- 10.1021/jacs.2c11908 is OK
- 10.1021/acs.chemmater.1c03349 is OK
- 10.1002/anie.198708461 is OK
- 10.1016/j.apsusc.2022.156064 is OK
- 10.1021/ja00349a027 is OK
- 10.1021/acs.jpcc.1c00718 is OK
- 10.1002/cplu.202200123 is OK
- 10.1002/adfm.202314565 is OK
- 10.1063/1.4812323 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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👋 @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5055, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@editorialbot editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Feb 26, 2024
@JaGeo
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JaGeo commented Feb 27, 2024

@RMeli Thank you so much! And thanks also for the great review experience! 😀

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RMeli commented Feb 27, 2024

Thank you @JaGeo for engaging so well with this review. I was happy to recommend publication, according to the reviewers suggestions. Now the EiC will do the final checks.

Thank you again to @srmnitc and @berquist for the in depth and constructive review!

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@RMeli thanks for editing this one. It looks like perhaps @editorialbot create post-review checklist was not used yet. I'll call it now and take it from here. I recommend using it in the future to prevent overlooking some of the last steps. In this case for instance the license on the archive link doesn't match up yet. No worries though we'll sort this out now. Thanks again.

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Kevin-Mattheus-Moerman commented Feb 27, 2024

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

  • Double check authors and affiliations (including ORCIDs)
  • Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
  • Archive the release on Zenodo/figshare/etc and post the DOI here.
  • Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
  • Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

  • Read the text of the paper and offer comments/corrections (as either a list or a pull request)
  • Check that the archive title, author list, version tag, and the license are correct
  • Set archive DOI with @editorialbot set <DOI here> as archive
  • Set version with @editorialbot set <version here> as version
  • Double check rendering of paper with @editorialbot generate pdf
  • Specifically check the references with @editorialbot check references and ask author(s) to update as needed
  • Recommend acceptance with @editorialbot recommend-accept

@Kevin-Mattheus-Moerman
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@JaGeo As AEiC on this track I will now help process the final steps to help with acceptance in JOSS. I have just checked the paper, this review, your repository, and the archive link. Most seems in order. I'd only ask you to please ensure that the license listed on the archive link matches your software license. Can you edit this please?

@JaGeo
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JaGeo commented Feb 27, 2024

@Kevin-Mattheus-Moerman Thank you. I have edited the repo metadata and changed the license to the 'BSD 3-Clause "New" or "Revised" License"

(see https://doi.org/10.5281/zenodo.10713348)

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@editorialbot accept

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

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Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Naik
  given-names: Aakash Ashok
  orcid: "https://orcid.org/0000-0002-6071-6786"
- family-names: Ueltzen
  given-names: Katharina
  orcid: "https://orcid.org/0009-0003-2967-1182"
- family-names: Ertural
  given-names: Christina
  orcid: "https://orcid.org/0000-0002-7696-5824"
- family-names: Jackson
  given-names: Adam J.
  orcid: "https://orcid.org/0000-0001-5272-6530"
- family-names: George
  given-names: Janine
  orcid: "https://orcid.org/0000-0001-8907-0336"
doi: 10.5281/zenodo.10713348
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Naik
    given-names: Aakash Ashok
    orcid: "https://orcid.org/0000-0002-6071-6786"
  - family-names: Ueltzen
    given-names: Katharina
    orcid: "https://orcid.org/0009-0003-2967-1182"
  - family-names: Ertural
    given-names: Christina
    orcid: "https://orcid.org/0000-0002-7696-5824"
  - family-names: Jackson
    given-names: Adam J.
    orcid: "https://orcid.org/0000-0001-5272-6530"
  - family-names: George
    given-names: Janine
    orcid: "https://orcid.org/0000-0001-8907-0336"
  date-published: 2024-02-27
  doi: 10.21105/joss.06286
  issn: 2475-9066
  issue: 94
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6286
  title: "LobsterPy: A package to automatically analyze LOBSTER runs"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06286"
  volume: 9
title: "LobsterPy: A package to automatically analyze LOBSTER runs"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

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🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.06286 joss-papers#5060
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06286
  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...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Feb 27, 2024
@JaGeo
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JaGeo commented Feb 28, 2024

Thank you very much, @Kevin-Mattheus-Moerman .

And, of course, thank you so mich, @srmnitc and @berquist for your reviews, as well!

@RMeli
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RMeli commented Feb 28, 2024

Congratulations @JaGeo!

@Kevin-Mattheus-Moerman this was my very fist time editing, thank you for double checking everything carefully and suggesting the "Post-Review Checklist" (I used the one on the Editorial Guide, but clearly slipped on the last point).

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RMeli commented Mar 1, 2024

@Kevin-Mattheus-Moerman can I close the issue once the paper is accepted? (I expected the bot to close it automatically, but I just noticed that it's still open.)

@Kevin-Mattheus-Moerman
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I'll do that shortly after some thanks/congratulations messages. Thanks

@Kevin-Mattheus-Moerman
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@JaGeo congratulations on this JOSS publication!!!

@RMeli Thanks for editing!

And a special thank you to the reviewers: @berquist, @srmnitc !!

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🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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.06286/status.svg)](https://doi.org/10.21105/joss.06286)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06286">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06286/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06286/status.svg
   :target: https://doi.org/10.21105/joss.06286

This is how it will look in your documentation:

DOI

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