[REVIEW]: libEnsemble: A complete Python toolkit for dynamic ensembles of calculations #6031

editorialbot · 2023-11-07T18:33:12Z

Submitting author: @jmlarson1 (Jeffrey Larson)
Repository: https://github.com/Libensemble/libensemble
Branch with paper.md (empty if default branch): joss-develop
Version: v1.1.0
Editor: @jbytecode
Reviewers: @jsoishi, @SergeyYakubov
Archive: 10.5281/zenodo.10391387

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/8d3b1a704c83affe55284dd00857bdb0"><img src="https://joss.theoj.org/papers/8d3b1a704c83affe55284dd00857bdb0/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/8d3b1a704c83affe55284dd00857bdb0/status.svg)](https://joss.theoj.org/papers/8d3b1a704c83affe55284dd00857bdb0)

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

@jsoishi & @SergeyYakubov, 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 @jbytecode 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 @jsoishi

📝 Checklist for @SergeyYakubov

The text was updated successfully, but these errors were encountered:

editorialbot · 2023-11-07T18:33:14Z

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:

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editorialbot · 2023-11-07T18:33:17Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.45 s (996.4 files/s, 121671.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         253           7849           7098          22684
reStructuredText                97           2562           3208           3228
TeX                              5            146             27           1220
C                               10            304            180           1147
Bourne Shell                    32            271            407            813
YAML                            16             93             15            669
Markdown                        10            243              0            532
Jupyter Notebook                 3              0            963            207
JSON                             2              0              0             78
Perl                             3              9             26             65
TOML                             3              8              0             59
MATLAB                           3             14             57             48
Fortran 90                       1             14              3             39
make                             2              9             10             25
XML                              3              0              0              5
CSS                              1              0              0              3
SVG                              1              0              0              1
-------------------------------------------------------------------------------
SUM:                           445          11522          11994          30823
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-11-07T18:33:19Z

Wordcount for paper.md is 1189

editorialbot · 2023-11-07T18:33:20Z

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

OK DOIs

- 10.1109/TPDS.2021.3082815 is OK
- 10.1007/s11081-020-09571-2 is OK
- 10.1109/TQE.2021.3140190 is OK
- 10.1016/j.cpc.2022.108566 is OK
- 10.1080/00401706.2023.2210170 is OK
- 10.1080/00401706.2023.2246157 is OK
- 10.48550/arXiv.2304.06881 is OK
- 10.1103/PhysRevAccelBeams.26.084601 is OK
- 10.18429/JACoW-IPAC2022-WEPOST030 is OK
- 10.1109/MLHPC54614.2021.00007 is OK
- 10.1109/ICPP.2016.59 is OK
- 10.1145/3307681.3325400 is OK
- 10.1109/xloop49562.2019.00010 is OK
- 10.1016/j.jpdc.2007.09.005 is OK
- 10.2172/1968587 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-11-07T18:34:44Z

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

jbytecode · 2023-11-07T18:39:10Z

@jsoishi, @SergeyYakubov - Thank you for accepting our invitation. This is the review thread. In this GitHub issue please firstly type

@editorialbot generate my checklist

to generate your checklist. In that list, each reviewer has a checklist of review items. When you complete a corresponding task, please check the box. The review is interactive, so you can open new issues in the software repository and interact with the other reviewers, the author, and the editor. Do not hesitate to ask me anything when you get into any trouble.

Have a nice reviewing!

jsoishi · 2023-11-10T19:29:37Z

Review checklist for @jsoishi

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

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/Libensemble/libensemble?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@jmlarson1) 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?

SergeyYakubov · 2023-11-12T17:15:00Z

Review checklist for @SergeyYakubov

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

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/Libensemble/libensemble?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@jmlarson1) 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?

SergeyYakubov · 2023-11-12T18:48:26Z

Hi @jmlarson1, I started looking into your paper.

Looks pretty interesting. Couple of issues as of now:

In the "statement of need," I do not see a clear description of the "target audience" as required by the checklist. Could you please add this to the paper (and maybe to the docs as well)?
Cannot run simple tutorial - see Problems running "Simple introduction tutorial" Libensemble/libensemble#1167

shuds13 · 2023-11-16T20:23:21Z

Hi @SergeyYakubov, we have fixed the tutorial. I have also updated our local copy of the paper to provide a target audience. The addition is quite brief, but I think as we describe example use cases above, this may be sufficient. Let me know if you think it would be useful to add more clarification.

jbytecode · 2023-11-19T17:50:44Z

@jsoishi, @SergeyYakubov - Could you please update your status and continue to review? Thank you in advance, have a nice week.

SergeyYakubov · 2023-11-26T15:32:40Z

@jbytecode - I've completed my review. I think the paper is well-written, and the software itself is promising. It is somewhat similar to what Apache Spark & Co does in the cloud, but more lightweight and developed with HPC in mind (I was not able to verify it works properly on a large supercomputer, though).

Thank you for inviting me.

jbytecode · 2023-11-27T11:14:37Z

@SergeyYakubov - Thank you!

jsoishi · 2023-12-06T01:06:43Z

@jbytecode I apologize for the delay in my review. I should have it finished by the end of this week.

jbytecode · 2023-12-06T16:10:37Z

@jsoishi - no worries, thank you for the reply.

jsoishi · 2023-12-08T15:01:07Z

@editorialbot generate pdf

editorialbot · 2023-12-08T15:02:48Z

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

jsoishi · 2023-12-11T18:20:59Z

@jbytecode I have finished my review. I am also generally impressed with the paper and software. I was able to test the examples on our SLURM-managed cluster.

jbytecode · 2023-12-11T18:23:25Z

@jsoishi - thank you for your review.

@jmlarson1 - now we can go on with our editorial tasks

jbytecode · 2023-12-11T18:26:09Z

@editorialbot check references

editorialbot · 2023-12-11T18:27:04Z

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

OK DOIs

- 10.1109/TPDS.2021.3082815 is OK
- 10.1007/s11081-020-09571-2 is OK
- 10.1109/TQE.2021.3140190 is OK
- 10.1016/j.cpc.2022.108566 is OK
- 10.1080/00401706.2023.2210170 is OK
- 10.1080/00401706.2023.2246157 is OK
- 10.48550/arXiv.2304.06881 is OK
- 10.1103/PhysRevAccelBeams.26.084601 is OK
- 10.18429/JACoW-IPAC2022-WEPOST030 is OK
- 10.1109/MLHPC54614.2021.00007 is OK
- 10.1109/ICPP.2016.59 is OK
- 10.1145/3307681.3325400 is OK
- 10.1109/xloop49562.2019.00010 is OK
- 10.1016/j.jpdc.2007.09.005 is OK
- 10.2172/1968587 is OK

MISSING DOIs

- None

INVALID DOIs

- None

jbytecode · 2023-12-11T18:28:42Z

@editorialbot generate pdf

editorialbot · 2023-12-11T18:29:59Z

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

jmlarson1 · 2023-12-18T14:00:29Z

@editorialbot generate pdf

editorialbot · 2023-12-18T14:01:35Z

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

jmlarson1 · 2023-12-18T14:04:00Z

@jbytecode The anchor/crossref to the section header wasn't working correctly, so I've explicitly added a markdown anchor.

I find that pointing to that has resolved the issue, right?

jbytecode · 2023-12-18T14:20:29Z

@editorialbot recommend-accept

editorialbot · 2023-12-18T14:20:31Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-12-18T14:20:42Z

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

OK DOIs

- 10.1109/TPDS.2021.3082815 is OK
- 10.1007/s11081-020-09571-2 is OK
- 10.1109/TQE.2021.3140190 is OK
- 10.1016/j.cpc.2022.108566 is OK
- 10.1080/00401706.2023.2210170 is OK
- 10.1080/00401706.2023.2246157 is OK
- 10.48550/arXiv.2304.06881 is OK
- 10.1103/PhysRevAccelBeams.26.084601 is OK
- 10.18429/JACoW-IPAC2022-WEPOST030 is OK
- 10.1109/MLHPC54614.2021.00007 is OK
- 10.1109/ICPP.2016.59 is OK
- 10.1145/3307681.3325400 is OK
- 10.1109/xloop49562.2019.00010 is OK
- 10.1016/j.jpdc.2007.09.005 is OK
- 10.2172/1968587 is OK
- 10.1038/s41586-020-2649-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-12-18T14:21:48Z

👋 @openjournals/csism-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#4850, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz · 2023-12-18T14:30:57Z

@jmlarson1 - as track editor, I'll proofread this later today and let you know what else, if anything, is needed

danielskatz · 2023-12-18T16:18:47Z

@jmlarson1 - I note the author order in the zenodo archive is different than in the paper. I'm just pointing this out in case you want to make them consistent.

danielskatz · 2023-12-18T16:24:10Z

@jmlarson1 - I've suggested a few small changes in Libensemble/libensemble#1199 - please merge this, or let me know what you disagree with, and then we can proceed

danielskatz · 2023-12-18T16:38:13Z

@editorialbot recommend-accept

editorialbot · 2023-12-18T16:38:15Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-12-18T16:38:33Z

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

OK DOIs

- 10.1109/TPDS.2021.3082815 is OK
- 10.1007/s11081-020-09571-2 is OK
- 10.1109/TQE.2021.3140190 is OK
- 10.1016/j.cpc.2022.108566 is OK
- 10.1080/00401706.2023.2210170 is OK
- 10.1080/00401706.2023.2246157 is OK
- 10.48550/arXiv.2304.06881 is OK
- 10.1103/PhysRevAccelBeams.26.084601 is OK
- 10.18429/JACoW-IPAC2022-WEPOST030 is OK
- 10.1109/MLHPC54614.2021.00007 is OK
- 10.1109/ICPP.2016.59 is OK
- 10.1145/3307681.3325400 is OK
- 10.1109/xloop49562.2019.00010 is OK
- 10.1016/j.jpdc.2007.09.005 is OK
- 10.2172/1968587 is OK
- 10.1038/s41586-020-2649-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-12-18T16:39:57Z

👋 @openjournals/csism-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#4851, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz · 2023-12-18T16:41:06Z

@editorialbot accept

editorialbot · 2023-12-18T16:41:08Z

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

editorialbot · 2023-12-18T16:42:37Z

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: Hudson
  given-names: Stephen
  orcid: "https://orcid.org/0000-0002-7500-6138"
- family-names: Larson
  given-names: Jeffrey
  orcid: "https://orcid.org/0000-0001-9924-2082"
- family-names: Navarro
  given-names: John-Luke
  orcid: "https://orcid.org/0000-0002-9916-9038"
- family-names: Wild
  given-names: Stefan M.
  orcid: "https://orcid.org/0000-0002-6099-2772"
contact:
- family-names: Hudson
  given-names: Stephen
  orcid: "https://orcid.org/0000-0002-7500-6138"
doi: 10.5281/zenodo.10391387
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Hudson
    given-names: Stephen
    orcid: "https://orcid.org/0000-0002-7500-6138"
  - family-names: Larson
    given-names: Jeffrey
    orcid: "https://orcid.org/0000-0001-9924-2082"
  - family-names: Navarro
    given-names: John-Luke
    orcid: "https://orcid.org/0000-0002-9916-9038"
  - family-names: Wild
    given-names: Stefan M.
    orcid: "https://orcid.org/0000-0002-6099-2772"
  date-published: 2023-12-18
  doi: 10.21105/joss.06031
  issn: 2475-9066
  issue: 92
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6031
  title: "libEnsemble: A complete Python toolkit for dynamic ensembles
    of calculations"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06031"
  volume: 8
title: "libEnsemble: A complete Python toolkit for dynamic ensembles of
  calculations"

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.

editorialbot · 2023-12-18T16:42:41Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2023-12-18T16:42:41Z

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.06031 joss-papers#4852
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06031
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

jmlarson1 · 2023-12-18T16:48:18Z

@jmlarson1 - I note the author order in the zenodo archive is different than in the paper. I'm just pointing this out in case you want to make them consistent.

Thank you for your edits. I've updated the Zenodo author order.

danielskatz · 2023-12-18T16:50:59Z

Congratulations to @jmlarson1 (Jeffrey Larson) and co-authors on your publication!!

And thanks to @jsoishi and @SergeyYakubov for reviewing, and to @jbytecode for editing!
JOSS completely depends on volunteers, and we couldn't be successful without you

editorialbot · 2023-12-18T16:51:01Z

🎉🎉🎉 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.06031/status.svg)](https://doi.org/10.21105/joss.06031)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06031">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06031/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06031/status.svg
   :target: https://doi.org/10.21105/joss.06031

This is how it will look in your documentation:

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editorialbot added Matlab Python review Shell Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Nov 7, 2023

editorialbot assigned jbytecode Nov 7, 2023

editorialbot mentioned this issue Nov 7, 2023

[PRE REVIEW]: libEnsemble: A complete Python toolkit for dynamic ensembles of calculations #6004

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Dec 18, 2023

editorialbot added accepted published Papers published in JOSS labels Dec 18, 2023

danielskatz closed this as completed Dec 18, 2023

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Open

[REVIEW]: libEnsemble: A complete Python toolkit for dynamic ensembles of calculations #6031

[REVIEW]: libEnsemble: A complete Python toolkit for dynamic ensembles of calculations #6031

Comments

editorialbot commented Nov 7, 2023 • edited Loading

Status

Reviewer instructions & questions

Checklists

editorialbot commented Nov 7, 2023

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jbytecode commented Nov 7, 2023

jsoishi commented Nov 10, 2023 • edited Loading

Review checklist for @jsoishi

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

SergeyYakubov commented Nov 12, 2023 • edited Loading

Review checklist for @SergeyYakubov

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

SergeyYakubov commented Nov 12, 2023 • edited Loading

shuds13 commented Nov 16, 2023

jbytecode commented Nov 19, 2023

SergeyYakubov commented Nov 26, 2023

jbytecode commented Nov 27, 2023

jsoishi commented Dec 6, 2023

jbytecode commented Dec 6, 2023

jsoishi commented Dec 8, 2023

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jsoishi commented Dec 11, 2023

jbytecode commented Dec 11, 2023

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editorialbot commented Nov 7, 2023 •

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jsoishi commented Nov 10, 2023 •

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SergeyYakubov commented Nov 12, 2023 •

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SergeyYakubov commented Nov 12, 2023 •

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