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[REVIEW]: Melissa: coordinating large-scale ensemble runs for deep learning and sensitivity analyses #5291

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editorialbot opened this issue Mar 22, 2023 · 83 comments
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accepted C CMake Dockerfile published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. review Track: 7 (CSISM) Computer science, Information Science, and Mathematics

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editorialbot commented Mar 22, 2023

Submitting author: @robcaulk (Robert Caulk)
Repository: https://gitlab.inria.fr/melissa/melissa
Branch with paper.md (empty if default branch): JOSS-paper
Version: JOSS_v2
Editor: @diehlpk
Reviewers: @acrlakshman, @NoujoudNader
Archive: 10.5281/zenodo.8046630

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/9da8b88c8ea947557b3ac144e909ac0b"><img src="https://joss.theoj.org/papers/9da8b88c8ea947557b3ac144e909ac0b/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/9da8b88c8ea947557b3ac144e909ac0b/status.svg)](https://joss.theoj.org/papers/9da8b88c8ea947557b3ac144e909ac0b)

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

@acrlakshman & @NoujoudNader, 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 @diehlpk 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 @acrlakshman

📝 Checklist for @NoujoudNader

@editorialbot editorialbot added C CMake Dockerfile review Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Mar 22, 2023
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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=0.34 s (441.6 files/s, 79552.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          76           1993           2269           8309
SVG                              5              3              4           4462
C                                7            286            603           2247
Markdown                        24            633              0           1683
JSON                             9              0              0            534
Jupyter Notebook                 1              0            948            383
Fortran 90                       3            121             80            350
TeX                              2             49              0            345
C/C++ Header                     6            101            113            256
CMake                            7             72            144            249
YAML                             2             16              5            211
Dockerfile                       1             12              5             41
Fortran 77                       1              9             15             38
Bourne Shell                     3             30             17             20
TOML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                           148           3325           4203          19131
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 1714

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

OK DOIs

- 10.1109/SC41405.2020.00005 is OK
- 10.1007/978-3-030-81627-8_6 is OK
- 10.1109/CLUSTER.2012.26 is OK
- 10.1145/1851476.1851481 is OK
- 10.1145/3426462.3426468 is OK
- 10.1177/10943420221110507 is OK
- 10.1115/1.4046020 is OK
- 10.1145/3281464.3281470 is OK
- 10.1109/CLUSTER51413.2022.00051 is OK
- 10.1109/TPDS.2021.3105994 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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

@acrlakshman
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acrlakshman commented Mar 22, 2023

Review checklist for @acrlakshman

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://gitlab.inria.fr/melissa/melissa?
  • 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 (@robcaulk) 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?

@robcaulk
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Thank you @acrlakshman and @NoujoudNader for accepting the review :-)

While we are available for any questions you may have (here or in our Melissa discourse https://melissa.discourse.group/ ), I’d like to help you test the code as efficiently as possible. If you do not have a supercomputer that you can install Melissa on, it is OK, Melissa can be run locally as well :-).

https://melissa.gitlabpages.inria.fr/melissa/first-dl-study/

this tutorial is executed locally with MPI, and our CI runs the same example with only 3 cores required.

On the other hand, if you have access to a supercomputer, we have templates for OAR and Slurm schedulers:

https://gitlab.inria.fr/melissa/melissa/-/tree/develop/examples/heat-pde/heat-pde-dl

Most of this will be repeated in the documentation but I just wanted to make sure you knew that a supercomputer is great (it’s the target usecase for sure) but not required for running/testing/debugging Melissa machinery.

Thanks again and do not hesitate to reach out during your review!

@NoujoudNader
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NoujoudNader commented Mar 23, 2023

Review checklist for @NoujoudNader

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://gitlab.inria.fr/melissa/melissa?
  • 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 (@robcaulk) 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?

@danielskatz
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@diehlpk - How is this review coming along? The progress appears somewhat slow.

@diehlpk
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diehlpk commented Apr 20, 2023

Hi @acrlakshman, @NoujoudNader how is your review going?

@diehlpk
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diehlpk commented Apr 20, 2023

@diehlpk - How is this review coming along? The progress appears somewhat slow.

Just checked in with the reviewers.

@acrlakshman
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Hi @acrlakshman, @NoujoudNader how is your review going?

Hi, sorry for the delay. This slipped my calendar, shall get back to this over the weekend.

@NoujoudNader
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@editorialbot generate pdf

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

@NoujoudNader
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NoujoudNader commented Apr 24, 2023

Hey,
@diehlpk thanks for inviting me to review this work.
@robcaulk Melissa is well built and the paper explain very well the work. I intalled Melissa on Ubunto and everything went well. However, i tried to install it also localy on windows and macos M1. This step was hard, and confusing. I wish if you can add explicit installation guide for mac and windows (https://melissa.gitlabpages.inria.fr/melissa/install/).

Thank you
Noujoud

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diehlpk commented Apr 26, 2023

Hi @acrlakshman how is your review going?

@diehlpk
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diehlpk commented Apr 26, 2023

Hey, @diehlpk thanks for inviting me to review this work. @robcaulk Melissa is well built and the paper explain very well the work. I intalled Melissa on Ubunto and everything went well. However, i tried to install it also localy on windows and macos M1. This step was hard, and confusing. I wish if you can add explicit installation guide for mac and windows (https://melissa.gitlabpages.inria.fr/melissa/install/).

Thank you Noujoud

@robcaulk would it be possible to add instructions for Windows and Mac OS?

Or mention that you are not supporting these?

@robcaulk
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Hey, @diehlpk thanks for inviting me to review this work. @robcaulk Melissa is well built and the paper explain very well the work. I intalled Melissa on Ubunto and everything went well. However, i tried to install it also localy on windows and macos M1. This step was hard, and confusing. I wish if you can add explicit installation guide for mac and windows (https://melissa.gitlabpages.inria.fr/melissa/install/).
Thank you Noujoud

@robcaulk would it be possible to add instructions for Windows and Mac OS?

Or mention that you are not supporting these?

Hey @diehlpk , yes, I have created the PR for warning users against Windows and MacOS here.

I am also working on making a pre built docker image available for these Windows/Mac users - I hope to have that completed in the near future. I will update here if we are successful distributing it properly and adding usage instructions :-).

@diehlpk
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diehlpk commented May 2, 2023

Hi @acrlakshman how is your review going?

@acrlakshman
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Hi @acrlakshman how is your review going?

Sorry for the delay @diehlpk . I shall get back to this, over the remaining part of this week.

@acrlakshman
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Doing some final tests, faced some issues while running heat-pde example on Ubuntu docker image. Shall update soon.

@robcaulk
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robcaulk commented May 8, 2023

Hello,

The docker solution is still not fully supported beyond our CI. But we do, however, fully support running an LXD container. We have a tutorial for installation and running LXD here: https://melissa.gitlabpages.inria.fr/melissa/virtual-cluster/

I hope it helps,

Robert

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diehlpk commented May 9, 2023

@acrlakshman could you please have a look?

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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

- 10.1109/SC41405.2020.00005 is OK
- 10.1007/978-3-030-81627-8_6 is OK
- 10.1109/CLUSTER.2012.26 is OK
- 10.1145/1851476.1851481 is OK
- 10.1145/3426462.3426468 is OK
- 10.1177/10943420221110507 is OK
- 10.1115/1.4046020 is OK
- 10.1145/3281464.3281470 is OK
- 10.1109/CLUSTER51413.2022.00051 is OK
- 10.1109/TPDS.2021.3105994 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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👋 @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#4318, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@robcaulk
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Looks great to me.

@danielskatz
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@robcaulk - I was going to make a PR to suggest some text changes in the paper, but I can't make a PR to the repo without getting an account from an INRIA member, it says. I think this goes against JOSS requirements, at least in spirit (see https://joss.readthedocs.io/en/latest/submitting.html). How would users make PRs/contributions to the code if they are not at INRIA?

@danielskatz
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Since I can't make a PR, here is an updated paper.md with my suggested changes.
paper.md

@danielskatz
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Also, here's an updated paper.bib with some more minor changes (except github won't let me upload a .bib extension, so I've added an extra .md extension that you can remove...
paper.bib.md

@robcaulk
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robcaulk commented Jun 16, 2023

@robcaulk - I was going to make a PR to suggest some text changes in the paper, but I can't make a PR to the repo without getting an account from an INRIA member, it says. I think this goes against JOSS requirements, at least in spirit (see https://joss.readthedocs.io/en/latest/submitting.html). How would users make PRs/contributions to the code if they are not at INRIA?

You are right that it is a frustrating hurdle for a user who wants to quickly submit a PR. However, we do encourage users to contact us for a free account with the following instructions here. We use this same approach for another software, SPAM, which we published on JOSS a few years back. Both projects, SPAM and Melissa are institutional softwares which means they benefit from living on the institutional gitlab servers (where the runners and storage are free and supporting the open-source nature of the project).

In an effort to make it even easier to report issues, at Melissa we have the discourse which does not require any permissions to log in and report issues or discuss enhancements.

I would be happy to make you an account on the INRIA gitlab if you would like to share your email (you can privately message me at if this is an avenue you wish to follow).

Otherwise, I am happy to incorporate the changes you provided here directly into the JOSS branch.

@danielskatz
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I guess that's meeting the strict requirements for JOSS...

Please go ahead and check my changes, and either merge them or let me know what you disagree with.

@robcaulk
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Thanks for those improvements @danielskatz - here is the MR:

https://gitlab.inria.fr/melissa/melissa/-/merge_requests/130

I believe this means I should tag a new version JOSS_v3 and update the sources + DOI on zenodo, right?

@danielskatz
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No, we don't even need the paper source in the repo, as we archive the PDF generated from it separately. Though you can if you want to.

@robcaulk
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Great, I just merged in edits, so we can have the bot rebuild the PDF.

@danielskatz
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@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

- 10.1109/SC41405.2020.00005 is OK
- 10.1007/978-3-030-81627-8_6 is OK
- 10.1109/CLUSTER.2012.26 is OK
- 10.1145/1851476.1851481 is OK
- 10.1145/3426462.3426468 is OK
- 10.1177/10943420221110507 is OK
- 10.1115/1.4046020 is OK
- 10.1145/3281464.3281470 is OK
- 10.1109/CLUSTER51413.2022.00051 is OK
- 10.1109/TPDS.2021.3105994 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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👋 @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#4319, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@danielskatz
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@robcaulk - please take a look at this and make sure you are ok with it - I will do the same

@robcaulk
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looks good to me :)

@danielskatz
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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: Schouler
  given-names: Marc
  orcid: "https://orcid.org/0000-0002-3708-4135"
- family-names: Caulk
  given-names: Robert Alexander
  orcid: "https://orcid.org/0000-0001-5618-8629"
- family-names: Meyer
  given-names: Lucas
  orcid: "https://orcid.org/0000-0001-5386-5997"
- family-names: Terraz
  given-names: Théophile
- family-names: Conrads
  given-names: Christoph
- family-names: Friedemann
  given-names: Sebastian
- family-names: Agarwal
  given-names: Achal
  orcid: "https://orcid.org/0000-0002-3216-4769"
- family-names: Baldonado
  given-names: Juan Manuel
- family-names: Pogodziński
  given-names: Bartłomiej
- family-names: Sekuła
  given-names: Anna
  orcid: "https://orcid.org/0000-0003-3524-3160"
- family-names: Ribes
  given-names: Alejandro
- family-names: Raffin
  given-names: Bruno
doi: 10.5281/zenodo.8046630
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Schouler
    given-names: Marc
    orcid: "https://orcid.org/0000-0002-3708-4135"
  - family-names: Caulk
    given-names: Robert Alexander
    orcid: "https://orcid.org/0000-0001-5618-8629"
  - family-names: Meyer
    given-names: Lucas
    orcid: "https://orcid.org/0000-0001-5386-5997"
  - family-names: Terraz
    given-names: Théophile
  - family-names: Conrads
    given-names: Christoph
  - family-names: Friedemann
    given-names: Sebastian
  - family-names: Agarwal
    given-names: Achal
    orcid: "https://orcid.org/0000-0002-3216-4769"
  - family-names: Baldonado
    given-names: Juan Manuel
  - family-names: Pogodziński
    given-names: Bartłomiej
  - family-names: Sekuła
    given-names: Anna
    orcid: "https://orcid.org/0000-0003-3524-3160"
  - family-names: Ribes
    given-names: Alejandro
  - family-names: Raffin
    given-names: Bruno
  date-published: 2023-06-16
  doi: 10.21105/joss.05291
  issn: 2475-9066
  issue: 86
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5291
  title: "Melissa: coordinating large-scale ensemble runs for deep
    learning and sensitivity analyses"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05291"
  volume: 8
title: "`Melissa`: coordinating large-scale ensemble runs for deep
  learning and sensitivity analyses"

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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🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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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.05291 joss-papers#4320
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05291
  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 Jun 16, 2023
@danielskatz
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Congratulations to @robcaulk (Robert Caulk) and co-authors on your JOSS publication!!

And thanks to @acrlakshman and @NoujoudNader for reviewing, and to @diehlpk for editing.
JOSS couldn't be successful without lots of volunteer effort, including yours!

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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.05291/status.svg)](https://doi.org/10.21105/joss.05291)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05291">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05291/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05291/status.svg
   :target: https://doi.org/10.21105/joss.05291

This is how it will look in your documentation:

DOI

We need your help!

The 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:

@robcaulk
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Thanks @danielskatz @diehlpk @acrlakshman and @NoujoudNader for all your help on reviewing and publishing this paper!

The badge looks pretty, we will add it to our README/doc :-)

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