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[REVIEW]: A GPU-Accelerated Open-Source Python Package for Calculating Powder Diffraction, Small-Angle-, and Total Scattering with the Debye Scattering Equation #6024

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editorialbot opened this issue Nov 6, 2023 · 74 comments
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editorialbot commented Nov 6, 2023

Submitting author: @AndySAnker (Andy Sode Anker)
Repository: https://github.com/FrederikLizakJohansen/DebyeCalculator
Branch with paper.md (empty if default branch):
Version: v1.0.7
Editor: @phibeck
Reviewers: @marcocamma, @elena-pascal, @KedoKudo
Archive: 10.5281/zenodo.10659528

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/08b1afc8d8341f95553a28dbd5cb3f09"><img src="https://joss.theoj.org/papers/08b1afc8d8341f95553a28dbd5cb3f09/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/08b1afc8d8341f95553a28dbd5cb3f09/status.svg)](https://joss.theoj.org/papers/08b1afc8d8341f95553a28dbd5cb3f09)

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

@marcocamma & @elena-pascal & @KedoKudo, 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 @phibeck 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 @elena-pascal

📝 Checklist for @KedoKudo

📝 Checklist for @marcocamma

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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:

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.08 s (403.8 files/s, 211633.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                             6              0              0           2285
Python                           8            380            355           1437
JavaScript                       6            106            120            557
YAML                             3              5             24            264
Jupyter Notebook                 2              0           9733            257
Markdown                         2             59              0            194
CSS                              1            143              3            145
TeX                              1             14              0            125
TOML                             1              2              0             39
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                            31            709          10235           5304
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 1397

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

OK DOIs

- 10.1016/c2010-0-66357-7 is OK
- 10.1107/s2053273315014473 is OK
- 10.1002/prot.24838 is OK
- 10.1107/S0108767394013292 is OK
- 10.1016/0022-4596(77)90020-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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

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elena-pascal commented Nov 7, 2023

Review checklist for @elena-pascal

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/FrederikLizakJohansen/DebyeCalculator?
  • 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 (@AndySAnker) 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?

@phibeck
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phibeck commented Nov 27, 2023

@marcocamma, @KedoKudo, @elena-pascal thanks again for reviewing! Just checking in on your review. Please let me know if you have any questions about the process. Feel free to create issues in project repository directly or write them down as comments here, but please do link the issues in this review so it's easy to follow for everyone.

@KedoKudo
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KedoKudo commented Nov 28, 2023

Review checklist for @KedoKudo

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/FrederikLizakJohansen/DebyeCalculator?
  • 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 (@AndySAnker) 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?

@KedoKudo
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@marcocamma
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@marcocamma, @KedoKudo, @elena-pascal thanks again for reviewing! Just checking in on your review. Please let me know if you have any questions about the process. Feel free to create issues in project repository directly or write them down as comments here, but please do link the issues in this review so it's easy to follow for everyone.

Thanks for the reminder ... honestly I had forgotten ... I am very sorry, I will try to speed up !

@marcocamma
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marcocamma commented Nov 28, 2023

Review checklist for @marcocamma

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/FrederikLizakJohansen/DebyeCalculator?
  • 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 (@AndySAnker) 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?

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Hello @marcocamma, here are the things you can ask me to do:


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# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

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@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

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

@marcocamma
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So I spent a bit of time working with the debyecalculator.

  • I have to say that the installation has been less straightforward that I would have hoped:
    • in none of the computer I has the right python version (so I had to install it ... that needs some time)
    • in those computers with GPU that I have access to, the NVIDIA driver was too old so I could not really test GPU implementation
    • can the author clairfy why such a tight constrain on the python version ?
    • it makes me worry that unless the package is very well maintained, it may quickly become difficult to install/use
      Here my comments on the library iteself:
  • I would improve a bit the bench-marking with a script that test
    • with/without GPU
    • structures with different sizes
    • test different batch_size
  • execution times on a decent device could be added to the script to have some reference value.
  • this script would quickly allow to test how fast the program can run on a particular device... or even test different devices to see where it might make more sense to run long calculations.
  • I am less and less fun of simple tuples as return values ... did the authors consider a named_tuple (or a dictionary instead) ?
  • last, but not least, I find that providing the input structure as CIF or XYZ file is a limitation
    • I would add the possibility of providing the input as tuple (atoms_list,xyz_array)
      • If one has thousands of structures (for example from MD simulations) that are neatly stored in a file, it would be a pity to write one file per structure just to calculate the G(r) or S(q)
    • related to the point above, would it make sense to move generate_nanoparticles as standalone utility function.
      • it could take a cif and a radius and return atom_list,xyz_position ?
  • I think it would be nice to be able to calculate the partial g(r). Of course this can be done by "filtering the inputs" (one more reasons to have non-file based atom_list,xyz_positions). But maybe g(r) could return the partial g(r) as well ?

As for the paper itself:

  • I think it would make sense to spend a bit more words on the comparison with other packages in terms of capabilities.
  • Also benchmark comparison with other software (and not only with DiffPy-CMI) would be welcomes.
  • Different softwares/papers use different definitions for G(r), S(q), etc. It is important to add what is used for this package

I wait for changes/comment before doing a second round. Keep up the good work !

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phibeck commented Feb 19, 2024

@AndySAnker here are a few more comments/suggestions for the manuscript. Please have a look when you have a moment.

  • line 12 and all other citations: please add a whitespace before references
  • line 36: I would use backticks for `DebyeCalculator`, to produce DebyeCalculator
  • line 37: similarly for xyz-files or CIF-files I would opt for .xyz files or .CIF files
  • line 45f: please insert the links to GitHub and PyPI as hyperlinks
  • line 50: citation before comma
  • line 52: perhaps link to Fig. 3 directly in Supporting Information or have a section link to SI
  • Figure 1 caption Fig 1, last line: please use a hyperlink
  • line 78: I would prefer: "Moreover, it can be installed conveniently via pip..."
  • line 78: please fix hyperlink

References:

  • line 92: Debye; missing DOI
  • line 94: Debye; missing DOI
  • line 96: Röntgenstrahlen; Annalen der Physik; missing DOI
  • line 97: Bragg
  • line 99: missing DOI
  • line 103: please correct the rendering of the material $V_{0.985}Al_{0.015}O_2$
  • line 110f: missing DOI
  • line 112f: missing DOI
  • line 114f: BCL::SAXS:; Debye; X-ray
  • line 117: Debye; missing DOI
  • line 120: missing DOI

AndySAnker added a commit to FrederikLizakJohansen/DebyeCalculator that referenced this issue Feb 19, 2024
Updated based on Editor comments in during review process:
openjournals/joss-reviews#6024 (comment)
@FrederikLizakJohansen
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@phibeck, thank you! @AndySAnker and I have gone through the points that you have raised and made the necessary adjustments to the paper.

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phibeck commented Feb 20, 2024

@editorialbot generate pdf

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

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phibeck commented Feb 20, 2024

@editorialbot check references

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

OK DOIs

- 10.1107/S2053273316015680 is OK
- 10.1002/andp.19153510606 is OK
- 10.1109/6.591665 is OK
- 10.1109/MM.2008.57 is OK
- 10.1016/c2010-0-66357-7 is OK
- 10.1107/s2053273315014473 is OK
- 10.1107/S0021889810041889 is OK
- 10.1107/S1600576715020488 is OK
- 10.1107/S1600576718000183 is OK
- 10.1107/S0021889899004860 is OK
- 10.1107/S002188989600934X is OK
- 10.1002/prot.24838 is OK
- 10.1107/S0108767394013292 is OK
- 10.1016/0022-4596(77)90020-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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phibeck commented Feb 20, 2024

@phibeck, thank you! @AndySAnker and I have gone through the points that you have raised and made the necessary adjustments to the paper.

Looks good, thanks! Seems like we're ready to hand this over to the Track Editor-in-chief!

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phibeck commented Feb 20, 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

- 10.1107/S2053273316015680 is OK
- 10.1002/andp.19153510606 is OK
- 10.1109/6.591665 is OK
- 10.1109/MM.2008.57 is OK
- 10.1016/c2010-0-66357-7 is OK
- 10.1107/s2053273315014473 is OK
- 10.1107/S0021889810041889 is OK
- 10.1107/S1600576715020488 is OK
- 10.1107/S1600576718000183 is OK
- 10.1107/S0021889899004860 is OK
- 10.1107/S002188989600934X is OK
- 10.1002/prot.24838 is OK
- 10.1107/S0108767394013292 is OK
- 10.1016/0022-4596(77)90020-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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👋 @openjournals/pe-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#5026, 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 20, 2024
@kyleniemeyer
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Hi @AndySAnker, I'm doing some final checks before publishing.

My only comment is that the reference to the NVIDIA article seems a bit off - there's no title, and normally for a web page you would add a note about when it was accessed (like note = {Accessed: 2024-02-20}.

@AndySAnker
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Hi @kyleniemeyer, that is a great point - thanks!

I have now updated the paper to state:
"With the advancements of GPUs like NVIDIA's Grace Hopper Superchip [@NVIDIA], which boasts 624GB of fast-access to memory" Instead of "576GB" which was the fast-access memory of the chip when we submitted the paper.

I have also added a title and a note to the reference, which now looks like this:
Screenshot 2024-02-20 at 17 26 00

If we add the note as suggested, it does not appear in the reference and readers would have to open the .bib file to see the note. Therefore, I have added this to the title.

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

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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: Johansen
  given-names: Frederik L.
  orcid: "https://orcid.org/0000-0002-8049-8624"
- family-names: Anker
  given-names: Andy S.
  orcid: "https://orcid.org/0000-0002-7403-6642"
- family-names: Friis-Jensen
  given-names: Ulrik
  orcid: "https://orcid.org/0000-0001-6154-1167"
- family-names: Dam
  given-names: Erik B.
  orcid: "https://orcid.org/0000-0002-8888-2524"
- family-names: Jensen
  given-names: Kirsten M. Ø.
  orcid: "https://orcid.org/0000-0003-0291-217X"
- family-names: Selvan
  given-names: Raghavendra
  orcid: "https://orcid.org/0000-0003-4302-0207"
contact:
- family-names: Johansen
  given-names: Frederik L.
  orcid: "https://orcid.org/0000-0002-8049-8624"
- family-names: Anker
  given-names: Andy S.
  orcid: "https://orcid.org/0000-0002-7403-6642"
- family-names: Jensen
  given-names: Kirsten M. Ø.
  orcid: "https://orcid.org/0000-0003-0291-217X"
- family-names: Selvan
  given-names: Raghavendra
  orcid: "https://orcid.org/0000-0003-4302-0207"
doi: 10.5281/zenodo.10659528
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Johansen
    given-names: Frederik L.
    orcid: "https://orcid.org/0000-0002-8049-8624"
  - family-names: Anker
    given-names: Andy S.
    orcid: "https://orcid.org/0000-0002-7403-6642"
  - family-names: Friis-Jensen
    given-names: Ulrik
    orcid: "https://orcid.org/0000-0001-6154-1167"
  - family-names: Dam
    given-names: Erik B.
    orcid: "https://orcid.org/0000-0002-8888-2524"
  - family-names: Jensen
    given-names: Kirsten M. Ø.
    orcid: "https://orcid.org/0000-0003-0291-217X"
  - family-names: Selvan
    given-names: Raghavendra
    orcid: "https://orcid.org/0000-0003-4302-0207"
  date-published: 2024-02-20
  doi: 10.21105/joss.06024
  issn: 2475-9066
  issue: 94
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6024
  title: A GPU-Accelerated Open-Source Python Package for Calculating
    Powder Diffraction, Small-Angle-, and Total Scattering with the
    Debye Scattering Equation
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06024"
  volume: 9
title: A GPU-Accelerated Open-Source Python Package for Calculating
  Powder Diffraction, Small-Angle-, and Total Scattering with the Debye
  Scattering Equation

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.06024 joss-papers#5028
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06024
  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 20, 2024
@kyleniemeyer
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Congratulations @AndySAnker on your article's publication in JOSS! Please consider signing up as a reviewer if you haven't already.

Many thanks to @marcocamma, @elena-pascal, and @KedoKudo for reviewing this submission, and @phibeck for editing.

@editorialbot
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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.06024/status.svg)](https://doi.org/10.21105/joss.06024)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06024">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06024/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06024/status.svg
   :target: https://doi.org/10.21105/joss.06024

This is how it will look in your documentation:

DOI

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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:

@AndySAnker
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Thank you everyone, it has been a pleasure working with you!

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