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[REVIEW]: BurnMan -- a Python toolkit for planetary geophysics, geochemistry and thermodynamics #5389

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editorialbot opened this issue Apr 20, 2023 · 69 comments
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accepted Jupyter Notebook published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review Shell Track: 6 (ESE) Earth Sciences and Ecology waitlisted Submissions in the JOSS backlog due to reduced service mode.

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editorialbot commented Apr 20, 2023

Submitting author: @bobmyhill (Robert Myhill)
Repository: https://github.com/geodynamics/burnman
Branch with paper.md (empty if default branch): paper
Version: v1.2.0
Editor: @jedbrown
Reviewers: @simonwmatthews, @kaylai
Archive: 10.5281/zenodo.8104293

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/b9b95117098cf85598bb01dadbe62ee2"><img src="https://joss.theoj.org/papers/b9b95117098cf85598bb01dadbe62ee2/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/b9b95117098cf85598bb01dadbe62ee2/status.svg)](https://joss.theoj.org/papers/b9b95117098cf85598bb01dadbe62ee2)

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

@simonwmatthews & @kaylai, 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 @jedbrown 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 @simonwmatthews

📝 Checklist for @kaylai

@editorialbot editorialbot added Jupyter Notebook Python review Shell Track: 6 (ESE) Earth Sciences and Ecology waitlisted Submissions in the JOSS backlog due to reduced service mode. labels Apr 20, 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=0.95 s (289.7 files/s, 114281.1 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Python                          211          10112          12535          75958
TeX                               2             97              0           1656
SQL                               1              0              0           1651
Jupyter Notebook                  8              0           3070           1087
reStructuredText                 41            467            313            531
Markdown                          6             98              0            404
Bourne Shell                      1             35              6            153
make                              1             24              5            126
YAML                              3              8              7             63
Bourne Again Shell                1             14             25             37
--------------------------------------------------------------------------------
SUM:                            275          10855          15961          81666
--------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 1654

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

OK DOIs

- 10.1016/0031-9201(81)90046-7 is OK
- 10.1111/j.1365-246X.2012.05609.x is OK
- 10.5281/zenodo.6903424 is OK
- 10.6084/m9.figshare.4865333 is OK
- 10.1029/2009GC002540 is OK
- 10.1029/2022GC010427 is OK
- 10.2138/am.2010.3354 is OK
- 10.1093/gji/ggab394 is OK
- 10.1016/S0364-5916(02)00035-4 is OK
- 10.5194/se-5-425-2014 is OK
- 10.1038/s41586-019-1483-x is OK
- 10.1016/j.pepi.2020.106552 is OK
- 10.1029/2018JE005844 is OK
- 10.1038/ngeo2898 is OK
- 10.1111/j.1365-246X.1981.tb04891.x is OK
- 10.1098/rsta.1982.0063 is OK
- 10.1080/00107510701529653 is OK
- 10.1016/0031-9201(77)90096-6 is OK
- 10.1029/96JB03270 is OK
- 10.2138/am-2003-2-307 is OK
- 10.1126/science.1233514 is OK
- 10.1111/j.1525-1314.1998.00140.x is OK
- 10.1111/j.1525-1314.2010.00923.x is OK
- 10.1111/j.1365-246X.2010.04890.x is OK
- 10.1093/petrology/egv020 is OK
- 10.1002/2013GC005122 is OK
- 10.1016/j.gca.2016.05.027 is OK
- 10.1007/s00410-017-1436-z is OK
- 10.1093/gji/ggac180 is OK
- 10.1093/gji/ggab242 is OK
- 10.1016/j.epsl.2016.11.031 is OK
- 10.1093/gji/ggu244 is OK
- 10.1007/s00410-021-01825-1 is OK
- 10.1038/s41561-019-0452-1 is OK
- 10.1126/sciadv.aar2538 is OK
- 10.1093/gji/ggx195 is OK
- 10.3847/0004-637X/819/1/32 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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

@jedbrown
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👋 @kaylai and @simonwmatthews Welcome to JOSS and thanks for agreeing to review! The comments from @editorialbot above outline the review process, which takes place in this thread (possibly with issues filed in the BurnMan repository). I'll be watching this thread if you have any questions.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention this issue so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within a month or two. Please let me know if you require some more time. We can also use editorialbot to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@jedbrown) if you have any questions/concerns.

@simonwmatthews
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simonwmatthews commented May 22, 2023

Review checklist for @simonwmatthews

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/geodynamics/burnman?
  • 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 (@bobmyhill) 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?

@kaylai
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kaylai commented May 24, 2023

Review checklist for @kaylai

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/geodynamics/burnman?
  • 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 (@bobmyhill) 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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kaylai commented May 24, 2023

@editorialbot commands

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


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# 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

# Generates a LaTeX preprint file
@editorialbot generate preprint

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

@simonwmatthews
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I have completed my review of Burnman. I recommend that Burnman should be accepted for publication following resolution of the issues I raised on the repository (which all reference this issue).

@bobmyhill
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@editorialbot generate pdf

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

@jedbrown
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jedbrown commented Jul 1, 2023

@bobmyhill Could you update the metadata for your archive so the author list matches that of the paper?

@bobmyhill
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@jedbrown Yes, sorry. Done!

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jedbrown commented Jul 1, 2023

@editorialbot set 10.5281/zenodo.8104293 as archive

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Done! archive is now 10.5281/zenodo.8104293

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jedbrown commented Jul 1, 2023

@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

- 10.1016/0031-9201(81)90046-7 is OK
- 10.1111/j.1365-246X.2012.05609.x is OK
- 10.5281/zenodo.6903424 is OK
- 10.6084/m9.figshare.4865333 is OK
- 10.1029/2009GC002540 is OK
- 10.1029/2022GC010427 is OK
- 10.2138/am.2010.3354 is OK
- 10.1016/j.epsl.2012.11.026 is OK
- 10.1093/gji/ggab394 is OK
- 10.1016/S0364-5916(02)00035-4 is OK
- 10.5194/se-5-425-2014 is OK
- 10.1038/s41586-019-1483-x is OK
- 10.1016/j.pepi.2020.106552 is OK
- 10.1029/2018JE005844 is OK
- 10.1038/ngeo2898 is OK
- 10.1111/j.1365-246X.1981.tb04891.x is OK
- 10.1098/rsta.1982.0063 is OK
- 10.1080/00107510701529653 is OK
- 10.1016/0031-9201(77)90096-6 is OK
- 10.1029/96JB03270 is OK
- 10.2138/am-2003-2-307 is OK
- 10.1126/science.1233514 is OK
- 10.1111/j.1525-1314.1998.00140.x is OK
- 10.1111/j.1525-1314.2010.00923.x is OK
- 10.1111/j.1365-246X.2010.04890.x is OK
- 10.1093/petrology/egv020 is OK
- 10.1002/2013GC005122 is OK
- 10.1016/j.gca.2016.05.027 is OK
- 10.1007/s00410-017-1436-z is OK
- 10.1093/gji/ggac180 is OK
- 10.1093/gji/ggab242 is OK
- 10.1016/j.epsl.2016.11.031 is OK
- 10.1093/gji/ggu244 is OK
- 10.1007/s00410-021-01825-1 is OK
- 10.1038/s41561-019-0452-1 is OK
- 10.1126/sciadv.aar2538 is OK
- 10.1093/gji/ggx195 is OK
- 10.3847/0004-637X/819/1/32 is OK
- 10.1007/BF00307281 is OK
- 10.48550/arXiv.1603.00943 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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⚠️ Error preparing paper acceptance. The generated XML metadata file is invalid.

Element isbn: [facet 'minLength'] The value has a length of '9'; this underruns the allowed minimum length of '10'.

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jedbrown commented Jul 1, 2023

@bobmyhill I think you can just remove that isbn from Ghiorso:1995 -- it has a DOI already and that other number is not an ISBN.

@bobmyhill
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@jedbrown Done! Thanks for checking the source of the error.

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jedbrown commented Jul 1, 2023

@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

- 10.1016/0031-9201(81)90046-7 is OK
- 10.1111/j.1365-246X.2012.05609.x is OK
- 10.5281/zenodo.6903424 is OK
- 10.6084/m9.figshare.4865333 is OK
- 10.1029/2009GC002540 is OK
- 10.1029/2022GC010427 is OK
- 10.2138/am.2010.3354 is OK
- 10.1016/j.epsl.2012.11.026 is OK
- 10.1093/gji/ggab394 is OK
- 10.1016/S0364-5916(02)00035-4 is OK
- 10.5194/se-5-425-2014 is OK
- 10.1038/s41586-019-1483-x is OK
- 10.1016/j.pepi.2020.106552 is OK
- 10.1029/2018JE005844 is OK
- 10.1038/ngeo2898 is OK
- 10.1111/j.1365-246X.1981.tb04891.x is OK
- 10.1098/rsta.1982.0063 is OK
- 10.1080/00107510701529653 is OK
- 10.1016/0031-9201(77)90096-6 is OK
- 10.1029/96JB03270 is OK
- 10.2138/am-2003-2-307 is OK
- 10.1126/science.1233514 is OK
- 10.1111/j.1525-1314.1998.00140.x is OK
- 10.1111/j.1525-1314.2010.00923.x is OK
- 10.1111/j.1365-246X.2010.04890.x is OK
- 10.1093/petrology/egv020 is OK
- 10.1002/2013GC005122 is OK
- 10.1016/j.gca.2016.05.027 is OK
- 10.1007/s00410-017-1436-z is OK
- 10.1093/gji/ggac180 is OK
- 10.1093/gji/ggab242 is OK
- 10.1016/j.epsl.2016.11.031 is OK
- 10.1093/gji/ggu244 is OK
- 10.1007/s00410-021-01825-1 is OK
- 10.1038/s41561-019-0452-1 is OK
- 10.1126/sciadv.aar2538 is OK
- 10.1093/gji/ggx195 is OK
- 10.3847/0004-637X/819/1/32 is OK
- 10.1007/BF00307281 is OK
- 10.48550/arXiv.1603.00943 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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👋 @openjournals/ese-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#4370, 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 Jul 1, 2023
@bobmyhill
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@jedbrown Brilliant, the proof looks good to me, with the exception of a couple of typos (now fixed in the paper branch).

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bobmyhill commented Jul 8, 2023

@jedbrown is this ok now? Thank you for all your efforts over the last few months :)

@kthyng
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kthyng commented Jul 11, 2023

Hi @bobmyhill! I am here to finalize the acceptance process.

  • Check that version was updated
  • Check that software archive exists, has been input to JOSS, and title and author list look good
  • Check paper

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kthyng commented Jul 11, 2023

Everything looks good so we are done!

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kthyng commented Jul 11, 2023

@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: Myhill
  given-names: Robert
  orcid: "https://orcid.org/0000-0001-9489-5236"
- family-names: Cottaar
  given-names: Sanne
  orcid: "https://orcid.org/0000-0003-0493-6570"
- family-names: Heister
  given-names: Timo
  orcid: "https://orcid.org/0000-0002-8137-3903"
- family-names: Rose
  given-names: Ian
- family-names: Unterborn
  given-names: Cayman
  orcid: "https://orcid.org/0000-0001-8991-3110"
- family-names: Dannberg
  given-names: Juliane
  orcid: "https://orcid.org/0000-0003-0357-7115"
- family-names: Gassmoeller
  given-names: Rene
  orcid: "https://orcid.org/0000-0001-7098-8198"
contact:
- family-names: Myhill
  given-names: Robert
  orcid: "https://orcid.org/0000-0001-9489-5236"
doi: 10.5281/zenodo.8104293
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Myhill
    given-names: Robert
    orcid: "https://orcid.org/0000-0001-9489-5236"
  - family-names: Cottaar
    given-names: Sanne
    orcid: "https://orcid.org/0000-0003-0493-6570"
  - family-names: Heister
    given-names: Timo
    orcid: "https://orcid.org/0000-0002-8137-3903"
  - family-names: Rose
    given-names: Ian
  - family-names: Unterborn
    given-names: Cayman
    orcid: "https://orcid.org/0000-0001-8991-3110"
  - family-names: Dannberg
    given-names: Juliane
    orcid: "https://orcid.org/0000-0003-0357-7115"
  - family-names: Gassmoeller
    given-names: Rene
    orcid: "https://orcid.org/0000-0001-7098-8198"
  date-published: 2023-07-11
  doi: 10.21105/joss.05389
  issn: 2475-9066
  issue: 87
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5389
  title: BurnMan -- a Python toolkit for planetary geophysics,
    geochemistry and thermodynamics
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05389"
  volume: 8
title: BurnMan -- a Python toolkit for planetary geophysics,
  geochemistry and thermodynamics

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.05389 joss-papers#4397
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05389
  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 Jul 11, 2023
@kthyng
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kthyng commented Jul 11, 2023

Congrats on your new publication @bobmyhill!! Many thanks to editor @jedbrown and reviewers @simonwmatthews and @kaylai for your time, hard work, and expertise!!

@kthyng kthyng closed this as completed Jul 11, 2023
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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.05389/status.svg)](https://doi.org/10.21105/joss.05389)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05389">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05389/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05389/status.svg
   :target: https://doi.org/10.21105/joss.05389

This is how it will look in your documentation:

DOI

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