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[REVIEW]: Qiskit Dynamics: A Python package for simulating the time dynamics of quantum systems #5853

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editorialbot opened this issue Sep 18, 2023 · 64 comments
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accepted published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review Shell TeX Track: 7 (CSISM) Computer science, Information Science, and Mathematics

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editorialbot commented Sep 18, 2023

Submitting author: @DanPuzzuoli (Daniel Puzzuoli)
Repository: https://github.com/Qiskit-Extensions/qiskit-dynamics
Branch with paper.md (empty if default branch): paper
Version: 0.4.2
Editor: @danielskatz
Reviewers: @babreu-ncsa, @goerz, @hodgestar
Archive: 10.5281/zenodo.10034642

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/3cc07f787f550f53fbf9dd05e4503348"><img src="https://joss.theoj.org/papers/3cc07f787f550f53fbf9dd05e4503348/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/3cc07f787f550f53fbf9dd05e4503348/status.svg)](https://joss.theoj.org/papers/3cc07f787f550f53fbf9dd05e4503348)

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

@babreu-ncsa & @goerz & @hodgestar, 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 @danielskatz 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 @goerz

📝 Checklist for @hodgestar

📝 Checklist for @babreu-ncsa

@editorialbot editorialbot added Python review Shell TeX Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Sep 18, 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=0.28 s (554.6 files/s, 140855.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         101           6913           8093          20594
reStructuredText                26            892           1191            970
YAML                            17             12              5            507
Markdown                         8            134              0            388
TeX                              3             27              0            306
INI                              1              7              0             47
Bourne Shell                     1              8             15             12
TOML                             1              1              0              6
-------------------------------------------------------------------------------
SUM:                           158           7994           9304          22830
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 620

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

OK DOIs

- 10.1016/j.cpc.2012.11.019 is OK
- 10.1109/hpca53966.2022.00057 is OK
- 10.1103/physrevapplied.15.034080 is OK
- 10.21468/SciPostPhysCore.6.2.037 is OK
- 10.1038/s42005-022-00887-2 is OK
- 10.48550/arXiv.2110.10310 is OK
- 10.1016/j.jmr.2010.11.008 is OK
- 10.1016/j.jcp.2023.112262 is OK
- 10.1088/2058-9565/aba404 is OK
- 10.5281/zenodo.2573505 is OK
- 10.21105/joss.05329 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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

@danielskatz
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👋 @babreu-ncsa, @goerz, @hodgestar - Thanks for agreeing to review this submission.
This is the review thread for the paper. All of our communications will happen here from now on.

As you can see above, you each should use the command @editorialbot generate my checklist to create your review checklist. @editorialbot commands need to be the first thing in a new comment.

As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

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 openjournals/joss-reviews#5853 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 about 2-4 weeks. Please let me know if either of you require some more time. We can also use editorialbot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

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

@goerz
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goerz commented Sep 18, 2023

Review checklist for @goerz

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/Qiskit-Extensions/qiskit-dynamics?
  • 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 (@DanPuzzuoli) 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?

@hodgestar
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hodgestar commented Sep 27, 2023

Review checklist for @hodgestar

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/Qiskit-Extensions/qiskit-dynamics?
  • 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 (@DanPuzzuoli) 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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@babreu-ncsa - can you generate your checklist too, and at least check off the conflict of interest and code of conduct items, to make sure things are working?

@babreu-ncsa
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babreu-ncsa commented Oct 3, 2023

Review checklist for @babreu-ncsa

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/Qiskit-Extensions/qiskit-dynamics?
  • 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 (@DanPuzzuoli) 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?

@goerz
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goerz commented Oct 3, 2023

The paper and underlying software package are of exemplary quality. I have no objections to publication, up to two trivial "typo" issues in the manuscript (which is why I've left the "Quality of writing" and "References" unchecked for now).

qiskit-community/qiskit-dynamics#261
qiskit-community/qiskit-dynamics#262

Edit: The issues have been resolved, so the paper is good to go, as far as I'm concerned.

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goerz commented Oct 4, 2023

@editorialbot generate pdf

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

@danielskatz
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Thanks @goerz !

@danielskatz
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👋 @babreu-ncsa and @hodgestar - how are your reviews coming? Is there anything blocking your progress I can help with?

@babreu-ncsa
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@danielskatz thanks for the reminder. Sorry for the delay, I returned this week from back-to-back conferences. I'll get the review done within the next week.

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@editorialbot generate pdf

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

@babreu-ncsa
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babreu-ncsa commented Oct 13, 2023

There are some issues with installing the package along with JAX for OSX + Apple Silicon that may be worth a note in the Installation section of the repo's README, although they are related to JAX and not necessarily Qiskit-Dynamics... I'll let the authors decide what to do and mark the installation check box.

$ conda create --name qiskit-dynamics-jax-cpu -c conda-forge python=3.11
$ conda activate qiskit-dynamics-jax-cpu
$ pip install "qiskit-dynamics[jax]"
$ python
>>> import jax
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/babreu/opt/anaconda3/envs/qiskit-dynamics-jax-cpu/lib/python3.11/site-packages/jax/__init__.py", line 35, in <module>
    from jax import config as _config_module
  File "/Users/babreu/opt/anaconda3/envs/qiskit-dynamics-jax-cpu/lib/python3.11/site-packages/jax/config.py", line 17, in <module>
    from jax._src.config import config  # noqa: F401
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/babreu/opt/anaconda3/envs/qiskit-dynamics-jax-cpu/lib/python3.11/site-packages/jax/_src/config.py", line 25, in <module>
    from jax._src import lib
  File "/Users/babreu/opt/anaconda3/envs/qiskit-dynamics-jax-cpu/lib/python3.11/site-packages/jax/_src/lib/__init__.py", line 85, in <module>
    cpu_feature_guard.check_cpu_features()
RuntimeError: This version of jaxlib was built using AVX instructions, which your CPU and/or operating system do not support. You may be able work around this issue by building jaxlib from source.
$ system_profiler SPSoftwareDataType
Software:

    System Software Overview:

      System Version: macOS 13.6 (22G120)
      Kernel Version: Darwin 22.6.0
$ system_profiler SPHardwareDataType
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Model Number: Z14W0010BLL/A
      Chip: Apple M1 Max

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babreu-ncsa commented Oct 13, 2023

There is just one thing blocking me from completing the review (everything else is great and I'm able to reproduce what's in the tutorials):

Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?

I see there are tests in the repository (https://github.com/Qiskit-Extensions/qiskit-dynamics/tree/main/test), but it's not clear to me when these are run and if they can be triggered manually by the user. (I don't mean to be lengthy in this thread but also don't think this is worth opening an issue).

@goerz
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goerz commented Oct 13, 2023

@babreu-ncsa They do run automatically via the main.yml workflow.

You can run them locally using tox (running more or less the same commands as in the main.yml). I've done this on my laptop, and the tests pass.

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@editorialbot check references

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

OK DOIs

- 10.1016/j.cpc.2012.11.019 is OK
- 10.1109/hpca53966.2022.00057 is OK
- 10.1103/physrevapplied.15.034080 is OK
- 10.21468/SciPostPhysCore.6.2.037 is OK
- 10.1038/s42005-022-00887-2 is OK
- 10.48550/arXiv.2110.10310 is OK
- 10.1016/j.jmr.2010.11.008 is OK
- 10.1016/j.jcp.2023.112262 is OK
- 10.1088/2058-9565/aba404 is OK
- 10.5281/zenodo.2573505 is OK
- 10.21105/joss.05329 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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

@danielskatz
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@DanPuzzuoli - I've suggested some minor changes in qiskit-community/qiskit-dynamics#276 Please merge this, or let me know what you disagree with, then we can proceed to acceptance and publication.

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@editorialbot recommend-accept

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Paper is not ready for acceptance yet, the archive is missing

@danielskatz
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@DanPuzzuoli - At this point could you:

  • Make a tagged release of your software, and list the version tag of the archived version here.
  • Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
  • Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
  • Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

@DanPuzzuoli
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@goerz @hodgestar @babreu-ncsa thank you for your reviews, and thank you @danielskatz for editing!

@danielskatz I plan to make a minor change to documentation based on a suggestion by @hodgestar here that was not a blocker on their review. Aside from this, there will have been no changes made based on the reviews. Is it okay if I just stick with the latest tagged version for the archiving (0.4.2, which is what the reviewers used for review) and have this change included in the next natural release? I wouldn't normally make a new release solely for a change like this, and it'd be nice to conclude the process for the paper.

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yes, that's fine

@babreu-ncsa
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@DanPuzzuoli thanks for writing good software and making it open-source :)

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@danielskatz

  • The version tag of the reviewed software is 0.4.2
  • DOI for the zenodo archive of the above version: 10.5281/zenodo.10034642 - I've edited the title and author list to match the paper.

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@editorialbot set 0.4.2 as version

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Done! version is now 0.4.2

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@editorialbot set 10.5281/zenodo.10034642 as archive

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Done! archive is now 10.5281/zenodo.10034642

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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

- 10.1016/j.cpc.2012.11.019 is OK
- 10.1109/hpca53966.2022.00057 is OK
- 10.1103/physrevapplied.15.034080 is OK
- 10.21468/SciPostPhysCore.6.2.037 is OK
- 10.1038/s42005-022-00887-2 is OK
- 10.48550/arXiv.2110.10310 is OK
- 10.1016/j.jmr.2010.11.008 is OK
- 10.1016/j.jcp.2023.112262 is OK
- 10.1088/2058-9565/aba404 is OK
- 10.5281/zenodo.2573505 is OK
- 10.21105/joss.05329 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#4719, 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 Oct 24, 2023
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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: Puzzuoli
  given-names: Daniel
- family-names: Wood
  given-names: Christopher J.
- family-names: Egger
  given-names: Daniel J.
- family-names: Rosand
  given-names: Benjamin
- family-names: Ueda
  given-names: Kento
contact:
- family-names: Puzzuoli
  given-names: Daniel
doi: 10.5281/zenodo.10034642
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Puzzuoli
    given-names: Daniel
  - family-names: Wood
    given-names: Christopher J.
  - family-names: Egger
    given-names: Daniel J.
  - family-names: Rosand
    given-names: Benjamin
  - family-names: Ueda
    given-names: Kento
  date-published: 2023-10-24
  doi: 10.21105/joss.05853
  issn: 2475-9066
  issue: 90
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5853
  title: "Qiskit Dynamics: A Python package for simulating the time
    dynamics of quantum systems"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05853"
  volume: 8
title: "Qiskit Dynamics: A Python package for simulating the time
  dynamics of quantum systems"

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.05853 joss-papers#4720
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05853
  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 Oct 24, 2023
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Congratulations to @DanPuzzuoli (Daniel Puzzuoli) and co-authors on your publication!!

And thanks to @babreu-ncsa, @goerz, and @hodgestar for reviewing!
JOSS depends on volunteers and couldn't be successful without you

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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.05853/status.svg)](https://doi.org/10.21105/joss.05853)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05853">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05853/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05853/status.svg
   :target: https://doi.org/10.21105/joss.05853

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