[REVIEW]: 'HallThruster.jl: a Julia package for 1D Hall thruster discharge simulation'

[editorialbot]

Submitting author: !--author-handle-->@archermarx<!--end-author-handle-- (Thomas Marks) Repository: https://github.com/UM-PEPL/HallThruster.jl Branch with paper.md (empty if default branch): Version: v0.8.3 Editor: !--editor-->@lucydot<!--end-editor-- Reviewers: @Rupali-Sahu, @TomGoffrey, @lucydot Archive: 10.5281/zenodo.8066246

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/ce9cb7aa54df10d69ed248912e584f53"><img src="https://joss.theoj.org/papers/ce9cb7aa54df10d69ed248912e584f53/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/ce9cb7aa54df10d69ed248912e584f53/status.svg)](https://joss.theoj.org/papers/ce9cb7aa54df10d69ed248912e584f53)

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

@StanczakDominik & @Rupali-Sahu, 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 @lucydot 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 @Rupali-Sahu

📝 Checklist for @TomGoffrey

📝 Checklist for @lucydot

[archermarx]

Here are some other people i found in the JOSS list of reviewers that may be suitable

benjaminbolling rangsimanketkaew pkairys amorenobr p-ortmann TomGoffrey joglekara CFGrote sigvaldm rogeriojorge michaeltouati akaptano OsAmaro hasantahir

[lucydot]

@akaptano @hasantahir @OsAmaro - are any of you available to review this repo? Review has been underway for a while: one reviewer has finished but we really need another set of eyes on it. Please let me know if you have capacity to help!

[hasantahir]

Hi @lucydot

Sorry. I am starting teaching next week so can't commit. All the best to this repo!

[lucydot]

@sigvaldm, @rogeriojorge, @michaeltouati - are any of you available to review this repo? Review has been underway for a while: one reviewer has finished but we really need another set of eyes on it. Please let me know if you have capacity to help!

[lucydot]

@TomGoffrey @joglekara - are either of you available to review this repo? Review has been underway for a while: one reviewer has finished but we really need another set of eyes on it. Please let me know if you have capacity to help!

[TomGoffrey]

@lucydot I could probably take a look, but won't be able to do so for a few weeks. Would this work?

[joglekara]

Happy to take it on but I’m away for a couple of weeks

On Sun, Mar 5, 2023 at 1:43 PM Tom Goffrey @.***> wrote:

@lucydot https://github.com/lucydot I could probably take a look, but won't be able to do so for a few weeks. Would this work?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4672#issuecomment-1455215442, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADGQZ7TVGYJHKBDICWLOUCLW2UCGHANCNFSM56I255IA . You are receiving this because you were mentioned.Message ID: @.***>

[rogeriojorge]

Hi,

Thank you for reaching out. Although the repository appears intriguing, unfortunately I am presently unavailable for a review. I anticipate having more availability in the future.

Best, Rogerio

On 28 Feb 2023, at 15:08, Lucy Whalley @.***> wrote:

@sigvaldm https://github.com/sigvaldm, @rogeriojorge https://github.com/rogeriojorge, @michaeltouati https://github.com/michaeltouati - are any of you available to review this repo? Review has been underway for a while: one reviewer has finished but we really need another set of eyes on it. Please let me know if you have capacity to help!

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4672#issuecomment-1448351670, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABUAHSAKRVI7WJWBKJZ7JI3WZYIHBANCNFSM56I255IA. You are receiving this because you were mentioned.

[lucydot]

@TomGoffrey thank-you very much. Does a timeline where we aim to complete the review in 4-6 weeks work for you?

[TomGoffrey]

@lucydot Should be fine - I'm back at work late next week, but feel free to start the review process now.

[lucydot]

@TomGoffrey thats great. I'll add you as a reviewer. The review has already been underway for quite some time - however originally assigned reviewer is unavailable, so we need another set of eyes on it. Thank you for stepping in. The first step will be to generate a checklist with @editorialbot generate my checklist.

[lucydot]

@editorialbot add @TomGoffrey as reviewer

[editorialbot]

@TomGoffrey added to the reviewers list!

[lucydot]

@editorialbot remove @StanczakDominik as reviewer

[editorialbot]

@StanczakDominik removed from the reviewers list!

[TomGoffrey]

Review checklist for @TomGoffrey

Conflict of interest

• [x] 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

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the https://github.com/UM-PEPL/HallThruster.jl?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@archermarx) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• [x] 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.
• [x] 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

• [x] Installation: Does installation proceed as outlined in the documentation?
• [ ] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] 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).
• [x] 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?
• [x] 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?
• [x] 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?

[lucydot]

Hi @TomGoffrey a friendly reminder/prompt for your review ✅

[TomGoffrey]

Hi @TomGoffrey a friendly reminder/prompt for your review ✅

Sorry for the delay, managed to catch covid on my flight home so my return to work has been a bit delayed, getting started on the review today!

[TomGoffrey]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[archermarx]

Hi, just checking in to see if there have been any updates on this. Thanks!

[lucydot]

@TomGoffrey - just to echo @archermarx comment above, any updates on your review would be much appreciated.

[lucydot]

Hi @TomGoffrey I can see from tickboxes you are quite far through the review process ✅ - a prompt to please complete the review when possible and update us here.

[lucydot]

A note here that I have contacted @TomGoffrey via email - I know how easy it is to miss those github mentions!

[archermarx]

@TomGoffrey Another ping. Hopefully we can finish this up soon!

[lucydot]

Oh dear we really are having a tough time with this review process.

As it has already been signed off by one reviewer working in the field, and most of the review is complete by a second person in the field, I will ask the editorial team if I (or someone else in the editorial team) can complete the outstanding parts.

[lucydot]

In the meantime @TomGoffrey if you do have time to complete the review, that would be the preferred option.

[lucydot]

ok @archermarx I have been given the go-ahead to review myself, given that we have one person from the field that has already signed off, and one half-complete review.

I am a little snowed under with other review commitments at the moment, but I will aim to get this done in the next 2-3 weeks.

In the meantime @TomGoffrey if you are able to finish your review that would be the strongly preferred option.

[archermarx]

Thanks Lucy. Hopefully we can finally wrap this up.

[lucydot]

@editorialbot add @lucydot as reviewer

[editorialbot]

@lucydot added to the reviewers list!

[lucydot]

Review checklist for @lucydot

Conflict of interest

• [x] 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

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the https://github.com/UM-PEPL/HallThruster.jl?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@archermarx) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• [x] 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.
• [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• [x] 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

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [x] 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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] 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?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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?

[lucydot]

@editorialbot generate pdf

[lucydot]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1063/5.0021474 is OK
- 10.2514/6.2001-3505 is OK
- 10.1088/1361-6595/ab0f70 is OK
- 10.1063/1.368529 is OK
- 10.1063/1.1371519 is OK
- 10.1088/0963-0252/14/4/011 is OK
- 10.1063/1.5055750 is OK
- 10.1002/9780470436448.ch7 is OK
- 10.1063/1.4972269 is OK
- 10.1145/3511528.3511535 is OK
- 10.1137/141000671 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[lucydot]

Hi @archermarx I've just started working through the checklist.

• I couldn't find guidelines for "Report issues or problems with the software" or "Seek support". This could be fixed with a couple of sentences on the "Home" page of your documentation, for example.
• Link to tutorial from the README is broken
• PR with very small update to install instruction here: https://github.com/UM-PEPL/HallThruster.jl/pull/83 (tested on Julia 1.9)

[lucydot]

Paper:

• should one-dimensional fluid code be one-dimensional fluid dynamics code?
• you should be able to place the list of references on page 2 into a single bracket: [@boeuf1998; @ahedo2001; @haraquasineutralfluid; @sahu_ffm; @mikellides_1D]
• .(Thomas, 1949) --> (Thomas, 1949)(additional period removed)
• The Landmark 1D fluid test case weblink is broken (in reference list). Please be sure to use correct citation syntax.
• I think Gowda et al has now been peer reviewed+published (currently referencing the arxiv paper)

[lucydot]

Tutorials:

• I had to add show=true when using plot! within a user-defined function. For example, in the tutorial function plot_current: plot!(p, t_ms, ion_current, label = "Ion current (cathode)") -->plot!(p, t_ms, ion_current, label = "Ion current (cathode)",show=true)` (would also need updating at other places).

It may be that your system is setup to output plot as default. I am using a fresh install of Julia and IJulia. May catch others out so may be worth making a note of behaviour if don't want to add additional keyword argument to every plot call (which does feel clunky way to handle).

• There are some warnings towards the end of the tutorial. Is this acceptable? May be worth making a note if so, or fix if not.

[archermarx]

Hi Lucy! Thanks for taking the time to review. I can respond to your comments here:

Paper:

* should `one-dimensional fluid code` be `one-dimensional fluid dynamics code`?

In this case, no. Fluid is used here in contrast to kinetic or particle-in-cell. To clarify, I have changed the sentence to "...one dimensional fluid Hall thruster code".

* you should be able to place the list of references on page 2 into a single bracket: `[@boeuf1998; @ahedo2001; @haraquasineutralfluid; @sahu_ffm; @mikellides_1D]`

* `.(Thomas, 1949)` --> ` (Thomas, 1949)`(additional period removed)

* The `Landmark 1D fluid test case` weblink is broken (in reference list). Please be sure to use correct [citation syntax](https://pandoc.org/MANUAL.html#extension-citations).

* I think Gowda et al has now been peer reviewed+published (currently referencing the arxiv paper)

Thanks for these notes on the references. I have updated the links.

[archermarx]

Hi @archermarx I've just started working through the checklist.

* I couldn't find guidelines for "Report issues or problems with the software" or "Seek support". This could be fixed with a couple of sentences on the "Home" page of your documentation, for example.

* Link to tutorial from the README is broken

* PR with very small update to install instruction here: [Update installation instructions UM-PEPL/HallThruster.jl#83](https://github.com/UM-PEPL/HallThruster.jl/pull/83) (tested on Julia 1.9)

Thanks for catching this! I've accepted your PR and made the relevant changes.

Tutorials:

* I had to add `show=true` when using `plot!` within a user-defined function. For example, in the tutorial function `plot_current`: `plot!(p, t_ms, ion_current, label = "Ion current (cathode)") --> `plot!(p, t_ms, ion_current, label = "Ion current (cathode)",show=true)` (would also need updating at other places).

It may be that your system is setup to output plot as default. I am using a fresh install of Julia and IJulia. May catch others out so may be worth making a note of behaviour if don't want to add additional keyword argument to every plot call (which does feel clunky way to handle).

* There are some warnings towards the end of the tutorial. Is this acceptable? May be worth making a note if so, or fix if not.

Thanks for this. I added a note about the warnings to the tutorial and changed the plot parts of the tutorial to explicitly call display.

[archermarx]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[archermarx]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1063/5.0021474 is OK
- 10.2514/6.2001-3505 is OK
- 10.1088/1361-6595/ab0f70 is OK
- 10.1063/1.368529 is OK
- 10.1063/1.1371519 is OK
- 10.1088/0963-0252/14/4/011 is OK
- 10.1063/1.5055750 is OK
- 10.1002/9780470436448.ch7 is OK
- 10.1063/1.4972269 is OK
- 10.1145/3511528.3511535 is OK
- 10.1137/141000671 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[archermarx]

Thanks editorialbot!

[lucydot]

Hi @archermarx - my previous PR missed an @ sign in the citation list, I think this caused it not to format correctly. Just put in a PR that fixes. Can you merge? https://github.com/UM-PEPL/HallThruster.jl/pull/84

[lucydot]

That is my review complete! Now back into editor-mode.

[lucydot]

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

• [x] Double check authors and affiliations (including ORCIDs)
• [x] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
• [x] Archive the release on Zenodo/figshare/etc and post the DOI here.
• [x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• [x] Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

• [x] Read the text of the paper and offer comments/corrections (as either a list or a PR)
• [x] Check the references in the paper for corrections (e.g. capitalization)
• [x] Check that the archive title, author list, version tag, and the license are correct
• [x] Set archive DOI with @editorialbot set <DOI here> as archive
• [x] Set version with @editorialbot set <version here> as version
• [x] Double check rendering of paper with @editorialbot generate pdf
• [x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
• [ ] Recommend acceptance with @editorialbot recommend-accept

[lucydot]

@archermarx please can you work through the checklist above? You won't be able to tick them off; just let me know when they are complete in this thread.