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[REVIEW]: nudustc++: C++ Code for Modeling Dust Nucleation and Destruction in Gaseous Sysytems
Submitting author: @sarahstangl-lanl (Sarah Stangl) Repository: https://github.com/lanl/nuDustC Branch with paper.md (empty if default branch): Version: v1.0.0 Editor: @plaplant Reviewers: @guadabsb15, @steven-murray Archive: Pending
Status
Status badge code:
HTML: <a href="https://joss.theoj.org/papers/ea89ab59edf606e5a26f26c5170cc506"><img src="https://joss.theoj.org/papers/ea89ab59edf606e5a26f26c5170cc506/status.svg"></a>
Markdown: [](https://joss.theoj.org/papers/ea89ab59edf606e5a26f26c5170cc506)
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
@guadabsb15 & @steven-murray, 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 @plaplant 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 @steven-murray
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
Software report:
github.com/AlDanial/cloc v 1.90 T=0.03 s (1265.7 files/s, 294666.0 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
JSON 2 1 0 3676
C++ 7 193 249 1564
C/C++ Header 15 191 166 765
Markdown 2 96 0 178
TeX 1 12 2 164
CMake 1 23 6 98
INI 2 0 0 34
Python 1 9 1 20
YAML 1 0 0 2
-------------------------------------------------------------------------------
SUM: 32 525 424 6501
-------------------------------------------------------------------------------
Commit count by author:
51 Sarah Stangl (sarahstangl, stang277)
41 Sarah Stangl (sarahstangl-lanl, stang277)
6 Christopher Mauney
3 Sarah Marie Stangl
3 Sarah Marie Stangl - 329726
1 Sarah Stangl
Paper file info:
📄 Wordcount for paper.md is 0
✅ The paper includes a Statement of need section
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1146/annurev.astro.41.011802.094840 is OK
- 10.1111/j.1365-2966.2007.11829.x is OK
- 10.1046/j.1365-8711.2001.04486.x is OK
- 10.1086/379011 is OK
- 10.1086/505639 is OK
- 10.3847/1538-4357/ac57c3 is OK
- 10.3847/1538-4357/ac7d58 is OK
MISSING DOIs
- No DOI given, and none found for title: Astrochem: Abundances of chemical species in the i...
- 10.1143/ptp.77.1402 may be a valid DOI for title: Grain formation through nucleation process in astr...
- 10.3847/1538-4357/acf5e3 may be a valid DOI for title: Dust Coagulation in Oxygen-rich Circumstellar Outf...
- No DOI given, and none found for title: Kinetic Nucleation Theory and Thermal Fluctuations...
- No DOI given, and none found for title: StarChem
INVALID DOIs
- None
License info:
✅ License found: BSD 3-Clause "New" or "Revised" License (Valid open source OSI approved license)
@guadabsb15 @steven-murray thank you again for agreeing to review this submission! When you get a chance, please comment in this thread:
@editorialbot generate my checklist
Then you can go through the checklist items, and make issues on the upstream repo for any changes you recommend. Let me know if you have any questions!
@sarahstangl-lanl it seems like there are still some issues with rendering the PDF, which I think are related to the figure referencing issue I mentioned in the pre-review thread. When you get a chance, please try to update the paper so that the PDF renders correctly, as reviewing the paper is something the reviewers are required to do.
Also, some of the DOIs in the paper references are missing or do not resolve appropriately. See the comment here for a list of references with issues. If you have questions about how to resolve these issues, please let me know.
Review checklist for @guadabsb15
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/lanl/nuDustC?
- [x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
- [x] Contribution and authorship: Has the submitting author (@sarahstangl-lanl) 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?
- [ ] 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?
Review checklist for @steven-murray
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/lanl/nuDustC?
- [x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
- [x] Contribution and authorship: Has the submitting author (@sarahstangl-lanl) 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
- [ ] 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?
- [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
- [ ] 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?
Hi @sarahstangl-lanl, I've tried a first-pass through the checklist, and I have left a couple of issues on the repo (see above). I can't move forward without at least issue number 3 being solved, and it would be great to get a copy of the paper itself to review!
Is number 3 the "reproducibility" from the checklist? I added a pdf version of the paper: https://github.com/lanl/nuDustC/blob/main/joss_nudustc.pdf
What is the issue with rendering the image in the paper? It comes up for me using markdown.
@sarahstangl-lanl I was referring to https://github.com/lanl/nuDustC/issues/3 on your repo.
Thanks for the PDF!
@sarahstangl-lanl it would be good if the paper could be generated in the JOSS style as well.
@sarahstangl-lanl it looks like there is a paper.md file both in the top-level of the directory, as well as inside of the JOSS Paper directory. In addition to duplicating the paper content (which we should probably avoid), it seems like the space in the directory name is what is causing the paper generation to fail. Would you be able to reorganize the repo so that there is only a single copy of the paper.md file? And if it's in a directory, please rename the directory so that there are no spaces in the full path to the paper.md file. Thanks!
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@sarahstangl-lanl thanks for reorganizing the repo! The paper generation succeeded 🎉
@guadabsb15 @steven-murray thanks very much for starting your reviews and providing feedback! The paper is now available in this comment.
@guadabsb15 @steven-murray 👋 thanks again for starting your reviews! When you get a chance, please keep making your way through the issues, especially as they relate to the paper now that it is available. Let me know if you have any questions!
@sarahstangl-lanl I am sorry for my slowness getting back to this review. I have added a couple of comments to @guadabsb15 's issue on the repo in which I am finding it difficult to get the code installed, given the instructions on the readme. This could be my own unfamiliarity with the tools, but it is holding me up getting further in the review. Thanks!
@sarahstangl-lanl 👋 just checking in on the status of this review. It sounds like the reviewers are having issues building and installing the code (from the above issues). Do you know if they have been resolved? It sounds like these issues might be blocking further review of the code.
@plaplant yes there is some discussion about installation issues over on the repo -- I will try the installation process again in the coming week.
@steven-murray @guadabsb15 👋 just checking in on the status of this review. It looks like there are some points in the checklist that have been completed, but others that are outstanding. If you need anything from me or the authors in order to move forward, please just let me know!
@plaplant I think both @guadabsb15 and I are experiencing difficulties getting the code installed. There are a few open issues on the repo.
@steven-murray thanks for the update!
@sarahstangl-lanl it sounds like the reviewers are still having issues with installation. When the issues have been addressed, please respond to this thread so the reviewers know they can move forward with the rest of the review process. Let me know if you have any questions!
@sarahstangl-lanl as we have not heard from you in several months, I am going to go ahead and withdraw this submission from consideration for publication. You are able to re-submit this for publication in the future if you decide you would like to publish in JOSS.
@steven-murray @guadabsb15 thank you very much for the time and effort invested in reviewing this submission. We appreciate your help with this review! Because this submission will be withdrawn, no further action is needed.