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[REVIEW]: WATTS: Workflow and template toolkit for simulation
Submitting author: @paulromano (Paul Romano) Repository: https://github.com/watts-dev/watts Branch with paper.md (empty if default branch): joss-paper Version: v0.3.0 Editor: @danielskatz Reviewers: @sskutnik, @munkm, @yadudoc Archive: Pending
Status
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HTML: <a href="https://joss.theoj.org/papers/04749c75d05fbad296833e3f0fe7c822"><img src="https://joss.theoj.org/papers/04749c75d05fbad296833e3f0fe7c822/status.svg"></a>
Markdown: [](https://joss.theoj.org/papers/04749c75d05fbad296833e3f0fe7c822)
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
@sskutnik & @munkm & @yadudoc, 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
Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.
For a list of things I can do to help you, just type:
@editorialbot commands
For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
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Software report:
github.com/AlDanial/cloc v 1.88 T=0.10 s (959.9 files/s, 124465.3 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
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XML 1 1 0 2968
Python 44 848 1414 2366
SWIG 7 152 0 2106
reStructuredText 11 315 237 579
Markdown 21 178 0 472
TeX 1 19 0 229
YAML 4 17 4 95
SVG 1 0 1 57
TOML 1 3 0 51
DOS Batch 1 8 1 26
JSON 1 0 0 22
make 1 4 7 9
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SUM: 94 1545 1664 8980
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gitinspector failed to run statistical information for the repository
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1016/j.anucene.2014.07.048 is OK
- 10.5281/zenodo.591748 is OK
- 10.5281/zenodo.5761067 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.2172/1419730 is OK
- 10.1016/j.softx.2020.100430 is OK
- 10.1016/j.anucene.2014.08.024 is OK
- 10.2172/1817318 is OK
- 10.12688/f1000research.29032.2 is OK
- 10.1016/j.future.2022.01.024 is OK
- 10.1016/j.commatsci.2020.110086 is OK
- 10.1093/gigascience/giz044 is OK
- 10.1145/3307681.3325400 is OK
- 10.48550/arxiv.1909.08704 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@sskutnik & @munkm & @yadudoc - 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#4735 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.
👋 @sskutnik, @munkm, @yadudoc - how are things going? It doesn't look like any of you have created your checklists and gotten started yet. Please do.
Review checklist for @sskutnik
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/watts-dev/watts?
- [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 (@paulromano) 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?
Comment / suggestion on the paper; not well-formed enough to form a PR yet, but I wanted to put this out for discussion with the authors and other reviewers:
It seems like a substantial component of the "lift" being done by Watts specifically is in the plugin class That is, it acts as a functional adapter to the output generated by specific codes (like MCNP, MOOSE, OpenMC, etc.). The input generation largely seems like a function of Jinja (which is good and useful) with some supplemental physical unit conversion (also useful! but implemented outside this).
Assuming this is the case, I feel like the "plugin" interface as a core component of the Watts framework deserves a bit more attention / highlighting in the paper. The "what it does" part is fine, but from the perspective of a potential power user / contributor, part of what I would want to understand is what makes this all "tick"; how do I expand upon it to fit my code system of interest? Even just briefly going over the basic idea of the plugin in terms of what it's providing the framework (i.e., what's being implemented under the hood) would be useful to better contextualizing what's going on.
@munkm @yadudoc what do you think?
Other comments; It would probably be a good idea to explicitly document required Python modules, beyond what is managed by Pip. Installation is easy and is readily reproduced from the instructions, but an explicit list of dependencies would be useful for users installing offline.
Repo has good documentation for developer contributions and use examples; ~I don't know how stringent we want to be with respect to "user support" documentation. Possibly this could be cleared up a little in the top-level package overview.~
Otherwise, I think my one and only sticking point would be to flesh out a bit more how the plugin architecture works; with respect to WATTS, including some brief discussion of how this is bespoke to each package supported.
Update: PR 60 handles the above documentation request; this satisfies my above concern.
Review checklist for @yadudoc
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/watts-dev/watts?
- [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 (@paulromano) 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?
👋 @munkm - when do you think you will get a chance to create your checklist and start your review? (it was also nice seeing you briefly in person last week 🙂)
@danielskatz, I was away for a bit, and haven't had a chance to look at this closely. I'm aiming to have this review completed this weekend.
I've completed my review for the most part, and I've added three issues over on the github repo for watts detailing missing items. I'll come back and check off the missing boxes once the authors have had a chance to take a look.
Overall, I think this package provides values, the documentation is clean and understandable and the article does a good job of framing the problem. I think the plugin architecture for updating the application templates is quite nice, and I do wonder if the authors have considered integration with other python based workflow tools (as a workflow dev for parsl, this is cool!). Another point to note is that "workflow" means many different things in different communities, it might be useful to define what it means to you. For, eg. is it possible to compose any DAG? Similarly, I only figured out what the execution context looks like after going over the "Detailed Usage" section in the documentation. As a user, I would like to know whether any task-parallelism is supported or whether the tasks run serially. The last couple of comments are purely from my curiosity and not necessary to move the review forward. Apologies to the authors on the delay in getting this review completed.
Pending issues from docs and tests:
- https://github.com/watts-dev/watts/issues/63
- https://github.com/watts-dev/watts/issues/62
- https://github.com/watts-dev/watts/issues/61
Review checklist for @munkm
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/watts-dev/watts?
- [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 (@paulromano) 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)?
- [ ] 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!!! I am really excited about this package and thank you for your contribution to JOSS. I opened two issues that I think will help clarify things in the documentation for your future users, but watts-dev/watts#65 is not blocking for my review. However, I do think it's related and complementary to the original comment made by @sskutnik about power users. I have finished my review but I have two questions on your references:
- Are the MNCP 6.2 release notes the preferred reference for MCNP? I am not totally sure based on their website, but it seems for 6.3 their main reference is the user's manual. https://mcnp.lanl.gov/reference_collection.html#mcnp6_refs
- ABCE is a plugin mentioned in the docs, but I don't see it referenced in the paper. Is there no reference? Perhaps you could add a sentence describing it too.
👋 @paulromano - note you have issues and comments to respond to from @yadudoc and @munkm. When do you think you will be able to respond to them?
Thanks all for the excellent comments! I'm hoping to respond to them next week and will put a note here once I believe they've been addressed.
Hi @danielskatz There is indeed. I've had a few PRs to the watts repo addressing the reviewer feedback. Most of these have already been merged and I'm just waiting on one more (watts-dev/watts#71). I've also made some local updates to the text of the paper based on these updates and will push that once the review of the aforementioned PR is complete. I'll add another comment here once I believe all the feedback has been addressed and it's ready for another look.
Thanks for checking in!
Alright, the final PR has been merged and I've made corresponding updates in the joss-paper branch of watts. To respond specifically to a few of the comments made here:
Assuming this is the case, I feel like the "plugin" interface as a core component of the Watts framework deserves a bit more attention / highlighting in the paper. The "what it does" part is fine, but from the perspective of a potential power user / contributor, part of what I would want to understand is what makes this all "tick"; how do I expand upon it to fit my code system of interest? Even just briefly going over the basic idea of the plugin in terms of what it's providing the framework (i.e., what's being implemented under the hood) would be useful to better contextualizing what's going on.
@sskutnik This is a really good point. I've expanded the description of the Plugin classes in the paper to describe in more detail how they fit in to the overall system. I've also added a new section in our developer's guide that goes over how to connect new codes into watts.
Another point to note is that "workflow" means many different things in different communities, it might be useful to define what it means to you. For, eg. is it possible to compose any DAG? Similarly, I only figured out what the execution context looks like after going over the "Detailed Usage" section in the documentation. As a user, I would like to know whether any task-parallelism is supported or whether the tasks run serially.
@yadudoc This is discussed a bit in the paper itself, namely the relationship of watts to other workflow systems and specifically what watts does not do. It's a really interesting question though and I'm planning on spending some time after this to explore how watts and other workflow systems like Parsl could fit together! Thanks for all your helpful comments and suggestions :pray:
- Are the MNCP 6.2 release notes the preferred reference for MCNP? I am not totally sure based on their website, but it seems for 6.3 their main reference is the user's manual. https://mcnp.lanl.gov/reference_collection.html#mcnp6_refs
- ABCE is a plugin mentioned in the docs, but I don't see it referenced in the paper. Is there no reference? Perhaps you could add a sentence describing it too.
@munkm Thanks for pointing out the MCNP 6.3 release notes. Looks like those are hot off the press; I've updated the paper to cite those instead of the older 6.2 notes.
Regarding ABCE, unfortunately there is no reference at present. If it's OK with you, we can add a reference 1) in the documentation of watts once a reference becomes available and 2) in a future update of the paper for a new release.
Once again, thanks to all for the excellent feedback and helping to improve the software further!
@danielskatz The paper and the repo are in good order, and the issues I raised have been addressed by @paulromano. I recommend this work for publication.
@munkm - I see you have one unchecked item on your list - Can you now check it off? If not, what would enable you to do so?
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1016/j.anucene.2014.07.048 is OK
- 10.5281/zenodo.591748 is OK
- 10.5281/zenodo.5761067 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.2172/1419730 is OK
- 10.1016/j.softx.2020.100430 is OK
- 10.1016/j.anucene.2014.08.024 is OK
- 10.2172/1817318 is OK
- 10.12688/f1000research.29032.2 is OK
- 10.1016/j.future.2022.01.024 is OK
- 10.1016/j.commatsci.2020.110086 is OK
- 10.1093/gigascience/giz044 is OK
- 10.1145/3307681.3325400 is OK
- 10.48550/arxiv.1909.08704 is OK
MISSING DOIs
- None
INVALID DOIs
- None