[REVIEW]: Mat-dp: An open-source Python model for analysing material demand projections and their environmental implications, which result from building low-carbon systems

[editorialbot]

Submitting author: @kcerva (Karla Cervantes Barron)
Repository: https://github.com/Mat-dp/mat-dp-core
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @crvernon
Reviewers: @MoLi7, @nick-gorman
Archive: 10.5281/zenodo.7002733

Status

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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

@MoLi7 & @nick-gorman, 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 @crvernon 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 @MoLi7

📝 Checklist for @nick-gorman

[editorialbot]

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:

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.07 s (614.8 files/s, 112677.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          22            515            195           4633
Markdown                        13            664              0           1350
YAML                             3              5              4             77
TOML                             1              6              0             30
TeX                              1              0              0             29
Bourne Shell                     1              0              0              6
-------------------------------------------------------------------------------
SUM:                            41           1190            199           6125
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

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

OK DOIs

- 10.1021/es902909k is OK
- 10.5281/zenodo.3542680 is OK

MISSING DOIs

- 10.31235/osf.io/y4xcv may be a valid DOI for title: Documentation of part IVof the RECC model framework: Open Dynamic Material Systems Model for the Resource Efficiency-Climate Change Nexus (ODYM-RECC), v2.2

INVALID DOIs

- None

[editorialbot]

Wordcount for paper.md is 817

[editorialbot]

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

[crvernon]

👋 @kcerva @MoLi7 @nick-gorman This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above.

Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. 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, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention #4460 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 the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

[crvernon]

@kcerva regarding your question about name customization: https://github.com/openjournals/inara/blob/main/docs/names.md

Let me know if you have any questions.

[MoLi7]

Review checklist for @MoLi7

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

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

General checks

• Repository: Is the source code for this software available at the https://github.com/Mat-dp/mat-dp-core?
• 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 (@kcerva) 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

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?

[kcerva]

@editorialbot generate pdf

Thanks a lot @crvernon! I've updated my last name as needed, so hopefully that shows properly in the regenerated pdf.

[editorialbot]

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

[nick-gorman]

Review checklist for @nick-gorman

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

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

General checks

• Repository: Is the source code for this software available at the https://github.com/Mat-dp/mat-dp-core?
• 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 (@kcerva) 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

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?

[nick-gorman]

Hi @kcerva, At the start of the paper there is broad claim about the ability of MAT-dp to calculate the resources needed in any system or supply chain. However, the examples given in the documentation are all simplistic, demonstrating the functionality on system of real world complexity would makeit much easier to confirm the software's stated functionality claim. The hydro dam example doesn't seem to use main the optimisation functionality, and I'm not sure what it accomplishes that couldn't be done in a simple spreadsheet. Do you think you can add an example that better demonstrates how MAT-dp would be used to solve a real-world problem?

[nick-gorman]

Hi @kcerva, According to the review process the documentation also needs to include a statement of need. Do you think you can add a bit to the project intro in the docs explaining the need being met?

[nick-gorman]

A few extra notes on the paper:

• The summary at the start could be revised for greater clarity:
  • For example, mentioning that the underlying model is a linear program
  • Also the key thing driving the optimisation is the objective function, alongside the constraints you mention
  • I'm not sure it's entirely correct to say that the "system can be optimised by using three types of inbuilt contraints". The system is optimised by a solver to minimise an objective function subject to constraints.
• I think there is a typo on line 36, do you mean "other" rather than as
• The target audience section seems to continue talking about the functionality of Mat-dp. Could this be re-framed more specifically in terms of potential users?

[kcerva]

@editorialbot generate pdf

@nick-gorman thanks for your comments! We've addressed the ones related to the notes you had on the paper, so you should be able to see them on the regenerated pdf. We will be working on the remaining comments and keep you posted.

[editorialbot]

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

[kcerva]

Hello @nick-gorman. I'll address the remaining points you had made here:

• The example's complexity: The Complex Example in the Cookbook is assuming that the users are familiar with how to set up the key inputs and shows a full working example of setting a model up including different constraints, which can be implemented in a more "complex" manner. We figured that as long as users understand how to link processes and set up their constraints and objective function, the rest would be straight forward regarding the optimisation given the rest of the documentation. Also, I don't know if you have seen that the Function Reference sections also contain working examples, culminating in the example shown here. Those should be a little bit more complex in terms of the number of power plants involved, i.e. hopefully having the complexity you were hoping to see in your comment.

• Adding statement of need to documentation: We have added the section called "What gap does Mat-dp fill?" to the docs here. Hopefully this helps clarify this point.

As far as I can tell, these last comments and those I made before fully address all the points you raised, but please let us know if you have more questions.

[crvernon]

Thanks @kcerva ! Once you confirm that all is well from your perspective @nick-gorman let me know and check off your remaining boxes and I'll take a look.

Great work!

[nick-gorman]

Hi @kcerva and @crvernon,

I think the only outstanding point is a question I still have on the documentation: Mat-dp/mat-dp-core#23

Regarding example complexity happy to accept it as is, they are definitely sufficient to explain how to use Mat-dp.

However, just as general feedback, I still think it would be really useful to see Mat-dp simulating a system of real world complexity, or answering a real-world question. From the ones you've provided it's hard to see the use case. Generally, models of energy systems capture much more of the system complexity than the one presented in the Function Reference, Calliope is great example of a tool that does this, and lets the user model multiple resource flows and co2 production: https://www.callio.pe/model-gallery/. The complex example in the cookbook leaves me a bit confused, the hydro damn is modelled as a process that consumes raw materials and produces a fixed quantity of energy. However, the role of hydro in energy systems is much more nuanced than this, for instances it will have huge value in low carbon systems providing energy when wind and solar production are low. If modelling doesn't capture these dynamics it will provide misleading answers about how best to build low carbon energy systems.

Pardon the rant. I'm really not trying to question the value of Mat-dp. Just trying to explain why different examples might better communicate how Mat-dp could be used.

Cheers,
Nick

[editorialbot]

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

OK DOIs

- 10.1021/es902909k is OK
- 10.5281/zenodo.3542680 is OK
- 10.31235/osf.io/y4xcv is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/joss-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#3456, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[arfon]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04460 joss-papers#3457
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2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[arfon]

@MoLi7, @nick-gorman – many thanks for your reviews here and to @crvernon for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@kcerva – your paper is now accepted and published in JOSS ⚡🚀💥

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[kcerva]

Thanks so much for all your help and comments @arfon @MoLi7 @nick-gorman and @crvernon! Really happy this is out!

[MoLi7]

Congratulations!! Great work @kcerva 👏

[kcerva]

Hello @arfon. I am doing some admin of publications and I realised that the ORCID associated to this paper for my name is wrong. It should be https://orcid.org/my-orcid?orcid=0000-0001-9185-3022, but instead it has someone else's account. Is there a way to fix this?

[kthyng]

@openjournals/dev Could you help with this?

[xuanxu]

@kthyng the orcid should be updated in the metadata section of the paper.md file. Then reaccepting the submission (@editorialbot reaccept) will regenerate the paper with the correct orcid.

[kcerva]

@xuanxu should I do the update to the paper.md file or does someone else need to?

[xuanxu]

@kcerva yeah, please update it with your correct orcid.

[kcerva]

@xuanxu done!

[xuanxu]

@arfon / @kthyng: this should be ready for reacceptance

[kthyng]

@editorialbot reaccept

[editorialbot]

Rebuilding paper!

[editorialbot]

🌈 Paper updated!

New PDF and metadata files 👉 openjournals/joss-papers#3785

[kthyng]

Thanks @xuanxu!

@kcerva take a look and make sure everything looks right!

[kcerva]

Thank you @kthyng. It looks right!