[REVIEW]: sfctools - A toolbox for stock-flow consistent, agent-based models

[editorialbot]

Submitting author: @fuadlabgit (Thomas Baldauf)
Repository: https://gitlab.com/dlr-ve/esy/sfctools/framework/
Branch with paper.md (empty if default branch): paper
Version: joss_final
Editor: @sbenthall
Reviewers: @npalmer-professional, @alanlujan91
Archive: 10.5281/zenodo.8118870

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/1ba3edb21815b1031c14eb36911e9b21/status.svg)](https://joss.theoj.org/papers/1ba3edb21815b1031c14eb36911e9b21)

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

@npalmer-professional & @alanlujan91, 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 @sbenthall 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 @alanlujan91

📝 Checklist for @npalmer-professional

[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:

@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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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.36 s (400.1 files/s, 64172.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          88           4348           3261           9102
Qt                               7             43              0           3753
TeX                              2             70              0            558
reStructuredText                29            521            743            382
Markdown                         7             81              0            135
YAML                             9             26             12            123
TOML                             1              6              4             36
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                           145           5107           4028          14124
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1365

[editorialbot]

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

[editorialbot]

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

OK DOIs

- 10.21105/joss.03065 is OK

MISSING DOIs

- 10.2139/ssrn.305080 may be a valid DOI for title: Agent-based computational economics: Growing economies from the bottom up
- 10.1016/j.erss.2018.10.021 may be a valid DOI for title: Agent-based modelling and socio-technical energy transitions: A systematic literature review
- 10.1007/s43253-022-00071-w may be a valid DOI for title: Why do we need agent-based macroeconomics?
- 10.2139/ssrn.2664125 may be a valid DOI for title: Agent based-stock flow consistent macroeconomics: Towards a benchmark model
- 10.2139/ssrn.2741107 may be a valid DOI for title: Making visible “the invisible hand”: The mission of social simulation
- 10.1111/joes.12221 may be a valid DOI for title: Stock-Flow Consistent macroeconomic models: a survey
- 10.1093/cje/beu021 may be a valid DOI for title: Post-Keynesian stock-flow-consistent modelling: a survey

INVALID DOIs

- None

[sbenthall]

👋🏼 @fuadlabgit @alanlujan91 @npalmer-professional this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains 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 #4980 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 any 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 (@sbenthall) if you have any questions/concerns.

[alanlujan91]

Review checklist for @alanlujan91

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://gitlab.com/dlr-ve/esy/sfctools/framework/?
• 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 (@fuadlabgit) 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?

[sbenthall]

Ping @npalmer-professional is there anything I can do to help you get started with your review? Please don't hesitate to reach out to me on this thread, or by email if you prefer.

[fuadlabgit]

Dear @sbenthall and @npalmer-professional, belated happy new year and thank you so much for keeping the review process up. In the meantime, The code has been cleaned up and developed a bit further.

Therefore, I have merged back the development branch 'spotykach' to the paper branch. This should make the review a little easier (slightly cleaner code) and also includes some more tests. In order to distinguish the originally submitted version, I have created a tag in the paper branch. The original version is joss-initial-submission and the new version is tagged joss-pre-review. Hope this helps you.

In case the extent of the framework exceeds the capacities of the reviewer, I am also willing to discuss cutting parts off the repository for a more lightweight review.

All the best, Thomas

[oliviaguest]

@editorialbot generate pdf

[editorialbot]

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

[sbenthall]

@fuadlabgit I believe that it is just fine that you merged in progress during the review period, since reviews at JOSS are potentially interactive. It sounds like you've made some good improvements and unless I hear an objection from the reviewers, I'll trust that didn't create a problem in terms of scope.

[npalmer-professional]

Review checklist for @npalmer-professional

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://gitlab.com/dlr-ve/esy/sfctools/framework/?
• 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 (@fuadlabgit) 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?

[alanlujan91]

Reproducibility/Functionality/Performance: https://gitlab.com/dlr-ve/esy/sfctools/framework/-/issues/15

Having a hard time reproducing the paper example to test out functionality and performance.

[alanlujan91]

State of the field: Brief discussion of other software (1 sentence). More in depth discussion might be needed. Quick search also brought up https://github.com/AB-CE/abce and https://github.com/salesforce/ai-economist. Are these unrelated?

[fuadlabgit]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

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

[editorialbot]

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

[fuadlabgit]

State of the field: Brief discussion of other software (1 sentence). More in depth discussion might be needed. Quick search also brought up https://github.com/AB-CE/abce and https://github.com/salesforce/ai-economist. Are these unrelated?

@alanlujan91 , thank you so much for reviewing this part! Indeed, it would be valuable to mention more frameworks. I have
added an additional sentence to the paragraph, and have created a table for comparison. Also, I have added a reference to Abar et al. (2017) for a detailed review. If there are any more suggestions for citations concerning ABM comparison papers, I will be happy to add them there. It might be that the table makes the paper too long and bulky. Therefore, please indicate your preference about if and where to put table 1.

[fuadlabgit]

Reproducibility/Functionality/Performance: https://gitlab.com/dlr-ve/esy/sfctools/framework/-/issues/15

Having a hard time reproducing the paper example to test out functionality and performance.

@alanlujan91 thank you for testing the example. Improvements have been made about the reproducability and description of the paper example. See the issue page in Gitlab and my answers therein. You might need to run pip install --upgrade sfctools to get the latest version before running the example file. I have replaced the numerical values with sympy expressions "x" and "d" in order to get a result which is not too confusing and which better reflects the paper example. However, symbolic expressions are only supported in the latest version of sfctools.

[sbenthall]

@npalmer-professional Any updates on this?

[fuadlabgit]

Dear @npalmer-professional, thank you so much for reviewing and for your interest in the project! I will try to give some answers / further explanations about the points left open (see comments below)

Review checklist for @npalmer-professional

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://gitlab.com/dlr-ve/esy/sfctools/framework/?
• 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 (@fuadlabgit) 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.

There is no data involved in the framework, as it represents a general modeling framework, rather than a specific calibrated model.

• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.

Please have a look at the responses to alanlujan91 from March 2023. The paper example should be running and replicating exactly the transactions-flow table given in the paper.

• 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?

Here, I want to point out to the documentation page. There is a readthedocs page available here
https://sfctools-framework.readthedocs.io/en/latest/
The installation is explained under 'getting started' https://sfctools-framework.readthedocs.io/en/latest/doc_intro/installation.html

• 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.)

We do not explicitly claim performance gains, but point out methodological gains from using framework vs. other frameworks/methods such as programming models in MS Excel (as sometimes done in the field).

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.

Sfctools is registerd at Pypi, see https://pypi.org/project/sfctools/

• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).

The examples are placed under sfctools/examples and are also included in the API documentation: https://sfctools-framework.readthedocs.io/en/latest/doc_api_examples/examples_framework.html

• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?

An overview of the core modules is given here https://sfctools-framework.readthedocs.io/en/latest/doc_software/structure.html
We tried to split the functionality into three pillars, 'Automation and parameters', 'Bottom-Up Tools' and 'Data Structrures'.

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

The gitlab repository uses automated tests within its CI pipeline. You can check the pipeline history at https://gitlab.com/dlr-ve/esy/sfctools/framework/-/pipelines
I have added also a minimal GUI test, which tests if the paper example can be automatically reconstructed by clicking some buttons without errors.

• 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?

The 'Context and Scope' page of the documentation aims at giving a glimpse into the state of the field, different perspectives of modeling etc. and also gives 14 references. Further, a table has been added to the paper to show a comparison of sfctools to other modeling frameworks used in the community.
See https://sfctools-framework.readthedocs.io/en/latest/doc_software/software.html

• 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?

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.21105/joss.05087 is OK
- 10.2139/ssrn.305080 is OK
- 10.1016/j.erss.2018.10.021 is OK
- 10.1007/s43253-022-00071-w is OK
- 10.2139/ssrn.2664125 is OK
- 10.21105/joss.03065 is OK
- 10.1016/j.cosrev.2017.03.001 is OK
- 10.2139/ssrn.2741107 is OK
- 10.1111/joes.12221 is OK
- 10.1093/cje/beu021 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/sbcs-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#4382, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[fuadlabgit]

@editorialbot generate pdf

[editorialbot]

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

[fuadlabgit]

Sorry, the link to the documentation page was cyan and not clickable -> now it works.

[sbenthall]

Hmm. @fuadlabgit did you make a change to the repository? If so, I think I need to ask you to make another archive/DOI and release. Or have I misunderstood?

[fuadlabgit]

@sbenthall so sorry for the confusion. I was not aware this was producing inconveniences. Here is the updated, final version

I have created a tag https://gitlab.com/dlr-ve/esy/sfctools/framework/-/releases/joss_final
and a new Zenodo version with the DOI 10.5281/zenodo.8118870 (https://zenodo.org/record/8118870)

[oliviaguest]

@sbenthall is this now ready? 😊

[sbenthall]

@editorialbot set joss_final as version

[editorialbot]

Done! version is now joss_final

[sbenthall]

@editorialbot set 10.5281/zenodo.8118870 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.8118870

[sbenthall]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.21105/joss.05087 is OK
- 10.2139/ssrn.305080 is OK
- 10.1016/j.erss.2018.10.021 is OK
- 10.1007/s43253-022-00071-w is OK
- 10.2139/ssrn.2664125 is OK
- 10.21105/joss.03065 is OK
- 10.1016/j.cosrev.2017.03.001 is OK
- 10.2139/ssrn.2741107 is OK
- 10.1111/joes.12221 is OK
- 10.1093/cje/beu021 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[sbenthall]

@fuadlabgit It should be all good now. I've updated the submission.

@oliviaguest I once again recommend this submission for acceptance!

[editorialbot]

👋 @openjournals/sbcs-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#4387, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[fuadlabgit]

@sbenthall @alanlujan91 @npalmer-professional Wonderful. Thank you so much again for your effort, for reviewing and for the extremely valuable feedback, especially about the examples!

[oliviaguest]

@editorialbot accept

[editorialbot]

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

[editorialbot]

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: Baldauf
  given-names: Thomas
  orcid: "https://orcid.org/0000-0002-9119-7413"
doi: 10.5281/zenodo.8118870
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Baldauf
    given-names: Thomas
    orcid: "https://orcid.org/0000-0002-9119-7413"
  date-published: 2023-07-12
  doi: 10.21105/joss.04980
  issn: 2475-9066
  issue: 87
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 4980
  title: sfctools - A toolbox for stock-flow consistent, agent-based
    models
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.04980"
  volume: 8
title: sfctools - A toolbox for stock-flow consistent, agent-based
  models

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.

[editorialbot]

🐘🐘🐘 👉 Toot 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.04980 joss-papers#4398
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04980
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...

[oliviaguest]

Congratulations @fuadlabgit! Huge thanks to @sbenthall and the reviewers @npalmer-professional, @alanlujan91. 🥳 👏

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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