[REVIEW]: MF6RTM: a python package for predictive reactive transport modeling via the MODFLOW 6 and PHREEQC APIs

[editorialbot]

Submitting author: @p-ortega (Pablo Ortega-Tong)
Repository: https://github.com/p-ortega/mf6rtm
Branch with paper.md (empty if default branch): JOSS
Version: v0.3.0
Editor: @mengqi-z
Reviewers: @martinvonk, @vcantarella
Archive: Pending

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/25365e1a8ad29b420a7e09a796df546b"><img src="https://joss.theoj.org/papers/25365e1a8ad29b420a7e09a796df546b/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/25365e1a8ad29b420a7e09a796df546b/status.svg)](https://joss.theoj.org/papers/25365e1a8ad29b420a7e09a796df546b)

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

@martinvonk & @vcantarella, 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 @mengqi-z know.

✨ Please start on your review when you are able; the expectation is that it will take 2-4 weeks to complete. ✨

Checklists

📝 Checklist for @martinvonk

📝 Checklist for @vcantarella

[editorialbot]

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[editorialbot]

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

✅ OK DOIs

- 10.1016/j.envsoft.2018.06.009 is OK
- 10.2138/gselements.15.2.87 is OK
- 10.1016/j.advwatres.2015.06.001 is OK
- 10.1111/j.1745-6584.2003.tb02588.x is OK
- 10.1111/j.1745-6584.2010.00732.x is OK
- 10.3133/tm6A43 is OK
- 10.5194/gmd-15-1659-2022 is OK
- 10.1007/s12665-012-1546-x is OK
- 10.1111/gwat.13351 is OK
- 10.1016/j.envsoft.2016.08.017 is OK
- 10.1007/s10596-014-9443-x is OK
- 10.1016/j.envsoft.2021.105257 is OK
- 10.1177/1094342006064503 is OK
- 10.1016/S0883-2927(97)00070-X is OK
- 10.21105/joss.02317 is OK
- 10.1111/gwat.12413 is OK
- 10.1111/j.1745-6584.2012.00937.x is OK
- 10.1111/gwat.12558 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: CrunchFlow: User’s manual

❌ MISSING DOIs

- 10.3133/tm6a45 may be a valid DOI for title: MODFLOW – USG Version 1: An Unstructured Grid Vers...
- 10.3133/tm6a35 may be a valid DOI for title: PHAST Version 2 - A program for simulating groundw...

❌ INVALID DOIs

- None

[editorialbot]

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

[editorialbot]

Repository Analysis Report

Code breakdown

github.com/AlDanial/cloc v 1.98  T=0.13 s (816.8 files/s, 408821.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
CSV                             27              0              0          36157
Python                          33           1070           2109           3935
Jupyter Notebook                 8              0           4920           3155
TeX                              2             52              5            338
Markdown                         3            107              2            231
YAML                             7             35             41            210
MATLAB                           7              0              0            119
Text                             3             11              0            114
reStructuredText                10             79             94            113
TOML                             2             11              8             70
DOS Batch                        2              8              1             27
INI                              1              1              0             11
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                           106           1378           7187          44489
-------------------------------------------------------------------------------

Commit Count by Author

446	portega
    31	Anthony Aufdenkampe
    12	Pablo Ortega
     8	Paul Tomasula
     5	lkmancewicz-erdc
     2	Allan Foster
     2	Andres Prieto-Estrada
     1	dependabot[bot]

Repository History

Repository age: First commit on May 10, 2024

Code distribution (top 3 48-hour windows):

Period	Insertions	% of Total	Signal	View Changes
Jul 10, 2024 - Jul 12, 2024	1325642	32.6%	🟡	View diff
May 29, 2024 - May 31, 2024	576707	14.2%	🟢	View diff
Nov 29, 2025 - Dec 01, 2025	352410	8.7%	🟢	View diff

GitHub Activity Metrics

Metric	Count
GitHub stars	19
Forks	8
GitHub contributors	8
Releases	13
Total issues	19
Total pull requests	60
Unique commenters/reviewers (excluding authors)	6

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1653

✅ The paper includes a Statement of need section

✅ The paper includes a State of the field section

✅ The paper includes a Software design section

✅ The paper includes a Research impact statement section

✅ The paper includes an AI usage disclosure section

[editorialbot]

License info:

✅ License found: BSD 3-Clause "New" or "Revised" License (Valid open source OSI approved license)

[mengqi-z]

👋 @martinvonk, @vcantarella - 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 openjournals/joss-reviews#11173 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 4-6 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (@editorialbot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@mengqi-z) if you have any questions/concerns.

[editorialbot]

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[martinvonk]

Review checklist for @martinvonk

AI usage

• I confirm that I have read the JOSS AI policy and understand that:
  • AI may only be used for non-substantive assistance (e.g., grammar checking my review text, contextualizing public materials)
  • All evaluative decisions—including scoring, accept/reject recommendations, and assessments of originality, correctness, significance, and ethics compliance—must be made exclusively by me, not AI
  • I bear full responsibility for all judgments, recommendations, and technical claims in my review
  • I will disclose any AI assistance at the conclusion of my review

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/p-ortega/mf6rtm?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@p-ortega) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Scope and significance: Does this submission demonstrate clear research impact or credible scholarly significance as 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.

Development history and open-source practice

• Development timeline: Does the project show evidence of sustained development over time (preferably months or years) rather than rapid, recent code generation?
• Open development: Was the software developed openly from early stages? For projects with recent public repositories, is there at least six months of public development history with evidence of releases, public issues/pull requests, and ideally external engagement?
• Collaborative effort: Does the project show evidence of community engagement — such as contributions from multiple developers, issues/discussions from external users, or community influence on development — in the repo or as described in the paper?
• Good practices: Does the project look like a reusable, non-throwaway research software project that follows good open-source practices (license, documentation, tests and/or verification processes, releases, and clear contribution/support pathways).

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 (required section): 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 (required section): 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 (required section): Do the authors describe how this software compares to other commonly-used packages? If related tools exist, do they provide a clear "build vs. contribute" justification explaining their unique scholarly contribution and why alternatives are insufficient?
• Software Design (required section): Does the paper include a "Software Design" section that explains the trade-offs weighed, the design/architecture chosen, and why it matters? Is the content compelling and does it demonstrate meaningful design thinking?
• Research Impact Statement (required section): Does the paper include a "Research Impact Statement" section providing evidence of realized impact (publications, external use, integrations) or credible near-term significance (benchmarks, reproducible materials, community-readiness signals)? Is the evidence presented compelling?
• AI usage disclosure (required section): Does the paper include an "AI usage disclosure" section that transparently discloses any use of generative AI in the software creation, documentation, or paper authoring?
• 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?

[vcantarella]

Review checklist for @vcantarella

AI usage

• I confirm that I have read the JOSS AI policy and understand that:
  • AI may only be used for non-substantive assistance (e.g., grammar checking my review text, contextualizing public materials)
  • All evaluative decisions—including scoring, accept/reject recommendations, and assessments of originality, correctness, significance, and ethics compliance—must be made exclusively by me, not AI
  • I bear full responsibility for all judgments, recommendations, and technical claims in my review
  • I will disclose any AI assistance at the conclusion of my review

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/p-ortega/mf6rtm?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@p-ortega) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Scope and significance: Does this submission demonstrate clear research impact or credible scholarly significance as 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.

Development history and open-source practice

• Development timeline: Does the project show evidence of sustained development over time (preferably months or years) rather than rapid, recent code generation?
• Open development: Was the software developed openly from early stages? For projects with recent public repositories, is there at least six months of public development history with evidence of releases, public issues/pull requests, and ideally external engagement?
• Collaborative effort: Does the project show evidence of community engagement — such as contributions from multiple developers, issues/discussions from external users, or community influence on development — in the repo or as described in the paper?
• Good practices: Does the project look like a reusable, non-throwaway research software project that follows good open-source practices (license, documentation, tests and/or verification processes, releases, and clear contribution/support pathways).

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 (required section): 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 (required section): 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 (required section): Do the authors describe how this software compares to other commonly-used packages? If related tools exist, do they provide a clear "build vs. contribute" justification explaining their unique scholarly contribution and why alternatives are insufficient?
• Software Design (required section): Does the paper include a "Software Design" section that explains the trade-offs weighed, the design/architecture chosen, and why it matters? Is the content compelling and does it demonstrate meaningful design thinking?
• Research Impact Statement (required section): Does the paper include a "Research Impact Statement" section providing evidence of realized impact (publications, external use, integrations) or credible near-term significance (benchmarks, reproducible materials, community-readiness signals)? Is the evidence presented compelling?
• AI usage disclosure (required section): Does the paper include an "AI usage disclosure" section that transparently discloses any use of generative AI in the software creation, documentation, or paper authoring?
• 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?