[REVIEW]: The Causal Testing Framework

[editorialbot]

Submitting author: @jmafoster1 (Michael Foster)
Repository: https://github.com/CITCOM-project/CausalTestingFramework
Branch with paper.md (empty if default branch):
Version: v9.0.2
Editor: @danielskatz
Reviewers: @akothen, @yinfangchen, @FATelarico
Archive: Pending

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

@akothen & @yinfangchen & @FATelarico, 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

📝 Checklist for @akothen

📝 Checklist for @yinfangchen

📝 Checklist for @FATelarico

📝 Checklist for @FATelarico

[editorialbot]

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[editorialbot]

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

✅ OK DOIs

- 10.1109/ICST57152.2023.00023 is OK
- 10.1145/3607184 is OK
- 10.1109/ICST60714.2024.00023 is OK
- 10.1109/QSIC.2007.4385527 is OK
- 10.2139/ssrn.4732706 is OK
- 10.1093/ije/dyw341 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: DoWhy-GCM: An Extension of DoWhy for Causal Infere...
- No DOI given, and none found for title: Metamorphic testing: A new approach for generating...
- No DOI given, and none found for title: Causal Inference: What if
- No DOI given, and none found for title: Causality
- No DOI given, and none found for title: DoWhy: An End-to-End Library for Causal Inference

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.98  T=0.12 s (1026.6 files/s, 255058.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
CSV                             23              0              0          19228
Python                          54           1522           1642           6558
JSON                             5              0              0            646
Markdown                        12             89              0            379
reStructuredText                14            268            244            376
YAML                            12             37             19            329
TeX                              2             31              1            234
TOML                             1              8              1             69
DOS Batch                        1              8              1             26
CSS                              1              9              4             16
Dockerfile                       1              7             11             15
make                             1              4              7              9
Text                             1              0              0              4
-------------------------------------------------------------------------------
SUM:                           128           1983           1930          27889
-------------------------------------------------------------------------------

Commit count by author:

   512	cwild-UoS
   202	Michael Foster
   142	AndrewC19
   141	Michael
    58	Richard Somers
    52	f-allian
    33	Andrew Clark
    32	Robert (Bob) Turner
    17	Farhad Allian
    16	bobturneruk
     6	[email protected]
     1	Michae Foster
     1	Richard

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1016

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[editorialbot]

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

[danielskatz]

@akothen & @yinfangchen & @FATelarico - 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#7739 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.

[yinfangchen]

Review checklist for @yinfangchen

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/CITCOM-project/CausalTestingFramework?
• 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 (@jmafoster1) 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?

[akothen]

Review checklist for @akothen

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/CITCOM-project/CausalTestingFramework?
• 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 (@jmafoster1) 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?

[FATelarico]

Review checklist for @FATelarico

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/CITCOM-project/CausalTestingFramework?
• 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 (@jmafoster1) 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?

[FATelarico]

Hi there!

Almost all boxes are ticked for me. I just have comments about two issues.

First, authorship. Obviously commits are not the only (but perhaps the main) indicator of contributions to a piece of software's development. Still, I could only see more than a few commits by the submitting author, but not all of the collaborators. Whether there are other sufficient reasons to grant authorship to each and every other coauthor, it's only up to the development team. But it's part of our duty to double check.

Second Installation. Everything went smoothly on a 64-bit machine running both Ubuntu 22LTS and Windows 10, as well as on another one with Windows 11. However, the installation seems to break with no explicit error statement on a Debian 32-bit machine. I wonder whether you know why. And whether you think that could find place in the installation instructions.

Best 🚀

[jmafoster1]

Thanks @FATelarico for your review. In terms of authorship, I included everyone who has made a substantial contribution to the project, whether they have contributed code or not. I summarise contributions below:

• Michael Foster: Me, researcher on the CITCoM project and current lead developer
• Andrew Clark: PhD student who laid the groundwork for this project and initially led development
• Christopher Wild: RSE, helped with documentation, refactoring, and other non-core research related development
• Farhad Allian: RSE, helped with documentation, refactoring, and other non-core research related development. Took over when Robert Turner left
• Robert Turner: RSE, helped with documentation, refactoring, and other non-core research related development. Unfortunately left us fairly early on in the project, but was extremely helpful in directing the initial setup.
• Richard Somers: PhD student on the project, who led the development of the surrogate modelling modules.
• Nicholas Latimer: Co-I on CITCoM. He was extremely helpful in providing technical advice for implementing temporal estimation. While he has not directly contributed code to this project, he graciously provided me with Stata and R implementations of the estimation algorithms from his own research for me to generalise and translate into Python, which was also tremendously helpful for testing.
• Neil Walkinshaw: PI of the CITCoM project. He has not committed code himself, but has directed the research project and advised on both technical and non-technical aspects of the code and its evaluation.
• Rob Hierons: Co-I on CITCoM. He has not committed code himself, but has directed the research project and advised on both technical and non-technical aspects of the code and its evaluation.

As for your installation issue on Debian, I've never used Debian so I'm afraid I'm not sure. We initially had some issues with pygraphviz requiring libgraphviz-dev on ubuntu, and graphviz to be installed and on the path on Windows. Perhaps it could be something similar, or requiring some other lower level dependency like GCC or G++ or something? Or it could be the 32 bit nature of the machine as I'm not sure we've tried it on that. With no error message, it's very hard to look into it. Is there really no output at all from the failed install? @f-allian, do you have any ideas on this? Is it something that's worth looking into do you think, or should we simply put a note to the effect of "There have been reports on this failing to install on 32 bit Debian. Feel free to try and let us know if you have any issues." in the install notes?

[FATelarico]

As I said, there's no defined policy on authorship. So, as long as everyone on the submitting side is comfortable with the authors listed, and given that there's only so much to be inferred from GitHub commits, I ticked also that box.

Is there really no output at all from the failed install? f-allian, do you have any ideas on this?

The terminal just crushes, it's possible that there's a message being printed shortly before that, but I wasn't able to make sure of it.

Is it something that's worth looking into do you think, or should we simply put a note to the effect of "There have been reports on this failing to install on 32 bit Debian. Feel free to try and let us know if you have any issues." in the install notes?

I think that except for some older machines in developing-countries institutions, most user will have a 64-bit machine. So, I am not suggesting much deep analysis of it — especially if no apparent reason comes to mind. I'd suggest adding a note about 32-bit systems for the aforementioned user group, but there's not much more to be done about it.

[f-allian]

@FATelarico Thanks for your comments above.

I think that except for some older machines in developing-countries institutions, most user will have a 64-bit machine. So, I am not suggesting much deep analysis of it — especially if no apparent reason comes to mind. I'd suggest adding a note about 32-bit systems for the aforementioned user group, but there's not much more to be done about it.

I've run some tests using a Docker container consisting of a Debian 32-bit OS and the installation does indeed hang. The verbose mode shows that the problem arises from installing the newer versions of numpy, which our framework depends on. @jmafoster1 has already opened a PR to include this information for users in our README, so I'll approve that now. Thanks again.