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[REVIEW]: python-ags4: A Python library to read, write, and validate AGS4 geodata files
Submitting author: @asitha-sena (Asitha Senanayake) Repository: https://gitlab.com/ags-data-format-wg/ags-python-library Branch with paper.md (empty if default branch): joss_paper Version: 0.3.7 Editor: @jedbrown Reviewers: @PaulDebus, @banesullivan, @snakesonabrain Archive: Pending
Status
Status badge code:
HTML: <a href="https://joss.theoj.org/papers/3691899744cb0bf7d6482cbb5de0d563"><img src="https://joss.theoj.org/papers/3691899744cb0bf7d6482cbb5de0d563/status.svg"></a>
Markdown: [](https://joss.theoj.org/papers/3691899744cb0bf7d6482cbb5de0d563)
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
@PaulDebus & @banesullivan & @jessepisel, 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 @jedbrown 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 @snakesonabrain
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:
@editorialbot generate pdf
Software report:
github.com/AlDanial/cloc v 1.88 T=0.07 s (228.8 files/s, 64432.0 lines/s)
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Language files blank comment code
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Python 8 909 774 1670
Markdown 2 63 0 165
TeX 1 5 0 89
YAML 2 10 2 68
Jupyter Notebook 1 0 392 50
TOML 1 4 0 24
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SUM: 15 991 1168 2066
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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
- 10.5281/zenodo.3509134 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.5281/zenodo.3946761 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:
:wave: @PaulDebus, @banesullivan, @jessepisel :wave: Welcome to JOSS and thanks for agreeing to review! The comments from @editorialbot above outline the review process, which takes place in this thread (possibly with issues filed in the python-ags4 repository). I'll be watching this thread if you have any questions.
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. 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 a month or so. Please let me know if you require some more time. We can also use editorialbot to set automatic reminders if you know you'll be away for a known period of time.
Please feel free to ping me (@jedbrown) if you have any questions/concerns.
Review checklist for @PaulDebus
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://gitlab.com/ags-data-format-wg/ags-python-library?
- [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 (@asitha-sena) 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
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?
Welcome @snakesonabrain (author of Groundhog)! Please make a comment here with
@editorialbot generate my checklist
to get started, and let me know if you have any questions.
Now that we have direct AGS4 expertise thanks to Bruno, if one of the reviewers who hasn't started yet would like to rotate off this submission, please just let us know here. Of course you're welcome to stay.
Review checklist for @snakesonabrain
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://gitlab.com/ags-data-format-wg/ags-python-library?
- [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 (@asitha-sena) 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
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?
@jedbrown I am happy to rotate off this review now that Bruno has agreed to review the repository.
Hey,
I started my review but ran into issues pretty early on while trying to load files. I opened an an issue in the repository and only link here for the breadcrumbs.
I will update here, once the issue is resolved.
Cheers
@PaulDebus Tried the same files and does seem to work for me. Also tried on several ags files from my own archives and no issues sofar. Only thing which could be improved is automatic recognition of legacy AGS3.1 files, for which the code will not work.
My review is essentially complete. The only thing I'm missing in the package is some autogenerated docs for the core modules of the package. Also, a state of the field is missing in the paper.
Thanks for taking the time to review the paper and the repo.
@PaulDebus I added responses to the issues opened in the Gitlab repository. Hope that clarifies things. I'll be happy to answer any follow-up questions or concerns.
@snakesonabrain We did not add a "State of Field" as it is not listed in the guidelines (https://joss.readthedocs.io/en/latest/submitting.html). However, we would be happy to add this information if required. As for the documentation, is the information provided in the README file, the example Jupyter Notebook, and the doc strings not sufficient? Is a separate autogenerated readthedocs style site mandatory? (especially given the limited scope of this library).
There doesn't need to be a section called "State of the Field", but there should be enough comparison with related tools for a prospective user to make an informed choice.
@asitha-sena I'm happy to accept the README and examples as documentation. I just read API method documentation in the review requirements. But if that is not mandatory for the journal, we can leave things as they are.
I think the question is what is useful/expected by the target audience. If they'll be happy with inline help via docstrings rendered in their IDE, then that's enough. If you'll miss a sizable fraction of the audience by not having a sphinx site that users can browse and link to, then you can recommend creating one.
I believe the readme and examples are sufficient, so I will tick this box now.
@editorialbot generate pdf
@snakesonabrain I added some information about the "state of field" and related tools. Please have a look at the updated paper and let me know if it's sufficient.
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@asitha-sena Thanks for updating!
@jedbrown That concludes my review, all boxes ticked.
Thanks, @asitha-sena for answering my issue in the original repository. It clarified many issues and I think, we can resolve it soon. It is the only thing blocking me review from being complete.
For the rest, I mostly agree with @snakesonabrain, especially with the documentation of the methods. The docstrings are well designed and if you think those are sufficient, I will not object. Especially since the number of exposed functions is small, a full blown website would probably be overkill.
When this last issue is resolved, I will finish my review.
@PaulDebus Thanks for the update. I added some more information to the README as suggested. Hope that addresses your final concern.
@asitha-sena thanks for addressing my concerns and updating the README in a way that helps people with the same confusion I had. Therefore, I can finish my review.
The collaboration on the review was enjoyable and I am confident you will provide the same support for users of the software if any issues should arise. Further, I learned about some interesting tools and formats, which I liked.
@jedbrown I conclude my review, all boxes ticked and ready to go. There is one small stylistic difference between me and the authors, but as coding style is not part of the review, I have no objections left, as all issues have been addressed.