[REVIEW]: AirTrafficSim: An open-source web-based air traffic simulation platform. about joss-reviews HOT 70 CLOSED

@AoifeHughes Hope you had a nice break! Apologies for the huge delay in writing the review, I started it last week and plan to submit this week.

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Hi @xoolive and @gmingas,

Thank you for the comments. The paper and documentation have been updated and corrected. We will continue to further enhance the software and collaborate with other open-source packages to create a more robust platform for the community. We would like to extend our heartfelt gratitude for your time, effort, and constructive feedback throughout the review process. Thank you very much.

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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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Software report:

github.com/AlDanial/cloc v 1.88  T=0.01 s (281.0 files/s, 21171.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                              1             10              0            109
Markdown                         1             18              0             43
YAML                             1              8             16             22
-------------------------------------------------------------------------------
SUM:                             3             36             16            174
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 825

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Failed to discover a valid open source license

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@editorialbot set main as branch

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

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Done! branch is now main

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@editorialbot check repository

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.70 s (389.7 files/s, 41695.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                     118             47           6854          13225
Python                          22            877           2177           2447
SVG                             12             20             10            864
TypeScript                      12             79             97            699
Markdown                        15            268              0            588
JSON                            37              2              0            247
CSS                             29             36             27            202
YAML                             3             13             32             59
reStructuredText                19             27             67             42
DOS Batch                        1              8              1             26
HTML                             2              6              1             24
XML                              1              0              0             14
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                           272           1387           9273          18446
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Failed to discover a Statement of need section in paper

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@editorialbot set paper as branch

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Done! branch is now paper

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

OK DOIs

- 10.1080/01441640110074773 is OK
- 10.3390/aerospace9060294 is OK
- 10.1109/ACCESS.2020.2984488 is OK
- 10.3390/aerospace7030024 is OK
- 10.1002/qj.3803 is OK
- 10.1002/acs.1176 is OK
- 10.3390/aerospace7080104 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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Hi everyone, thank you so much for helping to review this paper!

A demo of AirTrafficSim is temporarily hosted at http://airtrafficsim.eastasia.cloudapp.azure.com:6111/ to assist the review process as currently the BADA 3.X performance data license from EuroControl is required to run the simulations. However, AirTrafficSim is extensible to use other open-source performance data such as OpenAP in the future.

Feel free to let me know you if have any questions!

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Review checklist for @xoolive

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/HKUST-OCTAD-LAB/AirTrafficSim?
• 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 (@kyfrankie) 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?

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Review checklist for @gmingas

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/HKUST-OCTAD-LAB/AirTrafficSim?
• 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 (@kyfrankie) 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?

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@kyfrankie thank you for the help, but it looks your link is down!

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Hi, thank you for pointing it out. I have restarted the service and it should be working now at http://airtrafficsim.eastasia.cloudapp.azure.com:6111/. Sorry for the inconvenience caused and feel free to let me know if you have any questions.

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First, thank you for this initiative, I am very much looking forward to using it more (and contribute possibly as a matter of fact!)

About the review now :)

General checks

I am not sure about the data sharing part. I have the BADA files, so I could run the software, but it may be relevant to provide the OpenAP implementation before publishing, so people can really reproduce? I assume this is a more editorial question here.

Let me put boxes to tick as I find it quite convenient too:

• OpenAP implementation (tick if BADA is non-blocking for the editor)
• Specify BADA v3 in the documentation + readme (There is also BADA 4...)
• Explain the content of the model should be unzipped in the BADA folder (or check if you have an archive to unzip), how about multiple versions of BADA 3

Functionality

• Consider making a proper package with an executable that you can run from any folder (poetry is a nice option). You wouldn't require the conda environment.yml (or this one would contain your library) and the package would pull the dependencies by itself upon installation. I didn't tick the "installation" item, as what you describe is more how to prepare your environment (you don't install anything)
• there are few dead imports (e.g. cartopy.crs is not required in weather.py), also why is openap a required dependency if it's not implemented yet? (There are tools for detecting that, like flake8)
• one flight per CSV is really not a reasonable option, also CSV is not a reasonable format (tick if future work, I don't think it is blocking for functionality, but definitely is for performance)
• explain how to switch between "flight plan" mode and "trajectory replay" mode
• careful: many data providers mislabel heading for a track angle. Please consider renaming accordingly.

Documentation

Please consider being more diligent (than me! 🤣) in the documentation but I ticked the box anyway.

However, I cannot tick the box for unit tests as I couldn't see any.

• implement unit tests
• the community guideline item is to be better specified
• I couldn't find how to input a flight plan in ICAO format (e.g. for LFPO to LFBO, N0448F350 ERIXU5B ERIXU DCT ETAMO DCT GUERE DCT NARAK NARAK6L, but I have more with airways, the area implements free route here) and export the result of a simulation to a new file

Software paper

• explain how AirTrafficSim brings added value to BlueSky (apart from using different technology)
• you mention an algorithm for sticking to published airways, but I couldn't find any trace of it (also I don't really understand as a flight plan describes the airways...)

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Hi @kyfrankie, have you had a chance to read over @xoolive 's notes?

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Hi @AoifeHughes, I am one of the co-authors of this paper, Go Nam Lui. I'm sorry for not getting back to you sooner. We read over @xoolive 's notes two weeks ago, and we plan to respond to him after taking care of all his comments. We will update you here in a few days.

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Hi all,

Could I firstly say happy new year to everyone and hope you had a nice winter break! Have we any updates on this review. Please do let me know if there are any issues from either the reviewers' side or if authors' have concerns or questions. Very happy to help!

@harrylui1995 @gmingas @xoolive @kyfrankie

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Thanks for the submission. This is a very interesting and potentially useful piece of software.

At the moment there are a few missing items for me that prevent me from ticking all the boxes in the review. I created issues for each one in the software repo and a list is included here:

• Tests and a CI should be added see here
• One statement in the paper needs further clarification see here
• The Simulation button in the UI fails see here
• Map sometimes fails to render see here
• More installation instructions needed for BADA see here
• Docstrings missing/incomplete and formatted inconsistently see here
• Contribution guide could be added see here

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Dear Reviewers,

Thank you for your thorough comments. Your suggestions help a lot. Since we are all amateurs in managing open-source projects, the process is slow. We mainly draw @xoolive's comments here.

We have implemented a series of unit tests on the core functions and debugged some of the problems.

For the OpenAP implementation, we still plan to include it in the future, owing to the workload. We have updated documentation to specify the BADA version and the associated installation guidance and deleted the content related to OpenAP in the documentation and Readme.

As for building a python package, we found that because of the dependencies with the Cartopy package, Conda is better than pip. The current status is that we are still dealing with the conda build and the recipes. We will update you once it works.

Thanks for your kind suggestion for the data format. CSV format is first deployed to log aircraft movements in our software because of its row-major format. Besides, it facilitates monitoring purposes since it's human-readable. Later, we will implement the Parquet format to reduce storage consumption.

Regarding the ICAO format for the flight plan, the software only considers waypoints' ICAO name to build its plan currently. We plan to implement the function to read an ICAO format flight plan. We also updated the documentation for more clarity. The "simulation" and "replay" codes are explained in Navigating the UI - AirTrafficSim (hkust-octad-lab.github.io). The algorithm to detect published airways is being developed and has yet to be available. The sentence has been removed to avoid confusion. Thank you for the suggestion.

We also notice @gmingas' comments. We will update everyone again once the software has been updated to address the issues.

Lastly, happy Lunar New Year, everyone!

Best,
Frankie

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@kyfrankie @harrylui1995 恭禧發財!

About pip vs conda, your package should describe the dependencies, regardless of pip and conda. If some of your dependencies require some external dependencies, you should leave the choice to the user to use one option or the other for the installation.

As a matter of fact, publishing a package on conda-forge requires that you have a package on pip as well...

Good luck anyway, don't hesitate to ping if you need help

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Hi @kyfrankie, just wanting to check in with how you're getting on? Reviewers also, do let me know if U can help with anything.

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Pinging again @kyfrankie.

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Hi, I am sorry for the delayed response. I was distracted with other commitments but we are working on updating the software to meet the suggestions from reviewers (mainly to incorporate the automated testing and openAP library which requires various modifications to the code). We aim to complete everything by the end of April. Sorry for the delay once again.

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That's no problem. I've made a note of this and can check back in with you at the start of May. Otherwise, you're very welcome to update here when you have an update yourself. Absolutely no pressure or worries, I completely understand. Hope all is well!

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Hi @kyfrankie no worries on timings, I just wanted to see if we had an update and to make sure this doesn't get forgotten about (by me 😊)

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Dear editor and reviewers,

Thank you a lot for your patience and all your comments. They are very useful and have helped us to develop a better open-source software package. We have improved AirTrafficSim to address the comments and suggestions and I would like to provide a summary below:

• Completed set up of automated testing with pytest and Coverage.py. Integration testing has been implemented.
• Packaged and published AirTrafficSim on the conda-forge channel. Related installation instruction has been updated.
• Initial integration of OpenAP open-source aircraft performance model.
• Fixed and improved code quality, dead imports and docstrings.
• Clarified and improved paper and documentation wording.
• Added contribution guideline.
• Specified BADA version and updated installation guide.
• Updated UI to address issue

We hope this can address the issues and we would like to express our sincere gratitude for your patience and time to edit and review this work. We will continue to work on developing AirTrafficSim to improve its code quality and features, for example, using better file structure than CSV files, using ICAO flight plan format, using the Traffic package to handle OpenSky data, improving UI, adding more test cases, and more.

Please feel free to let me know if you have any questions. Thanks.

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@editorialbot generate pdf

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

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Hi all, I wonder with these changes that @kyfrankie has made could the reviewers confirm if they are happy with this and can proceed in completing their checklists?

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Hi @kyfrankie @harrylui1995 @AoifeHughes

Very good job!! There has been significant improvement since last time.

Few remarks though.

About the paper:

• line 11: I would recommend that you don't use the qualifier "microscopic" for ATM research. There's not much that is microscopic in ATM...
• line 22: typo: "compare d to"
• line 23: maybe "control the aircraft with external modules" rather than limiting yourself to "reinforcement learning"
• line 42: can we use other sources of (possibly closed) sources of navigation data
• general comment: why not mentioning the ability to replay existing traffic (from ADS-B for instance)

In the documentation:

• fix -- init to --init

There are still quite some glitches in the code, but nothing critical to me.
I will tick all the boxes, so I am not blocking the process, but please consider these comments.

Please keep in touch for integration with traffic

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@kyfrankie @harrylui1995 Thanks so much for the changes, it looks really food now and congrats for packaging the library and putting it in conda.

I updated my checklist and the only things left to do I think are a couple of changes to the documentation:

• Make sure docs point to BADA website where users can get a license, to avoid them having to search for it.
• Change the -- init to --init, as it currently fails (mentioned above by @xoolive)

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@xoolive @gmingas Thank you so much for your valuable comments on this software, they really help us improve the platform entirely. *Also looking forward to integrating this platform with https://github.com/xoolive/traffic

We also would like to express our deep gratitude to the editor in charge @AoifeHughes, for actively keeping the process up since November.

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Morning @harrylui1995, Just a few quick thoughts on the paper.md

• "timestep" -> "time step"
• "an easy-to-use API..." this sentence could be reworked, I wouldn't say that "reinforcement learning" is an algorithm. So maybe even just dropping the "such as" part of the sentence.
• Figure 1, could you add more text to the legend so that the figure can be more easily understood
• Add a citation for "Iconic react"
  • and Flask + other key libraries you've mentioned.

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@editorialbot generate pdf

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

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Good morning @AoifeHughes, thanks for your comments. We just drawed your first two comments, and will update the Figure 1 and citations soon.

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Thanks @AoifeHughes and @harrylui1995 for the comments and help, they are all addressed now. Please feel free to let me know if further improvement is needed.

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Hi @kyfrankie At this point could you:

• Update the figure legend as @harrylui1995 mentioned
• Update the citations

Then the next steps will be to:

• Make a tagged release of your software, and list the version tag of the archived version here.
• Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
• Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
• Please list the DOI of the archived version here.

I can then move forward with recommending acceptance of the submission.

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@editorialbot generate pdf

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

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Hi @AoifeHughes, thanks for the comments.

The figures and citations should have been updated in the paper already. Please let me know if further adjustment is needed. In addition, the software was tagged with release 0.1.0 and the archive was uploaded to Zenodo with doi 10.5281/zenodo.8070119.

Thank you for much for the guidance along the process.

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@editorialbot set 10.5281/zenodo.8070119 as archive

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Done! archive is now 10.5281/zenodo.8070119

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@editorialbot set 0.1.0 as version

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Done! version is now 0.1.0

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@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

OK DOIs

- 10.1080/01441640110074773 is OK
- 10.3390/aerospace9060294 is OK
- 10.1109/ACCESS.2020.2984488 is OK
- 10.3390/aerospace7030024 is OK
- 10.1002/qj.3803 is OK
- 10.1002/acs.1176 is OK
- 10.3390/aerospace7080104 is OK

MISSING DOIs

- 10.1016/j.trc.2022.103811 may be a valid DOI for title: Weather impact quantification on airport arrival on-time performance through a Bayesian statistics modeling approach
- 10.1088/1755-1315/569/1/012067 may be a valid DOI for title: Towards understanding the impact of convective weather on aircraft arrival traffic at the Hong Kong International Airport
- 10.1109/ipsn.2014.6846743 may be a valid DOI for title: Bringing up OpenSky: A large-scale ADS-B sensor network for research

INVALID DOIs

- None

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👋 @openjournals/pe-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#4333, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

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Updated the doi reference

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@editorialbot generate pdf

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

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This looks good to me!

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@editorialbot check references

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

OK DOIs

- 10.1080/01441640110074773 is OK
- 10.3390/aerospace9060294 is OK
- 10.1109/ACCESS.2020.2984488 is OK
- 10.3390/aerospace7030024 is OK
- 10.1002/qj.3803 is OK
- 10.1002/acs.1176 is OK
- 10.3390/aerospace7080104 is OK
- 10.1016/j.trc.2022.103811 is OK
- 10.1088/1755-1315/569/1/012067 is OK
- 10.1109/ipsn.2014.6846743 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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@editorialbot accept

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

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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:

cff-version: "1.2.0"
authors:
- family-names: Hui
  given-names: Ka Yiu
- family-names: Nguyen
  given-names: Chris HC.
- family-names: Lui
  given-names: Go Nam
- family-names: Liem
  given-names: Rhea P.
contact:
- family-names: Lui
  given-names: Go Nam
- family-names: Liem
  given-names: Rhea P.
doi: 10.5281/zenodo.8070119
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Hui
    given-names: Ka Yiu
  - family-names: Nguyen
    given-names: Chris HC.
  - family-names: Lui
    given-names: Go Nam
  - family-names: Liem
    given-names: Rhea P.
  date-published: 2023-06-22
  doi: 10.21105/joss.04916
  issn: 2475-9066
  issue: 86
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 4916
  title: "AirTrafficSim: An open-source web-based air traffic simulation
    platform."
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.04916"
  volume: 8
title: "AirTrafficSim: An open-source web-based air traffic simulation
  platform."

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.

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🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

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🚨🚨🚨 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 👉 openjournals/joss-papers#4334
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04916
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...

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Congratulations @kyfrankie on your article's publication in JOSS! Please sign up as a reviewer to help with future submissions, if you haven't already.

Many thanks to @gmingas and @xoolive for reviewing this, and @AoifeHughes for editing.

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

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reStructuredText:
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This is how it will look in your documentation:

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The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://reviewers.joss.theoj.org/join
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

from joss-reviews.