[REVIEW]: PyNGHam: A Python library of the NGHam protocol

[editorialbot]

Submitting author: @mgm8 (Gabriel Marcelino)
Repository: https://github.com/mgm8/pyngham
Branch with paper.md (empty if default branch): main
Version: v1.1.1
Editor: @jbytecode
Reviewers: @pritchardn, @0xCoto
Archive: 10.5281/zenodo.7555428

Status

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Markdown: [![status](https://joss.theoj.org/papers/cf5b9150f924d3fbb6adee6cd253e040/status.svg)](https://joss.theoj.org/papers/cf5b9150f924d3fbb6adee6cd253e040)

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Checklists

📝 Checklist for @0xCoto

📝 Checklist for @pritchardn

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (730.4 files/s, 76310.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          11            329            531            945
reStructuredText                 8            228            149            403
Markdown                         4             74              0            122
YAML                             4             22             33             99
TeX                              1              8              0             67
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            29            665            720           1645
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1143

[editorialbot]

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

[editorialbot]

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

OK DOIs

- 10.13140/RG.2.1.1806.0408 is OK
- 10.1137/0108018 is OK
- 10.1109/TLA.2020.9085277 is OK

MISSING DOIs

- Errored finding suggestions for "NGHam protocol", please try later

INVALID DOIs

- None

[jbytecode]

Dear @pritchardn, @0xCoto

Thank you again, for accepting our invitation to review.

This is the review thread. Please, firstly type

@editorialbot generate my checklist

to generate your own checklist. In that checklist, there are ~20 check items. Whenever you complete the corresponding task, you can check off them.

Please write your comments as separate posts and do not modify your checklist descriptions.

The review process is interactive so you can always interact with the authors, reviewers, and the editor. You can also create issues and pull requests in the target repo. Please do mention this thread's URL in the issues so we can keep tracking what is going on out of our world.

Please do not hesitate to ask me about anything, anytime.

Thank you in advance!

[0xCoto]

Review checklist for @0xCoto

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/mgm8/pyngham?
• 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 (@mgm8) 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?

[pritchardn]

Review checklist for @pritchardn

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/mgm8/pyngham?
• 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 (@mgm8) 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?

[0xCoto]

@mgm8 - Could you please comment on how this library compares against conventional DSP tools (such as GNU Radio, whose versatility may permit similar processing pipelines)? Considering GNU Radio's increasing popularity in the field of satellite communications, I think it would be useful for readers to understand the cases where PyNGHam could replace/complement the functionality of GNU Radio-based modules, such as gr-nuts.

Some initial minor comments (language suggestions to improve the quality of the manuscript):

• Line 9: improves considerably → considerably improves
• Line 10: of a communication link → of the communication link
• Line 10: uses → applications
• Line 11: in → (remove)
• Line 11-12: as the protocol of the radio links between stations on Earth and a satellite → supporting a reliable communication link between the ground station and the satellite
• Line 12: allows → enables
• Line 15: was developed → was originally developed (to make its initial development clear and distinguish it from the work being presented in the paper)
• Line 16: After that, it was → It was later on
• Line 17: in the → `on the
• Line 17: it's being used → is being used or has been used (if not all missions are still active).
• Line 21-25: Consider linking relevant references for each satellite mission (where available)
• Line 26: on the list above, → of the above list
• Line 28: which was the context → (remove)
• Line 30-32: This paragraph needs rewording; "this way" does not quite seem to link the two sentences in a manner that appears fully relevant to one another.
• Line 33-35: This library is already being used in the development of the satellites of the SpaceLab, specifically in the ground station software [@spacelab-decoder] [@spacelab-transmitter], that sends telecommand and receives data to/from the satellites. → This library is already being used in the design of satellites by SpaceLab, as part of the ground station software [@spacelab-decoder; @spacelab-transmitter] responsible for the uplink of telecommands and downlink of telemetry/payload data.
• Line 37: idea → intention
• Line 38: using an FEC → using a FEC
• Line 38: and a well-defined → on a well-defined
• Line 40: is used → is employed
• Line 42: "GMSK" is an undefined acronym (should be "Gaussian minimum-shift keying")
• Line 42: 0xAAAAAAAA → `0xAAAAAAAA` (i.e., surround sequence with "`" to differentiate it from the font/format of the rest of the paragraph)
• Line 44-45: The size tag field has seven different options, indicating seven different packet sizes, as described below. → The size tag field has seven different options, each corresponding to a unique packet size described in Table 1.

(More to come)

Also, it might be useful to mention what "NGHam" stands for (i.e. "Next Generation Ham Radio") somewhere, as it does not appear to be a very well-known protocol. The reader currently has to head to the Skagmo (2014) reference to figure this out.

[pritchardn]

I'll be adding my comments as I go, I plan to have my review completed in the next two weeks 😄

Documentation - Statement of Need: There is a space in the overview page for explaining the point of the protocol however the last sentence, where the statement of need actually is seems unfinished - ending with , and so far.

Consider elaborating a little more about why an easy-to-use Python-based implementation is useful (I think it is, but I'd like to see it written) - especially since this is a pure-python implementation, rather than a binding of the original implementation,

[jbytecode]

@mgm8 - Our reviewers have suggested some corrections, could you please update your status? Thank you in advance.

[pritchardn]

Documentation - Community Guidlines
I can see the CONTRIBUTING.md file, I would suggest:

• Mentioning its existence in the main README.md and main documentation (users just installing through pip may never look at the source).
• Mentioning how to reach out for support, not just bug reporting and code-contributions

Just makes things super clear and easily accessible 😄

[pritchardn]

Functionality documentation
I appreciate the description of the protocol itself, but documenting the API is necessary to make it clear how to use the library.

As a good start, writing proper docstrings in the main classes and methods will populate tooltips in IDEs and be a good start towards automating API doc generation - Sphinx has some pretty powerful autodoc features that make life easier.

[jbytecode]

@mgm8 - could you please update your status?

[mgm8]

@mgm8 - Could you please comment on how this library compares against conventional DSP tools (such as GNU Radio, whose versatility may permit similar processing pipelines)? Considering GNU Radio's increasing popularity in the field of satellite communications, I think it would be useful for readers to understand the cases where PyNGHam could replace/complement the functionality of GNU Radio-based modules, such as gr-nuts.

Some initial minor comments (language suggestions to improve the quality of the manuscript):

• Line 9: improves considerably → considerably improves
• Line 10: of a communication link → of the communication link
• Line 10: uses → applications
• Line 11: in → (remove)
• Line 11-12: as the protocol of the radio links between stations on Earth and a satellite → supporting a reliable communication link between the ground station and the satellite
• Line 12: allows → enables
• Line 15: was developed → was originally developed (to make its initial development clear and distinguish it from the work being presented in the paper)
• Line 16: After that, it was → It was later on
• Line 17: in the → `on the
• Line 17: it's being used → is being used or has been used (if not all missions are still active).
• Line 21-25: Consider linking relevant references for each satellite mission (where available)
• Line 26: on the list above, → of the above list
• Line 28: which was the context → (remove)
• Line 30-32: This paragraph needs rewording; "this way" does not quite seem to link the two sentences in a manner that appears fully relevant to one another.
• Line 33-35: This library is already being used in the development of the satellites of the SpaceLab, specifically in the ground station software [@spacelab-decoder] [@spacelab-transmitter], that sends telecommand and receives data to/from the satellites. → This library is already being used in the design of satellites by SpaceLab, as part of the ground station software [@spacelab-decoder; @spacelab-transmitter] responsible for the uplink of telecommands and downlink of telemetry/payload data.
• Line 37: idea → intention
• Line 38: using an FEC → using a FEC
• Line 38: and a well-defined → on a well-defined
• Line 40: is used → is employed
• Line 42: "GMSK" is an undefined acronym (should be "Gaussian minimum-shift keying")
• Line 42: 0xAAAAAAAA → `0xAAAAAAAA` (i.e., surround sequence with "`" to differentiate it from the font/format of the rest of the paragraph)
• Line 44-45: The size tag field has seven different options, indicating seven different packet sizes, as described below. → The size tag field has seven different options, each corresponding to a unique packet size described in Table 1.

(More to come)

Also, it might be useful to mention what "NGHam" stands for (i.e. "Next Generation Ham Radio") somewhere, as it does not appear to be a very well-known protocol. The reader currently has to head to the Skagmo (2014) reference to figure this out.

@0xCoto thanks for your comments and suggestions!

All suggestions were fixed in this commit: 913f9e8

About the first comment: This library is independent from high level frameworks like GNURadio. The intention is to use it in final user applications, like satellite decoders used in real satellite missions. It is an alternative to the GNURadio blocks such as the gr-nuts, but independent from the GNURadio ecosystem. It is also useful as a simulation or research/education tool, that can be used in simple Python scripts.

Do you think this explanation should be added to the paper and/or documentation?

[0xCoto]

@mgm8

Do you think this explanation should be added to the paper and/or documentation?

Yes, this is definitely something worth addressing, as readers may be curious as to why they should give this package a try instead of GNU Radio. The potential applications and purpose of the package should be made clear in the manuscript.

You can also briefly state the advantages NGHam offers compared to other modulation/encoding schemes used in CubeSats, to emphasize the importance of having a Python-based solution for something like this.

[mgm8]

@mgm8

Do you think this explanation should be added to the paper and/or documentation?

Yes, this is definitely something worth addressing, as readers may be curious as to why they should give this package a try instead of GNU Radio. The potential applications and purpose of the package should be made clear in the manuscript.

You can also briefly state the advantages NGHam offers compared to other modulation/encoding schemes used in CubeSats, to emphasize the importance of having a Python-based solution for something like this.

@0xCoto Ok, fixed in 3e4b63d!

Documentation - Statement of Need: There is a space in the overview page for explaining the point of the protocol however the last sentence, where the statement of need actually is seems unfinished - ending with , and so far.

Consider elaborating a little more about why an easy-to-use Python-based implementation is useful (I think it is, but I'd like to see it written) - especially since this is a pure-python implementation, rather than a binding of the original implementation,

@pritchardn I think this commit also solves your first suggestion.

[mgm8]

Documentation - Community Guidlines I can see the CONTRIBUTING.md file, I would suggest:

• Mentioning its existence in the main README.md and main documentation (users just installing through pip may never look at the source).
• Mentioning how to reach out for support, not just bug reporting and code-contributions

Just makes things super clear and easily accessible smile

@pritchardn Thanks for your suggestions! I improved the references to the contributing instructions in 4533d5c and cebe889.

[0xCoto]

@editorialbot generate pdf

[editorialbot]

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

[mgm8]

@editorialbot generate pdf

@0xCoto Sorry, I made the last changes in a different branch and I think the generated article proof is outdated. I just merged the dev branch to the main and now the article proof should be updated.

[mgm8]

@editorialbot generate pdf

[editorialbot]

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

[0xCoto]

@mgm8 - Comments for the rest of the manuscript:

• "Statement of need" → "Statement of Need" (section capitalization is inconsistent)
• In Table 1, the "up to" prefixes can be neglected, since the header "Max. Data Size" already indicates the upper limit.
• Line 32-33: "GNURadio" → "GNU Radio" (and should be cited for those unfamiliar with the GNU Radio framework)
• Line 52: "Inside the code block, there are two types of fields" → "The code block consists of two types of fields"
• Line 53-54: "The packet [...] divided in into four fields" needs to be reworded.
• Line 54: "Header" → "header"
• Line 54: Define the "CRC" acronym (Cyclic-Redundancy Code)
• Line 58-59: Since you're referencing CCSDS 131.0-B-3, could CCSDS 131.0-B-3 be more relevant than CCSDS 132.0-B-3? Also, could you please point me to where exactly the polynomial is brought up in the standard? In the manuscript, the polynomial is $x^8+x^7+x^5+x^3+1$. However, the only polynomial I see in the CCSDS 131.0-B-3 standard is on p. 29, which looks a bit different: $F(x) = x^8+x^7+x^2+x+1$. Are these two irrelevant?
• Line 61: "RS code block and gets the original content of the RS part of the packet" → "RS code block, ultimately retrieving the original content of the RS part of the packet."
• Line 62: "sequence" → "sequences"
• Line 62: "avoided," → "mitigated" (remove comma)
• Line 62-63: Change sentence to: "By scrambling the packets via bit transition, long sequences of ones or zeros are avoided."
• Line 63-64: This sentence can be shrunk down to just the citation alone, merged on the previous sentence (which does not have to be a separate paragraph, i.e. can merge with the previous sentence). Also, I do not see Section 8.3 in the cited standard (the last Section appears to be 6.6).
• Line 66: "Besides the RF transmissions using the NGHam protocol" → "While the NGHam protocol can be used to support wireless communications"
• Line 68: "there is no FEC algorithm involved, just" → "no FEC algorithm is involved, but merely"
• Line 68: "if" → "whether"
• Line 69: "or not" → remove
• Line 69: "Both RF and serial protocols" - protocols does not sound like the appropriate term (since the protocol is NGHam). I would suggest "Both the RF and serial options"?
• Line 69: "following" → "subsequent"
• Line 75: What is meant by "repeating information"? Are you referring to a (communication) repeater/relay?
• Line 76: "the" → remove
• Line 78: "was inspired in part" → "was partly inspired"
• Line 80: "there is a class [...] protocol" → "a class [...] protocol is available"
• Line 80: "The" → "the"
• Line 82: Try to reword to avoid two nearby instances of ":" which introduces a bit of confusion. You could also shorten the beginning of line 83 to "packet encoding and decoding"
• Line 84: "or the payload data" unless this is different from "NGHam packet" you could wrap in parentheses or separate by a /, i.e., "NGHam packet/payload data"
• Line 86-87: Change to "The objective of this library is to offer an alternative to the original NGHam library, purely written in Python."
• Line 87: "This way, this" → "In this manner, such package"
• Line 87: "can be easily used in" → "can easily be used to carry out"
• Line 87-88: "packet decoding and encoding software, telecommunication classes, and so on" → "develop packet encoding and decoding tools, introduce telecommunication concepts to students, among others"
• Line 88-90: Sentence requires rewording.
• Line 90-91: This sentence belongs to the previous section (Python Implementation). Also, "in its Sphinx" can be neglected (it is an unimportant detail for the reader). As for the reference, a direct link would be more useful.
• "Acknowledgement" → "Acknowledgements"

[jbytecode]

@editorialbot set 10.5281/zenodo.7555428 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.7555428

[jbytecode]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.13140/RG.2.1.1806.0408 is OK
- 10.1137/0108018 is OK
- 10.1109/TLA.2020.9085277 is OK
- 10.3390/s22103715 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[jbytecode]

@editorialbot generate pdf

[editorialbot]

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

[jbytecode]

Dear @mgm8

Everything seems okay to me. I am now recommending an acceptance. Our track editor will make the final decision.

I hope your library will get more users and your paper gets lots of citations!

Thank you in advance

[jbytecode]

@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

- 10.13140/RG.2.1.1806.0408 is OK
- 10.1137/0108018 is OK
- 10.1109/TLA.2020.9085277 is OK
- 10.3390/s22103715 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/csism-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#3892, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

@mgm8 - I'm the track editor for this submission, and I'll now proofread it, and then move the process towards publication

[danielskatz]

I've suggested some minor changes to the paper in mgm8/pyngham#28 - please merge this, or let e know what you disagree with, then we can continue.

[mgm8]

I've suggested some minor changes to the paper in mgm8/pyngham#28 - please merge this, or let e know what you disagree with, then we can continue.

@danielskatz Done! I accepted the pull request!

[danielskatz]

@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

- 10.13140/RG.2.1.1806.0408 is OK
- 10.1137/0108018 is OK
- 10.1109/TLA.2020.9085277 is OK
- 10.3390/s22103715 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/csism-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#3898, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[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.04915 joss-papers#3899
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04915
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...

[danielskatz]

Congratulations to @mgm8 (Gabriel Marcelino)!!

And thanks to @pritchardn and @0xCoto for reviewing, and to @jbytecode for editing!
We couldn't do this without you

[editorialbot]

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