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[REVIEW]: PyIRD: A Python-Based Data Reduction Pipeline for Subaru/IRD and REACH #9126
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@editorialbot generate pdfReference check summary (note 'MISSING' DOIs are suggestions that need verification): ✅ OK DOIs - 10.1117/12.2311836 is OK - 10.1117/12.2561755 is OK - 10.1117/12.968154 is OK - 10.48550/arXiv.2410.11561 is OK - 10.3847/1538-4357/ad8cdd is OK - 10.48550/arXiv.2410.06900 is OK 🟡 SKIP DOIs - No DOI given, and none found for title: IRAF in the Nineties - No DOI given, and none found for title: gpkron ❌ MISSING DOIs - None ❌ INVALID DOIs - NoneSoftware report:
github.com/AlDanial/cloc v 1.98 T=0.19 s (569.9 files/s, 109727.9 lines/s) ------------------------------------------------------------------------------- Language files blank comment code ------------------------------------------------------------------------------- Python 79 1233 1584 4552 reStructuredText 11 641 1017 347 Jupyter Notebook 5 0 10453 242 C 1 2 0 229 Markdown 7 69 3 180 TeX 1 9 0 115 YAML 2 12 11 71 make 1 4 7 9 TOML 1 0 0 3 ------------------------------------------------------------------------------- SUM: 108 1970 13075 5748 -------------------------------------------------------------------------------Commit count by author:
174 Hajime Kawahara 128 Yui Kasagi 5 ZiyingGu 3 Kento Masuda 1 YuiKasagiPaper file info:
📄 Wordcount for
paper.mdis 740✅ The paper includes a
Statement of needsectionLicense info:
✅ License found:
MIT License(Valid open source OSI approved license)@crhea93, @shihyuntang, @profxj – This is the review thread for the paper. All of our communications will happen here from now on.
Please read the "Reviewer instructions & questions" in the first comment above. Please create your checklist typing:
@editorialbot generate my checklistAs 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, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention
https://github.com/openjournals/joss-reviews/issues/9126so 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 the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.
Review checklist for @crhea93
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/prvjapan/pyird?
- 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 (@YuiKasagi) 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?
Minor Notes:
- The example is very good and detailed! However, it would be very convenient if an jupyter notebook mimicking the example was provided.
- On a similar note, could the authors please provide more detail on how the flat fielding and calibration is done.
Thanks @crhea93! @shihyuntang, @profxj – a friendly reminder to get started on your reviews soon please.
Review checklist for @shihyuntang
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/prvjapan/pyird?
- 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 (@YuiKasagi) 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?
Review checklist for @profxj
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/prvjapan/pyird?
- 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 (@YuiKasagi) 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?
Additional comments
My main concern is that some fraction of this code base would greatly benefit from integration within PypeIt. But, oddly, it appears were unaware of PypeIt, even though it is now used for several Subaru instruments. In full disclosure, I am a lead developer of PypeIt.
Anyhow, I don't think this should delay publication of the JOSS paper. But I would encourage them to work with PypeIt going forward.
Thank you very much for your comment, @profxj !
Following your comment, I have now confirmed that PypeIt supports echelle spectrographs similar to IRD. Our concept for developing PyIRD was to create a package that is easy to maintain by specializing it for IRD and REACH, and also optimized for extracting spectra of faint objects. That said, we would be happy to consider integration with PypeIt in the future.
We have also added a brief mention of PypeIt in the revised paper.
You can find the other revisions in thejoss-reviewbranch, and we would appreciate it if you could take a look at them together with release v1.1 (the currentmasterbranch). Once the review-related updates are finalized, we plan to mergejoss-reviewintomaster.14 remaining items
Reference check summary (note 'MISSING' DOIs are suggestions that need verification): ✅ OK DOIs - 10.1117/12.2311836 is OK - 10.1117/12.2561755 is OK - 10.1117/12.968154 is OK - 10.1088/1538-3873/ad1b38 is OK - 10.1016/j.asr.2014.02.024 is OK - 10.21105/joss.02308 is OK - 10.3847/1538-4357/ac7c74 is OK - 10.1038/s41586-020-2649-2 is OK - 10.1038/s41592-019-0686-2 is OK - 10.5281/zenodo.3509134 is OK - 10.3847/1538-3881/adf730 is OK - 10.3847/1538-4357/adddbd is OK - 10.3847/1538-4357/ad8cdd is OK - 10.3847/1538-4357/adcba2 is OK 🟡 SKIP DOIs - No DOI given, and none found for title: IRAF in the Nineties - No DOI given, and none found for title: gpkron ❌ MISSING DOIs - None ❌ INVALID DOIs - None👋 @openjournals/aass-eics, this paper is ready to be accepted and published.
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Doing it live! Attempting automated processing of paper acceptance...Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.
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cff-version: "1.2.0" authors: - family-names: Kasagi given-names: Yui orcid: "https://orcid.org/0000-0002-8607-358X" - family-names: Kawahara given-names: Hajime orcid: "https://orcid.org/0000-0003-3309-9134" - family-names: Gu given-names: Ziying - family-names: Hirano given-names: Teruyuki orcid: "https://orcid.org/0000-0003-3618-7535" - family-names: Kotani given-names: Takayuki orcid: "https://orcid.org/0000-0001-6181-3142" - family-names: Kuzuhara given-names: Masayuki orcid: "https://orcid.org/0000-0002-4677-9182" - family-names: Masuda given-names: Kento orcid: "https://orcid.org/0000-0003-1298-9699" doi: 10.5281/zenodo.18264940 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Kasagi given-names: Yui orcid: "https://orcid.org/0000-0002-8607-358X" - family-names: Kawahara given-names: Hajime orcid: "https://orcid.org/0000-0003-3309-9134" - family-names: Gu given-names: Ziying - family-names: Hirano given-names: Teruyuki orcid: "https://orcid.org/0000-0003-3618-7535" - family-names: Kotani given-names: Takayuki orcid: "https://orcid.org/0000-0001-6181-3142" - family-names: Kuzuhara given-names: Masayuki orcid: "https://orcid.org/0000-0002-4677-9182" - family-names: Masuda given-names: Kento orcid: "https://orcid.org/0000-0003-1298-9699" date-published: 2026-01-17 doi: 10.21105/joss.09126 issn: 2475-9066 issue: 117 journal: Journal of Open Source Software publisher: name: Open Journals start: 9126 title: "PyIRD: A Python-Based Data Reduction Pipeline for Subaru/IRD and REACH" type: article url: "https://joss.theoj.org/papers/10.21105/joss.09126" volume: 11 title: "PyIRD: A Python-Based Data Reduction Pipeline for Subaru/IRD and REACH"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.
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@crhea93, @shihyuntang, @profxj – many thanks for your reviews here! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨
@YuiKasagi – your paper is now accepted and published in JOSS ⚡🚀💥
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@arfon Many thanks for your support and coordination during the review!
@crhea93 @shihyuntang @profxj Thank you for the detailed and constructive feedback — it was incredibly helpful.
☺️ 🙌
Submitting author: @YuiKasagi (Yui Kasagi)
Repository: https://github.com/prvjapan/pyird
Branch with paper.md (empty if default branch): master
Version: v1.2.0
Editor: @arfon
Reviewers: @crhea93, @shihyuntang, @profxj
Archive: 10.5281/zenodo.18264940
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