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[REVIEW]: ShOpt.jl: A Julia Package for Empirical Point Spread Function Characterization of JWST NIRCam Data #6144

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editorialbot opened this issue Dec 13, 2023 · 108 comments
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AAS Papers being published together with a AAS submission HTML Julia Jupyter Notebook paused review TeX Track: 1 (AASS) Astronomy, Astrophysics, and Space Sciences

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editorialbot commented Dec 13, 2023

Submitting author: @EdwardBerman (Edward Berman)
Repository: https://github.com/EdwardBerman/shopt
Branch with paper.md (empty if default branch):
Version: v2.0.1
Editor: @ivastar
Reviewers: @kevinmicha, @jpierel14, @aymgal
Archive: Pending

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/23d4688dd417e29f321349f0126f50f8"><img src="https://joss.theoj.org/papers/23d4688dd417e29f321349f0126f50f8/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/23d4688dd417e29f321349f0126f50f8/status.svg)](https://joss.theoj.org/papers/23d4688dd417e29f321349f0126f50f8)

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

@kevinmicha & @jpierel14, 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 @ivastar 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 @kevinmicha

📝 Checklist for @jpierel14

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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:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.48 s (72.8 files/s, 10202.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           19            415            453           1892
Markdown                         4            235              0            698
TeX                              2             63              0            385
YAML                             3             15              4             59
HTML                             1              5              0             40
Jupyter Notebook                 2              0            579             30
Python                           1              3              1             13
Bourne Shell                     2              5              0              7
SVG                              1              0              0              1
-------------------------------------------------------------------------------
SUM:                            35            741           1037           3125
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 1833

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

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

OK DOIs

- 10.1177/0278364918784361 is OK
- 10.1017/9781009166164 is OK
- 10.21105/joss.03866 is OK
- 10.21105/joss.00615 is OK
- 10.21105/joss.00602 is OK
- 10.1086/338085 is OK
- 10.1093/mnras/staa3679 is OK
- 10.1117/12.489103 is OK
- 10.1117/12.925447 is OK
- 10.1088/1538-3873/acac53 is OK
- 10.1088/0004-6256/150/5/150 is OK
- 10.3847/1538-4357/ac7c74 is OK
- 10.1117/12.2056689 is OK
- 10.1117/12.925230 is OK
- 10.1007/s11214-006-8315-7 is OK
- 10.1111/j.1365-2966.2010.16277.x is OK
- 10.1086/131977 is OK
- 10.1117/12.925447 is OK
- 10.1117/12.615554 is OK
- 10.3847/1538-4357/ac7c74 is OK
- 10.1007/s41781-021-00053-3 is OK

MISSING DOIs

- 10.1016/j.ascom.2015.02.002 may be a valid DOI for title: GalSim: The modular galaxy image simulation toolkit

INVALID DOIs

- None

@kevinmicha
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kevinmicha commented Dec 13, 2023

Review checklist for @kevinmicha

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/EdwardBerman/shopt?
  • 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 (@EdwardBerman) 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?

@kevinmicha
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kevinmicha commented Dec 17, 2023

Hi @EdwardBerman et al., I have been reviewing the ShOpt.jl repository (and paper), and I must say this is a solid contribution to the PSF modelling field!

I have opened two issues in your repository so far; please let me know when they are fixed so I can continue to check the boxes:

[JOSS] Reproducibility: Figure 2
[JOSS] Paper comments

@jpierel14
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jpierel14 commented Jan 4, 2024

Review checklist for @jpierel14

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/EdwardBerman/shopt?
  • 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 (@EdwardBerman) 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?

@kevinmicha
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Hi,

@EdwardBerman et al. have solved the issues I opened via the Dec 23, 2023 and Jan 4, 2024 commits.

@ivastar I have ticked all the boxes and am happy to recommend ShOpt for publication in JOSS. Well done @EdwardBerman et al.!

@ivastar
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ivastar commented Jan 9, 2024

@kevinmicha thank you for the expeditious review!

Pinging @jpierel14 with a reminder to please complete the outstanding items in the checklist. Let me know if I can be of assistance.

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ivastar commented Jan 10, 2024

@editorialbot add @aymgal as reviewer

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@aymgal added to the reviewers list!

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ivastar commented Jan 10, 2024

@EdwardBerman, adding one more reviewer as @jpierel14 reported issues with the functionality testing due to IT issues at his institute. @aymgal, please only do the functionality testing part of the checklist. Let me know if there are questions.

@jpierel14
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@ivastar Sorry can you point me to where the most recent version of the paper is? I read the version linked above, but then noticed in here that the paper had been updated. I see in the repo, the pdf has not been updated but the markdown version of the paper has, and does not match the pdf linked above by the bot. I have read the paper though and am ready to give comments, just want to make sure I'm on the most recent version!

@EdwardBerman
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@editorialbot generate pdf

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Does this update the PDF for you? Otherwise I'll push an updated PDF to the repository.

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

@jpierel14
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@EdwardBerman ah yep that one is updated, thank you!

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@editorialbot generate pdf

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Regenerated pdf to fix one last typo

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@editorialbot check references

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Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "primaryClass" (NAME) [#<BibTeX::Bibliography data=[29]>, "@", #<BibTeX::Entry >, {:title=>["COSMOS-Web: Intrinsically Luminous z$\\gtrsim$10 Galaxy Candidates Test Early Stellar Mass Assembly"], :author=>["Caitlin M. Casey and Hollis B. Akins and Marko Shuntov and Olivier Ilbert and Louise Paquereau and Maximilien Franco and Christopher C. Hayward and Steven L. Finkelstein and Michael Boylan-Kolchin and Brant E. Robertson and Natalie Allen and Malte Brinch and Olivia R. Cooper and Xuheng Ding and Nicole E. Drakos and Andreas L. Faisst and Seiji Fujimoto and Steven Gillman and Santosh Harish and Michaela Hirschmann and Shuowen Jin and Jeyhan S. Kartaltepe and Anton M. Koekemoer and Vasily Kokorev and Daizhong Liu and Arianna S. Long and Georgios Magdis and Claudia Maraston and Crystal L. Martin and Henry Joy McCracken and Jed McKinney and Bahram Mobasher and Jason Rhodes and R. Michael Rich and David B. Sanders and John D. Silverman and Sune Toft and Aswin P. Vijayan and John R. Weaver and Stephen M. Wilkins and Lilan Yang and Jorge A. Zavala"], :year=>["2023"], :eprint=>["2308.10932"], :archiveprefix=>["arXiv"], :doi=>["10.48550/arXiv.2308.10932"]}]

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Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "archivePrefix" (NAME) [#<BibTeX::Bibliography data=[31]>, "@", #<BibTeX::Entry >, {:title=>["JADES + JEMS: A Detailed Look at the Buildup of Central Stellar Cores and Suppression of Star Formation in Galaxies at Redshifts 3 < z < 4.5"], :author=>["Zhiyuan Ji and Christina C. Williams and Sandro Tacchella and Katherine A. Suess and William M. Baker and Stacey Alberts and Andrew J. Bunker and Benjamin D. Johnson and Brant Robertson and Fengwu Sun and Daniel J. Eisenstein and Marcia Rieke and Michael V. Maseda and Kevin Hainline and Ryan Hausen and George Rieke and Christopher N. A. Willmer and Eiichi Egami and Irene Shivaei and Stefano Carniani and Stephane Charlot and Jacopo Chevallard and Emma Curtis-Lake and Tobias J. Looser and Roberto Maiolino and Chris Willott and Zuyi Chen and Jakob M. Helton and Jianwei Lyu and Erica Nelson and Rachana Bhatawdekar and Kristan Boyett and Lester Sandles"], :year=>["2023"], :eprint=>["2305.18518"], :doi=>["10.48550/arXiv.2305.18518"]}]

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

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

OK DOIs

- 10.3847/1538-3881/ace7ca is OK
- 10.1177/0278364918784361 is OK
- 10.1515/9781400830244 is OK
- 10.1017/9781009166164 is OK
- 10.21105/joss.03866 is OK
- 10.21105/joss.00615 is OK
- 10.21105/joss.00602 is OK
- 10.1086/338085 is OK
- 10.1093/mnras/staa3679 is OK
- 10.3847/1538-4357/acc2bc is OK
- 10.1117/12.489103 is OK
- 10.1117/12.925447 is OK
- 10.1088/1538-3873/acac53 is OK
- 10.1088/0004-6256/150/5/150 is OK
- 10.3847/1538-4357/ac7c74 is OK
- 10.1117/12.2056689 is OK
- 10.1117/12.925230 is OK
- 10.1007/s11214-006-8315-7 is OK
- 10.1111/j.1365-2966.2010.16277.x is OK
- 10.1086/131977 is OK
- 10.1117/12.925447 is OK
- 10.1117/12.615554 is OK
- 10.3847/1538-3881/ad14f7 is OK
- 10.3847/1538-4357/ac7c74 is OK
- 10.48550/arXiv.2308.10932 is OK
- 10.1007/s41781-021-00053-3 is OK
- 10.48550/arXiv.2305.18518 is OK
- 10.3847/2041-8213/ac9586 is OK
- 10.3847/2041-8213/ac8f93 is OK
- 10.3847/2041-8213/ac8803 is OK
- 10.3847/2041-8213/ac9c02 is OK
- 10.21105/joss.05340 is OK

MISSING DOIs

- 10.1016/j.ascom.2015.02.002 may be a valid DOI for title: GalSim: The modular galaxy image simulation toolki...
- No DOI given, and none found for title: PSFEx: Point Spread Function Extractor
- No DOI given, and none found for title: Automated Morphometry with SExtractor and PSFEx
- 10.3847/1538-4357/ad1183 may be a valid DOI for title: Characterization of JWST NIRCam PSFs and Implicati...

INVALID DOIs

- https://doi.org/10.48550/arXiv.1607.07892 is INVALID because of 'https://doi.org/' prefix

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

OK DOIs

- 10.3847/1538-3881/ace7ca is OK
- 10.1177/0278364918784361 is OK
- 10.1515/9781400830244 is OK
- 10.1017/9781009166164 is OK
- 10.21105/joss.03866 is OK
- 10.21105/joss.00615 is OK
- 10.48550/arXiv.1607.07892 is OK
- 10.21105/joss.00602 is OK
- 10.1086/338085 is OK
- 10.1093/mnras/staa3679 is OK
- 10.3847/1538-4357/acc2bc is OK
- 10.1117/12.489103 is OK
- 10.1117/12.925447 is OK
- 10.1088/1538-3873/acac53 is OK
- 10.1088/0004-6256/150/5/150 is OK
- 10.3847/1538-4357/ac7c74 is OK
- 10.1016/j.ascom.2015.02.002 is OK
- 10.1117/12.2056689 is OK
- 10.1117/12.925230 is OK
- 10.1007/s11214-006-8315-7 is OK
- 10.1111/j.1365-2966.2010.16277.x is OK
- 10.1086/131977 is OK
- 10.1117/12.925447 is OK
- 10.1117/12.615554 is OK
- 10.3847/1538-3881/ad14f7 is OK
- 10.3847/1538-4357/ac7c74 is OK
- 10.48550/arXiv.2304.13776 is OK
- 10.48550/arXiv.2308.10932 is OK
- 10.1007/s41781-021-00053-3 is OK
- 10.48550/arXiv.2305.18518 is OK
- 10.3847/2041-8213/ac9586 is OK
- 10.3847/2041-8213/ac8f93 is OK
- 10.3847/2041-8213/ac8803 is OK
- 10.3847/2041-8213/ac9c02 is OK
- 10.21105/joss.05340 is OK

MISSING DOIs

- No DOI given, and none found for title: Automated Morphometry with SExtractor and PSFEx

INVALID DOIs

- ascl:1301.001 is INVALID (failed connection)

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

OK DOIs

- 10.3847/1538-3881/ace7ca is OK
- 10.1177/0278364918784361 is OK
- 10.1515/9781400830244 is OK
- 10.1017/9781009166164 is OK
- 10.21105/joss.03866 is OK
- 10.21105/joss.00615 is OK
- 10.48550/arXiv.1607.07892 is OK
- 10.21105/joss.00602 is OK
- 10.1086/338085 is OK
- 10.1093/mnras/staa3679 is OK
- 10.3847/1538-4357/acc2bc is OK
- 10.1117/12.489103 is OK
- 10.1117/12.925447 is OK
- 10.1088/1538-3873/acac53 is OK
- 10.1088/0004-6256/150/5/150 is OK
- 10.3847/1538-4357/ac7c74 is OK
- 10.1016/j.ascom.2015.02.002 is OK
- 10.1051/aas:1996164 is OK
- 10.1117/12.2056689 is OK
- 10.1117/12.925230 is OK
- 10.1007/s11214-006-8315-7 is OK
- 10.1111/j.1365-2966.2010.16277.x is OK
- 10.1086/131977 is OK
- 10.1117/12.925447 is OK
- 10.1117/12.615554 is OK
- 10.3847/1538-3881/ad14f7 is OK
- 10.3847/1538-4357/ac7c74 is OK
- 10.48550/arXiv.2304.13776 is OK
- 10.48550/arXiv.2308.10932 is OK
- 10.1007/s41781-021-00053-3 is OK
- 10.48550/arXiv.2305.18518 is OK
- 10.3847/2041-8213/ac9586 is OK
- 10.3847/2041-8213/ac8f93 is OK
- 10.3847/2041-8213/ac8803 is OK
- 10.3847/2041-8213/ac9c02 is OK
- 10.21105/joss.05340 is OK

MISSING DOIs

- No DOI given, and none found for title: PSFEx: Point Spread Function Extractor

INVALID DOIs

- None

@EdwardBerman
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@ivastar I've updated all references to published versions and tracked down all of the DOI's except for one. I can't seem to find the one for PSFex anywhere, not on NASA ADS, google scholar, or any publishing site. I'm not sure it exists? Can you suggest to me a next step.

Beyond that, I have one more writing change I'd like to make per your editorial comments, and then I will have addressed everything. Thanks!

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ivastar commented Mar 21, 2024

Doh. This is the only thing I can find for PSFex:

https://ui.adsabs.harvard.edu/abs/2013ascl.soft01001B/exportcitation

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

OK DOIs

- 10.3847/1538-3881/ace7ca is OK
- 10.1177/0278364918784361 is OK
- 10.1515/9781400830244 is OK
- 10.1017/9781009166164 is OK
- 10.21105/joss.03866 is OK
- 10.21105/joss.00615 is OK
- 10.48550/arXiv.1607.07892 is OK
- 10.21105/joss.00602 is OK
- 10.1086/338085 is OK
- 10.1093/mnras/staa3679 is OK
- 10.3847/1538-4357/acc2bc is OK
- 10.1117/12.489103 is OK
- 10.1117/12.925447 is OK
- 10.1088/1538-3873/acac53 is OK
- 10.1088/0004-6256/150/5/150 is OK
- 10.3847/1538-4357/ac7c74 is OK
- 10.1016/j.ascom.2015.02.002 is OK
- 10.1051/aas:1996164 is OK
- 10.1051/aas:1996164 is OK
- 10.1117/12.2056689 is OK
- 10.1117/12.925230 is OK
- 10.1007/s11214-006-8315-7 is OK
- 10.1111/j.1365-2966.2010.16277.x is OK
- 10.1086/131977 is OK
- 10.1117/12.925447 is OK
- 10.1117/12.615554 is OK
- 10.3847/1538-3881/ad14f7 is OK
- 10.3847/1538-4357/ac7c74 is OK
- 10.48550/arXiv.2304.13776 is OK
- 10.48550/arXiv.2308.10932 is OK
- 10.1007/s41781-021-00053-3 is OK
- 10.48550/arXiv.2305.18518 is OK
- 10.3847/2041-8213/ac9586 is OK
- 10.3847/2041-8213/ac8f93 is OK
- 10.3847/2041-8213/ac8803 is OK
- 10.3847/2041-8213/ac9c02 is OK
- 10.21105/joss.05340 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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

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📄 Preprint file created: Find it here in the Artifacts list 📄

@EdwardBerman
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@ivastar I've finished going through your editorial comments and tracking down the correct DOI's. We've received our referee report for our AAS companion paper in the last couple days, and are making our way through the necessary revisions at this time. Let me know if you need anything else on our end, otherwise, I think all that is left is for my coauthors and I to work through the AAS review process. Thanks again for your help!

@ivastar
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ivastar commented Mar 25, 2024

Excellent! Do you think that the code will change in response to the AAS comments? If not, we can may be move ahead with the post-review checklist:

#6144 (comment)

@EdwardBerman
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For the most part any code changes should just be minor edits. I don't anticipate any major changes, although, I'll have to dig deeper into these comments before I can say this for certain.

@ivastar ivastar added the paused label Apr 29, 2024
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ivastar commented Apr 29, 2024

@EdwardBerman following up on this review. Please let me know if there are any developments.

@EdwardBerman
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Hi @ivastar thank you for checking in. I've made a handful of small edits which are now pushed. I'm hoping to finish things up soon for resubmitting the AAS companion paper. I will keep you updated when that happens and any major developments along the way!

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AAS Papers being published together with a AAS submission HTML Julia Jupyter Notebook paused review TeX Track: 1 (AASS) Astronomy, Astrophysics, and Space Sciences
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