Closed editorialbot closed 1 month ago
Thanks for your suggestions @Sbozzolo
I've updated the paper to include more citations and detail.
I've also modified the code such that users can use it with the most recent python version as long as they don't want to do center-of-mass corrections. In the case they do want to do center-of-mass corrections, it will tell them they need to downgrade to 3.10. Thanks for that suggestion!
I've also uploaded the recent updates to pypi and zenodo as a new version.
Thanks!
I fully ackowledge my bias here, but I think that the paper is not fairly and fully representing the state of the field.
The paper reads
There are several existing tools to analyze ETK simulations including, but not limited to, Kuibit, Power, PyCactus, and SimulationTools. [...] Each of these tools tackles specific aspects of studying numerical relativity simulations, but more versatile tools are needed. Several of these tools require proprietary software and others still require signicant expertise in numerical relativity data.
This implies that existing tools are limited, not versatile enough, and/or not user friendly enough. However, I think that all these problems are already solved by kuibit. Kuibit was also designed around the idea of exposing physical concepts instead of technical details, so I think it's unfair to say that mayawaves is unique in this (as the paragraph below the quoted one does).
While I think I could be perfectly objective in my review, I do reckognize that I have personal interests here in this particular point. So, I'll let @eloisabentivegna comment on this. This is my last point before giving green light.
Thanks again @deborahferguson for all your hard work during this review!
@Sbozzolo Thanks for your candor, you're correct that it wasn't worded very well. Designing it for intuition and physical concepts are some of my favorite aspects of the library, but you're right that Kuibit is similar in that way and I shouldn't say otherwise. I've done some rephrasing that will hopefully be acceptable. Thanks for all your feedback, it's been very helpful.
Thanks @Sbozzolo for the comments and for disclosing your bias -- I find your viewpoint useful nonetheless. My own perspective is no less biased (I have family connections to SimulationTools), but I have looked at the current wording and find it fair.
It is, however, less descriptive than before. Can we find a description of Mayawaves' unique contributions that we can all agree upon? The creation of Mayawaves must have surely stemmed from shortcomings in the other solutions; the latter should not be understated. @deborahferguson: thanks for the effort so far; could you possibly add a sentence or two explaining your package's unique value to new users?
I've done some additional rephrasing and added some text to make sure it is clear what the unique benefits of Mayawaves are, and I believe the second and third paragraphs of the Statement of Need describe it well. Part of the challenge has been that Mayawaves and Kuibit were being developed at the same time, clearly with a lot of the same ideas, and I want to be sure to give an accurate and fair representation of both.
I appreciate all of your help to improve this paper and library!
Thanks @deborahferguson. I understand the complexities of creating software in a very active field. The new text seems fair to me. @Sbozzolo, could you share your thoughts?
@cjoana, it appears you are done with your checklist -- can you confirm your recommendation?
Hi @eloisabentivegna, please read the follow keeping my bias in mind, and feel free to ignore it if you think my position it too biased. :)
I think the new text is fair, but I don't think it answers the question "Do the authors describe how this software compares to other commonly-used packages?": the other packages are just mentioned and nothing is said about them.
If I were to discuss the state of the field in software for post-processing Einstein Toolkit simulations, I would mention:
watpy
seems to be similar to mayawaves
in working with catalogs (the CoRe one), rugutils
seems to work with grid variables.I think the more accurate representation of the state of the field is that there was an underlying issue with usability and user-friendlines that both kuibit
and mayawaves
tackled approximately at the same time. The directions ended up being slightly different: kuibit is a general purpose library, but it doesn't implement anything to work with catalogs and it is less sophisticated in the analysis of gravitational waves, areas where mayawaves shines.
Hi @eloisabentivegna, @deborahferguson
Yes, I am done with the checklist, for me the paper is ready to go. I do recommend the paper for publication.
@Sbozzolo, thanks for the detailed viewpoint. The description you give is extremely useful and will remain on the record for this review.
At the same time, the Statement of Need and, to a lesser extent, the State of the Field often end up being somewhat subjective to who writes them and when. Others may not agree on the state-of-the-art assessment and the feeling that specific functionality is needed, and the review process is not meant to resolve these divergences but to confirm that the authors have fully documented their motivations for writing a given package at a given point in time. This now seems to have been done.
If this is the last point on your list, can you provide your final recommendation for Mayawaves?
Yes, @eloisabentivegna, I recommend mayawaves for publication in JOSS and I wholeheartely welcome this new user-friendly public code to the community's shared toolkit.
Thanks @cjoana and @Sbozzolo! I will now start pre-publication.
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1088/1361-6382/aa7929 is OK
- 10.1103/PhysRevD.99.023003 is OK
- 10.1038/s41550-021-01568-w is OK
- 10.1088/0264-9381/32/7/074001 is OK
- 10.1088/0264-9381/32/2/024001 is OK
- 10.1103/physrevlett.116.061102 is OK
- 10.1103/physrevx.11.021053 is OK
- 10.1103/physrevx.9.031040 is OK
- 10.1103/physrevx.13.041039 is OK
- 10.1103/physrevlett.119.161101 is OK
- 10.3847/2041-8213/ab75f5 is OK
- 10.1103/PhysRevD.96.123012 is OK
- 10.1103/PhysRevLett.113.151101 is OK
- 10.1103/physrevd.95.044028 is OK
- 10.1103/PhysRevD.93.044007 is OK
- 10.1103/PhysRevD.96.024058 is OK
- 10.1103/PhysRevD.93.044006 is OK
- 10.1103/physrevd.93.122004 is OK
- 10.1103/physrevd.96.104041 is OK
- 10.1088/0264-9381/24/12/S04 is OK
- 10.1088/0264-9381/33/20/204001 is OK
- 10.1088/0264-9381/29/11/115001 is OK
- 10.1103/PhysRevD.76.084020 is OK
- 10.1103/PhysRevLett.103.131101 is OK
- 10.1103/PhysRevD.88.024040 is OK
- 10.1103/PhysRevD.74.104005 is OK
- 10.1103/PhysRevD.77.064032 is OK
- 10.1103/PhysRevD.77.081501 is OK
- 10.1103/PhysRevD.77.104018 is OK
- 10.1103/PhysRevD.79.084010 is OK
- 10.1103/PhysRevD.78.101503 is OK
- 10.1103/PhysRevD.91.104022 is OK
- 10.1088/0264-9381/28/19/195015 is OK
- 10.1201/b12985 is OK
- 10.21105/joss.03099 is OK
- 10.1103/PhysRevD.59.024007 is OK
- 10.1103/PhysRevD.52.5428 is OK
- 10.1088/0264-9381/21/6/014 is OK
MISSING DOIs
- No DOI given, and none found for title: Numerical Relativity Injection Infrastructure
- No DOI given, and none found for title: Overview of KAGRA : KAGRA science
- Entry without DOI or title found
- Entry without DOI or title found
- Entry without DOI or title found
- 10.1007/3-540-36569-9_13 may be a valid DOI for title: The Cactus Framework and Toolkit: Design and Appli...
- No DOI given, and none found for title: Second MAYA Catalog of Binary Black Hole Numerical...
- No DOI given, and none found for title: Accuracy limitations of existing numerical relativ...
- No DOI given, and none found for title: Black Hole - Neutron Star Binary Mergers: The Impa...
INVALID DOIs
- None
@deborahferguson, could you inspect the missing DOIs listed above? I understand that a DOI is not applicable to every reference, but please include it wherever possible.
Hi @eloisabentivegna,
Excellent! Thanks for all your work on this. I've added all the missing DOIs I could find. I still can't find ones for SimulationTools, PyCactus, or POWER.
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.48550/arXiv.1703.01076 is OK
- 10.1088/1361-6382/aa7929 is OK
- 10.1103/PhysRevD.99.023003 is OK
- 10.1038/s41550-021-01568-w is OK
- 10.1088/0264-9381/32/7/074001 is OK
- 10.1088/0264-9381/32/2/024001 is OK
- 10.1093/ptep/ptaa120 is OK
- 10.1103/physrevlett.116.061102 is OK
- 10.1103/physrevx.11.021053 is OK
- 10.1103/physrevx.9.031040 is OK
- 10.1103/physrevx.13.041039 is OK
- 10.1103/physrevlett.119.161101 is OK
- 10.3847/2041-8213/ab75f5 is OK
- 10.1103/PhysRevD.96.123012 is OK
- 10.1103/PhysRevLett.113.151101 is OK
- 10.1103/physrevd.95.044028 is OK
- 10.1103/PhysRevD.93.044007 is OK
- 10.1103/PhysRevD.96.024058 is OK
- 10.1103/PhysRevD.93.044006 is OK
- 10.1103/physrevd.93.122004 is OK
- 10.1103/physrevd.96.104041 is OK
- 10.1088/0264-9381/24/12/S04 is OK
- 10.1088/0264-9381/33/20/204001 is OK
- 10.1088/0264-9381/29/11/115001 is OK
- 10.1103/PhysRevD.76.084020 is OK
- 10.1103/PhysRevLett.103.131101 is OK
- 10.1103/PhysRevD.88.024040 is OK
- 10.1103/PhysRevD.74.104005 is OK
- 10.1103/PhysRevD.77.064032 is OK
- 10.1103/PhysRevD.77.081501 is OK
- 10.1103/PhysRevD.77.104018 is OK
- 10.1103/PhysRevD.79.084010 is OK
- 10.1103/PhysRevD.78.101503 is OK
- 10.1103/PhysRevD.91.104022 is OK
- 10.1088/0264-9381/28/19/195015 is OK
- 10.1201/b12985 is OK
- 10.21105/joss.03099 is OK
- 10.1103/PhysRevD.59.024007 is OK
- 10.1103/PhysRevD.52.5428 is OK
- 10.1088/0264-9381/21/6/014 is OK
- 10.1007/3-540-36569-9_13 is OK
- 10.48550/arXiv.2309.00262 is OK
- 10.48550/arXiv.2312.10241 is OK
- 10.48550/arXiv.2404.09924 is OK
MISSING DOIs
- No DOI given, and none found for title: SimulationTools
- No DOI given, and none found for title: PyCactus: Post-processing tools for Cactus computa...
- No DOI given, and none found for title: POWER
INVALID DOIs
- None
POWER: https://doi.org/10.1088/1361-6382/aa9cad (CQG publication) source code (currently) https://github.com/NCSAGravity/Gravitational_Waveform_Extractor
SimulationTools: Ian may now what to use
PyCactus: no idea, Wolfgang may have something other than the source code repo. Astrophysics code library has this https://ascl.net/2107.017
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.48550/arXiv.1703.01076 is OK
- 10.1088/1361-6382/aa7929 is OK
- 10.1103/PhysRevD.99.023003 is OK
- 10.1038/s41550-021-01568-w is OK
- 10.1088/0264-9381/32/7/074001 is OK
- 10.1088/0264-9381/32/2/024001 is OK
- 10.1093/ptep/ptaa120 is OK
- 10.1103/physrevlett.116.061102 is OK
- 10.1103/physrevx.11.021053 is OK
- 10.1103/physrevx.9.031040 is OK
- 10.1103/physrevx.13.041039 is OK
- 10.1103/physrevlett.119.161101 is OK
- 10.3847/2041-8213/ab75f5 is OK
- 10.1103/PhysRevD.96.123012 is OK
- 10.1103/PhysRevLett.113.151101 is OK
- 10.1103/physrevd.95.044028 is OK
- 10.1103/PhysRevD.93.044007 is OK
- 10.1103/PhysRevD.96.024058 is OK
- 10.1103/PhysRevD.93.044006 is OK
- 10.1103/physrevd.93.122004 is OK
- 10.1103/physrevd.96.104041 is OK
- 10.1088/0264-9381/24/12/S04 is OK
- 10.1088/0264-9381/33/20/204001 is OK
- 10.1088/0264-9381/29/11/115001 is OK
- 10.1103/PhysRevD.76.084020 is OK
- 10.1103/PhysRevLett.103.131101 is OK
- 10.1103/PhysRevD.88.024040 is OK
- 10.1103/PhysRevD.74.104005 is OK
- 10.1103/PhysRevD.77.064032 is OK
- 10.1103/PhysRevD.77.081501 is OK
- 10.1103/PhysRevD.77.104018 is OK
- 10.1103/PhysRevD.79.084010 is OK
- 10.1103/PhysRevD.78.101503 is OK
- 10.1103/PhysRevD.91.104022 is OK
- 10.1088/0264-9381/28/19/195015 is OK
- 10.1201/b12985 is OK
- 10.21105/joss.03099 is OK
- 10.1088/1361-6382/aa9cad is OK
- 10.1103/PhysRevD.59.024007 is OK
- 10.1103/PhysRevD.52.5428 is OK
- 10.1088/0264-9381/21/6/014 is OK
- 10.1007/3-540-36569-9_13 is OK
- 10.48550/arXiv.2309.00262 is OK
- 10.48550/arXiv.2312.10241 is OK
- 10.48550/arXiv.2404.09924 is OK
MISSING DOIs
- No DOI given, and none found for title: SimulationTools
- No DOI given, and none found for title: PyCactus: Post-processing tools for Cactus computa...
INVALID DOIs
- None
Thanks @rhaas80! I updated the citation for POWER
Thanks @rhaas80 for filling the gaps, and @deborahferguson for updating the references.
Unless @ianhinder and @wokast object, I would leave the remaining two references as they are, as I can't find a recommended DOId publication to cite for either package.
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Unless @ianhinder and @wkast object, I would leave the remaining two references as they are, as I can't find a recommended DOId publication to cite for either package.
It is fine as it is; there is no other reference for SimulationTools.
@deborahferguson, I've just noted a few text improvements in an issue under the code repo. Please take a look, and if happy apply and move on to the post-review checklist below.
@editorialbot set <DOI here> as archive
@editorialbot set <version here> as version
@editorialbot generate pdf
@editorialbot check references
and ask author(s) to update as needed@editorialbot recommend-accept
@deborahferguson, could you take a look at the tasks above, and proceed with the version/archive creation?
Hi @eloisabentivegna I believe I've completed all the tasks listed above.
Release version on GitHub: v2024.6 DOI of release on Zenodo: 10.5281/zenodo.11551465
The authors and license appear to match.
@editorialbot set version as v2024.6
I'm sorry human, I don't understand that. You can see what commands I support by typing:
@editorialbot commands
@editorialbot set v2024.6 as version
Done! version is now v2024.6
@editorialbot set 10.5281/zenodo.11551465 as archive
Done! archive is now 10.5281/zenodo.11551465
@deborahferguson, can you change the Zenodo title to match this submission's title exactly?
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.48550/arXiv.1703.01076 is OK
- 10.1088/1361-6382/aa7929 is OK
- 10.1103/PhysRevD.99.023003 is OK
- 10.1038/s41550-021-01568-w is OK
- 10.1088/0264-9381/32/7/074001 is OK
- 10.1088/0264-9381/32/2/024001 is OK
- 10.1093/ptep/ptaa120 is OK
- 10.1103/physrevlett.116.061102 is OK
- 10.1103/physrevx.11.021053 is OK
- 10.1103/physrevx.9.031040 is OK
- 10.1103/physrevx.13.041039 is OK
- 10.1103/physrevlett.119.161101 is OK
- 10.3847/2041-8213/ab75f5 is OK
- 10.1103/PhysRevD.96.123012 is OK
- 10.1103/PhysRevLett.113.151101 is OK
- 10.1103/physrevd.95.044028 is OK
- 10.1103/PhysRevD.93.044007 is OK
- 10.1103/PhysRevD.96.024058 is OK
- 10.1103/PhysRevD.93.044006 is OK
- 10.1103/physrevd.93.122004 is OK
- 10.1103/physrevd.96.104041 is OK
- 10.1088/0264-9381/24/12/S04 is OK
- 10.1088/0264-9381/33/20/204001 is OK
- 10.1088/0264-9381/29/11/115001 is OK
- 10.1103/PhysRevD.76.084020 is OK
- 10.1103/PhysRevLett.103.131101 is OK
- 10.1103/PhysRevD.88.024040 is OK
- 10.1103/PhysRevD.74.104005 is OK
- 10.1103/PhysRevD.77.064032 is OK
- 10.1103/PhysRevD.77.081501 is OK
- 10.1103/PhysRevD.77.104018 is OK
- 10.1103/PhysRevD.79.084010 is OK
- 10.1103/PhysRevD.78.101503 is OK
- 10.1103/PhysRevD.91.104022 is OK
- 10.1088/0264-9381/28/19/195015 is OK
- 10.1201/b12985 is OK
- 10.21105/joss.03099 is OK
- 10.1088/1361-6382/aa9cad is OK
- 10.1103/PhysRevD.59.024007 is OK
- 10.1103/PhysRevD.52.5428 is OK
- 10.1088/0264-9381/21/6/014 is OK
- 10.1007/3-540-36569-9_13 is OK
- 10.48550/arXiv.2309.00262 is OK
- 10.48550/arXiv.2312.10241 is OK
- 10.48550/arXiv.2404.09924 is OK
MISSING DOIs
- No DOI given, and none found for title: SimulationTools
- No DOI given, and none found for title: PyCactus: Post-processing tools for Cactus computa...
INVALID DOIs
- None
I've changed the Zenodo title
@editorialbot recommend-accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.48550/arXiv.1703.01076 is OK
- 10.1088/1361-6382/aa7929 is OK
- 10.1103/PhysRevD.99.023003 is OK
- 10.1038/s41550-021-01568-w is OK
- 10.1088/0264-9381/32/7/074001 is OK
- 10.1088/0264-9381/32/2/024001 is OK
- 10.1093/ptep/ptaa120 is OK
- 10.1103/physrevlett.116.061102 is OK
- 10.1103/physrevx.11.021053 is OK
- 10.1103/physrevx.9.031040 is OK
- 10.1103/physrevx.13.041039 is OK
- 10.1103/physrevlett.119.161101 is OK
- 10.3847/2041-8213/ab75f5 is OK
- 10.1103/PhysRevD.96.123012 is OK
- 10.1103/PhysRevLett.113.151101 is OK
- 10.1103/physrevd.95.044028 is OK
- 10.1103/PhysRevD.93.044007 is OK
- 10.1103/PhysRevD.96.024058 is OK
- 10.1103/PhysRevD.93.044006 is OK
- 10.1103/physrevd.93.122004 is OK
- 10.1103/physrevd.96.104041 is OK
- 10.1088/0264-9381/24/12/S04 is OK
- 10.1088/0264-9381/33/20/204001 is OK
- 10.1088/0264-9381/29/11/115001 is OK
- 10.1103/PhysRevD.76.084020 is OK
- 10.1103/PhysRevLett.103.131101 is OK
- 10.1103/PhysRevD.88.024040 is OK
- 10.1103/PhysRevD.74.104005 is OK
- 10.1103/PhysRevD.77.064032 is OK
- 10.1103/PhysRevD.77.081501 is OK
- 10.1103/PhysRevD.77.104018 is OK
- 10.1103/PhysRevD.79.084010 is OK
- 10.1103/PhysRevD.78.101503 is OK
- 10.1103/PhysRevD.91.104022 is OK
- 10.1088/0264-9381/28/19/195015 is OK
- 10.1201/b12985 is OK
- 10.21105/joss.03099 is OK
- 10.1088/1361-6382/aa9cad is OK
- 10.1103/PhysRevD.59.024007 is OK
- 10.1103/PhysRevD.52.5428 is OK
- 10.1088/0264-9381/21/6/014 is OK
- 10.1007/3-540-36569-9_13 is OK
- 10.48550/arXiv.2309.00262 is OK
- 10.48550/arXiv.2312.10241 is OK
- 10.48550/arXiv.2404.09924 is OK
MISSING DOIs
- No DOI given, and none found for title: SimulationTools
- No DOI given, and none found for title: PyCactus: Post-processing tools for Cactus computa...
INVALID DOIs
- None
Just recommended acceptance for this submission. Congratulations @deborahferguson, and thanks for sharing your code; thanks also @cjoana and @Sbozzolo for your time and work on the reviews.
:wave: @openjournals/aass-eics, this paper is ready to be accepted and published.
Check final proof :point_right::page_facing_up: Download article
If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5500, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept
@editorialbot accept
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: Ferguson given-names: Deborah orcid: "https://orcid.org/0000-0002-4406-591X" - family-names: Anne given-names: Surendra - family-names: Gracia-Linares given-names: Miguel orcid: "https://orcid.org/0000-0002-5033-2973" - family-names: Iglesias given-names: Hector orcid: "https://orcid.org/0009-0008-1089-9239" - family-names: Jan given-names: Aasim orcid: "https://orcid.org/0000-0003-2050-7231" - family-names: Martinez given-names: Erick - family-names: Lu given-names: Lu - family-names: Meoni given-names: Filippo - family-names: Nowicki given-names: Ryan - family-names: Trostel given-names: Max L. orcid: "https://orcid.org/0000-0001-9743-0303" - family-names: Tsao given-names: Bing-Jyun orcid: "https://orcid.org/0000-0003-4614-0378" - family-names: Valorz given-names: Finny contact: - family-names: Ferguson given-names: Deborah orcid: "https://orcid.org/0000-0002-4406-591X" doi: 10.5281/zenodo.11551465 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Ferguson given-names: Deborah orcid: "https://orcid.org/0000-0002-4406-591X" - family-names: Anne given-names: Surendra - family-names: Gracia-Linares given-names: Miguel orcid: "https://orcid.org/0000-0002-5033-2973" - family-names: Iglesias given-names: Hector orcid: "https://orcid.org/0009-0008-1089-9239" - family-names: Jan given-names: Aasim orcid: "https://orcid.org/0000-0003-2050-7231" - family-names: Martinez given-names: Erick - family-names: Lu given-names: Lu - family-names: Meoni given-names: Filippo - family-names: Nowicki given-names: Ryan - family-names: Trostel given-names: Max L. orcid: "https://orcid.org/0000-0001-9743-0303" - family-names: Tsao given-names: Bing-Jyun orcid: "https://orcid.org/0000-0003-4614-0378" - family-names: Valorz given-names: Finny date-published: 2024-06-15 doi: 10.21105/joss.06032 issn: 2475-9066 issue: 98 journal: Journal of Open Source Software publisher: name: Open Journals start: 6032 title: "Mayawaves: Python Library for Interacting with the Einstein Toolkit and the MAYA Catalog" type: article url: "https://joss.theoj.org/papers/10.21105/joss.06032" volume: 9 title: "Mayawaves: Python Library for Interacting with the Einstein Toolkit and the MAYA Catalog" ```
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Submitting author: !--author-handle-->@deborahferguson<!--end-author-handle-- (Deborah Ferguson) Repository: https://github.com/MayaWaves/mayawaves Branch with paper.md (empty if default branch): paper Version: v2024.6 Editor: !--editor-->@eloisabentivegna<!--end-editor-- Reviewers: @cjoana, @Sbozzolo Archive: 10.5281/zenodo.11551465
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