Looks like this is fixed now. I'll let @kyleniemeyer take over from here.

from joss-reviews.

@mailhexu Not sure it will let me tag you as a reviewer, but here's the MR addressing issues 49 and 51:

nomad-coe/greenX#54

It seems I cannot review the MR. But I had a look and it seems the issues are well addressed.

from joss-reviews.

Dear Lucy,

Thanks for your comments on our manuscript.
We have revised it, and we hope it is now acceptable for publication in JOSS.
In view of the paper to be more “advert”-like, we agree that the length was a concern. We have thus carefully examined the whole content of the paper. The section “Structure of the library” did not fit in this picture, and we have moved it to the Web page of GreenX. The “Mathematical framework” section has been reduced by half : we only have kept the minimum needed for the section “Required Input and Output” to be understandable by the reader. The latter is not a detailed description of the input/output, but it allows the reader to understand what the code is doing. We think that the people potentially interested need such information even in an advert-type publication. We then also performed miscellaneous removals inside the manuscript. Altogether, the paper has been reduced from 10.5 pages to 7 pages, among those 2.5 pages being bibliography (that we think is just fair to keep).
This is not an exceptional length for a JOSS paper. In order to better realize whether we are in an acceptable range, we surveyed the 40 last published papers in JOSS. On Friday 25 August, joss.04913 was published. It is a 7 pages, and also includes 2.5 pages of bibliography. Thus its size is similar to ours. In the 40 last published papers, five of them are 7 pages or more (joss.04913, joss.05305,joss.05319, joss.05076, joss.05466). The longest is joss.05466 with 14 pages. We agree that we are still on the larger side, but such length is apparently acceptable.
May we thus respectfully ask you to accept our manuscript in the present form ?

With our best regards,
The authors

from joss-reviews.

Dear @lucydot,

The editorialbot encountered some issues during the paper acceptance process, primarily stemming from markdown problems. We have addressed these issues, and it appears that they have now been successfully resolved. We kindly request you to please rerun the "recommend-accept" function to confirm its functionality.

We apologize for any inconvenience this may have caused and sincerely appreciate your cooperation. Thank you in advance!

Best regards,
Maryam

from joss-reviews.

Dear @lucydot,
can you run the recommend-accept command again please? As far as we know, only editors can do this. We checked and fixed the warnings of the logs in the GitHub Action. We hope everything works now.

Best regards,
Dorothea

from joss-reviews.

Thanks @Panadestein and the rest of the team, got there in the end!

from joss-reviews.

@aziziph My suggestion is wait for the reviewer feedback, then open an MR off of this issue, which addresses the points. The reviewers can then check diff and confirm we have sufficiently addressed points/concerns.

from joss-reviews.

Hi @aziziph, re-pinging the message above.

The review process in JOSS is different from other journals in that it is more of a conversation back and forth (rather than a review that is completed in one go, which is then responded to in one go). My advice would be to start responding to points as they are raised. Usually the review process will include several merged PRs, and the reviewers keep track using the checklist.

As mentioned in the pre-review, I suggest renaming the license file to LICENSE.txt as that is standard for gh repos (and will be automatically recognised as a license by gh), and there are a couple of invalid DOIs reported in the thread above.

from joss-reviews.

Dear @lucydot

We would like to thank you for the acceptance. Subsequently, we have completed the "Author Tasks After Review is Complete".

• Double check authors and affiliations (including ORCIDs) DONE!
• Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper. DONE!
• Archive the release on Zenodo/figshare/etc and post the DOI here. DONE!
  doi:10.5281/zenodo.8321618
• Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper. DON!
• Make sure that the license listed for the archive is the same as the software license. DONE!

Best regards,
On behalf of the authors

from joss-reviews.

Dear @lucydot

It seems that there is a problem with the preparation of the acceptance. We have tried to fix it. May I ask if you run again recommend-accept to see if it works?

Thank you very much in advance!
Best regards,
Maryam

from joss-reviews.

Hi @DarioALeonValido - thanks for your expertise in reviewing the paper.

Hi @aziziph @AlexBuccheri - I agree that there is not space for the efficiency comparison in the JOSS paper. As this is the key performance claim of the software, a link to this comparison in the documentation or in a paper published elsewhere is required. Ideally it would be both. I note that the paper you link to is currently unpublished - is there a pre-print available?

I agree with @mailhexu that the documentation is quite inaccessible in its current form; requiring user installation to access (I think, it is not clear) function-level documentation. It is not easy for potential users to understand the software capabilities and use cases without reading the JOSS paper, which requires pdf download.

I suggest you make this information (software capabilities, use cases, API docs) available as webpages. This could be hosted on github pages, for example. At a minimum, this information (minus the API docs) need to be available on the README.md.

Happy to discuss this more if anything is unclear. Exploring previous repos published in JOSS can be a good way to find strong documentation examples. I can see this is being discussed on the issue here.

from joss-reviews.

Wr.t. the open issues, they were actually all addressed. I'm not sure why Github didn't automatically close them (in the instances they were linked in the MRs)

from joss-reviews.

Dear @lucydot @mailhexu @DarioALeonValido,

thank you very much for your throughout review and valuable comments. We continued working on the remaining comments (although several of the raised issued were already solved, as @AlexBuccheri said). Now we have set up a GitHub pages website for the project (nomad-coe.github.io/greenX/), which hopefully solves the documentation issue. The website includes benchmark results and detail usage instructions, including a mapping from the quantities defined in the paper to the actual variables in the code. This website will of course grow together with the library, and new components of GreenX will find similar entries in it.

We hope that with these adjustments, our paper now meets all requirements for acceptance. Thank you for your thoughtful review and continued guidance.

from joss-reviews.

It seems that papers < 10 pages in length are somewhat of a grey area. I'm happy to accept the paper at its current length, especially given that effort has already been put into editing down.

from joss-reviews.

Dear Green-X team (@aziziph @Panadestein @AlexBuccheri @fdelesma @dgolze)

• There is an invalid DOI ("--") that needs to be updated/removed - this is for the unpublished work cited.
• I'll generate the post-review checklist. You can't tick off the items, but please let me know when each item has been completed here in the thread.

from joss-reviews.

I think the issue here is that Pandoc is struggling to identify the equations labeled/linked in your document. Have you tried following these docs? https://joss.readthedocs.io/en/latest/submitting.html#equations

from joss-reviews.

ping @arfon

from joss-reviews.

@lucydot or @arfon we did more radical changes now:
i) removed all hspace's in the equations as you recommend
ii) removed all labels in the equations and replaced the reference in the text by hand
Could you please try again to run the recommend-accept command?

from joss-reviews.

@lucydot is action required from our side? Do we have to reply in openjournals/joss-papers#4641

from joss-reviews.

@dgolze nothing at the moment - I'm going to do some final checks before publishing. I'll let you know if we need any changes. You could review the final PDF, though!

from joss-reviews.

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

from joss-reviews.

Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (997.6 files/s, 197311.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Fortran 90                      15            261            416           5899
TeX                              1             21              0            754
Markdown                        10            133              0            441
Python                           7            150            134            398
CMake                           11            116            282            388
YAML                             2             12              6             70
C/C++ Header                     1              0              0             10
TOML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            48            693            838           7963
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 2761

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Failed to discover a valid open source license

from joss-reviews.

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

OK DOIs

- 10.1021/acs.jctc.1c00488 is OK
- 10.1103/PhysRevB.92.081104 is OK
- 10.1038/s41550-017-0220-3 is OK
- 10.2307/j.ctvc778ff is OK
- 10.1051/0004-6361/201629272 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.6084/m9.figshare.828487 is OK
- 10.1007/978-3-642-61609-9 is OK
- 10.3389/fchem.2019.00377 is OK
- 10.1103/PhysRevB.78.085125 is OK
- 10.1145/1874391.187410 is OK
- 10.1007/s00791-018-00308-4 is OK
- 10.1007/s00791-018-00308-4 is OK
- 10.1103/PhysRev.126.413 is OK
- 10.1103/PhysRev.129.62 is OK
- 10.1063/1.462485 is OK
- 10.1021/ct5001268 is OK
- 10.1103/PhysRevB.90.054115 is OK
- 10.1103/PhysRevB.94.165109 is OK
- 10.1021/acs.jctc.0c01282 is OK
- 10.1103/PhysRevLett.74.1827 is OK
- 10.1103/PhysRev.139.A796 is OK
- 10.1002/wcms.1344 is OK
- 10.1103/PhysRevB.84.241201 is OK
- 10.1103/PhysRevB.71.193102 is OK
- 10.1021/acs.jctc.6b00380 is OK
- 10.1038/s41597-020-0385-y is OK
- 10.1021/acs.jctc.0c00693 is OK
- 10.1021/acs.jpclett.7b02740 is OK
- 10.1021/acs.jctc.7b00770 is OK
- 10.1088/1367-2630/14/5/053020 is OK
- 10.1007/BF00655090 is OK
- 10.48550/arXiv.1108.4417 is OK
- 10.1016/S0010-4655(98)00174-X is OK
- 10.1103/PhysRevB.13.4274 is OK
- 10.1103/PhysRevA.73.012511 is OK
- 10.1103/PhysRevB.96.155207 is OK
- 10.1016/j.cpc.2018.09.003 is OK
- 10.1016/j.cpc.2014.10.021 is OK
- 10.1021/acs.jctc.9b01235 is OK
- 10.1021/acs.jctc.1c00101 is OK
- 10.1021/acs.jctc.1c00308 is OK
- 10.48550/arXiv.2303.09979 is OK
- 10.1021/acs.jctc.0c00600 is OK
- 10.1021/acs.jctc.8b00177 is OK
- 10.1021/acs.jctc.6b01235 is OK
- 10.1021/acs.jctc.2c00774 is OK
- 10.1063/1.5090605 is OK
- 10.1016/0009-2614(91)80078-C is OK
- 10.1063/1.1809602 is OK
- 10.1103/PhysRevB.94.035118 is OK
- 10.1007/s10853-012-6570-4 is OK
- 10.1007/s00214-011-1084-8 is OK
- 10.1021/ct4002202 is OK
- 10.1103/RevModPhys.74.601 is OK
- 10.1021/acs.jctc.6b00840 is OK
- 10.1021/acs.jctc.6b00840 is OK
- 10.1103/PhysRevB.85.155129 is OK
- 10.1016/j.cpc.2017.06.012 is OK

MISSING DOIs

- None

INVALID DOIs

- -- is INVALID
- 10.33892Ffchem.2021.736591 is INVALID

from joss-reviews.

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

from joss-reviews.

Review checklist for @DarioALeonValido

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/nomad-coe/greenX?
• 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 (@aziziph) 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?

from joss-reviews.

@aziziph

Dear Maryam and other authors, I find this library potentially very useful. However, my main concern so far is regarding validation and performance, that are left to an unpublished paper (Azizi et al 2023).

I suggest you to include here at lest a simple example illustrating the efficiency of the minimax grids. Maybe it could be done by integrating a toy function, but I also would like to see if you can get an estimate of how much it is reduced the prefactor of low-scaling MP2/RPA/GW calculations to justify the exclusive use of this particular quadrature.

Another related question. In line 150 of the pdf you specify that the number of time/frequency points in the library ranges from 2 to 64, how are these values related to the final accuracy of correlation and quasi-particle energies?

from joss-reviews.

Review checklist for @mailhexu

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/nomad-coe/greenX?
• 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 (@aziziph) 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?

from joss-reviews.

Hello @mailhexu @aziziph @DarioALeonValido
Just to let you know that I am at a conference for the next week; will check in again w/c 10th July.

from joss-reviews.

@aziziph Dear Mariam and other authors,

Thanks for making this library available! I think it can be very useful.

I found a few minor issues during the reviewing procedure:
I opened a few minor issues:
nomad-coe/greenX#48
nomad-coe/greenX#49
nomad-coe/greenX#51
nomad-coe/greenX#52
And a PR:
nomad-coe/greenX#50

I have some minor suggestions below:

• I find it unclear whether some part of the Summary is referring to GreenX as a whole or specifically discussing its time-frequency component. For instance, in line 22, "the package" appears to refer to the GreenX library, while the subsequent sentences seem to focus more on the time-frequency component. Using an acronym like GXTF for the component could potentially provide clarity even though the time-frequency library is currently the only functional component in GreenX, based on the presence of multiple directories with the prefix "GreenX-" with only "README" files inside the main branch (correct me if the other components are already developped). This might confuse the fut
• I didn't find the mentioning of the documentation of the API in the manuscript. The method of compiling and opening the documentation is indeed in the README.md, but it doesn't seem straightforward to know what is inside. Some introduction of the contents should be helpful. To put it online (e.g. in github pages or readthedocs.io) can also be helpful.
• An example code of using it (as provided in the doxygen documentation) is helpful if it is made more easily accessible (e.g. in an example directory).

from joss-reviews.

@mailhexu Not sure it will let me tag you as a reviewer, but here's the MR addressing issues 49 and 51:

nomad-coe/greenX#54

from joss-reviews.

@aziziph

Dear Maryam and other authors, I find this library potentially very useful. However, my main concern so far is regarding validation and performance, that are left to an unpublished paper (Azizi et al 2023).

I suggest you to include here at lest a simple example illustrating the efficiency of the minimax grids. Maybe it could be done by integrating a toy function, but I also would like to see if you can get an estimate of how much it is reduced the prefactor of low-scaling MP2/RPA/GW calculations to justify the exclusive use of this particular quadrature.

Another related question. In line 150 of the pdf you specify that the number of time/frequency points in the library ranges from 2 to 64, how are these values related to the final accuracy of correlation and quasi-particle energies?

We thank the referee for the suggestion. The editor already remarked on the length of the paper "JOSS papers are short advertisements for the software package, and as a guideline the word count is 250-1000 words. Your paper currently exceeds this guideline by a significant amount." Since it is not possible to shorten the paper without sacrificing clarity, it seems that adding further material to the paper is not appropriate. However, we agree that it is highly interesting to compare minimax grids against standard time and frequency grids, which we will report extensively in an unpublished work, referenced as Azizi2023. We are happy to provide here an example. In this test, we evaluate the RPA total energy of CH4 using a Gauss-Legendre grid, a modified Gauss-Legendre grid (so far the standard in FHI-aims and abinit), and minimax grids. An accuracy of 10^-6 eV is reached with 10 minimax grid points while the modified Gauss-Legendre grids requires 36 points for this accuracy (Please see the following figure).

Error differences of the total RPA energy [eV] of methane calculated using the Gauss-Legendre, modified Gauss-Legendre and minimax imaginary frequency grid points. These differences were calculated with respect to the lowest RPA energy obtained with 34 minimax grid points. The ground state energy was calculated using the PBE exchange correlation functional in combination of the Tier2 basis set. The global resolution of identity (RI-V) approach was used for the calculation of the exact exchange and RPA correlation energy. The auxiliary basis functions for the RI-V method were generated automatically on the fly. #

from joss-reviews.

@aziziph

Dear Maryam, thanks for providing this example. These results seem very promising indeed. Since you are using the minimax grid as a reference, I wonder if the Gauss-Legendre grid is converging to a different value around 10^-3 eV. I guess you will comment on this in the benchmarking paper.

I see that all the issues raised by the other referee have been corrected, so I am happy to recommend the paper for publication without further ado.

All the best,
Dario A. Leon

from joss-reviews.

A follow on note to say that by having a documentation webpage you will be able to cut the details in your JOSS paper. The JOSS paper is an advert for the repo, it does not need to go into details of the implementation (it is not the place for the e.g. mathematical framework section). This is better in the online docs.

from joss-reviews.

@lucydot

Dear Lucy, thank you very much for providing this possible solution. I coincide with you that an illustrative example in support of the claims of the library should be available at a preprint of the benchmarking reference or somewhere else beside this thread.

from joss-reviews.

Dear @aziziph @AlexBuccheri @Panadestein -

A heads up that I am going on annual leave until the 8th of August.

The primary outstanding issue relates to documentation, which I can see is under discussion (nomad-coe/greenX#59). If you have any questions relating to this I will briefly have access to internet this Monday 24th, otherwise I will be off-grid!

There are also some more minor issues raised by @mailhexu (nomad-coe/greenX#48 nomad-coe/greenX#49 nomad-coe/greenX#51 nomad-coe/greenX#52).

Hopefully this gives a good timeline for completion; I will check back here ASAP after returning from AL as I think we are getting close to the end!

Lucy

from joss-reviews.

Hi @lucydot, I've opened an MR to address the documentation concerns. After a discussion, we collectively decided on putting the benchmarks on Github pages. This will still reside in the repo, but not the JOSS paper. @DarioALeonValido and @mailhexu can follow the progress here

from joss-reviews.

Dear @lucydot @DarioALeonValido , @aziziph and other authors,
I think all the issues raised are solved. Thanks for the effort to make this software and the documentation available. I am happy to recommend the publication.
Best,
HeXu

from joss-reviews.

@editorialbot recommend-accept

from joss-reviews.

I'm sorry @mailhexu, I'm afraid I can't do that. That's something only editors are allowed to do.

from joss-reviews.

@editorialbot generate pdf

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

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

from joss-reviews.

Dear @aziziph @AlexBuccheri @Panadestein -

We are getting there - I have a few outstanding points:

• In your repo README you have the doxygen documentation listed but there is no link to the Github pages site; I think this should be added. I know there is a link at the top of the page but this can be missed when half way down, and I'd expect all docs to be listed under documentation section.
• Do you plan to update both forms of docs? This seems it might get a bit difficult to maintain and that there might be divergence. Users need to be clear about what is the master docs.
• The GH pages docs refer to an exascale library: perhaps wording such as exascale-ready library or exascale-optimised might be better - as the library itself is not exascale.
• Returning to a point made at the start of the review process: currently the paper is too long and goes into too deep a level of mathematical detail. I suggest you move the mathematical section to the online documentation. Even with this section removed from the paper you will pushing the allowed word limit I think. Detailed docs are meant to be hosted online, with the paper acting as a short 1/2-page advert for the code.
• I noticed slight inconsistencies with terminology. In the section required input and output of the library you make several references to a library when I think you are referring to the time-frequency component specifically. If so, this needs re-wording so that there is no confusion between the two.

Happy to discuss more here, please let me know if anything is unclear, this is very much as a two-way process.

Best,

Lucy

from joss-reviews.

Dear @aziziph @AlexBuccheri @Panadestein -

We are getting there - I have a few outstanding points:

* In your repo README you have the doxygen documentation listed but there is no link to the Github pages site; I think this should be added. I know there is a link at the top of the page but this can be missed when half way down, and I'd expect all docs to be listed under documentation section.

* Do you plan to update both forms of docs? This seems it might get a bit difficult to maintain and that there might be divergence. Users need to be clear about what is the master docs.

* The GH pages docs refer to an `exascale library`: perhaps wording such as `exascale-ready library` or `exascale-optimised` might be better - as the library itself is not exascale.

* Returning to a point made at the start of the review process: currently the paper is too long and goes into too deep a level of mathematical detail. I suggest you move the mathematical section to the online documentation. Even with this section removed from the paper you will pushing the allowed word limit I think. Detailed docs are meant to be hosted online, with the paper acting as a short 1/2-page advert for the code.

* I noticed slight inconsistencies with terminology. In the section `required input and output of the library` you make several references to a library when I think you are referring to the time-frequency component specifically. If so, this needs re-wording so that there is no confusion between the two.

Happy to discuss more here, please let me know if anything is unclear, this is very much as a two-way process.

Best,

Lucy

Dear @lucydot,
cc @aziziph @Panadestein @AlexBuccheri @fdelesma

We have addressed points 1-3 and 5. A short additional comment about point 2: we plan to update both forms and also want to point out that the information in the README and the website doesn't overlap. The README contains instruction how to compile etc. and further information for developers, while the website covers usage examples, benchmarks etc. We removed remaining redundancies. About point 4, we have to wait for the input of the project's PI @gonzex.
Best,
Dorothea

from joss-reviews.

Thanks for the update @dgolze 👍

from joss-reviews.

Hello,

Just to let you know that I will be away on leave for two weeks, so my replies will be slower than usual. Best,

Lucy

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@editorialbot generate pdf

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

from joss-reviews.

Thanks for the update and paper edits @gonzex and team.

I'm going to discuss this with the wider JOSS editorial team, as I think you have highlighted an inconsistency between what we ask for, and what is being published. I hope to get back to you in a week with this.

from joss-reviews.

@editorialbot check references

from joss-reviews.

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

OK DOIs

- 10.1038/s41550-017-0220-3 is OK
- 10.2307/j.ctvc778ff is OK
- 10.1051/0004-6361/201629272 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.6084/m9.figshare.828487 is OK
- 10.1007/978-3-642-61609-9 is OK
- 10.3389/fchem.2019.00377 is OK
- 10.1103/PhysRevB.78.085125 is OK
- 10.1145/1874391.187410 is OK
- 10.1007/s00791-018-00308-4 is OK
- 10.1021/acs.jctc.3c00555 is OK
- 10.1007/s00791-018-00308-4 is OK
- 10.1103/PhysRev.126.413 is OK
- 10.1103/PhysRev.129.62 is OK
- 10.1063/1.462485 is OK
- 10.1021/ct5001268 is OK
- 10.1103/PhysRevB.90.054115 is OK
- 10.1103/PhysRevB.94.165109 is OK
- 10.1021/acs.jctc.0c01282 is OK
- 10.1103/PhysRevLett.74.1827 is OK
- 10.1103/PhysRev.139.A796 is OK
- 10.1002/wcms.1344 is OK
- 10.1103/PhysRevB.84.241201 is OK
- 10.1103/PhysRevB.71.193102 is OK
- 10.1021/acs.jctc.6b00380 is OK
- 10.1038/s41597-020-0385-y is OK
- 10.1021/acs.jctc.0c00693 is OK
- 10.1021/acs.jpclett.7b02740 is OK
- 10.1021/acs.jctc.7b00770 is OK
- 10.1088/1367-2630/14/5/053020 is OK
- 10.1007/BF00655090 is OK
- 10.48550/arXiv.1108.4417 is OK
- 10.1016/S0010-4655(98)00174-X is OK
- 10.1103/PhysRevB.13.4274 is OK
- 10.1103/PhysRevA.73.012511 is OK
- 10.1103/PhysRevB.96.155207 is OK
- 10.1016/j.cpc.2018.09.003 is OK
- 10.1016/j.cpc.2014.10.021 is OK
- 10.1021/acs.jctc.9b01235 is OK
- 10.1021/acs.jctc.1c00101 is OK
- 10.1021/acs.jctc.1c00308 is OK
- 10.3389/fchem.2021.736591 is OK
- 10.1021/acs.jctc.3c00512 is OK
- 10.1021/acs.jctc.0c00600 is OK
- 10.1021/acs.jctc.8b00177 is OK
- 10.1021/acs.jctc.6b01235 is OK
- 10.1021/acs.jctc.2c00774 is OK
- 10.1063/1.5090605 is OK
- 10.1016/0009-2614(91)80078-C is OK
- 10.1063/1.1809602 is OK
- 10.1103/PhysRevB.94.035118 is OK
- 10.1007/s10853-012-6570-4 is OK
- 10.1007/s00214-011-1084-8 is OK
- 10.1021/ct4002202 is OK
- 10.1103/RevModPhys.74.601 is OK
- 10.1021/acs.jctc.6b00840 is OK
- 10.1103/PhysRevB.85.155129 is OK
- 10.1016/j.cpc.2017.06.012 is OK
- 10.48550/arXiv.2306.16066 is OK

MISSING DOIs

- None

INVALID DOIs

- -- is INVALID

from joss-reviews.

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

• Double check authors and affiliations (including ORCIDs)
• Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
• Archive the release on Zenodo/figshare/etc and post the DOI here.
• Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

• Read the text of the paper and offer comments/corrections (as either a list or a PR)
• Check the references in the paper for corrections (e.g. capitalization)
• Check that the archive title, author list, version tag, and the license are correct
• Set archive DOI with @editorialbot set <DOI here> as archive
• Set version with @editorialbot set <version here> as version
• Double check rendering of paper with @editorialbot generate pdf
• Specifically check the references with @editorialbot check references and ask author(s) to update as needed
• Recommend acceptance with @editorialbot recommend-accept

from joss-reviews.

Thanks for the acceptance ! I see that there is some (small) work on our side. This will be done soon ...

from joss-reviews.

@editorialbot generate pdf

from joss-reviews.

@editorialbot check references

from joss-reviews.

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

OK DOIs

- 10.1038/s41550-017-0220-3 is OK
- 10.2307/j.ctvc778ff is OK
- 10.1051/0004-6361/201629272 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.6084/m9.figshare.828487 is OK
- 10.1007/978-3-642-61609-9 is OK
- 10.3389/fchem.2019.00377 is OK
- 10.1103/PhysRevB.78.085125 is OK
- 10.1145/1874391.187410 is OK
- 10.1007/s00791-018-00308-4 is OK
- 10.1021/acs.jctc.3c00555 is OK
- 10.1007/s00791-018-00308-4 is OK
- 10.1103/PhysRev.126.413 is OK
- 10.1103/PhysRev.129.62 is OK
- 10.1063/1.462485 is OK
- 10.1021/ct5001268 is OK
- 10.1103/PhysRevB.90.054115 is OK
- 10.1103/PhysRevB.94.165109 is OK
- 10.1021/acs.jctc.0c01282 is OK
- 10.1103/PhysRevLett.74.1827 is OK
- 10.1103/PhysRev.139.A796 is OK
- 10.1002/wcms.1344 is OK
- 10.1103/PhysRevB.84.241201 is OK
- 10.1103/PhysRevB.71.193102 is OK
- 10.1021/acs.jctc.6b00380 is OK
- 10.1038/s41597-020-0385-y is OK
- 10.1021/acs.jctc.0c00693 is OK
- 10.1021/acs.jpclett.7b02740 is OK
- 10.1021/acs.jctc.7b00770 is OK
- 10.1088/1367-2630/14/5/053020 is OK
- 10.1007/BF00655090 is OK
- 10.48550/arXiv.1108.4417 is OK
- 10.1016/S0010-4655(98)00174-X is OK
- 10.1103/PhysRevB.13.4274 is OK
- 10.1103/PhysRevA.73.012511 is OK
- 10.1103/PhysRevB.96.155207 is OK
- 10.1016/j.cpc.2018.09.003 is OK
- 10.1016/j.cpc.2014.10.021 is OK
- 10.1021/acs.jctc.9b01235 is OK
- 10.1021/acs.jctc.1c00101 is OK
- 10.1021/acs.jctc.1c00308 is OK
- 10.3389/fchem.2021.736591 is OK
- 10.1021/acs.jctc.3c00512 is OK
- 10.1021/acs.jctc.0c00600 is OK
- 10.1021/acs.jctc.8b00177 is OK
- 10.1021/acs.jctc.6b01235 is OK
- 10.1021/acs.jctc.2c00774 is OK
- 10.1063/1.5090605 is OK
- 10.1016/0009-2614(91)80078-C is OK
- 10.1063/1.1809602 is OK
- 10.1103/PhysRevB.94.035118 is OK
- 10.1007/s10853-012-6570-4 is OK
- 10.1007/s00214-011-1084-8 is OK
- 10.1021/ct4002202 is OK
- 10.1103/RevModPhys.74.601 is OK
- 10.1021/acs.jctc.6b00840 is OK
- 10.1103/PhysRevB.85.155129 is OK
- 10.1016/j.cpc.2017.06.012 is OK
- 10.48550/arXiv.2306.16066 is OK

MISSING DOIs

- None

INVALID DOIs

- None

from joss-reviews.

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

from joss-reviews.

@editorialbot set v1.0.0 as version

from joss-reviews.

Done! version is now v1.0.0

from joss-reviews.

@editorialbot set 10.5281/zenodo.8321618 as archive

from joss-reviews.

Done! archive is now 10.5281/zenodo.8321618

from joss-reviews.

@editorialbot recommend-accept

from joss-reviews.

Attempting dry run of processing paper acceptance...

from joss-reviews.

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

OK DOIs

- 10.1038/s41550-017-0220-3 is OK
- 10.2307/j.ctvc778ff is OK
- 10.1051/0004-6361/201629272 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.6084/m9.figshare.828487 is OK
- 10.1007/978-3-642-61609-9 is OK
- 10.3389/fchem.2019.00377 is OK
- 10.1103/PhysRevB.78.085125 is OK
- 10.1145/1874391.187410 is OK
- 10.1007/s00791-018-00308-4 is OK
- 10.1021/acs.jctc.3c00555 is OK
- 10.1007/s00791-018-00308-4 is OK
- 10.1103/PhysRev.126.413 is OK
- 10.1103/PhysRev.129.62 is OK
- 10.1063/1.462485 is OK
- 10.1021/ct5001268 is OK
- 10.1103/PhysRevB.90.054115 is OK
- 10.1103/PhysRevB.94.165109 is OK
- 10.1021/acs.jctc.0c01282 is OK
- 10.1103/PhysRevLett.74.1827 is OK
- 10.1103/PhysRev.139.A796 is OK
- 10.1002/wcms.1344 is OK
- 10.1103/PhysRevB.84.241201 is OK
- 10.1103/PhysRevB.71.193102 is OK
- 10.1021/acs.jctc.6b00380 is OK
- 10.1038/s41597-020-0385-y is OK
- 10.1021/acs.jctc.0c00693 is OK
- 10.1021/acs.jpclett.7b02740 is OK
- 10.1021/acs.jctc.7b00770 is OK
- 10.1088/1367-2630/14/5/053020 is OK
- 10.1007/BF00655090 is OK
- 10.48550/arXiv.1108.4417 is OK
- 10.1016/S0010-4655(98)00174-X is OK
- 10.1103/PhysRevB.13.4274 is OK
- 10.1103/PhysRevA.73.012511 is OK
- 10.1103/PhysRevB.96.155207 is OK
- 10.1016/j.cpc.2018.09.003 is OK
- 10.1016/j.cpc.2014.10.021 is OK
- 10.1021/acs.jctc.9b01235 is OK
- 10.1021/acs.jctc.1c00101 is OK
- 10.1021/acs.jctc.1c00308 is OK
- 10.3389/fchem.2021.736591 is OK
- 10.1021/acs.jctc.3c00512 is OK
- 10.1021/acs.jctc.0c00600 is OK
- 10.1021/acs.jctc.8b00177 is OK
- 10.1021/acs.jctc.6b01235 is OK
- 10.1021/acs.jctc.2c00774 is OK
- 10.1063/1.5090605 is OK
- 10.1016/0009-2614(91)80078-C is OK
- 10.1063/1.1809602 is OK
- 10.1103/PhysRevB.94.035118 is OK
- 10.1007/s10853-012-6570-4 is OK
- 10.1007/s00214-011-1084-8 is OK
- 10.1021/ct4002202 is OK
- 10.1103/RevModPhys.74.601 is OK
- 10.1021/acs.jctc.6b00840 is OK
- 10.1103/PhysRevB.85.155129 is OK
- 10.1016/j.cpc.2017.06.012 is OK
- 10.48550/arXiv.2306.16066 is OK

MISSING DOIs

- None

INVALID DOIs

- None

from joss-reviews.

The paper's PDF and metadata files generation produced some warnings that could prevent the final paper from being published. Please fix them before the end of the review process.

d}(i\tau) \hspace{1.9em} &\text{and} \hs
                   ^
unexpected "."
expecting digit, "em", "pt", "in" or "cm"

    \hspace{-3em}F^\text{even}(i\omega_k
            ^
unexpected "-"
expecting white space or digit

from joss-reviews.

⚠️ Error preparing paper acceptance. The generated XML metadata file is invalid.

IDREFS attribute rid references an unknown ID "st_odd_t_to_w"
IDREFS attribute rid references an unknown ID "st_odd_t_to_w"
IDREFS attribute rid references an unknown ID "ct_st_even"
IDREFS attribute rid references an unknown ID "ct_st_even"
IDREFS attribute rid references an unknown ID "ct_st_even"

from joss-reviews.

@editorialbot recommend-accept

from joss-reviews.

Attempting dry run of processing paper acceptance...

from joss-reviews.

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

OK DOIs

- 10.1038/s41550-017-0220-3 is OK
- 10.2307/j.ctvc778ff is OK
- 10.1051/0004-6361/201629272 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.6084/m9.figshare.828487 is OK
- 10.1007/978-3-642-61609-9 is OK
- 10.3389/fchem.2019.00377 is OK
- 10.1103/PhysRevB.78.085125 is OK
- 10.1145/1874391.187410 is OK
- 10.1007/s00791-018-00308-4 is OK
- 10.1021/acs.jctc.3c00555 is OK
- 10.1007/s00791-018-00308-4 is OK
- 10.1103/PhysRev.126.413 is OK
- 10.1103/PhysRev.129.62 is OK
- 10.1063/1.462485 is OK
- 10.1021/ct5001268 is OK
- 10.1103/PhysRevB.90.054115 is OK
- 10.1103/PhysRevB.94.165109 is OK
- 10.1021/acs.jctc.0c01282 is OK
- 10.1103/PhysRevLett.74.1827 is OK
- 10.1103/PhysRev.139.A796 is OK
- 10.1002/wcms.1344 is OK
- 10.1103/PhysRevB.84.241201 is OK
- 10.1103/PhysRevB.71.193102 is OK
- 10.1021/acs.jctc.6b00380 is OK
- 10.1038/s41597-020-0385-y is OK
- 10.1021/acs.jctc.0c00693 is OK
- 10.1021/acs.jpclett.7b02740 is OK
- 10.1021/acs.jctc.7b00770 is OK
- 10.1088/1367-2630/14/5/053020 is OK
- 10.1007/BF00655090 is OK
- 10.48550/arXiv.1108.4417 is OK
- 10.1016/S0010-4655(98)00174-X is OK
- 10.1103/PhysRevB.13.4274 is OK
- 10.1103/PhysRevA.73.012511 is OK
- 10.1103/PhysRevB.96.155207 is OK
- 10.1016/j.cpc.2018.09.003 is OK
- 10.1016/j.cpc.2014.10.021 is OK
- 10.1021/acs.jctc.9b01235 is OK
- 10.1021/acs.jctc.1c00101 is OK
- 10.1021/acs.jctc.1c00308 is OK
- 10.3389/fchem.2021.736591 is OK
- 10.1021/acs.jctc.3c00512 is OK
- 10.1021/acs.jctc.0c00600 is OK
- 10.1021/acs.jctc.8b00177 is OK
- 10.1021/acs.jctc.6b01235 is OK
- 10.1021/acs.jctc.2c00774 is OK
- 10.1063/1.5090605 is OK
- 10.1016/0009-2614(91)80078-C is OK
- 10.1063/1.1809602 is OK
- 10.1103/PhysRevB.94.035118 is OK
- 10.1007/s10853-012-6570-4 is OK
- 10.1007/s00214-011-1084-8 is OK
- 10.1021/ct4002202 is OK
- 10.1103/RevModPhys.74.601 is OK
- 10.1021/acs.jctc.6b00840 is OK
- 10.1103/PhysRevB.85.155129 is OK
- 10.1016/j.cpc.2017.06.012 is OK
- 10.48550/arXiv.2306.16066 is OK

MISSING DOIs

- None

INVALID DOIs

- None

from joss-reviews.

The paper's PDF and metadata files generation produced some warnings that could prevent the final paper from being published. Please fix them before the end of the review process.

    {\color{white}.}\hspace{-3em}F^\text
           ^
unexpected control sequence \color
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

from joss-reviews.

⚠️ Error preparing paper acceptance. The generated XML metadata file is invalid.

IDREFS attribute rid references an unknown ID "ctsteven"
IDREFS attribute rid references an unknown ID "ctsteven"
IDREFS attribute rid references an unknown ID "ctsteven"
IDREFS attribute rid references an unknown ID "stoddttow"
IDREFS attribute rid references an unknown ID "stoddttow"

from joss-reviews.

Ping @lucydot

from joss-reviews.

@editorialbot recommend-accept

from joss-reviews.

Attempting dry run of processing paper acceptance...

from joss-reviews.

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

OK DOIs

- 10.1038/s41550-017-0220-3 is OK
- 10.2307/j.ctvc778ff is OK
- 10.1051/0004-6361/201629272 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.6084/m9.figshare.828487 is OK
- 10.1007/978-3-642-61609-9 is OK
- 10.3389/fchem.2019.00377 is OK
- 10.1103/PhysRevB.78.085125 is OK
- 10.1145/1874391.187410 is OK
- 10.1007/s00791-018-00308-4 is OK
- 10.1021/acs.jctc.3c00555 is OK
- 10.1007/s00791-018-00308-4 is OK
- 10.1103/PhysRev.126.413 is OK
- 10.1103/PhysRev.129.62 is OK
- 10.1063/1.462485 is OK
- 10.1021/ct5001268 is OK
- 10.1103/PhysRevB.90.054115 is OK
- 10.1103/PhysRevB.94.165109 is OK
- 10.1021/acs.jctc.0c01282 is OK
- 10.1103/PhysRevLett.74.1827 is OK
- 10.1103/PhysRev.139.A796 is OK
- 10.1002/wcms.1344 is OK
- 10.1103/PhysRevB.84.241201 is OK
- 10.1103/PhysRevB.71.193102 is OK
- 10.1021/acs.jctc.6b00380 is OK
- 10.1038/s41597-020-0385-y is OK
- 10.1021/acs.jctc.0c00693 is OK
- 10.1021/acs.jpclett.7b02740 is OK
- 10.1021/acs.jctc.7b00770 is OK
- 10.1088/1367-2630/14/5/053020 is OK
- 10.1007/BF00655090 is OK
- 10.48550/arXiv.1108.4417 is OK
- 10.1016/S0010-4655(98)00174-X is OK
- 10.1103/PhysRevB.13.4274 is OK
- 10.1103/PhysRevA.73.012511 is OK
- 10.1103/PhysRevB.96.155207 is OK
- 10.1016/j.cpc.2018.09.003 is OK
- 10.1016/j.cpc.2014.10.021 is OK
- 10.1021/acs.jctc.9b01235 is OK
- 10.1021/acs.jctc.1c00101 is OK
- 10.1021/acs.jctc.1c00308 is OK
- 10.3389/fchem.2021.736591 is OK
- 10.1021/acs.jctc.3c00512 is OK
- 10.1021/acs.jctc.0c00600 is OK
- 10.1021/acs.jctc.8b00177 is OK
- 10.1021/acs.jctc.6b01235 is OK
- 10.1021/acs.jctc.2c00774 is OK
- 10.1063/1.5090605 is OK
- 10.1016/0009-2614(91)80078-C is OK
- 10.1063/1.1809602 is OK
- 10.1103/PhysRevB.94.035118 is OK
- 10.1007/s10853-012-6570-4 is OK
- 10.1007/s00214-011-1084-8 is OK
- 10.1021/ct4002202 is OK
- 10.1103/RevModPhys.74.601 is OK
- 10.1021/acs.jctc.6b00840 is OK
- 10.1103/PhysRevB.85.155129 is OK
- 10.1016/j.cpc.2017.06.012 is OK
- 10.48550/arXiv.2306.16066 is OK

MISSING DOIs

- None

INVALID DOIs

- None

from joss-reviews.

The paper's PDF and metadata files generation produced some warnings that could prevent the final paper from being published. Please fix them before the end of the review process.

    \hspace{-2em}F^\text{even}(i\omega_k
            ^
unexpected "-"
expecting white space or digit

i\omega_k) \hspace{-1em}&=&\hspace{-1em}
                   ^
unexpected "-"
expecting white space or digit

from joss-reviews.

⚠️ Error preparing paper acceptance. The generated XML metadata file is invalid.

IDREFS attribute rid references an unknown ID "stoddttow"
IDREFS attribute rid references an unknown ID "stoddttow"
IDREFS attribute rid references an unknown ID "ctsteven"
IDREFS attribute rid references an unknown ID "ctsteven"
IDREFS attribute rid references an unknown ID "ctsteven"

from joss-reviews.

Hello @arfon, thanks for the recommend-accept. We have been facing this XML error for a while now. I looked in the documentation of JOSS, but did not find any entry about how to deal with it. Do you have any hint? Thanks a lot

from joss-reviews.

Dear @arfon,

We have updated the md file with the labeling format explained in the documentation. Could you please run the recommend-accept again to see if it works.

Thank you very much in advance!
Best,
Maryam

from joss-reviews.

@editorialbot recommend-accept

from joss-reviews.

Attempting dry run of processing paper acceptance...

from joss-reviews.

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

OK DOIs

- 10.1038/s41550-017-0220-3 is OK
- 10.2307/j.ctvc778ff is OK
- 10.1051/0004-6361/201629272 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.6084/m9.figshare.828487 is OK
- 10.1007/978-3-642-61609-9 is OK
- 10.3389/fchem.2019.00377 is OK
- 10.1103/PhysRevB.78.085125 is OK
- 10.1145/1874391.187410 is OK
- 10.1007/s00791-018-00308-4 is OK
- 10.1021/acs.jctc.3c00555 is OK
- 10.1007/s00791-018-00308-4 is OK
- 10.1103/PhysRev.126.413 is OK
- 10.1103/PhysRev.129.62 is OK
- 10.1063/1.462485 is OK
- 10.1021/ct5001268 is OK
- 10.1103/PhysRevB.90.054115 is OK
- 10.1103/PhysRevB.94.165109 is OK
- 10.1021/acs.jctc.0c01282 is OK
- 10.1103/PhysRevLett.74.1827 is OK
- 10.1103/PhysRev.139.A796 is OK
- 10.1002/wcms.1344 is OK
- 10.1103/PhysRevB.84.241201 is OK
- 10.1103/PhysRevB.71.193102 is OK
- 10.1021/acs.jctc.6b00380 is OK
- 10.1038/s41597-020-0385-y is OK
- 10.1021/acs.jctc.0c00693 is OK
- 10.1021/acs.jpclett.7b02740 is OK
- 10.1021/acs.jctc.7b00770 is OK
- 10.1088/1367-2630/14/5/053020 is OK
- 10.1007/BF00655090 is OK
- 10.48550/arXiv.1108.4417 is OK
- 10.1016/S0010-4655(98)00174-X is OK
- 10.1103/PhysRevB.13.4274 is OK
- 10.1103/PhysRevA.73.012511 is OK
- 10.1103/PhysRevB.96.155207 is OK
- 10.1016/j.cpc.2018.09.003 is OK
- 10.1016/j.cpc.2014.10.021 is OK
- 10.1021/acs.jctc.9b01235 is OK
- 10.1021/acs.jctc.1c00101 is OK
- 10.1021/acs.jctc.1c00308 is OK
- 10.3389/fchem.2021.736591 is OK
- 10.1021/acs.jctc.3c00512 is OK
- 10.1021/acs.jctc.0c00600 is OK
- 10.1021/acs.jctc.8b00177 is OK
- 10.1021/acs.jctc.6b01235 is OK
- 10.1021/acs.jctc.2c00774 is OK
- 10.1063/1.5090605 is OK
- 10.1016/0009-2614(91)80078-C is OK
- 10.1063/1.1809602 is OK
- 10.1103/PhysRevB.94.035118 is OK
- 10.1007/s10853-012-6570-4 is OK
- 10.1007/s00214-011-1084-8 is OK
- 10.1021/ct4002202 is OK
- 10.1103/RevModPhys.74.601 is OK
- 10.1021/acs.jctc.6b00840 is OK
- 10.1103/PhysRevB.85.155129 is OK
- 10.1016/j.cpc.2017.06.012 is OK
- 10.48550/arXiv.2306.16066 is OK

MISSING DOIs

- None

INVALID DOIs

- None

from joss-reviews.

The paper's PDF and metadata files generation produced some warnings that could prevent the final paper from being published. Please fix them before the end of the review process.

    \hspace{-2em}F^\text{even}(i\omega_k
            ^
unexpected "-"
expecting white space or digit

i\omega_k) \hspace{-1em}&=&\hspace{-1em}
                   ^
unexpected "-"
expecting white space or digit

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⚠️ Error preparing paper acceptance. The generated XML metadata file is invalid.

IDREFS attribute rid references an unknown ID "stoddttow"
IDREFS attribute rid references an unknown ID "stoddttow"
IDREFS attribute rid references an unknown ID "ctsteven"
IDREFS attribute rid references an unknown ID "ctsteven"
IDREFS attribute rid references an unknown ID "ctsteven"

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@aziziph @dgolze apologies for my late reply to your earlier messages.

It seems there is still a problem @arfon, will raise with other editors in case they have seen similar.

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Is the hspace necessary @aziziph? As a test could we try removing it to see if that is where the problem is? Just to check, is the hspace being used in math mode? I don't think valid latex if so.

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Is the hspace necessary @aziziph? As a test could we try removing it to see if that is where the problem is? Just to check, is the hspace being used in math mode? I don't think valid latex if so.@lucydot
we will remove the hspace, trying right now

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Hi @lucydot I believe I fixed the compilation warnings in nomad-coe/greenX@3df7ff1 Would you mind recommending again? Apologies for the long iterations

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ping @lucydot @arfon

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ping @lucydot @arfon

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@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

OK DOIs

- 10.1038/s41550-017-0220-3 is OK
- 10.2307/j.ctvc778ff is OK
- 10.1051/0004-6361/201629272 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.6084/m9.figshare.828487 is OK
- 10.1007/978-3-642-61609-9 is OK
- 10.3389/fchem.2019.00377 is OK
- 10.1103/PhysRevB.78.085125 is OK
- 10.1145/1874391.187410 is OK
- 10.1007/s00791-018-00308-4 is OK
- 10.1021/acs.jctc.3c00555 is OK
- 10.1007/s00791-018-00308-4 is OK
- 10.1103/PhysRev.126.413 is OK
- 10.1103/PhysRev.129.62 is OK
- 10.1063/1.462485 is OK
- 10.1021/ct5001268 is OK
- 10.1103/PhysRevB.90.054115 is OK
- 10.1103/PhysRevB.94.165109 is OK
- 10.1021/acs.jctc.0c01282 is OK
- 10.1103/PhysRevLett.74.1827 is OK
- 10.1103/PhysRev.139.A796 is OK
- 10.1002/wcms.1344 is OK
- 10.1103/PhysRevB.84.241201 is OK
- 10.1103/PhysRevB.71.193102 is OK
- 10.1021/acs.jctc.6b00380 is OK
- 10.1038/s41597-020-0385-y is OK
- 10.1021/acs.jctc.0c00693 is OK
- 10.1021/acs.jpclett.7b02740 is OK
- 10.1021/acs.jctc.7b00770 is OK
- 10.1088/1367-2630/14/5/053020 is OK
- 10.1007/BF00655090 is OK
- 10.48550/arXiv.1108.4417 is OK
- 10.1016/S0010-4655(98)00174-X is OK
- 10.1103/PhysRevB.13.4274 is OK
- 10.1103/PhysRevA.73.012511 is OK
- 10.1103/PhysRevB.96.155207 is OK
- 10.1016/j.cpc.2018.09.003 is OK
- 10.1016/j.cpc.2014.10.021 is OK
- 10.1021/acs.jctc.9b01235 is OK
- 10.1021/acs.jctc.1c00101 is OK
- 10.1021/acs.jctc.1c00308 is OK
- 10.3389/fchem.2021.736591 is OK
- 10.1021/acs.jctc.3c00512 is OK
- 10.1021/acs.jctc.0c00600 is OK
- 10.1021/acs.jctc.8b00177 is OK
- 10.1021/acs.jctc.6b01235 is OK
- 10.1021/acs.jctc.2c00774 is OK
- 10.1063/1.5090605 is OK
- 10.1016/0009-2614(91)80078-C is OK
- 10.1063/1.1809602 is OK
- 10.1103/PhysRevB.94.035118 is OK
- 10.1007/s10853-012-6570-4 is OK
- 10.1007/s00214-011-1084-8 is OK
- 10.1021/ct4002202 is OK
- 10.1103/RevModPhys.74.601 is OK
- 10.1021/acs.jctc.6b00840 is OK
- 10.1103/PhysRevB.85.155129 is OK
- 10.1016/j.cpc.2017.06.012 is OK
- 10.48550/arXiv.2306.16066 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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👋 @openjournals/pe-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4641, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

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@dgolze just a question: can you explain why GW is italicized in the title and text, while other acronyms like RPA are not?

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It's in Italic because of convention.
@kyleniemeyer

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OK, thanks @aziziph!

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@editorialbot accept

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