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[PRE REVIEW]: elsa: an elegant framework for tomographic reconstruction #6164

Closed editorialbot closed 10 months ago

editorialbot commented 10 months ago

Submitting author: !--author-handle-->@ner0-m<!--end-author-handle-- (David Frank) Repository: https://gitlab.com/tum-ciip/elsa Branch with paper.md (empty if default branch): df/joss-paper Version: 0.8.0 Editor: !--editor-->@jbytecode<!--end-editor-- Reviewers: @uellue, @DanNixon Managing EiC: Daniel S. Katz

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HTML: <a href="https://joss.theoj.org/papers/cd26f77e40404f0403c91531e61b07e9"><img src="https://joss.theoj.org/papers/cd26f77e40404f0403c91531e61b07e9/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/cd26f77e40404f0403c91531e61b07e9/status.svg)](https://joss.theoj.org/papers/cd26f77e40404f0403c91531e61b07e9)

Author instructions

Thanks for submitting your paper to JOSS @ner0-m. Currently, there isn't a JOSS editor assigned to your paper.

@ner0-m if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands
editorialbot commented 10 months ago

Hello human, 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
editorialbot commented 10 months ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.48 s (1609.6 files/s, 271551.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                            359          14455           4912          70039
C/C++ Header                   239           3693           7752          12964
CMake                           57            523            584           3004
Python                          38            945            585           2794
CUDA                            14            317            345           1449
Markdown                        15            444              0           1275
YAML                             5             86            116            661
Bourne Shell                    16            148             82            647
reStructuredText                20            397            289            596
TeX                              1             16              0            236
JSON                             1              3              0            153
make                             2             42             16            152
TOML                             1              3              0             15
JavaScript                       1              0              0              1
-------------------------------------------------------------------------------
SUM:                           769          21072          14681          93986
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 10 months ago

Wordcount for paper.md is 1104

editorialbot commented 10 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.04722 is OK
- 10.1098/rsta.2020.0192 is OK
- 10.1098/rsta.2020.0193 is OK
- 10.1364/oe.24.025129 is OK
- 10.1117/12.2534833 is OK
- 10.1088/2631-8695/ac8224 is OK
- 10.1117/12.2646492 is OK
- 10.1088/2631-8695/ad08fd is OK
- 10.1109/tci.2023.3240078 is OK
- 10.48550/ARXIV.2304.14505 is OK
- 10.5281/zenodo.6986012 is OK
- 10.5281/zenodo.6983008 is OK
- 10.1103/PhysRevLett.117.158101 is OK
- 10.1038/nphys265 is OK

MISSING DOIs

- None

INVALID DOIs

- arXiv:2310.16846 is INVALID (failed connection)
editorialbot commented 10 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

editorialbot commented 10 months ago

Five most similar historical JOSS papers:

uDALES: large-eddy-simulation software for urban flow, dispersion, and microclimate modelling Submitting author: @tomgrylls Handling editor: @Kevin-Mattheus-Moerman (Active) Reviewers: @wimvanderbauwhede, @p-costa, @ashwinvis Similarity score: 0.8173

AXITOM: A Python package for reconstruction of axisymmetric tomograms acquired by a conical beam Submitting author: @PolymerGuy Handling editor: @katyhuff (Retired) Reviewers: @PingjunChen, @dgursoy Similarity score: 0.8162

LiberTEM: Software platform for scalable multidimensional data processing in transmission electron microscopy Submitting author: @uellue Handling editor: @majensen (Active) Reviewers: @alvarolopez, @fedorov Similarity score: 0.8123

Open Source Optical Coherence Tomography Software Submitting author: @spectralcode Handling editor: @arfon (Active) Reviewers: @jdavidli, @brandondube Similarity score: 0.8120

TE-dependent analysis of multi-echo fMRI with tedana Submitting author: @tsalo Handling editor: @oliviaguest (Active) Reviewers: @martinagvilas, @stebo85 Similarity score: 0.8120

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

danielskatz commented 10 months ago

@ner0-m - thanks for your submission.

As a minor point, the doi in your frank2023 bib entry should be 10.48550/arXiv.2310.16846 rather than arXiv:2310.16846, which is not a valid doi. Please changes this, then use the command @editorialbot check references to check again, and then the command @editorialbot generate pdf to make a new PDF. editorialbot commands need to be the first entry in a new comment.

Second, based on your submission information, this ended up in our "Computer science, Information Science, and Mathematics" track, which I lead. Does this seem correct to you? Please see https://joss.theoj.org/about#editorial_board for our seven tracks (each with a track editor), and let me know if you think this should be in a different track. Once I hear back from you on this, either I or another track editor will start by looking for an editor for this submission.

ner0-m commented 10 months ago

@editorialbot check references

editorialbot commented 10 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.04722 is OK
- 10.1098/rsta.2020.0192 is OK
- 10.1098/rsta.2020.0193 is OK
- 10.1364/oe.24.025129 is OK
- 10.1117/12.2534833 is OK
- 10.1088/2631-8695/ac8224 is OK
- 10.1117/12.2646492 is OK
- 10.1088/2631-8695/ad08fd is OK
- 10.1109/tci.2023.3240078 is OK
- 10.48550/ARXIV.2304.14505 is OK
- 10.48550/arXiv.2310.16846 is OK
- 10.5281/zenodo.6986012 is OK
- 10.5281/zenodo.6983008 is OK
- 10.1103/PhysRevLett.117.158101 is OK
- 10.1038/nphys265 is OK

MISSING DOIs

- None

INVALID DOIs

- None
ner0-m commented 10 months ago

@editorialbot generate pdf

editorialbot commented 10 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

editorialbot commented 10 months ago

Five most similar historical JOSS papers:

uDALES: large-eddy-simulation software for urban flow, dispersion, and microclimate modelling Submitting author: @tomgrylls Handling editor: @Kevin-Mattheus-Moerman (Active) Reviewers: @wimvanderbauwhede, @p-costa, @ashwinvis Similarity score: 0.8173

AXITOM: A Python package for reconstruction of axisymmetric tomograms acquired by a conical beam Submitting author: @PolymerGuy Handling editor: @katyhuff (Retired) Reviewers: @PingjunChen, @dgursoy Similarity score: 0.8162

LiberTEM: Software platform for scalable multidimensional data processing in transmission electron microscopy Submitting author: @uellue Handling editor: @majensen (Active) Reviewers: @alvarolopez, @fedorov Similarity score: 0.8123

Open Source Optical Coherence Tomography Software Submitting author: @spectralcode Handling editor: @arfon (Active) Reviewers: @jdavidli, @brandondube Similarity score: 0.8120

TE-dependent analysis of multi-echo fMRI with tedana Submitting author: @tsalo Handling editor: @oliviaguest (Active) Reviewers: @martinagvilas, @stebo85 Similarity score: 0.8120

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

ner0-m commented 10 months ago

@danielskatz Thank you for the message! I fixed the incorrect DOI. Seems like it's now all good now.

The "Computer science, Information Science, and Mathematics" track sounds correct for me. At least it doesn't really fit into any of the other tracks.

If you need any more information please let me know!

danielskatz commented 10 months ago

👋 @jbytecode - do you think you would be able to edit this submission?

danielskatz commented 10 months ago

@editorialbot invite @jbytecode as editor

editorialbot commented 10 months ago

Invitation to edit this submission sent!

jbytecode commented 10 months ago

@editorialbot assign me as editor

@danielskatz - sure, gladly!

editorialbot commented 10 months ago

Assigned! @jbytecode is now the editor

jbytecode commented 10 months ago

@ner0-m - Hello, thank you for submitting your work to JOSS. I am the handling editor for this submission. The editorial bot has identified some previously published works that are similar to yours. Initially, I will attempt to invite the authors of these works to serve as reviewers. If we are unable to assign at least two reviewers through this process, I will then ask you to provide a list of potential reviewers from the suggested reviewers list. Thank you in advance.

jbytecode commented 10 months ago

👋👋👋 Dear @tomgrylls, @PolymerGuy , @uellue, @spectralcode, @tsalo 👋👋👋

Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)?

JOSS publishes articles about open source research software. The submission I'd like you to review is titled:

elsa: an elegant framework for tomographic reconstruction

You can find more information at the top of this Github issue (https://github.com/openjournals/joss-reviews/issues/6164).

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know.

This is the pre-review issue. After setting at least 2 reviewers we will start the review process in a separate thread. In that thread, there will be 23 check items for each single reviewer.

Thank you in advance!

uellue commented 10 months ago

Dear @jbytecode, it would be my pleasure to review this submission. With the upcoming Christmas holidays and a number of planned activities in my schedule I will only be able to work on this from the 3rd week of January on. I hope that is soon enough?

jbytecode commented 10 months ago

@editorialbot add @uellue as reviewer

@uellue - The starting date you've provided is okay to me. Thank you for your quick response. I am now assigning you as a reviewer. The review process will start in a separate thread whenever we assign the second reviewer.

jbytecode commented 10 months ago

@editorialbot add @uellue as reviewer

editorialbot commented 10 months ago

@uellue added to the reviewers list!

jbytecode commented 10 months ago

@ner0-m - Do you have suggestions for potential reviewers? You can use the search tool for finding a suitable list. Please mention their GitHub username without using the @ character.

ner0-m commented 10 months ago

Just looking at similar papers published by JOSS and the search tool:

I hope that we will find someone suitable from this list.

jbytecode commented 10 months ago

👋👋👋 Dear @DanNixon 👋👋👋

Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)?

JOSS publishes articles about open source research software. The submission I'd like you to review is titled:

elsa: an elegant framework for tomographic reconstruction

You can find more information at the top of this Github issue (https://github.com/openjournals/joss-reviews/issues/6164).

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know.

This is the pre-review issue. After setting at least 2 reviewers we will start the review process in a separate thread. In that thread, there will be 23 check items for each single reviewer.

The first reviewer is already assigned. We need an other reviewer as the second one. Here is the reviewing documentation.

Thank you in advance!

DanNixon commented 10 months ago

Hi @jbytecode, I'd be happy to be the second reviewer for this submission. I should be able to make a start in early January.

jbytecode commented 10 months ago

@editorialbot add @DanNixon as reviewer

editorialbot commented 10 months ago

@DanNixon added to the reviewers list!

jbytecode commented 10 months ago

@uellue, @DanNixon - thank you for accepting our invitation. the review will start in a separate GitHub issue. I will introduce the instructions there.

jbytecode commented 10 months ago

@editorialbot start review

editorialbot commented 10 months ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6174.