[REVIEW]: Connectome Mapper 3: A Flexible and Open-Source Pipeline Software for Multiscale Multimodal Human Connectome Mapping #4248

editorialbot · 2022-03-17T07:03:17Z

Submitting author: @sebastientourbier (Sebastien Tourbier)
Repository: https://github.com/connectomicslab/connectomemapper3
Branch with paper.md (empty if default branch):
Version: v3.0.4
Editor: @osorensen
Reviewers: @adbartni, @jsheunis
Archive: 10.5281/zenodo.6645256

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/fa1f416a4a6c23fe19bda6f36f123c1e/status.svg)](https://joss.theoj.org/papers/fa1f416a4a6c23fe19bda6f36f123c1e)

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

@adbartni & @jsheunis, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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Checklists

📝 Checklist for @jsheunis

📝 Checklist for @adbartni

The text was updated successfully, but these errors were encountered:

editorialbot · 2022-03-17T07:03:18Z

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:

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

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editorialbot · 2022-03-17T07:03:43Z

Software report:

github.com/AlDanial/cloc v 1.88  T=1.34 s (126.1 files/s, 93677.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              3              0             25          65623
Python                          95           6525           9108          25397
reStructuredText                18           1331            409           2152
XML                              2              0              0           1854
YAML                             9             77            115           1720
Jupyter Notebook                 7              0           5607           1196
INI                             10             54              0            917
CSS                              1              0              9            723
TeX                              1             60              0            668
Markdown                         3             81              0            493
HTML                             3             50              2            314
JSON                             6              0              0            228
Dockerfile                       1             43            111            192
DOS Batch                        1             23              1            166
make                             1             24              6            123
Bourne Shell                     7             15             40             66
JavaScript                       1              0              1              1
-------------------------------------------------------------------------------
SUM:                           169           8283          15434         101833
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2022-03-17T07:03:48Z

Wordcount for paper.md is 2739

editorialbot · 2022-03-17T07:03:52Z

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

OK DOIs

- 10.5281/zenodo.3475969 is OK
- 10.1016/J.NEUROIMAGE.2011.08.056 is OK
- 10.1038/nn.4500 is OK
- 10.5281/zenodo.3571874 is OK
- 10.3389/fninf.2019.00001 is OK
- 10.1038/s41592-018-0235-4 is OK
- 10.1038/nn.4502 is OK
- 10.1371/journal.pone.0048121 is OK
- 10.3389/conf.fninf.2013.09.00042 is OK
- 10.1016/j.neuroimage.2015.04.042 is OK
- 10.1101/188706 is OK
- 10.1016/j.neuroimage.2006.01.021 is OK
- 10.1016/j.neuroimage.2015.02.065 is OK
- 10.1371/journal.pcbi.1005209 is OK
- 10.1146/annurev-biodatasci-072018-021237 is OK
- 10.3389/fninf.2014.00008 is OK
- 10.1162/netn_e_00052 is OK
- 10.1016/j.neuroimage.2012.01.021 is OK
- 10.5075/epfl-thesis-3230 is OK
- 10.1016/J.NEUROIMAGE.2011.09.015 is OK
- 10.1016/j.clinph.2020.09.018 is OK
- 10.1038/sdata.2018.270 is OK
- 10.1016/j.jneumeth.2011.09.031 is OK
- 10.3389/fnins.2013.00267 is OK
- 10.1016/j.neuroimage.2019.116137 is OK
- 10.3389/fninf.2011.00013 is OK
- 10.1038/s41592-021-01185-5 is OK
- 10.5281/ZENODO.3712762 is OK
- 10.1371/journal.pone.0177459 is OK
- 10.21105/joss.01294 is OK
- 10.1038/sdata.2016.44 is OK
- 10.1371/journal.pcbi.0010042 is OK
- 10.1016/j.clinph.2019.09.006 is OK
- 10.1038/nn.4550 is OK
- 10.1016/j.nicl.2020.102336 is OK
- 10.1016/j.neuroimage.2020.117137 is OK
- 10.1162/netn_a_00147 is OK
- 10.1002/hbm.25365 is OK
- 10.1016/j.neuroimage.2021.118611 is OK
- 10.1162/netn_a_00218 is OK
- doi10.18112/openneuro.ds003505.v1.1.1 is OK
- 10.1038/s41597-021-01116-1 is OK
- 10.1016/j.clinph.2021.10.008 is OK
- 10.1016/j.neuroimage.2009.10.003 is OK
- 10.12688/f1000research.20887.3 is OK
- 10.1101/gr.1239303 is OK
- 10.1101/2022.01.31.478189 is OK
- 10.1162/netn_a_00114 is OK
- 10.1073/PNAS.1922248117 is OK
- 10.1016/j.media.2007.06.004 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-03-17T07:05:53Z

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

jsheunis · 2022-03-29T20:53:58Z

Review checklist for @jsheunis

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/connectomicslab/connectomemapper3?
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 (@sebastientourbier) 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

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 and who the target audience is?
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?

jsheunis · 2022-04-08T14:21:19Z

@osorensen @sebastientourbier

Review update: I've checked most of the boxes in my checklist. The ones that are still open are dependent on open issues, particularly:

sebastientourbier · 2022-04-09T06:17:02Z

Dear @jsheunis,

Thank you a lot for the time you spent reviewing CMP3 and its paper!
I am going to address your issues next week and I will reply directly inside them for the sake of clarity.
I will let you all know as soon as it is done.

Best regards

adbartni · 2022-04-18T13:56:27Z

Review checklist for @adbartni

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/connectomicslab/connectomemapper3?
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 (@sebastientourbier) 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

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 and who the target audience is?
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?

osorensen · 2022-06-10T04:53:45Z

@sebastientourbier can you please update us on how it is going addressing the points raised by the reviewers?

osorensen · 2022-06-23T20:54:31Z

Here are the lines: https://github.com/connectomicslab/connectomemapper3/search?q=isbn&type=

sebastientourbier · 2022-06-24T07:40:44Z

@osorensen All isbn fields have been removed 👍

osorensen · 2022-06-24T07:49:58Z

@editorialbot check references

osorensen · 2022-06-24T07:50:09Z

@editorialbot generate pdf

editorialbot · 2022-06-24T07:50:28Z

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

OK DOIs

- 10.5281/zenodo.3475969 is OK
- 10.1016/J.NEUROIMAGE.2011.08.056 is OK
- 10.1038/nn.4500 is OK
- 10.5281/zenodo.3571874 is OK
- 10.3389/fninf.2019.00001 is OK
- 10.1038/s41592-018-0235-4 is OK
- 10.1038/nn.4502 is OK
- 10.1371/journal.pone.0048121 is OK
- 10.3389/conf.fninf.2013.09.00042 is OK
- 10.1016/j.neuroimage.2015.04.042 is OK
- 10.1101/188706 is OK
- 10.1016/j.neuroimage.2006.01.021 is OK
- 10.1016/j.neuroimage.2015.02.065 is OK
- 10.1371/journal.pcbi.1005209 is OK
- 10.1146/annurev-biodatasci-072018-021237 is OK
- 10.3389/fninf.2014.00008 is OK
- 10.1162/netn_e_00052 is OK
- 10.1016/j.neuroimage.2012.01.021 is OK
- 10.5075/epfl-thesis-3230 is OK
- 10.1016/J.NEUROIMAGE.2011.09.015 is OK
- 10.1016/j.clinph.2020.09.018 is OK
- 10.1038/sdata.2018.270 is OK
- 10.1016/j.jneumeth.2011.09.031 is OK
- 10.3389/fnins.2013.00267 is OK
- 10.1016/j.neuroimage.2019.116137 is OK
- 10.3389/fninf.2011.00013 is OK
- 10.1038/s41592-021-01185-5 is OK
- 10.5281/ZENODO.3712762 is OK
- 10.1371/journal.pone.0177459 is OK
- 10.21105/joss.01294 is OK
- 10.1038/sdata.2016.44 is OK
- 10.1371/journal.pcbi.0010042 is OK
- 10.1016/j.clinph.2019.09.006 is OK
- 10.1038/nn.4550 is OK
- 10.1016/j.nicl.2020.102336 is OK
- 10.1016/j.neuroimage.2020.117137 is OK
- 10.1162/netn_a_00147 is OK
- 10.1002/hbm.25365 is OK
- 10.1016/j.neuroimage.2021.118611 is OK
- 10.1162/netn_a_00218 is OK
- 10.18112/openneuro.ds003505.v1.1.1 is OK
- 10.1038/s41597-021-01116-1 is OK
- 10.1016/j.clinph.2021.10.008 is OK
- 10.1016/j.neuroimage.2009.10.003 is OK
- 10.12688/f1000research.20887.3 is OK
- 10.1101/gr.1239303 is OK
- 10.1101/2022.01.31.478189 is OK
- 10.1162/netn_a_00114 is OK
- 10.1073/PNAS.1922248117 is OK
- 10.1016/j.media.2007.06.004 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-06-24T07:52:03Z

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

osorensen · 2022-06-24T07:55:06Z

@editorialbot recommend-accept

editorialbot · 2022-06-24T07:55:07Z

Attempting dry run of processing paper acceptance...

editorialbot · 2022-06-24T07:55:33Z

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

OK DOIs

- 10.5281/zenodo.3475969 is OK
- 10.1016/J.NEUROIMAGE.2011.08.056 is OK
- 10.1038/nn.4500 is OK
- 10.5281/zenodo.3571874 is OK
- 10.3389/fninf.2019.00001 is OK
- 10.1038/s41592-018-0235-4 is OK
- 10.1038/nn.4502 is OK
- 10.1371/journal.pone.0048121 is OK
- 10.3389/conf.fninf.2013.09.00042 is OK
- 10.1016/j.neuroimage.2015.04.042 is OK
- 10.1101/188706 is OK
- 10.1016/j.neuroimage.2006.01.021 is OK
- 10.1016/j.neuroimage.2015.02.065 is OK
- 10.1371/journal.pcbi.1005209 is OK
- 10.1146/annurev-biodatasci-072018-021237 is OK
- 10.3389/fninf.2014.00008 is OK
- 10.1162/netn_e_00052 is OK
- 10.1016/j.neuroimage.2012.01.021 is OK
- 10.5075/epfl-thesis-3230 is OK
- 10.1016/J.NEUROIMAGE.2011.09.015 is OK
- 10.1016/j.clinph.2020.09.018 is OK
- 10.1038/sdata.2018.270 is OK
- 10.1016/j.jneumeth.2011.09.031 is OK
- 10.3389/fnins.2013.00267 is OK
- 10.1016/j.neuroimage.2019.116137 is OK
- 10.3389/fninf.2011.00013 is OK
- 10.1038/s41592-021-01185-5 is OK
- 10.5281/ZENODO.3712762 is OK
- 10.1371/journal.pone.0177459 is OK
- 10.21105/joss.01294 is OK
- 10.1038/sdata.2016.44 is OK
- 10.1371/journal.pcbi.0010042 is OK
- 10.1016/j.clinph.2019.09.006 is OK
- 10.1038/nn.4550 is OK
- 10.1016/j.nicl.2020.102336 is OK
- 10.1016/j.neuroimage.2020.117137 is OK
- 10.1162/netn_a_00147 is OK
- 10.1002/hbm.25365 is OK
- 10.1016/j.neuroimage.2021.118611 is OK
- 10.1162/netn_a_00218 is OK
- 10.18112/openneuro.ds003505.v1.1.1 is OK
- 10.1038/s41597-021-01116-1 is OK
- 10.1016/j.clinph.2021.10.008 is OK
- 10.1016/j.neuroimage.2009.10.003 is OK
- 10.12688/f1000research.20887.3 is OK
- 10.1101/gr.1239303 is OK
- 10.1101/2022.01.31.478189 is OK
- 10.1162/netn_a_00114 is OK
- 10.1073/PNAS.1922248117 is OK
- 10.1016/j.media.2007.06.004 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-06-24T07:57:03Z

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

Check final proof 👉 openjournals/joss-papers#3299

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3299, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman · 2022-06-25T14:17:36Z

@sebastientourbier

I checked the archive meta-data and all looks good. 👍
I checked the version tag for the review and archive and verified they match 👍
I proofread the paper and have the following comment:
Introduce Magnetic Resonance Imaging (MRI) in the summary where MRI is first used.

sebastientourbier · 2022-06-27T08:20:26Z

Dear @Kevin-Mattheus-Moerman,

Thank you very much.

I just took care to introduce MRI the very first time it is used in the paper. I also took care of defining BIDS in the summary too. Finally, I noticed that I was redefining CMP3 acronym multiple times and this has been fixed. The changes can be viewed in connectomicslab/connectomemapper3#196.

Let me know if you need anything else.
Best

Kevin-Mattheus-Moerman · 2022-06-27T08:24:44Z

@editorialbot generate pdf

editorialbot · 2022-06-27T08:26:09Z

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

Kevin-Mattheus-Moerman · 2022-06-27T08:44:46Z

@editorialbot accept

editorialbot · 2022-06-27T08:44:47Z

Doing it live! Attempting automated processing of paper acceptance...

editorialbot · 2022-06-27T08:46:48Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2022-06-27T08:46:49Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04248 joss-papers#3312
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04248
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman · 2022-06-27T08:52:45Z

@sebastientourbier congratulations on your JOSS publication!

@osorensen thanks for editing this one!

And special thanks to @adbartni and @jsheunis for your review efforts!! 🎉

editorialbot · 2022-06-27T08:52:47Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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reStructuredText:
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   :target: https://doi.org/10.21105/joss.04248

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sebastientourbier · 2022-06-27T09:41:42Z

This is a really great 🎉
Thank you very much all for the time you invested in the reviewing/editing process. It really helped in improving the robustness and the documentation of CMP3, as well as the quality of the paper. 🙏

editorialbot added Dockerfile Python review Shell labels Mar 17, 2022

editorialbot assigned osorensen Mar 17, 2022

editorialbot mentioned this issue Mar 17, 2022

[PRE REVIEW]: Connectome Mapper 3: A Flexible and Open-Source Pipeline Software for Multiscale Multimodal Human Connectome Mapping #4194

Closed

jsheunis mentioned this issue Apr 15, 2022

BUG: Running cmpbidsappmanager just hangs, no GUI appearing connectomicslab/connectomemapper3#171

Closed

sebastientourbier mentioned this issue May 18, 2022

REL: v3.0.4 connectomicslab/connectomemapper3#184

Merged

sebastientourbier mentioned this issue Jun 2, 2022

REV: Add high-level paper summary connectomicslab/connectomemapper3#175

Merged

sebastientourbier mentioned this issue Jun 24, 2022

JOSS REV: Remove isbn in entries of paper.bib connectomicslab/connectomemapper3#195

Merged

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Jun 24, 2022

sebastientourbier mentioned this issue Jun 27, 2022

JOSS REV: Introduce MRI and BIDS in paper summary connectomicslab/connectomemapper3#196

Merged

editorialbot added accepted published Papers published in JOSS labels Jun 27, 2022

Kevin-Mattheus-Moerman closed this as completed Jun 27, 2022

editorialbot mentioned this issue Oct 30, 2023

[PRE REVIEW]: CM++ - A Meta-method for Well-Connected Community Detection #5998

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[PRE REVIEW]: Thresholdmann: A Web tool for interactively creating adaptive thresholds to segment MRI data. #6152

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[PRE REVIEW]: LabelProp: A semi-automatic segmentation tool for 3D medical images #6257

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[REVIEW]: Connectome Mapper 3: A Flexible and Open-Source Pipeline Software for Multiscale Multimodal Human Connectome Mapping #4248

[REVIEW]: Connectome Mapper 3: A Flexible and Open-Source Pipeline Software for Multiscale Multimodal Human Connectome Mapping #4248

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[REVIEW]: Connectome Mapper 3: A Flexible and Open-Source Pipeline Software for Multiscale Multimodal Human Connectome Mapping #4248

[REVIEW]: Connectome Mapper 3: A Flexible and Open-Source Pipeline Software for Multiscale Multimodal Human Connectome Mapping #4248

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jsheunis commented Mar 29, 2022 • edited Loading

Review checklist for @jsheunis

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

jsheunis commented Apr 8, 2022

sebastientourbier commented Apr 9, 2022

adbartni commented Apr 18, 2022 • edited Loading

Review checklist for @adbartni

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

osorensen commented Jun 10, 2022

osorensen commented Jun 23, 2022

sebastientourbier commented Jun 24, 2022

osorensen commented Jun 24, 2022

osorensen commented Jun 24, 2022

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editorialbot commented Jun 24, 2022

osorensen commented Jun 24, 2022

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editorialbot commented Jun 24, 2022

Kevin-Mattheus-Moerman commented Jun 25, 2022 • edited Loading

sebastientourbier commented Jun 27, 2022

Kevin-Mattheus-Moerman commented Jun 27, 2022

editorialbot commented Jun 27, 2022

Kevin-Mattheus-Moerman commented Jun 27, 2022

editorialbot commented Jun 27, 2022

editorialbot commented Jun 27, 2022

editorialbot commented Jun 27, 2022

Kevin-Mattheus-Moerman commented Jun 27, 2022

editorialbot commented Jun 27, 2022

sebastientourbier commented Jun 27, 2022

editorialbot commented Mar 17, 2022 •

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jsheunis commented Mar 29, 2022 •

edited

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adbartni commented Apr 18, 2022 •

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Kevin-Mattheus-Moerman commented Jun 25, 2022 •

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