[PRE REVIEW]: MetaSpread: A cancer growth and metastatic spread simulation program in Python

[editorialbot]

Submitting author: !--author-handle-->@alfredohernandezinostroza<!--end-author-handle-- (Alfredo Hernández) Repository: https://github.com/alfredohernandezinostroza/MetaSpread Branch with paper.md (empty if default branch): paper Version: 2024.0.2 Editor: !--editor-->@ppxasjsm<!--end-editor-- Reviewers: Pending Managing EiC: Kevin M. Moerman

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.01 s (522.4 files/s, 56812.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                         2             73              0            182
TeX                              1             16              0            141
YAML                             1              1              4             18
-------------------------------------------------------------------------------
SUM:                             4             90              4            341
-------------------------------------------------------------------------------

Commit count by author:

   180  Alfredo Hernández
     3  Alfredo A. Hernandez I

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 4655

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🔴 Failed to discover a valid open source license

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@editorialbot set main as branch

[editorialbot]

Done! branch is now main

[Kevin-Mattheus-Moerman]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.02 s (669.3 files/s, 90654.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          12            260            288           1470
JSON                             1              1              0             44
TOML                             1              2              0             41
CSV                              1              0              0             32
Markdown                         1             13              0             16
-------------------------------------------------------------------------------
SUM:                            16            276            288           1603
-------------------------------------------------------------------------------

Commit count by author:

   249  Alfredo Hernández
    30  VINICIUS DAMIN
     1  Murillo Teixeira
     1  Vinícius Schaedler Damin

[editorialbot]

Paper file info:

⚠️ Failed to find a paper file in https://github.com/alfredohernandezinostroza/MetaSpread (branch: main)

[editorialbot]

License info:

🟡 License found: GNU Affero General Public License v3.0 (Check here for OSI approval)

[Kevin-Mattheus-Moerman]

@editorialbot set paper as branch

[editorialbot]

Done! branch is now paper

[Kevin-Mattheus-Moerman]

@editorialbot check refereces

[editorialbot]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

[Kevin-Mattheus-Moerman]

@editorialbot check references

[Kevin-Mattheus-Moerman]

@alfredohernandezinostroza Dear author, thanks for this submission. I am the AEiC on this track and here to help process the initial steps. Before we proceed, please can you have a look at the following points:

• [ ] Your project appears to lack contributing guidelines at the moment. Please work to add these and to mention/link to them in your README. You could for instance create a CONTRIBUTING.md file (see here for some examples: https://contributing.md/example/).
• [ ] Your readme appears rather minimal apart from the above, it would be good to include links to testing and documentation.
• [ ] Please study the above reference check :point_up: (looks like it is a bit delayed today, I'll attempt it again later if it doesn't work) and see if you can address any potential DOI issues. You can add/amend DOI entries in your .bib file, and call @editorialbot check references here to check them again.

[Kevin-Mattheus-Moerman]

@editorialbot check references

[Kevin-Mattheus-Moerman]

@openjournals/dev @xuanxu the reference checking seems down for me today on several submissions. Are you able to help?

[editorialbot]

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

OK DOIs

- 10.1038/nature14971 is OK

MISSING DOIs

- 10.1007/s11538-019-00597-x may be a valid DOI for title: A mathematical framework for modelling the metasta...
- 10.1016/j.jtbi.2021.110677 may be a valid DOI for title: A novel 3D atomistic-continuum cancer invasion mod...
- 10.1016/j.jocs.2019.101067 may be a valid DOI for title: Computational modelling and simulation of cancer g...
- 10.1007/978-3-030-32857-3_7 may be a valid DOI for title: Multiscale modelling of cancer: micro-, meso-and m...
- 10.1007/s11517-022-02514-2 may be a valid DOI for title: A multi-layered hybrid model for cancer cell invas...
- 10.21105/joss.02436 may be a valid DOI for title: CancerSim: A Cancer Simulation Package for Python ...
- No DOI given, and none found for title: MESA: an agent-based modeling framework
- 10.1200/cci.18.00069 may be a valid DOI for title: A review of cell-based computational modeling in c...
- No DOI given, and none found for title: Protease-dependent versus-independent cancer cell ...
- 10.1038/npjbcancer.2015.18 may be a valid DOI for title: Spatiotemporal progression of metastatic breast ca...
- No DOI given, and none found for title: Continuous and discrete mathematical models of tum...
- No DOI given, and none found for title: Mathematical modelling of tumour invasion and meta...
- 10.7554/elife.84263 may be a valid DOI for title: A survey of open questions in adaptive therapy: Br...

INVALID DOIs

- None

[Kevin-Mattheus-Moerman]

@openjournals/dev @xuanxu okay, never mind it seems back, thanks

[alfredohernandezinostroza]

@alfredohernandezinostroza Dear author, thanks for this submission. I am the AEiC on this track and here to help process the initial steps. Before we proceed, please can you have a look at the following points:

* [ ]  Your project appears to lack contributing guidelines at the moment. Please work to add these and to mention/link to them in your README. You could for instance create a `CONTRIBUTING.md` file (see here for some examples: https://contributing.md/example/).

* [ ]  Your readme appears rather minimal apart from the above, it would be good to include links to testing and documentation.

* [ ]  Please study the above reference check ☝️ (looks like it is a bit delayed today, I'll attempt it again later if it doesn't work) and see if you can address any potential DOI issues. You can add/amend DOI entries in your `.bib` file, and call `@editorialbot check references` here to check them again.

Hello! Thank you so much for the information! I will address the first and third point as soon as possible. Regarding the second point, would a link to an example Jupyter notebook that showcases the program's capabilities suffice?

[Kevin-Mattheus-Moerman]

@alfredohernandezinostroza

On your question, I think a Jupyter notebook might serve as a nice demo/example. However the README typically has description, installation instructions, a getting started section, links to documentation, links to testing, links to the license, links to the contributing guidelines. So please extend the README to include these. For testing and documentation a Jupyter notebook would not be sufficient. Here are some example (albeit much larger) Pythons project featuring an extended README, dedicated documentation, and CI integration and automated testing: https://github.com/sunpy/sunpy, https://github.com/astropy/astropy, and here is one features in JOSS: https://github.com/dmey/synthia.

Let me know when you think you can complete the above. Note that if you do not have documentation and automated testing in place at the moment, it may be best to retract this submission at this point, and to resubmit once this has been completed.

[Kevin-Mattheus-Moerman]

@alfredohernandezinostroza :wave:

[Kevin-Mattheus-Moerman]

@alfredohernandezinostroza please respond to the above. We do need to hear from you in a timely fashion, and the changes should be processed as soon as you can. If we do not hear from you by the end of next week we'll need to assume you are no longer interested in pursuing a publication with JOSS and reject this submission.

[Kevin-Mattheus-Moerman]

@editorialbot invite @ppxasjsm as editor

[editorialbot]

Invitation to edit this submission sent!

[ppxasjsm]

Yes happy to!

[Kevin-Mattheus-Moerman]

@editorialbot assign @ppxasjsm as editor

[editorialbot]

Assigned! @ppxasjsm is now the editor

[alfredohernandezinostroza]

@alfredohernandezinostroza please respond to the above. We do need to hear from you in a timely fashion, and the changes should be processed as soon as you can. If we do not hear from you by the end of next week we'll need to assume you are no longer interested in pursuing a publication with JOSS and reject this submission.

Hello! Sorry for the delay, and thank you for your patience. We are currently working on implementing what you requested. As you said, maybe it would be better to retract the submission and then resubmit once it is finished. How should we proceed?

[ppxasjsm]

I think either works for me. I am happy to wait for your edit and you can let me know once they are done on here and I can pick up editing this then? Unless you want a clean submission then please feel free to suggest me as an editor on a resubmission and I am happy to manage your new submission.

[alfredohernandezinostroza]

I think a clean submission would be nice! We will proceed with that option then. Thank you very much!

[alfredohernandezinostroza]

@ppxasjsm Hello! I wanted to ask if it is necessary for us to make the publication shorter for the next submission. This is because we would like to keep it as it is, as it has all the information that a new user needs, from the background, to the installation, to how to run the program. But if it's too long we can make it shorter. Thanks!

[Kevin-Mattheus-Moerman]

@alfredohernandezinostroza yes please do shorten the paper significantly and only have the required components as per our guidelines. The information you mentioned (e.g. "information that a new user needs..") should instead be part of the documentation and README. I will now proceed to reject this submission. You may link to this issue when you plan to resubmit.

[Kevin-Mattheus-Moerman]

@editorialbot reject

[editorialbot]

Paper rejected.