[PRE REVIEW]: Decomposing Gaifman Structures

[editorialbot]

Submitting author: @balqui (José Luis Balcázar)
Repository: https://github.com/balqui/degais/
Branch with paper.md (empty if default branch):
Version: V1.4
Editor: @matthewfeickert
Reviewers: Pending
Managing EiC: Chris Vernon

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[editorialbot]

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "url" (NAME) [#<BibTeX::Bibliography data=[6]>, "@", #<BibTeX::Entry >, {:author=>["Andrzej Ehrenfeucht and Tero Harju and Grzegorz Rozenberg"], :title=>["The Theory of 2-Structures - {A} Framework for Decomposition and Transformation of Graphs"], :publisher=>["World Scientific"], :year=>["1999"]}, ",", "%"]

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.98  T=0.29 s (217.6 files/s, 511833.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Text                             6             39              0          76076
TableGen                        27              0              0          70763
Python                          25            418            912           1644
Markdown                         3            105             10            398
TeX                              1             16              1             95
YAML                             1              1              4             23
TOML                             1              3              0             21
-------------------------------------------------------------------------------
SUM:                            64            582            927         149020
-------------------------------------------------------------------------------

Commit count by author:

    95	balqui
    52	José Luis Balcázar, balqui at GitHub
     7	Balqui

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1433

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[editorialbot]

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

[editorialbot]

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[crvernon]

👋 @balqui

Could you explain this statement a bit? Why was the refactoring done and is any of the original code used directly in your work? Thanks.

Author: Jose Luis Balcazar, ORCID 0000-0003-4248-4528, relying in large parts on the functionality of code by Marie Ely Piceno, although fully rewritten.

[balqui]

Missatge de Chris Vernon ***@***.***> del dia dv., 17 de gen. 2025 a les 14:20:

👋 @balqui <https://github.com/balqui> Could you explain this statement a bit? Why was the refactoring done and is any of the original code used directly in your work? Thanks. Author: Jose Luis Balcazar, ORCID 0000-0003-4248-4528, relying in large parts on the functionality of code by Marie Ely Piceno <https://github.com/balqui/labgaif>, although fully rewritten.

Sure. First, let me point out that Ely is also a coauthor of this submission. As indicated in the paper, her original code was not really usable by anyone else. It was developed hand-in-hand with the research process constituting her PhD, of which I was the advisor, and was full of dead ends, inefficiencies, deprecated code, and undocumented behavior. Instead of cleaning it up, I decided to reconstruct it fully. A handful of lines of her code (labgaif GitHub repo, MIT License) may remain in the current submission, with her authorization, but no full function (or method or class as the OO-structure is now different). Similarly, the third author created a wholly different implementation of which no code remains at all but her ideas were deemed worth of coauthorship; that was for her graduation project of which I was also the advisor. All three coauthors contributed nontrivially to the conceptual intuitions that support the algorithmics implemented by the current code. The same three authors sign the 2018 paper where these ideas were first proposed and the 2021 paper where applications are described (both cited in the submission). Thanks for your efforts on JOSS. José. Message ID: ***@***.***>

…

[crvernon]

@editorialbot invite @matthewfeickert as editor

@balqui please reduce the word count of your paper to at or lower than 1000 words. Thank you.

[editorialbot]

Invitation to edit this submission sent!

[matthewfeickert]

@editorialbot assign @matthewfeickert as editor

[editorialbot]

Assigned! @matthewfeickert is now the editor

[matthewfeickert]

@balqui thanks for your submission to JOSS. Before I request any reviewer time to be spent on the submission though I'm going to ask you to reread the Submitting a paper to JOSS docs in detail as there are multiple problems with the submission that would result in it being automatically declined without large amounts of revisions by reviewers.

It might be helpful for you to read the Review Criteria docs but at a glance your submission has:

• No documentation (a doc.md is insufficient)
• Installation instructions are not prominent
• The directory structure for degais is wrong and does not package degais properly as a Python package.
  • Specifically it does not correctly follow a src/ directory layout of src/<package name>/ which is required to properly lay out the package in a distribution. Installation of degais as is incorrectly installs the Python source files directly under the virtual environment's site-packages/ directory, not under site-packages/degais/ (which doesn't exist).
• Only one example which is just text, no code, and so insufficient
• No API docs
• No tests that can be run in an automated way with a testing framework
• No CI

Please address all of these issues within one week (by 2025-02-13) if you would like to continue with a review.

My suggestion given the scope of work that would need to be done is that you instead withdraw your submission for now and resubmit in the future whenever you have had the time to carefully go through and prepare the project. That's totally fine and we would very much welcome a future submission from you if you chose to do so.

[matthewfeickert]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[balqui]

Understood, Matthew and Chris. We will follow the advice of withdrawing and possibly resubmitting as the issues raised require clearly more than one week to solve. Thanks for your help. José Luis Balcázar (@balqui)

[balqui]

@editorialbot withdraw

[editorialbot]

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

[balqui]

Sorry, I am told that I cannot withdraw through the editorial bot, and I cannot find on the submission page (which to me looks like https://joss.theoj.org/papers/2bc1b254b01c7202572d4d2d1dc07fb7) a way to withdraw. I do see a "paper actions" section with some text in it but no actual action available to perform. How should we do that?

[danielskatz]

As the error message says, Editors-in-Chief (eics) can do this, as I will now.

[danielskatz]

@editorialbot withdraw

[editorialbot]

Paper withdrawn.