[PRE REVIEW]: PGFinder — A Python package and web tool for peptidoglycomics

[editorialbot]

Submitting author: @TheLostLambda (Brooks Rady)
Repository: https://github.com/Mesnage-Org/pgfinder
Branch with paper.md (empty if default branch): ns-rse/109-joss
Version: v1.0.3
Editor: Pending
Reviewers: Pending
Managing EiC: Kevin M. Moerman

Status

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

OK DOIs

- 10.1093/femsre/fuaa044 is OK
- 10.1038/nbt.1511 is OK
- 10.1126/science.abj3986 is OK
- 10.1016/j.molmed.2020.05.003 is OK
- 10.7554/eLife.70597 is OK
- 10.1111/j.1574-6976.2007.00094.x is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.09 s (912.4 files/s, 85639.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
YAML                            13            359             38           2626
Python                          18            414            606            997
Markdown                        11            216              0            553
Svelte                          11             48              1            504
TypeScript                      13             41              7            286
SVG                              1              1              1            182
DOS Batch                        1             21              1            133
TOML                             1             13              2            124
TeX                              1              5              0            108
JSON                             3              0              0             93
JavaScript                       2              2              3             14
HTML                             1              2              2             12
make                             1              4              6             11
reStructuredText                 2              8             17              9
Jupyter Notebook                 1              0             39              0
-------------------------------------------------------------------------------
SUM:                            80           1134            723           5652
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 674

[editorialbot]

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

[editorialbot]

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[Kevin-Mattheus-Moerman]

@TheLostLambda thanks for this submission. I am the AEiC for this track and here to help with initial steps.
Given the relatively small size (in terms of lines of code), I have triggered a scope review by the editorial board. This includes assessing if this work conforms to our substantial scholarly effort criteria. This scope review should take about two weeks to complete.

[TheLostLambda]

Hi @Kevin-Mattheus-Moerman! Sounds good! I'm happy to help out however I can!

Between the Python, Svelte, and Typescript (where the proper code is — as opposed to other data and documentation files), I think things should come out at around 1800 lines or so (going off of the cloc output above).

In terms of citations, I think it helps that we've already got one paper out in eLife on the original version of the software, and we're working on another paper built on results from this tool at the moment! When it comes to use and citation by peers in the field, the existing PGFinder paper should have a couple of citations, and we recently presented this new and improved version at a conference where there seemed to be some decent interest!

I there is any more information that would be helpful for the editorial board, just let me know!

[TheLostLambda]

Oh, and perhaps to adjust the labels for this review, it might be good to remove TeX and Makefile tags (as those files are just part of the Sphinx documentation generation), and it would be good to add someone to take a look at the web side of things!

A Svelte specialist would be best, but it's pretty close to regular HTML, CSS, and Java/Typescript :)

[Kevin-Mattheus-Moerman]

@TheLostLambda thanks for the additional information. If in addition, you could summarise/clarify what significant changes were made since the elife paper (https://doi.org/10.7554/eLife.70597) that would be helpful.

[TheLostLambda]

Hi @Kevin-Mattheus-Moerman ! Sorry for the glacial delay! In rough order of effort / impact / importance:

1. The Web GUI was developed from scratch to replace the previously clunky Jupyter notebooks that were used to interact with PGFinder. This also meant porting the Python code to run in Pyodide (on the client-side, via WebAssembly).
2. The search outputs were overhauled — moving from a wide to a long data format. This took the output from something that was (in my opinion) difficult to process via downstream programs, and brought things in line with the "Tidy Data" standard. This required a particularly large overhaul of some of the PGFinder internals, and was a multi-month process started by Ankur Patel that I eventually helped to carry over the line.
3. Switching to this "long format" was a prerequisite for adding the very scientifically important "Delta PPM" column, that lets users know how closely the masses of the PGFinder-assigned structures match the masses experimentally observed.
4. That then also made it possible to add another step of data processing to the analysis, in which previously ambiguous matches (PGFinder assigns two structures to the same mass) can be resolved by picking the structure with the lowest absolute delta ppm. This consolidation process majorly aides in downstream analysis!

Beyond user features, substantial effort has gone into refactoring the codebase and bringing it in line with good open-source practices:

1. Use of the tool and it's API have been documented (with documentation automatically generated by Sphinx and uploaded to ReadTheDocs
2. The package has switched to semantic versioning and has been uploaded to PyPi for distribution
3. Both unit and integration tests have been added (including end-to-end tests of the Web GUI) and run automatically via GitHub actions
4. To make contributing easier for other developers, a contributing section of the documentation has been written and tools like precommit configured to standardize code style

These are just the highlights and I've almost certainly missed out on some details, but when the eLife paper was published, the v0.02 tag was created, so you can see all of the changes we've made since using this link: Mesnage-Org/pgfinder@v0.02...main

Looks like it's currently around 677 commits by 4 developers over the past two years or so :)

Sorry again for the delay and hopefully this information is helpful! Please let me know if you'd like any more detail or clarification :)

[TheLostLambda]

@Kevin-Mattheus-Moerman Hi Kevin!

I don't mean to pester, but do you know how long we should expect the pre-review process to take / is there anything you still need from us?

Thanks a ton,
Brooks

[Kevin-Mattheus-Moerman]

@TheLostLambda apologies for the delay encountered so far. We are combating a bit of a backlog in submissions and the board, as a consequence, has not been responding as fast as we'd like. I have spurred them on just now with a reminder and will conclude the scope review this week. Once again sorry for how long this has been going on.

[Kevin-Mattheus-Moerman]

@TheLostLambda Once again my apologies for the delay in processing this scope review. The editorial board has now concluded this scope review. Unfortunately the conclusion is that this work is not at present in scope in JOSS. Although the software itself is scientifically interesting, the core functionality has already been published through the recent eLife publication (https://doi.org/10.7554/eLife.70597). The advancement on top of that work was not deemed sufficient enough to warrant a JOSS publication.

We will now proceed to reject this submission.

Note that the above conclusion does not mean the software is not useful or not of a high quality.

We do hope you will consider JOSS for any future (re-)submissions.

Once again, my sincere apologies for the much slower than usual scope review process.

[Kevin-Mattheus-Moerman]

@editorialbot reject

[editorialbot]

Paper rejected.

[bobturneruk]

Hi @Kevin-Mattheus-Moerman, and other editors - thanks for taking the time to look at our work. We're very proud of the eLife paper, which demonstrates the scientific merit and usefulness of pgfinder via an excellent journal. I encouraged my co-authors to submit to JOSS as well in order to obtain a review of the software (i.e. the code etc.), which I felt was not something the eLife process (nor that of many other journals) covered in detail. We've done quite a bit of PR reviewing within the team, but it's not quite the same as an independant perspective. I hadn't spotted any review criteria around novelty or previous publication - if anyone has time to direct me to the right bit of the criteria, I'd appreciate it! Or maybe it should have been obvious to me. If this is the wrong place for me to make a comment like this, please let me know. I'm comfortable with the rejection, just thinking what to do with future work. I will continue to point to the JOSS criteria as the best available set for reviewing research software (I'm happy that pgfinder was improved by making changes to meet these) and I appreciate the work you're doing.