[PRE REVIEW]: Pycashier: cash in on DNA barcode tags

[editorialbot]

Submitting author: @daylinmorgan (Daylin Morgan)
Repository: https://github.com/brocklab/pycashier
Branch with paper.md (empty if default branch): joss
Version: v2024.1004
Editor: @lpantano
Reviewers: @adrientaudiere, @LTLA
Managing EiC: Kevin M. Moerman

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (1358.5 files/s, 139590.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          18            386            204           1952
SVG                              7             56              7           1083
Markdown                         7            143              0            431
YAML                             7             27             12            170
TeX                              1              9              0            144
TOML                             2             24              8            126
make                             3             18              3             54
Bourne Shell                     2             11              2             38
Dockerfile                       1              5              2             17
-------------------------------------------------------------------------------
SUM:                            48            679            238           4015
-------------------------------------------------------------------------------

Commit count by author:

   253	Daylin Morgan
     4	DaylinMorgan
     2	daylin

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 598

✅ 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 📄 👈

[Kevin-Mattheus-Moerman]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1021/acssynbio.8b00105 is OK
- 10.1093/bioinformatics/bty560 is OK
- 10.1016/j.ccell.2020.12.002 is OK
- 10.1007/978-1-0716-1811-0_8 is OK
- 10.1038/s43018-021-00222-8 is OK
- 10.1088/1478-3975/abb09c is OK
- 10.14806/ej.17.1.200 is OK
- 10.1093/bioinformatics/btv053 is OK

MISSING DOIs

- No DOI given, and none found for title: ClonMapper Barcoding System
- No DOI given, and none found for title: Pysam-Developers/Pysam

INVALID DOIs

- None

[Kevin-Mattheus-Moerman]

Dear author, @daylinmorgan 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:

• Please study the above reference check ☝️ and see if you can address any of the reported potential DOI issues (it is okay if those highlighted really do not have a DOI). You can add/amend DOI entries in your .bib file, and call @editorialbot check references here to check them again.
• 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/).
• The README is very short in general. Typically has clear description (usually not overly technical), installation instructions, as well as things like a getting started section, links to documentation (I think you have this but a small section could also work), links to testing, links to the license, links to the contributing guidelines. So please extend the README to include these.
• In your affiliation in the paper, please spell out USA as United States of America.

[daylinmorgan]

Thank you for the helpful comments!

As requested I've added a CONTRIBUTING.md and expanded the README.md. And spelled out USA within the affiliation in the paper.

I'm unable to provide DOI's for the two missing since both are citations directly to URL's that have no accompanying DOI's.

Let me know anything else that should be updated.

[Kevin-Mattheus-Moerman]

@editorialbot generate pdf

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@editorialbot invite @lpantano as editor

[editorialbot]

Invitation to edit this submission sent!

[lpantano]

I can work on this one

[Kevin-Mattheus-Moerman]

@editorialbot assign @lpantano as editor

[editorialbot]

Assigned! @lpantano is now the editor

[lpantano]

I am working on reviewing this before looking for reviewers, will come back this Friday. Thanks

[lpantano]

Hi @daylinmorgan,
It took me a little more than intended, but I think overall is good. I am missing a section in the statement of need to mention other tools and the main GAP this tool is filling. Can you add this? Then I can start the review. Thanks!

[daylinmorgan]

Thanks for the initial feedback @lpantano. I've expanded the statement of need to better highlight some of the alternatives and the specific niche filled by our tool.

[daylinmorgan]

@editorialbot generate pdf

[editorialbot]

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

[lpantano]

Thank you for adding that explanation in the code. Do you have some editors in mind?

[lpantano]

@editorialbot list reviewers

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Please log in the JOSS Reviewers site to search through the list of current reviewers.

[lpantano]

@adrientaudiere, @LTLA, would you be interested in reviewing this paper?

[adrientaudiere]

Hi @lpantano, I can do it!

[lpantano]

@editorialbot add @adrientaudiere as reviewer

[editorialbot]

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

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[LTLA]

@lpantano I need to deal with some mild life-related stuff so I probably won't be free until the end of the month. Happy to do it if I'm still needed at that point but don't feel obliged to wait for me.

[lpantano]

@Kevin-Mattheus-Moerman do you know why the bot didn't recognize the command? According to the docs, it seems fine.

[lpantano]

@editorialbot add @adrientaudiere to reviewers

[editorialbot]

@adrientaudiere added to the reviewers list!

[lpantano]

@editorialbot add @LTLA to reviewers

[editorialbot]

@LTLA added to the reviewers list!

[lpantano]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #6891.

[lpantano]

@LTLA , I think we can wait for you review then. Thank you for helping out with this work.