[PRE REVIEW]: Shear Mapping in Python (SMPy): Modular, Extensible, and Accessible Dark Matter Mapping

[editorialbot]

Submitting author: @GeorgeVassilakis (Georgios N. Vassilakis)
Repository: https://github.com/GeorgeVassilakis/SMPy
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: Pending
Reviewers: Pending
Managing EiC: Warrick Ball

Status

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

✅ OK DOIs

- 10.1007/s00159-020-00129-w is OK
- 10.3847/1538-3881/ad5840 is OK
- 10.3847/1538-4357/acff5f is OK
- 10.1093/mnras/stab1495 is OK
- 10.1093/pasj/psx070 is OK
- 10.1086/172297 is OK
- 10.1051/0004-6361/201936865 is OK
- 10.1111/j.1365-2966.2012.21133.x is OK
- 10.3847/1538-3881/ace7ca is OK
- 10.1051/0004-6361/202243054 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.5281/zenodo.10957263 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.3847/1538-4357/ac7c74 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.3390/aerospace10110960 is OK
- 10.3847/1538-4357/ab7c58 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Astropy: A community Python package for astronomy
- No DOI given, and none found for title: PyYAML

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.98  T=0.03 s (943.8 files/s, 163511.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          23            499           1138           1150
Jupyter Notebook                 3              0           1711            291
TeX                              1             22              0            279
YAML                             3             40             40            174
Markdown                         2             45              0            155
-------------------------------------------------------------------------------
SUM:                            32            606           2889           2049
-------------------------------------------------------------------------------

Commit count by author:

    70	GeorgeVassilakis
    58	George Vassilakis
     4	Maya Amit
     4	data_vadar
     4	mcclearyj
     3	EdwardBerman
     1	Sayan Saha

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 983

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

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

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[warrickball]

Hi @GeorgeVassilakis! Thanks for your (re)submission and sorry again for the delay in starting the submission process following the Easter break and backlog. I appreciate that you've taken on board the remarks from the previous submission of SMPy and have substantially extended the code, so I don't see a need for a new scope review (though an editor or reviewers may argue for one later).

All the suitable JOSS editors are currently working at capacity so I'm going to "waitlist" this review until an editor with the relevant expertise is available to take it on. With our current backlog, note that this might take 3-4 months. Thanks for your patience!

In the meantime, I think a major point in the review will be the documentation. Though a single README.md is technically satisfactory, the current "documentation" doesn't describe the interface to the code, which is a requirement in our review criteria. Normally the "interface" documentation would be API documentation but for a script-like tool like smpy.run I'd expect a description of the configuration file (i.e. the YAML file).

We vastly prefer (and usually get) Python projects that deploy documentation to GitHub/GitLab pages or Read the Docs via a documentation system like Sphinx or MkDocs. It'd be great if you could set this up while we wait for an editor.

I'd also suggest you rather demonstrate the use of the package by comparing convergence maps with all the available methods, rather than just the KS inversion. Having multiple methods is an additional feature of SMPy, beyond just getting the inversion in the first place. (Note also that the first few sentences of the README still imply the KS inversion is the only method available.)

Finally, as a detail in the paper itself, note that you can group citations together by replacing e.g. [@ACTDR62024] [@DESY32021] with [@ACTDR62024; @DESY32021]. Journal titles need to be written out in full, and our pipeline doesn't recognise NASA ADS shortcuts (e.g. replace \apj with "The Astrophysical Journal", which you've done in places but not everywhere).

[GeorgeVassilakis]

Good evening @warrickball, thank you kindly for the initial pass-through review. I totally understand the timeframe, and it is no worry to me! I've been meaning to update and upgrade the documentation for some time, and I love the idea of creating a Read the Docs-type website. I'll be sure to address this and your other comments well before the editor comes along. Thanks again for your time!