[PRE REVIEW]: spherical: A Comprehensive Database and Automated Pipeline for VLT/SPHERE High-Contrast Imaging

[editorialbot]

Submitting author: @m-samland (Matthias Samland)
Repository: https://github.com/m-samland/spherical
Branch with paper.md (empty if default branch): paper
Version: v2.1.1
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

- 10.48550/arXiv.1712.06948 is OK
- 10.5281/zenodo.6563998 is OK
- 10.1051/0004-6361/201834996 is OK
- 10.3847/1538-3881/aa73d7 is OK
- 10.21105/joss.04774 is OK
- 10.1051/0004-6361/201937308 is OK
- 10.1051/0004-6361/202244587 is OK
- 10.1117/1.JATIS.3.4.048002 is OK
- 10.1051/0004-6361/201937159 is OK
- 10.1051/0004-6361/201935251 is OK
- 10.1117/12.789786 is OK
- 10.1111/j.1365-2966.2010.16916.x is OK
- 10.1051/0004-6361/201834989 is OK
- 10.1051/0004-6361/201834996 is OK
- 10.1117/12.788366 is OK
- 10.1051/0004-6361/201423910 is OK
- 10.1051/0004-6361/202451751 is OK
- 10.1117/12.2231983 is OK
- 10.1051/0004-6361/201833620 is OK
- 10.1051/0004-6361:200810090 is OK
- 10.3847/1538-4357/ac7c74 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/aafc33 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.3509134 is OK
- 10.48550/arXiv.2003.05714 is OK
- 10.1117/12.2630154 is OK
- 10.1117/12.2629970 is OK
- 10.18727/0722-6691/5221 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: IRDAP: SPHERE-IRDIS polarimetric data reduction pi...
- No DOI given, and none found for title: pyKLIP: PSF Subtraction for Exoplanets and Disks
- No DOI given, and none found for title: SHINE, The SpHere INfrared survey for Exoplanets
- No DOI given, and none found for title: Data Reduction and Handling for SPHERE

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.98  T=0.16 s (396.8 files/s, 407555.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Text                            24              6              0          52619
Python                          28           1917           3358           6256
TeX                              1             33              0            540
Markdown                         6            151              0            287
TOML                             1             16              3             96
YAML                             3             14              4             75
Jupyter Notebook                 1              0            313             47
-------------------------------------------------------------------------------
SUM:                            64           2137           3678          59920
-------------------------------------------------------------------------------

Commit count by author:

    95	Matthias Samland
     1	Lukas Welzel

[editorialbot]

Paper file info:

⚠️ Wordcount for paper.md is 1509

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: BSD 3-Clause "New" or "Revised" License (Valid open source OSI approved license)

[editorialbot]

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

[editorialbot]

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[warrickball]

Hi @m-samland, thanks for your submission! 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. Unfortunately, owing to our current backlog, this will probably take at least 4 months. Sorry, and thanks for your patience!

In the meantime, there a few points that you can address before the review, since they'll need to be resolved before publication anyway.

1. It looks like you used NASA ADS to populate your BibTeX file, which means there are macros for the journal names (e.g. \apj) which our pipeline doesn't recognise. Please expand these into the full name of the journal (e.g. "The Astrophysical Journal").

2. You've variously used bold-faced text in the paper. This isn't JOSS style and should be removed. We try to write the names of software packages however they describe themselves in e.g. their docs, like "NumPy".

3. The paper is a touch long. Our docs say

   The paper should be between 250-1000 words. Authors submitting papers significantly longer than 1000 words may be asked to reduce the length of their paper.

   I don't expect it to really get down to 1000 words but it would be good to cut a few hundred if possible. You can check our word count by commenting here with @editorialbot check repository and regenerate the PDF with @editorialbot generate pdf.

4. At a glance, the current documentation (which is just the README, I think?) didn't make it clear whether spherical is to be used as a script/pipeline or a library (or both). I expect our reviewers will ask you to document the API to at least some extent, which JOSS requires, but there are docstrings throughout the code, so you could try using a standard documentation system (e.g. Sphinx, maybe MkDocs) to automatically build API docs. I'd also suggest turning the explore_database.ipynb notebook into a documentation page. It's very useful! Again, there are tools to generate docs pages from notebooks, though I'm not hugely familiar with them myself.

5. On a related note, if you are providing standard scripts as a command-line interface, you can configure the Python package to install these in a standard location so that they're added to the user's $PATH variable. I see some entry points are already defined but they don't seem to correspond to the SPHERE IFS analysis pipeline mentioned in the README.

Sorry again that there'll probably be some wait before an editor starts searching for reviewers. The points above won't affect your place in the queue, though as you approach the front it starts to depend more on editor expertise than exactly which submission is "first" in the queue.