[PRE REVIEW]: QhX: A Python package for periodicity detection in red noise

[editorialbot]

Submitting author: @lionandjelka (Andjelka Kovacevic)
Repository: https://github.com/lionandjelka/QhX1
Branch with paper.md (empty if default branch): paper-submission
Version: v0.2.0
Editor: Pending
Reviewers: Pending
Managing EiC: Warrick Ball

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/6bbd66b59696eabaee7c5b23b776174c"><img src="https://joss.theoj.org/papers/6bbd66b59696eabaee7c5b23b776174c/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/6bbd66b59696eabaee7c5b23b776174c/status.svg)](https://joss.theoj.org/papers/6bbd66b59696eabaee7c5b23b776174c)

Author instructions

Thanks for submitting your paper to JOSS @lionandjelka. Currently, there isn't a JOSS editor assigned to your paper.

@lionandjelka if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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[editorialbot]

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

✅ OK DOIs

- 10.1051/0004-6361/201833304 is OK
- 10.1177/00037028241241308 is OK
- 10.48550/arXiv.2310.16896 is OK
- 10.48550/arXiv.1811.06542 is OK
- 10.3390/universe9060287 is OK
- 10.3847/1538-4365/ac88ce is OK
- 10.1093/mnras/stv1230 is OK
- 10.1086/309985 is OK
- 10.1093/mnras/sty3466 is OK
- 10.3847/1538-4357/ace31a is OK
- 10.1051/0004-6361/202450886 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Time-frequency Analysis
- No DOI given, and none found for title: LSST: From Science Drivers to Reference Design and...
- No DOI given, and none found for title: Two-Dimensional Correlation Analysis of Periodicit...
- No DOI given, and none found for title: Fidgit: AGN DataChallenge

❌ MISSING DOIs

- 10.1086/170594 may be a valid DOI for title: 3C 345: Is the Variability of Quasars Nonlinear?
- 10.1093/mnras/sty1316 may be a valid DOI for title: Multifractality Signatures in Quasars Time Series ...
- 10.1038/159591a0 may be a valid DOI for title: Acoustical Quanta and the Theory of Hearing
- 10.3847/1538-3881/acb596 may be a valid DOI for title: Detecting Long-period Variability in the SDSS Stri...
- 10.1515/astro-2020-0007 may be a valid DOI for title: Two-Dimensional Correlation Analysis of Periodicit...
- 10.1093/mnras/staa737 may be a valid DOI for title: Confirmed Short Periodic Variability of Subparsec ...
- 10.3847/1538-4357/aaf731 may be a valid DOI for title: The Optical Variability of Supermassive Black Hole...
- 10.1093/mnras/stx3137 may be a valid DOI for title: Oscillatory Patterns in the Light curves of Five L...
- 10.1086/118137 may be a valid DOI for title: Wavelets for Period Analysis of Unevenly Sampled T...
- 10.1007/978-1-4612-2544-7_2 may be a valid DOI for title: Wavelets, Spectrum Analysis and 1/f Processes
- 10.1016/b978-0-12-811220-5.00002-2 may be a valid DOI for title: Advances in Two-Dimensional Correlation Spectrosco...

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=4.01 s (51.9 files/s, 326946.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
CSV                             15              1              0        1105043
HTML                            68           3388            272          41331
SVG                              4              0              0           5360
Jupyter Notebook                22              0         142481           2392
Python                          35            774           1760           1832
CSS                              6            223             57           1015
JavaScript                      12            131            221            880
reStructuredText                35            489            528            554
TeX                              1             46              0            315
Markdown                         2             61              0            146
YAML                             3             11              0             59
TOML                             1              7              0             54
make                             2             16             18             43
DOS Batch                        1              8              1             26
JSON                             1              0              0             23
-------------------------------------------------------------------------------
SUM:                           208           5155         145338        1159073
-------------------------------------------------------------------------------

Commit count by author:

    65	lionandjelka
    34	OS Kernel

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1421

✅ 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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[lionandjelka]

Thank you. Here are my suggestions for potential reviewers:
astrogilda
afeinstein20
sgeorge91
rmorgan10
jessie-dotson
bliiir

[warrickball]

Hi @lionandjelka, and thanks for your submission to JOSS. All our editors are currently busy so I'm going to place this on our current waiting list. In any case, the project you've submitted has a variety of issues that I've listed below that need to be addressed before we open this up for an editor to pick up, so I'm going to tag it as "paused" until the following points are addressed.

1. The repo description says it's a "test repo of Qhx". Is that still true? I see you have several different Qhx repos, so it isn't clear this is the one you intended to submit.

2. There are a lot of extra files in the repo, including at least

   • some files named 0, 1, 2 and 3,
   • a bunch of CSV files,
   • some Jupyter Notebooks (which might be part of the docs),
   • probably some profiling output in prof and
   • some build artefacts (e.g. Qhx.egg-info/ and build/).

   I don't think any of these should be in the repo and are only likely to confuse any potential reviewers.

3. The Qhx documentation describes two versions of the same code. A final step in the JOSS publication process will be to tag a new release version, which is difficult to reconcile with having two versions. Regardless, just for ease-of-use, it makes more sense to have a single package with appropriate options—be that different functions or relevant arguments—to select between two different modes of execution.

4. This is less important at the outset but the paper is also a bit long. The JOSS documentation says:

   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.

   The JOSS paper should be little more than a brief summary of the software, how it fills a current niche and how it would be (or has been) used in research. At the very least, your section describing the contents of the documentation page ("Documentation and Tutorials") can be removed.

Feel free to ask me any questions and keep me posted on your progress through these items.

[lionandjelka]

Hi @warrickball ,

Thank you so very much for taking the time to prereview our submission and for providing such clear and constructive feedback. We also appreciate the opportunity to share the steps we have taken to address the issues:

1. Repository Description:

   • We have clarified the repository description, which now states:
     "QhX - Quasar harmonics eXplorer: A Python package for detecting oscillations in red noise."
   • We made our other QhX-related repositories private and renamed them to avoid confusion, as they are unrelated to this submission.

2. Repository Content:

   • We thoroughly cleaned the repository, removing all unrelated files (e.g., CSV files, profiling outputs, build artifacts like Qhx.egg-info/ and build/, and other extraneous files). The repository now contains only files relevant to the package and its documentation.

3. Versioning:

   • We have tagged the repository with a new release version, v0.2.0.
   • References to the older version (v0.1.1) have been removed from the documentation, as we agree there is no need to explain the older code.
   • The new version, v0.2.0, synergizes both the fixed and dynamical modes through separate functions and appropriate arguments in some of them.

4. Paper Length:

   • We have streamlined the main body of the paper to ~<853 words (excluding references, author names, and affiliations).
   • We removed the section "Documentation and Tutorials", as per your recommendation.

Thank you again for your time and consideration.
We are happy to cooperate further and look forward to the next steps.

Best regards,

[warrickball]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.01 s (373.5 files/s, 63495.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                              1             46              0            315
Markdown                         1             38              0             87
YAML                             1              2              0             22
-------------------------------------------------------------------------------
SUM:                             3             86              0            424
-------------------------------------------------------------------------------

Commit count by author:

    75	lionandjelka
    34	OS Kernel

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 988

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🔴 Failed to discover a valid open source license

[warrickball]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

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[warrickball]

@editorialbot check references

[editorialbot]

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

✅ OK DOIs

- 10.1051/0004-6361/201833304 is OK
- 10.1177/00037028241241308 is OK
- 10.48550/arXiv.2310.16896 is OK
- 10.48550/arXiv.1811.06542 is OK
- 10.3390/universe9060287 is OK
- 10.3847/1538-4365/ac88ce is OK
- 10.1093/mnras/stv1230 is OK
- 10.1086/309985 is OK
- 10.1093/mnras/sty3466 is OK
- 10.3847/1538-4357/ace31a is OK
- 10.1051/0004-6361/202450886 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Time-frequency Analysis
- No DOI given, and none found for title: LSST: From Science Drivers to Reference Design and...
- No DOI given, and none found for title: Two-Dimensional Correlation Analysis of Periodicit...
- No DOI given, and none found for title: Fidgit: AGN DataChallenge

❌ MISSING DOIs

- 10.1086/170594 may be a valid DOI for title: 3C 345: Is the Variability of Quasars Nonlinear?
- 10.1093/mnras/sty1316 may be a valid DOI for title: Multifractality Signatures in Quasars Time Series ...
- 10.1038/159591a0 may be a valid DOI for title: Acoustical Quanta and the Theory of Hearing
- 10.3847/1538-3881/acb596 may be a valid DOI for title: Detecting Long-period Variability in the SDSS Stri...
- 10.1515/astro-2020-0007 may be a valid DOI for title: Two-Dimensional Correlation Analysis of Periodicit...
- 10.1093/mnras/staa737 may be a valid DOI for title: Confirmed Short Periodic Variability of Subparsec ...
- 10.3847/1538-4357/aaf731 may be a valid DOI for title: The Optical Variability of Supermassive Black Hole...
- 10.1093/mnras/stx3137 may be a valid DOI for title: Oscillatory Patterns in the Light curves of Five L...
- 10.1086/118137 may be a valid DOI for title: Wavelets for Period Analysis of Unevenly Sampled T...
- 10.1007/978-1-4612-2544-7_2 may be a valid DOI for title: Wavelets, Spectrum Analysis and 1/f Processes
- 10.1016/b978-0-12-811220-5.00002-2 may be a valid DOI for title: Advances in Two-Dimensional Correlation Spectrosco...

❌ INVALID DOIs

- None

[warrickball]

Thanks @lionandjelka for a quick and comprehensive response! The repo now looks much easier to navigate and review. I'll note that the failure to detect the MIT license is an issue on our side and nothing to worry about.

This is ready for an editor to pick up but all of them are currently busy, so I'll add this to the waitlist until someone is available. Sorry for the delay!

In the meantime, you may want to try to add some of the missing DOIs to the BibTeX. If you get your BibTeX from the NASA ADS, it should have the DOIs. We know not everything has a DOI (e.g. books often don't) but they should be present where available.

[lionandjelka]

Thank you so very much, @warrickball, for your kind support and guidance to navigate through the preview process.

We understand that the process might take some time, and we are grateful for the efforts of the Editors despite their busy schedules.

In the meantime, we have updated the BibTeX file to include the missing DOIs where available, as per your kind suggestion.

Thank you most sincerely again for all your support and for keeping us informed throughout the process.
We look forward to hearing from the Editorial Team when they are available.