[REVIEW]: fathon: A Python package for a fast computation of detrendend fluctuation analysis and related algorithms

whedon commented 4 years ago

Submitting author: @stfbnc (Stefano Bianchi) Repository: https://github.com/stfbnc/fathon.git Version: v0.1.2 Editor: @mbobra Reviewer: @ali-ramadhan, @ashwinvis Archive: 10.5281/zenodo.3601637

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/01daa29253660bd3539ee0f718a52a77"><img src="https://joss.theoj.org/papers/01daa29253660bd3539ee0f718a52a77/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/01daa29253660bd3539ee0f718a52a77/status.svg)](https://joss.theoj.org/papers/01daa29253660bd3539ee0f718a52a77)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@ali-ramadhan & @ashwinvis, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @mbobra know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @ali-ramadhan

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@stfbnc) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @ashwinvis

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@stfbnc) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

whedon commented 4 years ago

Reference check summary:

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.1016/j.physa.2010.10.022 may be missing for title: DCCA cross-correlation coefficient: quantifying level of cross-correlation.
- https://doi.org/10.1103/physrevlett.100.084102 may be missing for title: Detrended cross-correlation analysis: a new method for analyzing two nonstationary time series.
- https://doi.org/10.3389/fphys.2012.00141 may be missing for title: Introduction to multifractal detrended fluctuation analysis in Matlab.
- https://doi.org/10.1103/physreve.60.1390 may be missing for title: Statistical properties of the volatility of price fluctuations.
- https://doi.org/10.1103/physrevlett.90.108501 may be missing for title: Scaling of atmosphere and ocean temperature correlations in observations and climate models.
- https://doi.org/10.1103/physreve.47.3730 may be missing for title: Finite-size effects on long-range correlations: Implications for analyzing DNA sequences

INVALID DOIs

- None

mbobra commented 4 years ago

@stfbnc Can you update your paper.bib files with the appropriate DOIs, so they appear as links in the paper? For example, the podobnik_2008 entry in paper.bib file should be modified to include the DOI as follows:

@article{podobnik_2008,
    Author = {Podobnik, B. and Stanley, H.E.},
    Journal = {Physical Review Letters},
    Number = {8},
    Pages = {084102},
    Title = {Detrended cross-correlation analysis: a new method for analyzing two nonstationary time series.},
    Volume = {100},
    DOI = {10.1016/j.physa.2010.10.022},
    Year = {2008}}

stfbnc commented 4 years ago

@whedon check references

whedon commented 4 years ago

Reference check summary:

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.1016/j.physa.2010.10.022 may be missing for title: DCCA cross-correlation coefficient: quantifying level of cross-correlation.
- https://doi.org/10.1103/physrevlett.100.084102 may be missing for title: Detrended cross-correlation analysis: a new method for analyzing two nonstationary time series.
- https://doi.org/10.3389/fphys.2012.00141 may be missing for title: Introduction to multifractal detrended fluctuation analysis in Matlab.
- https://doi.org/10.1103/physreve.60.1390 may be missing for title: Statistical properties of the volatility of price fluctuations.
- https://doi.org/10.1103/physrevlett.90.108501 may be missing for title: Scaling of atmosphere and ocean temperature correlations in observations and climate models.
- https://doi.org/10.1103/physreve.47.3730 may be missing for title: Finite-size effects on long-range correlations: Implications for analyzing DNA sequences

INVALID DOIs

- None

stfbnc commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

stfbnc commented 4 years ago

@whedon check references

whedon commented 4 years ago

Reference check summary:

OK DOIs

- http://dx.doi.org/10.1016/j.physa.2010.10.022 is OK
- http://dx.doi.org/10.1103/PhysRevLett.100.084102 is OK
- http://dx.doi.org/10.3389/fphys.2012.00141 is OK
- http://dx.doi.org/10.1016/S0378-4371(02)01383-3 is OK
- http://dx.doi.org/10.1103/PhysRevE.69.056107 is OK
- http://dx.doi.org/10.1103/PhysRevE.60.1390 is OK
- http://dx.doi.org/10.1103/PhysRevLett.90.108501 is OK
- https://doi.org/10.5194/acp-7-629-2007 is OK
- http://dx.doi.org/10.1103/PhysRevE.47.3730 is OK

MISSING DOIs

- None

INVALID DOIs

- None

stfbnc commented 4 years ago

@mbobra DOIs added!

mbobra commented 4 years ago

@whedon set 10.5281/zenodo.3601637 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.3601637 is the archive.

mbobra commented 4 years ago

@whedon set v0.1.2 as version

whedon commented 4 years ago

OK. v0.1.2 is the version.

mbobra commented 4 years ago

@openjournals/joss-eics This paper is accepted and ready for final processing! Nice work, @stfbnc 🎉

danielskatz commented 4 years ago

Thanks @mbobra - just as a minor correction, let's call it "ready-to-accept" until the final processing is done :)

danielskatz commented 4 years ago

@whedon accept

whedon commented 4 years ago

Attempting dry run of processing paper acceptance...

whedon commented 4 years ago

Reference check summary:

OK DOIs

- http://dx.doi.org/10.1016/j.physa.2010.10.022 is OK
- http://dx.doi.org/10.1103/PhysRevLett.100.084102 is OK
- http://dx.doi.org/10.3389/fphys.2012.00141 is OK
- http://dx.doi.org/10.1016/S0378-4371(02)01383-3 is OK
- http://dx.doi.org/10.1103/PhysRevE.69.056107 is OK
- http://dx.doi.org/10.1103/PhysRevE.60.1390 is OK
- http://dx.doi.org/10.1103/PhysRevLett.90.108501 is OK
- https://doi.org/10.5194/acp-7-629-2007 is OK
- http://dx.doi.org/10.1103/PhysRevE.47.3730 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 4 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1209

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1209, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

danielskatz commented 4 years ago

👋 @stfbnc - please merge https://github.com/stfbnc/fathon/pull/6 or let me know what parts you disagree with

stfbnc commented 4 years ago

@danielskatz Thanks for the corrections, I've merged your pull request.

danielskatz commented 4 years ago

@whedon accept

whedon commented 4 years ago

Attempting dry run of processing paper acceptance...

whedon commented 4 years ago

Reference check summary:

OK DOIs

- http://dx.doi.org/10.1016/j.physa.2010.10.022 is OK
- http://dx.doi.org/10.1103/PhysRevLett.100.084102 is OK
- http://dx.doi.org/10.3389/fphys.2012.00141 is OK
- http://dx.doi.org/10.1016/S0378-4371(02)01383-3 is OK
- http://dx.doi.org/10.1103/PhysRevE.69.056107 is OK
- http://dx.doi.org/10.1103/PhysRevE.60.1390 is OK
- http://dx.doi.org/10.1103/PhysRevLett.90.108501 is OK
- https://doi.org/10.5194/acp-7-629-2007 is OK
- http://dx.doi.org/10.1103/PhysRevE.47.3730 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 4 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1210

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1210, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

danielskatz commented 4 years ago

@whedon accept deposit=true

whedon commented 4 years ago

Doing it live! Attempting automated processing of paper acceptance...

whedon commented 4 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 4 years ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1211
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01828
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

danielskatz commented 4 years ago

Thanks to @ali-ramadhan & @ashwinvis for reviewing, and @mbobra for editing! And congratulations to @stfbnc!!

whedon commented 4 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.01828/status.svg)](https://doi.org/10.21105/joss.01828)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01828">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01828/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01828/status.svg
   :target: https://doi.org/10.21105/joss.01828

This is how it will look in your documentation:

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

openjournals / joss-reviews