[REVIEW]: NoisySignalIntegration.jl: A Julia package for uncertainty evaluation of numeric integrals

[whedon]

Submitting author: @nluetts (Nils Lüttschwager)
Repository: https://github.com/nluetts/NoisySignalIntegration.jl
Version: v0.2.2
Editor: @jbytecode
Reviewer: @myousefi2016, @mseri
Archive: 10.5281/zenodo.5338743

⚠️ JOSS reduced service mode ⚠️

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Status

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Markdown: [![status](https://joss.theoj.org/papers/8d555b9e8738857733e2dad881f27088/status.svg)](https://joss.theoj.org/papers/8d555b9e8738857733e2dad881f27088)

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

@myousefi2016 & @mseri, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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

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✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @myousefi2016

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@nluetts) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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

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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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 @mseri

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@nluetts) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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

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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @myousefi2016, @mseri it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.03 s (1216.6 files/s, 132770.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           19            394            108           1647
Markdown                         9            298              0            859
TOML                             2              4              0             46
YAML                             1              2              0             25
-------------------------------------------------------------------------------
SUM:                            31            698            108           2577
-------------------------------------------------------------------------------


Statistical information for the repository '5d27fcc6329d35bddf46ec12' was
gathered on 2021/07/23.
No commited files with the specified extensions were found.

[whedon]

PDF failed to compile for issue #3526 with the following error:

 Can't find any papers to compile :-(

[jbytecode]

@whedon generate pdf from branch paper

[whedon]

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

[whedon]

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

[jbytecode]

Dear @myousefi2016 and @mseri,

Thank you for accepting our invitation.

This is the reviewing page for the current submission. In this page, there are 20 checkboxes for each reviewer. These boxes indicate the corresponding reviewing tasks. Please fill them whenever you complete the corresponding task.

Please have a look at the Reviewing Guidelines page for details of reviewing process of JOSS.

Please do not hesitate to ask me anything.

[nluetts]

Also thank you for accepting the review from my side!

[whedon]

👋 @mseri, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @myousefi2016, please update us on how your review is going (this is an automated reminder).

[jbytecode]

Dear @mseri,

Could you please inform us on how is your review going?

[mseri]

Sorry for the delay, I was busy with some conferences and then in holiday. I have read the documentation, successfully installed and tested the library following it (with julia 1.6.2). I also played around with some of the examples.

The only issue I ran into, was that I did not have the Interpolation package installed (used in the first example) but that was immediate to spot and solve from the error message.

The paper flows nicely and seems to fit with the JOSS requirements, the library is well documented, installs smoothly and seem to work as expected. For me it ticks all the boxes.

[jbytecode]

@mseri thank you for your review.

@myousefi2016 could you please update your status and let us know how is your reviewing going?

thank you!

[myousefi2016]

@jbytecode Sorry for the late reply. I believe the review is complete and I read the documentation and the paper, which is pretty informative and descriptive. Also, I was able to install and test the library in Julia. I checked all the requirements here. Thanks!

[jbytecode]

@whedon check references

[danielskatz]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #3526 with the following error:

 Can't find any papers to compile :-(

[danielskatz]

@whedon check references from branch paper

[whedon]

Attempting to check references... from custom branch paper

[whedon]

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

OK DOIs

- 10.1039/C9CP00435A is OK
- 10.1063/1.5009011 is OK
- 10.5281/zenodo.2647458 is OK
- 10.20944/preprints202107.0033.v1 is OK

MISSING DOIs

- 10.18637/jss.v098.i16 may be a valid DOI for title: Distributions.jl: Definition and Modeling of Probability Distributions in the JuliaStats Ecosystem

INVALID DOIs

- None

[jbytecode]

@whedon generate pdf from branch paper

[whedon]

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

[whedon]

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

[jbytecode]

Dear @nluetts

• Please correct the missing DOI issue reported by whedon.

• Please re-check the whole paper by means of both language and format. When it is finished, let whedon generate the pdf and check references here.

• make a tagged release and archive (e.g. with Zenodo) as described here, and report the version number (in format of vX.Y.Z) and archive DOI in this thread. Please verify that the archive deposit has the correct metadata (title and author list), or edit these if that is not the case.

Thank you in advance.

[jbytecode]

@mseri and @myousefi2016 thank you for your great effort.

hope we will work together again!

[jbytecode]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

PDF failed to compile for issue #3526 with the following error:

 Can't find any papers to compile :-(

[jbytecode]

@whedon recommend-accept from branch paper

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1039/C9CP00435A is OK
- 10.1063/1.5009011 is OK
- 10.18637/jss.v098.i16 is OK
- 10.5281/zenodo.2647458 is OK
- 10.3390/molecules26154523 is OK
- 10.3390/molecules26164883 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2549

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2549, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch paper 

[kyleniemeyer]

@whedon accept deposit=true from branch paper

Looks good to me, thanks all!

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03526 joss-papers#2555
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03526
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[kyleniemeyer]

Congratulations @nluetts on your article's publication in JOSS!

Many thanks to @myousefi2016 and @mseri for reviewing this submission, and @jbytecode for editing.

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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.03526/status.svg)](https://doi.org/10.21105/joss.03526)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03526">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03526/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03526/status.svg
   :target: https://doi.org/10.21105/joss.03526

This is how it will look in your documentation:

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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:

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[nluetts]

Dear @kyleniemeyer, is there a possibility to squeeze in a sentence in the acknowledgement, now that the paper is already published?

[kyleniemeyer]

@nluetts It is possible to update the paper if something was missing, but it's a bit unusual to add an acknowledgment so long after the fact.

cc @arfon

[nluetts]

Yes, I admit that this is a bit awkward.

Although I was not funded by it, a research training group which I am associated with was part of the motivation for me to develop the package (they require thorough uncertainty analysis.)

It was pointed out to me that the publication can be included in the research training group's publication list, but this requires that the RTG is mentioned in the acknowledgment of the paper. Therefore, I would like to revise the acknowledgement and add a sentence.

If that is OK, how would I go about it? Can I simply update the paper branch in my repository and you can instruct whedon to rebuild the paper and replace it on the JOSS website?

[arfon]

If that is OK, how would I go about it? Can I simply update the paper branch in my repository and you can instruct whedon to rebuild the paper and replace it on the JOSS website?

Yes, I can do this. Please let me know when the paper is updated in your repository.

[nluetts]

Thank you very much, @arfon!

I updated the paper in my repository.

[arfon]

OK, that should be updated now. The site make take ~24 hours to update with the new paper as there is caching in place.

[nluetts]

Many many thanks for making that happen! 👍
It seems to be online already!