[REVIEW]: LaplaceInterpolation.jl: A Julia package for fast interpolation on a grid interpolation on a grid

[whedon]

Submitting author: @lootie (Charlotte Haley)
Repository: https://github.com/vishwas1984/LaplaceInterpolation.jl
Version: v0.1.2
Editor: @VivianePons
Reviewer: @wkearn, @eviatarbach
Archive: 10.5281/zenodo.5942603

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

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Review checklist for @wkearn

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 (@lootie) 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 @eviatarbach

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 (@lootie) 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. @wkearn, @eviatarbach 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.

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[whedon]

Wordcount for paper.md is 931

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.50 s (95.3 files/s, 320080.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Jupyter Notebook                12              0         155843           1814
Julia                           21            346            163           1450
Markdown                         4            106              0            590
Python                           3            158            175            339
TeX                              1             11              0            116
YAML                             4              5              4            110
TOML                             3              3              0             44
-------------------------------------------------------------------------------
SUM:                            48            629         156185           4463
-------------------------------------------------------------------------------


Statistical information for the repository 'f3897dd68491f6e51dffaab6' was
gathered on 2021/09/27.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Charlotte Haley                 11          1063            421           95.25
Vishwas Rao                      3            52             22            4.75

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Charlotte Haley             669           62.9          1.2               26.46
Vishwas Rao                   3            5.8          1.8                0.00

[whedon]

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

[whedon]

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

[whedon]

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

[eviatarbach]

Before doing a more comprehensive review, I notice the example in the documentation has a few issues that prevent a user from running it, including:

• Please indicate that one must install the TestImages.jl and Images.jl package.
• Misspellings such as "TestImgaes" and "imgg"
• Forgotten imports, such as Plots, Random, and Images
• Undefined variables such as "holeyimage1"

[vishwas1984]

@eviatarbach : Thanks for these comments. We have updated our documentation with the suggested corrections.

[VivianePons]

Hi @eviatarbach and @wkearn can you update me on the review? Thanks!

[eviatarbach]

Hello @VivianePons, I was waiting for vishwas1984/LaplaceInterpolation.jl#3 to be resolved so that I can review the examples.

Also, I am not able to modify the checklist. It seems I may have not clicked the invitation link in time and it expired, sorry! Do you know how to fix this?

[VivianePons]

@whedon re-invite @eviatarbach as reviewer

[whedon]

OK, the reviewer has been re-invited.

@eviatarbach please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[lootie]

Hi, is there any way to add @vishwas1984 to the watchlist for this thread?

[vishwas1984]

@VivianePons : It has been about two months and we have not gotten any feedback. Could you please take a look into this?

[VivianePons]

Indeed,

please, @eviatarbach and @wkearn can you update us?

Thanks

[eviatarbach]

Apologies, I did not see that the notebook issue had been resolved. I commend the authors on the great contribution: having a fast interpolation algorithm available will be of interest to many communities. The checklist requirements have to be fully satisfied before it can be published, though. My comments follow.

First of all, the size of the repository is quite big, at 185 MB, due to git blobs (.git/objects/pack alone is 166 MB). Maybe consider using git-filter-branch or something like BFG.

Notebooks

Is there a smaller example you can use for the 3D interpolation in JOSS_Companion_Notebook? When I tried it, it consumed over 5 GB of RAM, which would be too much for many personal computers. At least add a warning to the notebook about this.

Documentation

Please add information about the notebooks to the documentation.

In addition, you are missing the following checklist items from the documentation:

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• 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

Paper

1. Please clarify the time complexity. Is the algorithm is linear in the number of points to be interpolated? In the volume of the space?
2. Please add a performance section, showing the scaling of the Matérn vs. Laplace interpolation.
3. Please add citations to the other packages you reference in the paper, not just links. Also, the link for gridinterppy is dead.

Minor edits:
L26: "d— dimensions" → "d dimensions"
L27: The j index is not italicized.
L36: "interpolation to solve" → "interpolation to be solved"
L63: "wrapperr" → "wrapper"

[wkearn]

My apologies on the delay. Thanks for the updates to the installation instructions and notebooks. Everything seems to work properly now.

This package provides an implementation of a fast algorithm for interpolation on grids of arbitrary dimensions. There are other Julia packages that do various kinds of interpolation, which are cited in this paper, though none as far as I know that implement this particular algorithm.

I don't necessarily think that this should hold up the review, but the examples in the documentation and notebooks of restoring images are somewhat contrived. Maybe there are other applications that would do a better job of illustrating the strength of this interpolation approach that could be included in the documentation?

As @eviatarbach stated, there is no statement of need in the documentation, though you could easily add it. There are, however, automated tests (Pkg.test("LaplaceInterpolation") runs them), and a brief set of contributing instructions in the README. It seems like you have already made the changes to the citations and typos.

[lootie]

@whedon generate pdf

[whedon]

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

[vishwas1984]

@eviatarbach
Thanks for the detailed comments. I have used BFG as suggested to remove the blobs and the size of the repo after blob deletion is 8.27 MB (from this site https://citizendot.github.io/gh-info/). Thanks a lot for the suggestion.

Notebooks:
I have added a toy example for demonstrating 3D case in the notebook and for this problem the memory requirements are much lesser. I have left the previous example as is and I have added a warning about system requirements.
My Colleague @lootie will address the remaining reviews.

[lootie]

@eviatarbach Thank you for your detailed comments. I have made the changes to the paper that you've suggested, and have recompiled the paper. Additional comments below.

Documentation

The docs/src/index.md file contains the text “The Notebooks folder contains this and other examples.“, but has been placed under its own heading, per your suggestion, for visibility.

Checklist items
A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?

The statement of need is located in the paper.md itself under its own heading. Thank you.

Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?

The testfile for the software is located in tests/runtests.jl and can be run from the Julia REPL using
pkg> test LaplaceInterpolation

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

Thank you. The community guidelines are in the README.md file on the github page under “Contributing”, and are as follows: “Contributions are welcome in the form of issues, pull requests. Support questions can be directed to vhebbur at anl.gov.”

The performance comparison I have added to the paper, as per your suggestion, can be reproduced using the notebook, included (Notebooks/Another_1D_Example.ipynb).

@wkearn Thank you for your input on the examples we’ve given. We developed this package in order to interpolate missing data from volumetric images of X-ray scattering. Specifically, an implementation on a 1000x1000x1000 image with identical spherical punches totaling about 1/10 of the dataset was taking half an hour on a local cluster using the astropy.convolve algorithm. Given the number of such datasets, and the desire to process the volumes as a data stream, we wrote this package. This basic use case is shown on the README page, and this algorithm has been written into a much larger software suite for processing X-ray images. While this example is important to us, we recognize that Laplace interpolation can be used by a much broader set - especially those interested in 2D images, and one finds more and more examples of 3D and 4D gridded datasets (geophysical data and space-time data), that we decided to make the package extensible to arbitrary dimensions.

[whedon]

OK. 10.5281/zenodo.5942603 is the archive.

[VivianePons]

@whedon set v0.1.2 as version

[whedon]

OK. v0.1.2 is the version.

[VivianePons]

Congratulation @lootie and @vishwas1984 I am moving the paper to acceptance! Thank you to both reviewers @wkearn, and @eviatarbach

[VivianePons]

@whedon recommand-accept

[whedon]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

[VivianePons]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1016/c2013-0-12559-7 is OK
- 10.1137/1.9781611970104 is OK
- 10.1007/s00211-011-0391-2 is OK
- 10.1007/978-1-4614-0772-0_4 is OK
- 10.1080/10618600.2019.1652616 is OK
- 10.1007/978-3-642-24785-9_3 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.1038/s41592-019-0686-2 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#2924

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2924, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[vishwas1984]

Thank you @VivianePons for handling this paper. Thanks also to @eviatarbach and @wkearn for helpful comments.

[vishwas1984]

@VivianePons : I checked the proofs and I okay the paper.

[whedon]

I'm sorry @lootie, I'm afraid I can't do that. That's something only editor-in-chiefs are allowed to do.

[lootie]

👍

[Kevin-Mattheus-Moerman]

@lootie @VivianePons I have read the paper and inspected the Zenodo archive and all seems in order. I will now proceed to process this submission for acceptance.

[Kevin-Mattheus-Moerman]

@whedon accept deposit=true

[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.03766 joss-papers#2927
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03766
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...

[Kevin-Mattheus-Moerman]

Congratulations on this publication @lootie

Thank you @wkearn and @eviatarbach for your review efforts, and thanks @VivianePons 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.03766/status.svg)](https://doi.org/10.21105/joss.03766)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.03766/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03766/status.svg
   :target: https://doi.org/10.21105/joss.03766

This is how it will look in your documentation:

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[tarleb]

Hi all! We are working towards a more unified archive of all JOSS papers. In this process, I noted that the Markdown sources for this paper contain markup to include an image that does not exist, namely images/Onedim_GP.png. It is therefore missing from the published PDF. It seems that the image was supposed to be a combination of three files in the figures folder. For best results, the figure caption should be given as the image description, as in ![figure caption, possibly spanning many lines](figures/Onedim_FP.png). @lootie could you take a look?