[REVIEW]: Applied Measure Theory for Probabilistic Modeling

whedon commented 2 years ago

Submitting author: @mschauer (Moritz Schauer) Repository: https://github.com/cscherrer/MeasureTheory.jl Version: v0.16.4 Reviewer: @ludgerpaehler, @femtomc Archive: 10.5281/zenodo.6707122

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Review checklist for @ludgerpaehler

Conflict of interest

[x] As the reviewer I confirm that I have read the JuliaCon conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

[x] I confirm that I read and will adhere to the JuliaCon 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] Authorship: Has the submitting author (@mschauer) 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

[ ] 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.
[ ] 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 function 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

Paper format

[x] Authors: Does the paper.tex file include a list of authors with their affiliations?
[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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
[x] Page limit: Is the page limit for full papers respected by the submitted document?

Content

[x] Context: is the scientific context motivating the work correctly presented?
[x] Methodology: is the approach taken in the work justified, presented with enough details and reference to reproduce it?
[x] Results: are the results presented and compared to approaches with similar goals?

Review checklist for @femtomc

Conflict of interest
[x] As the reviewer I confirm that I have read the JuliaCon conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

[x] I confirm that I read and will adhere to the JuliaCon 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] Authorship: Has the submitting author (@mschauer) 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 function 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 format

[x] Authors: Does the paper.tex file include a list of authors with their affiliations?
[ ] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[ ] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
[ ] Page limit: Is the page limit for full papers respected by the submitted document?

Content

[ ] Context: is the scientific context motivating the work correctly presented?
[ ] Methodology: is the approach taken in the work justified, presented with enough details and reference to reproduce it?
[ ] Results: are the results presented and compared to approaches with similar goals?

whedon commented 2 years ago

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

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whedon commented 2 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.05 s (1033.1 files/s, 67368.6 lines/s)
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Statistical information for the repository '0f1adcd6e7123f43c9e691e2' was
gathered on 2021/10/11.
No commited files with the specified extensions were found.

whedon commented 2 years ago

PDF failed to compile for issue #92 with the following error:

 Can't find any papers to compile :-(

cscherrer commented 2 years ago

@whedon generate pdf from branch paper

whedon commented 2 years ago

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

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

femtomc commented 2 years ago

I'll get to this tonight - sorry for delay.

whedon commented 2 years ago

:wave: @ludgerpaehler, please update us on how your review is going (this is an automated reminder).

whedon commented 2 years ago

:wave: @femtomc, please update us on how your review is going (this is an automated reminder).

ludgerpaehler commented 2 years ago

Really interesting package with a strong necessity for it.

Working through the checklist, there are two points which jumped my eyes:

Statement of Need: Do the authors clearly state what problems the software is designed to solve (..)?

https://github.com/cscherrer/MeasureTheory.jl/issues/179

Example Usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).

https://github.com/cscherrer/MeasureTheory.jl/issues/180

ludgerpaehler commented 2 years ago

I would furthermore encourage the authors to improve the reading flow of the paper. Two sections that the eye in this respect are

In "Why Measures?"

Also, there’s an elegant correspondence between frequentist and Bayesian methods, where regularization corresponds to a prior.

It is a really good analogy, but reads disconnected from the rest of the paragraph. Integration with the rest of the paragraph would elevate the reading flow greatly.

"Related Work" just lists the 5 related papers in their own respective paragraphs, without any leading thread between the 5 of them.

cscherrer commented 2 years ago

Thank you @ludgerpaehler! I'll discuss with @mschauer; we'll follow up in the issues you added.

femtomc commented 2 years ago

@cscherrer

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

Do you mind adopting a specific set of guidelines for contributions, and placing them in the repository? (e.g. ColPrac, or something else).

vchuravy commented 2 years ago

Gentle bump @cscherrer did you address the review points?

vchuravy commented 2 years ago

@whedon remind @cscherrer in two weeks

whedon commented 2 years ago

Reminder set for @cscherrer in two weeks

cscherrer commented 2 years ago

Hi, :wave:

I'd like to thank @vchuravy and our reviewers @ludgerpaehler and @femtomc for helpful feedback and patience. MeasureTheory has grown and matured steadily since our initial submission, so we had an issue of trying to hit a moving target with a paper that will soon be somewhat frozen. I think we're finally in a position to address this more thoroughly.

We have made some modifications to the repository which should now be visible. We've also made some significant edits to the paper, to make it match the current state of the package. These changes are in a separate branch. I expect @mschauer and I can get these pushed to the paper branch very soon, likely within the next day or two. After we merge these, the branch will still be available in case you'd like to see details of exactly what has changed.

I'll update again here when the changes are merged.

cscherrer commented 2 years ago

Edits are pushed! The paper branch is now updated.

cscherrer commented 2 years ago

@whedon generate pdf from branch paper

whedon commented 2 years ago

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

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

mschauer commented 2 years ago

@femtomc Do you think https://github.com/cscherrer/MeasureTheory.jl/pull/200 addresses your concerns in a way adequate for a small project?

femtomc commented 2 years ago

Yes, perfect.

femtomc commented 2 years ago

Should I read this again after the recent updates?

cscherrer commented 2 years ago

Up to you of course, but there are quite a few changes. There's a diff here in case that's helpful: https://github.com/cscherrer/MeasureTheory.jl/pull/201/files#diff-983b58b8186b0a4ed7f280f258cdab3eb0dd7d5136f8ac361ba982a43cfb7136

mschauer commented 2 years ago

Sorry, we should have said it: This is our revision.

cscherrer commented 2 years ago

@whedon generate pdf from branch paper

whedon commented 2 years ago

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

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

cscherrer commented 2 years ago

(minor updates to the bibliography)

vchuravy commented 1 year ago

@whedon help

whedon commented 1 year ago

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

@whedon commands

vchuravy commented 1 year ago

@whedon commands

whedon commented 1 year ago

Here are some things you can ask me to do:

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vchuravy commented 1 year ago

@whedon recommend-accept

whedon commented 1 year ago

No archive DOI set. Exiting...

vchuravy commented 1 year ago

@ludgerpaehler @femtomc is there any thing left from your perspective?

ludgerpaehler commented 1 year ago

From my side it looks good to publish!

vchuravy commented 1 year ago

@cscherrer I will need a Zenodo deposition see https://juliacon.github.io/proceedings-guide/author/#publication_phase

cscherrer commented 1 year ago

@vchuravy we have a DOI from arxiv, does that work? https://arxiv.org/abs/2110.00602

mschauer commented 1 year ago

The DOI on arxiv doesn't point to a specific version, so I made 10.5281/zenodo.6784068 (https://doi.org/10.48550/arXiv.2110.00602)

cscherrer commented 1 year ago

Thanks @mschauer . I was worried about violating some DOI uniqueness requirements, but I think your point about referring to a specific version makes sense.

mschauer commented 1 year ago

No worries, there is no uniqueness requirement for DOIs, I also linked them:

cscherrer commented 1 year ago

@whedon set 10.5281/zenodo.6784068 as archive

whedon commented 1 year ago

I'm sorry @cscherrer, I'm afraid I can't do that. That's something only editors are allowed to do.

vchuravy commented 1 year ago

@whedon set 10.5281/zenodo.6784068 as archive

whedon commented 1 year ago

OK. 10.5281/zenodo.6784068 is the archive.

vchuravy commented 1 year ago

Sorry folks this should be the DOI to the code-artifacts. Not the DOI to the paper, we will generate that later. @carstenbauer that's ambiguously worded in the docs.

vchuravy commented 1 year ago

The JOSS docs are clearer on that:

We ask that the authors issue a new tagged release of the software (if changed), and archive it (on Zenodo, figshare, or other). The authors then post the version number and archive DOI in the REVIEW issue. The handling editor executes the pre-publication steps, and pings the EiCs for final processing.

cscherrer commented 1 year ago

Ok here it is: That's for cscherrer/MeasureTheory.jl: v0.16.4

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