[REVIEW]: Applied Measure Theory for Probabilistic Modeling #92

whedon · 2021-10-11T16:10:58Z

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

Status badge code:

HTML: <a href="https://proceedings.juliacon.org/papers/7958be3512c592ee211c3a3e8b22165e"><img src="https://proceedings.juliacon.org/papers/7958be3512c592ee211c3a3e8b22165e/status.svg"></a>
Markdown: [![status](https://proceedings.juliacon.org/papers/7958be3512c592ee211c3a3e8b22165e/status.svg)](https://proceedings.juliacon.org/papers/7958be3512c592ee211c3a3e8b22165e)

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Reviewer instructions & questions

@ludgerpaehler & @femtomc, 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 @ludgerpaehler

Conflict of interest

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.

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

General checks

Repository: Is the source code for this software available at the repository url?
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Authorship: Has the submitting author (@mschauer) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 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

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?

Review checklist for @femtomc

Conflict of interest

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

I confirm that I read and will adhere to the JuliaCon 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?
Authorship: Has the submitting author (@mschauer) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 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

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?

The text was updated successfully, but these errors were encountered:

whedon · 2021-10-11T16:11:01Z

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 🎉.

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whedon · 2021-10-11T16:11:10Z

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.05 s (1033.1 files/s, 67368.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           32            577            263           1423
YAML                             8             19             12            321
Markdown                         4            118              0            261
TOML                             2              4              0             59
TeX                              1              0              0              8
-------------------------------------------------------------------------------
SUM:                            47            718            275           2072
-------------------------------------------------------------------------------


Statistical information for the repository '0f1adcd6e7123f43c9e691e2' was
gathered on 2021/10/11.
No commited files with the specified extensions were found.

whedon · 2021-10-11T16:11:11Z

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

 Can't find any papers to compile :-(

cscherrer · 2021-10-11T16:19:14Z

@whedon generate pdf from branch paper

whedon · 2021-10-11T16:19:17Z

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

whedon · 2021-10-11T16:19:26Z

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

femtomc · 2021-10-14T15:00:06Z

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

whedon · 2021-10-25T16:11:03Z

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

whedon · 2021-10-25T16:11:11Z

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

ludgerpaehler · 2021-12-10T00:20:04Z

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 (..)?

JuliaMath/MeasureTheory.jl#179

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

JuliaMath/MeasureTheory.jl#180

ludgerpaehler · 2021-12-10T00:41:21Z

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 · 2021-12-10T17:36:51Z

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

femtomc · 2021-12-14T20:47:57Z

@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 · 2022-01-27T15:38:42Z

Gentle bump @cscherrer did you address the review points?

vchuravy · 2022-05-05T14:11:25Z

@whedon remind @cscherrer in two weeks

whedon · 2022-05-05T14:11:28Z

Reminder set for @cscherrer in two weeks

cscherrer · 2022-05-18T00:20:27Z

Hi, 👋

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 · 2022-05-20T15:26:16Z

Edits are pushed! The paper branch is now updated.

cscherrer · 2022-05-20T15:26:37Z

@whedon generate pdf from branch paper

whedon · 2022-05-20T15:26:42Z

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

whedon · 2022-05-20T15:26:50Z

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

mschauer · 2022-05-20T15:31:29Z

@femtomc Do you think JuliaMath/MeasureTheory.jl#200 addresses your concerns in a way adequate for a small project?

femtomc · 2022-05-20T15:45:46Z

Yes, perfect.

femtomc · 2022-05-20T15:46:06Z

Should I read this again after the recent updates?

vchuravy · 2022-07-03T17:35:45Z

@whedon recommend-accept from branch paper

whedon · 2022-07-03T17:35:48Z

Attempting dry run of processing paper acceptance...

whedon · 2022-07-03T17:35:54Z

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "volume" (NAME) [#<BibTeX::Bibliography data=[3]>, "@", #<BibTeX::Entry >, {:title=>["Julia: {A} fresh approach to numerical computing"], :author=>["Bezanson, Jeff and Edelman, Alan and Karpinski, Stefan and Shah, Viral B"], :journal=>["SIAM review"], :doi=>["10.1137/141000671"]}]

whedon · 2022-07-03T17:35:59Z

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

 Latexmk: This is Latexmk, John Collins, 17 Jan. 2018, version: 4.55.
Rule 'pdflatex': Rules & subrules not known to be previously run:
   pdflatex
Rule 'pdflatex': The following rules & subrules became out-of-date:
      'pdflatex'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -recorder  "paper.tex"'
------------
Collected error summary (may duplicate other messages):
  pdflatex: Command for 'pdflatex' gave return code 1
      Refer to 'paper.log' for details
E, [2022-07-03 17:35:58#130] ERROR -- : Failed to parse BibTeX on value "volume" (NAME) [#<BibTeX::Bibliography data=[3]>, "@", #<BibTeX::Entry >, {:title=>["Julia: {A} fresh approach to numerical computing"], :author=>["Bezanson, Jeff and Edelman, Alan and Karpinski, Stefan and Shah, Viral B"], :journal=>["SIAM review"], :doi=>["10.1137/141000671"]}]
bibtex.y:138:in `on_error': Failed to parse BibTeX on value "volume" (NAME) [#<BibTeX::Bibliography data=[3]>, "@", #<BibTeX::Entry >, {:title=>["Julia: {A} fresh approach to numerical computing"], :author=>["Bezanson, Jeff and Edelman, Alan and Karpinski, Stefan and Shah, Viral B"], :journal=>["SIAM review"], :doi=>["10.1137/141000671"]}] (BibTeX::ParseError)
	from (eval):3:in `_racc_do_parse_c'
	from (eval):3:in `do_parse'
	from bibtex.y:111:in `parse'
	from /app/vendor/bundle/ruby/2.6.0/gems/bibtex-ruby-6.0.0/lib/bibtex/bibliography.rb:67:in `parse'
	from /app/vendor/bundle/ruby/2.6.0/gems/bibtex-ruby-6.0.0/lib/bibtex/bibliography.rb:50:in `open'
	from /app/vendor/bundle/ruby/2.6.0/gems/bibtex-ruby-6.0.0/lib/bibtex/utilities.rb:25:in `open'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/bibtex_parser.rb:38:in `generate_citations'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/compilers.rb:202:in `crossref_from_latex'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/compilers.rb:19:in `generate_crossref'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:100:in `compile'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:88:in `compile'
	from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:in `run'
	from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in `invoke_command'
	from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in `dispatch'
	from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in `start'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:131:in `<top (required)>'
	from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `load'
	from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `<main>'

vchuravy · 2022-07-03T17:40:02Z

@whedon check references

mschauer · 2022-07-03T19:19:30Z

@cscherrer commata missing in JuliaMath/MeasureTheory.jl@1f907a7

mschauer · 2022-07-03T20:09:27Z

@whedon check references

mschauer · 2022-07-03T20:17:03Z

@whedon generate pdf from branch paper

whedon · 2022-07-03T20:17:06Z

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

whedon · 2022-07-03T20:17:15Z

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

cscherrer · 2022-07-03T20:17:27Z

Thanks @mschauer , just accepted your changes

vchuravy · 2022-07-03T20:32:44Z

@whedon check references

mschauer · 2022-07-03T20:50:10Z

@whedon check references from branch paper

whedon · 2022-07-03T20:50:13Z

Attempting to check references... from custom branch paper

whedon · 2022-07-03T20:51:03Z

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

OK DOIs

- 10.1007/978-3-642-17905-1 is OK
- 10.1007/978-1-4757-2539-1 is OK
- 10.1137/141000671 is OK
- 10.5281/ZENODO.1005091 is OK
- 10.5281/ZENODO.3931118 is OK
- 10.18637/jss.v098.i16 is OK
- 10.5281/zenodo.2647458 is OK
- 10.1214/18-AOS1715 is OK
- 10.3389/fphy.2021.663457 is OK
- 10.1007/s11222-021-10008-8 is OK
- 10.48550/ARXIV.2103.08478 is OK
- 10.1016/j.spl.2018.02.021 is OK
- 10.2168/lmcs-9(3:11)2013 is OK
- 10.1145/3374208 is OK
- 10.1214/088342307000000014 is OK
- 10.1016/j.jmva.2009.04.008 is OK
- 10.1007/978-3-319-29604-3_5 is OK
- 10.5281/zenodo.5520061 is OK
- 10.18637/jss.v076.i01 is OK
- 10.1145/503272.503288 is OK

MISSING DOIs

- None

INVALID DOIs

- None

vchuravy · 2022-07-03T21:20:00Z

@whedon recommend-accept from branch paper

whedon · 2022-07-03T21:20:03Z

Attempting dry run of processing paper acceptance...

whedon · 2022-07-03T21:20:17Z

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

Check final proof 👉 JuliaCon/proceedings-papers#61

If the paper PDF and Crossref deposit XML look good in JuliaCon/proceedings-papers#61, 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

whedon · 2022-07-03T21:20:50Z

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

OK DOIs

- 10.1007/978-3-642-17905-1 is OK
- 10.1007/978-1-4757-2539-1 is OK
- 10.1137/141000671 is OK
- 10.5281/ZENODO.1005091 is OK
- 10.5281/ZENODO.3931118 is OK
- 10.18637/jss.v098.i16 is OK
- 10.5281/zenodo.2647458 is OK
- 10.1214/18-AOS1715 is OK
- 10.3389/fphy.2021.663457 is OK
- 10.1007/s11222-021-10008-8 is OK
- 10.48550/ARXIV.2103.08478 is OK
- 10.1016/j.spl.2018.02.021 is OK
- 10.2168/lmcs-9(3:11)2013 is OK
- 10.1145/3374208 is OK
- 10.1214/088342307000000014 is OK
- 10.1016/j.jmva.2009.04.008 is OK
- 10.1007/978-3-319-29604-3_5 is OK
- 10.5281/zenodo.5520061 is OK
- 10.18637/jss.v076.i01 is OK
- 10.1145/503272.503288 is OK

MISSING DOIs

- None

INVALID DOIs

- None

vchuravy · 2022-07-03T21:22:05Z

@whedon accept deposit=true from branch paper

whedon · 2022-07-03T21:22:08Z

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

whedon · 2022-07-03T21:22:31Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.jcon.00092 proceedings-papers#62
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/jcon.00092
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

whedon · 2022-07-03T21:24:06Z

🎉🎉🎉 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://proceedings.juliacon.org/papers/10.21105/jcon.00092/status.svg)](https://doi.org/10.21105/jcon.00092)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/jcon.00092">
  <img src="https://proceedings.juliacon.org/papers/10.21105/jcon.00092/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://proceedings.juliacon.org/papers/10.21105/jcon.00092/status.svg
   :target: https://doi.org/10.21105/jcon.00092

This is how it will look in your documentation:

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Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://forms.gle/yANMe4c9YmuW9MWcA
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mschauer · 2022-07-04T08:02:02Z

Thank you for the reviews @femtomc and @ludgerpaehler and the editorial work @vchuravy

cscherrer · 2022-07-04T13:18:34Z

Reviews were very helpful for improving readability and catching some repository issues we had missed. Thank you!

whedon added Julia review TeX labels Oct 11, 2021

whedon assigned vchuravy Oct 11, 2021

whedon mentioned this issue Oct 11, 2021

[PRE REVIEW]: Applied Measure Theory for Probabilistic Modeling #89

Closed

[REVIEW]: Applied Measure Theory for Probabilistic Modeling #92

[REVIEW]: Applied Measure Theory for Probabilistic Modeling #92

Comments

whedon commented Oct 11, 2021 • edited Loading

Reviewer instructions & questions

Review checklist for @ludgerpaehler

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Paper format

Content

Review checklist for @femtomc

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Paper format

Content

whedon commented Oct 11, 2021

whedon commented Oct 11, 2021

whedon commented Oct 11, 2021

cscherrer commented Oct 11, 2021

whedon commented Oct 11, 2021

whedon commented Oct 11, 2021

femtomc commented Oct 14, 2021 • edited Loading

whedon commented Oct 25, 2021

whedon commented Oct 25, 2021

ludgerpaehler commented Dec 10, 2021

ludgerpaehler commented Dec 10, 2021

cscherrer commented Dec 10, 2021

femtomc commented Dec 14, 2021

vchuravy commented Jan 27, 2022

vchuravy commented May 5, 2022

whedon commented May 5, 2022

cscherrer commented May 18, 2022

cscherrer commented May 20, 2022

cscherrer commented May 20, 2022

whedon commented May 20, 2022

whedon commented May 20, 2022

mschauer commented May 20, 2022 • edited Loading

femtomc commented May 20, 2022

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vchuravy commented Jul 3, 2022

whedon commented Jul 3, 2022

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vchuravy commented Jul 3, 2022

mschauer commented Jul 3, 2022

mschauer commented Jul 3, 2022

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mschauer commented Jul 3, 2022

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vchuravy commented Jul 3, 2022

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mschauer commented Jul 4, 2022

cscherrer commented Jul 4, 2022

whedon commented Oct 11, 2021 •

edited

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mschauer commented May 20, 2022 •

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