[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

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)

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

@ludgerpaehler & @femtomc, 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 @vchuravy know.

✨ 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 @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?

vchuravy commented 2 years ago

@whedon set 10.5281/zenodo.6707122 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.6707122 is the archive.

vchuravy commented 2 years ago

@whedon set v0.16.4 as version

whedon commented 2 years ago

OK. v0.16.4 is the version.

vchuravy commented 2 years ago

@whedon recommend-accept

whedon commented 2 years ago

Attempting dry run of processing paper acceptance...

whedon commented 2 years ago

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

 Can't find any papers to compile :-(

vchuravy commented 2 years ago

@whedon recommend-accept from branch paper

whedon commented 2 years ago

Attempting dry run of processing paper acceptance...

whedon commented 2 years ago

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

Check final proof :point_right: https://github.com/JuliaCon/proceedings-papers/pull/60

If the paper PDF and Crossref deposit XML look good in https://github.com/JuliaCon/proceedings-papers/pull/60, 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 commented 2 years ago

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
- 10.5281/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
- 10.1007/978-3-319-29604-3_5 is OK
- 10.5281/zenodo.5520061 is OK
- 10.18637/jss.v076.i01 is OK

MISSING DOIs

- 10.1137/141000671 may be a valid DOI for title: Julia: A fresh approach to numerical computing
- 10.1145/503272.503288 may be a valid DOI for title: Stochastic lambda calculus and monads of probability distributions

INVALID DOIs

- https://doi.org/10.1016/j.jmva.2009.04.008 is INVALID because of 'https://doi.org/' prefix

vchuravy commented 2 years ago

@cscherrer can you fix up the DOI in your references?

cscherrer commented 2 years ago

Just the one, right? I've just pushed the fix

cscherrer commented 2 years ago

Oh wait I can add the missing ones

cscherrer commented 2 years ago

Ok think it's done

cscherrer commented 2 years ago

Guess I should ping you now @vchuravy :)

vchuravy commented 1 year ago

@whedon recommend-accept from branch paper

whedon commented 1 year ago

Attempting dry run of processing paper acceptance...

whedon commented 1 year ago

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "volume" (NAME) [#, "@", #, {: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 commented 1 year ago

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 17:31:39#45] 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 commented 1 year ago

@whedon generate pdf from branch paper

whedon commented 1 year ago

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

whedon commented 1 year ago

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

vchuravy commented 1 year ago

@whedon recommend-accept from branch paper

whedon commented 1 year ago

Attempting dry run of processing paper acceptance...

whedon commented 1 year ago

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "volume" (NAME) [#, "@", #, {: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 commented 1 year ago

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 commented 1 year ago

@whedon check references

mschauer commented 1 year ago

@cscherrer commata missing in https://github.com/cscherrer/MeasureTheory.jl/commit/1f907a7b8d0f045da4e8be5026b5a2fbdf0aa1d1

mschauer commented 1 year ago

@whedon check references

mschauer commented 1 year ago

@whedon generate pdf from branch paper

whedon commented 1 year ago

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

mschauer commented 1 year ago

@whedon generate pdf from branch paper

whedon commented 1 year ago

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

whedon commented 1 year ago

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

cscherrer commented 1 year ago

Thanks @mschauer , just accepted your changes

vchuravy commented 1 year ago

@whedon check references

mschauer commented 1 year ago

@whedon check references from branch paper

whedon commented 1 year ago

Attempting to check references... from custom branch paper

whedon commented 1 year ago

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 commented 1 year ago

@whedon recommend-accept from branch paper

whedon commented 1 year ago

Attempting dry run of processing paper acceptance...

whedon commented 1 year ago

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

Check final proof :point_right: https://github.com/JuliaCon/proceedings-papers/pull/61

If the paper PDF and Crossref deposit XML look good in https://github.com/JuliaCon/proceedings-papers/pull/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 commented 1 year ago

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 commented 1 year ago

@whedon accept deposit=true from branch paper

whedon commented 1 year ago

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

whedon commented 1 year ago

🚨🚨🚨 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 :point_right: https://github.com/JuliaCon/proceedings-papers/pull/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 commented 1 year 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://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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mschauer commented 1 year ago

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

cscherrer commented 1 year ago

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

JuliaCon / proceedings-review