search

openjournals / joss-reviews

Reviews for the Journal of Open Source Software
Creative Commons Zero v1.0 Universal
707 stars 37 forks source link

[REVIEW]: sbi - a toolkit for simulation-based inference #2505

Closed whedon closed 4 years ago

whedon commented 4 years ago

Submitting author: @janfb (Jan Boelts) Repository: https://github.com/mackelab/sbi Version: v0.12.1 Editor: @dfm Reviewer: @EiffL, @cranmer Archive: 10.5281/zenodo.3993098

:warning: JOSS reduced service mode :warning:

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.

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/b8711046da9237288492863bb0384ca7"><img src="https://joss.theoj.org/papers/b8711046da9237288492863bb0384ca7/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/b8711046da9237288492863bb0384ca7/status.svg)](https://joss.theoj.org/papers/b8711046da9237288492863bb0384ca7)

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

@EiffL & @cranmer, 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

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @dfm 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 @EiffL

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @cranmer

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 4 years ago

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

:warning: JOSS reduced service mode :warning:

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.

:star: Important :star:

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:

watching

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

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 commented 4 years ago

PDF failed to compile for issue #2505 with the following error:

Can't find any papers to compile :-(

dfm commented 4 years ago

@whedon generate pdf from branch joss-submission

whedon commented 4 years ago 
Attempting PDF compilation from custom branch joss-submission. Reticulating splines etc...
whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

dfm commented 4 years ago

@EiffL, @cranmer: I just wanted to check in with you guys to keep this review on your radar. Let me know if you have any questions!

EiffL commented 4 years ago

I've just finally found some free time, doing this now, all my apologies for the delay.

dfm commented 4 years ago

@whedon re-invite @EiffL as reviewer

whedon commented 4 years ago

OK, the reviewer has been re-invited.

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

EiffL commented 4 years ago

@janfb just making sure I resolve all authors correctly, can you confirm that @meteore is in fact Alvaro ? :-)

alvorithm commented 4 years ago

Hi François, I can confirm I am Álvaro ;). I added my name on my GitHub profile page now.

EiffL commented 4 years ago

Thank you :-D

EiffL commented 4 years ago

Everything looks great, install is a breeze, runs on colab, nice documentation, nice test suite, very useful package! Very happy to recommend publication, and many thanks to the team for this tool :-)

cranmer commented 4 years ago

Hello,

Sorry for the delay, a few unexpected things fell on me.

I have time now, but my invitation has expired.

Kyle

On Aug 8, 2020, at 9:07 AM, Dan Foreman-Mackey notifications@github.com wrote:

@EiffL https://github.com/EiffL, @cranmer https://github.com/cranmer: I just wanted to check in with you guys to keep this review on your radar. Let me know if you have any questions!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/2505#issuecomment-670933114, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABCATCSXASHLVGRMI47FM4LR7VL2BANCNFSM4PE6EFAQ.

dfm commented 4 years ago

@whedon re-invite @cranmer as reviewer

whedon commented 4 years ago

OK, the reviewer has been re-invited.

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

dfm commented 4 years ago

No worries - that's where we all are these days! You should have a new invitation now.

cranmer commented 4 years ago

The check list has:

Contribution and authorship: Has the submitting author (@janfb) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

I wasn't sure where to find what is considered the “paper authors” at first, and then I found the PDF for the article proof.

@dfm Misc feedback for JOSS would be to have link to the PDF in the checklist. (Or maybe it would normally be there and it just failed for some reason).

cranmer commented 4 years ago

I know that Jakob H. Macke is part of this effort and belongs on author list (GitHub organization is Mackelab) but noting it since he doesn't show up on contributor list.

cranmer commented 4 years ago

Ok, I'm basically done. I don't know if I needed to explicitly run all the tests, they take a while. I did install the environment locally and can confirm that the tests are running.

The package is very nice, the interface to simulators seems natural, and I was able to run tutorial examples! The examples themselves are well chosen.

I created a few issues recommending improvements in documentation, but I don't see them as show stoppers.

There is one issue that had me uncheck the Functionality documentation:: https://github.com/mackelab/sbi/issues/298 The package would be useful even if this isn't possible, but the software paper says it is, and I haven't been able to confirm that yet. If it isn't possible, then I think a small tweak to the sentence in the software paper would be sufficient for publication.

cranmer commented 4 years ago

Thanks to @michaeldeistler of SBI team to quickly address problem. There is a PR that will fix the API documentation, and an example is planned to follow @dfm I'm not really sure about the procedure here. Do we wait for the PR to be merged and new API docs to be generated, or do we proceed assuming that it's in progress and on the way? (The example demonstrating this feature is nice, but I don't think it is essential).

As I wrote earlier, I think SBI is great and the submission is publishable even without this feature being there, except for that it is explicitly called out in the software paper so it should be in the API docs.

dfm commented 4 years ago

@cranmer: Thanks for the update! If you think that the functionality claims in the paper are sufficiently well justified once the embedding_net, etc. parameters are documented then I think it would be fine to proceed once that pull request has been merged without waiting for the full example in the docs.

janfb commented 4 years ago

@cranmer @dfm Please note we just released a new version of sbi adressing the above issues: https://github.com/mackelab/sbi/releases

The docs should be up to date now as well.

cranmer commented 4 years ago

Looks great!

Sign off from me @dfm. Congratulations @janfb and SBI team.

dfm commented 4 years ago

@whedon generate pdf from branch joss-submission

whedon commented 4 years ago 
Attempting PDF compilation from custom branch joss-submission. Reticulating splines etc...
whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

dfm commented 4 years ago

@whedon check references from branch joss-submission

whedon commented 4 years ago 
Attempting to check references... from custom branch joss-submission
whedon commented 4 years ago 
Reference check summary:

OK DOIs

- 10.1145/3295500.3356180 is OK
- 10.1093/biomet/asp052 is OK
- 10.1073/pnas.1912789117 is OK
- 10.1101/838383  is OK
- 10.1214/17-EJS1340SI is OK
- 10.1093/bioinformatics/bty361 is OK
- 10.21105/joss.00011 is OK
- 10.1063/1.1699114 is OK
- 10.1214/aos/1056562461  is OK
- 10.1093/oxfordjournals.molbev.a026091 is OK
- 10.1073/pnas.0607208104 is OK
- 10.1201/9781315117195 is OK
- 10.1098/rsif.2008.0172 is OK

MISSING DOIs

- https://doi.org/10.1145/3093172.3093233 may be missing for title: ABCpy

INVALID DOIs

- None
dfm commented 4 years ago

@janfb: Looks good! I just opened a pull request with some formatting edits for the manuscript. The following steps for you:

dfm commented 4 years ago

I'd also like to send a huge thanks to @EiffL and @cranmer for their constructive reviews!

janfb commented 4 years ago

@dfm thanks for the instructions! And many thanks again for editing this paper!

janfb commented 4 years ago

@whedon generate pdf from branch joss-submission

whedon commented 4 years ago 
Attempting PDF compilation from custom branch joss-submission. Reticulating splines etc...
whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

janfb commented 4 years ago

Regarding the version, yes, the most recent one is 0.12.1.

Two questions @dfm 1) we already have a version on arxiv: https://arxiv.org/abs/2007.09114 Is OK if we just make a new version of this submission with the most recent version of the paper?

2) The JOSS version of the article already has a DOI (10.21105/joss.02505) no? Or shall I create a new DOI using Zenodo?

janfb commented 4 years ago

I double-checked the article -- all looks good! I created a DOI using Zenodo and upload the zipped code of v0.12.1 (and not the paper PDF), the DOI is 10.5281/zenodo.3993098 Is this how it should be?

dfm commented 4 years ago

@janfb: This all looks good and you're definitely welcome to upload the JOSS manuscript to arXiv, although there have been some issues in the past (https://github.com/openjournals/joss/issues/132 might be relevant/helpful). The Zenodo archive is good - thanks!

dfm commented 4 years ago

@whedon set v0.12.1 as version

whedon commented 4 years ago

OK. v0.12.1 is the version.

dfm commented 4 years ago

@whedon set 10.5281/zenodo.3993098 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.3993098 is the archive.

dfm commented 4 years ago

@whedon accept

whedon commented 4 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 4 years ago

PDF failed to compile for issue #2505 with the following error:

Can't find any papers to compile :-(

dfm commented 4 years ago

@whedon accept from branch joss-submission

whedon commented 4 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 4 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1650

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1650, 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 joss-submission
whedon commented 4 years ago 
Reference check summary:

OK DOIs

- 10.1145/3093172.3093233 is OK
- 10.1145/3295500.3356180 is OK
- 10.1093/biomet/asp052 is OK
- 10.1073/pnas.1912789117 is OK
- 10.1101/838383  is OK
- 10.1214/17-EJS1340SI is OK
- 10.1093/bioinformatics/bty361 is OK
- 10.21105/joss.00011 is OK
- 10.1063/1.1699114 is OK
- 10.1214/aos/1056562461  is OK
- 10.1093/oxfordjournals.molbev.a026091 is OK
- 10.1073/pnas.0607208104 is OK
- 10.1201/9781315117195 is OK
- 10.1098/rsif.2008.0172 is OK

MISSING DOIs

- None

INVALID DOIs

- None