editorialbot commented 1 year ago

Submitting author: !--author-handle-->@marvinschmitt@osorensen<!--end-editor-- Reviewers: @sandeshkatakam, @LoryPack Archive: 10.5281/zenodo.8346393

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/4e59f48f4a948bc62b0e31fc04b05a89"><img src="https://joss.theoj.org/papers/4e59f48f4a948bc62b0e31fc04b05a89/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/4e59f48f4a948bc62b0e31fc04b05a89/status.svg)](https://joss.theoj.org/papers/4e59f48f4a948bc62b0e31fc04b05a89)

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

@sandeshkatakam & @LoryPack, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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

Checklists

📝 Checklist for @sandeshkatakam

📝 Checklist for @LoryPack

editorialbot commented 1 year ago

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

editorialbot commented 1 year ago

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

OK DOIs

- 10.21468/SciPostPhys.10.6.126 is OK
- 10.1007/s42113-023-00167-4 is OK
- 10.3390/s22145408 is OK
- 10.1109/TNNLS.2021.3124052 is OK
- 10.1371/journal.pcbi.1009472 is OK
- 10.1109/TNNLS.2020.3042395 is OK
- 10.1007/s11222-022-10090-6 is OK
- 10.7717/peerj-cs.55 is OK
- 10.21105/joss.04304 is OK
- 10.1016/j.jedc.2021.104082 is OK
- 10.1190/geo2022-0472.1 is OK
- 10.1016/j.jocm.2023.100418 is OK
- 10.2514/6.2022-0631 is OK
- PhysRevE.106.055311 is OK
- 10.1038/s41562-021-01282-7 is OK
- 10.20982/tqmp.16.2.p120 is OK
- 10.1007/s13349-022-00638-5 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.19 s (421.0 files/s, 172609.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          49           2767           6017           6373
Jupyter Notebook                10              0          12927           2428
TeX                              1             37              0            329
Markdown                         3            126              0            307
reStructuredText                 6            112            157            143
YAML                             5             15             21             98
INI                              1              5              0             30
TOML                             1              4              0             28
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            78           3078          19130           9771
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 1495

editorialbot 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:

sandeshkatakam commented 1 year ago

Review checklist for @sandeshkatakam

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/stefanradev93/BayesFlow?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@marvinschmitt) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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 functionality 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

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

osorensen commented 1 year ago

@editorialbot remind @LoryPack in 2 weeks

editorialbot commented 1 year ago

Reminder set for @LoryPack in 2 weeks

sandeshkatakam commented 1 year ago

@editorialbot remind @LoryPack in 2 weeks

Whom should I contact regarding an issue I am facing with the review? Do i have to contact the authors of the code on GitHub directly or raise an issue on the respective github repo?

osorensen commented 1 year ago

@sandeshkatakam, please open an issue in the source repository but include a link to this issue (i.e., https://github.com/openjournals/joss-reviews/issues/5702) in the issue that you create. That way we keep track.

For smaller issues you're also welcome to post them right here in the review thread.

editorialbot commented 1 year ago

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

sandeshkatakam commented 1 year ago

@osorensen I have finished my review checklist. How should I proceed further?

osorensen commented 1 year ago

Thanks a lot @sandeshkatakam. Then your done with your job, so no need to proceed further.

LoryPack commented 1 year ago

Review checklist for @LoryPack

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/stefanradev93/BayesFlow?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@marvinschmitt) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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 functionality 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

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

LoryPack commented 1 year ago

I'm done with my review @osorensen

osorensen commented 1 year ago

@editorialbot generate pdf

osorensen commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.18637/jss.v100.i07 is OK
- 10.21468/SciPostPhys.10.6.126 is OK
- 10.1007/s42113-023-00167-4 is OK
- 10.3390/s22145408 is OK
- 10.1109/TNNLS.2021.3124052 is OK
- 10.1371/journal.pcbi.1009472 is OK
- 10.1109/TNNLS.2020.3042395 is OK
- 10.1007/s11222-022-10090-6 is OK
- 10.7717/peerj-cs.55 is OK
- 10.21105/joss.04304 is OK
- 10.1016/j.jedc.2021.104082 is OK
- 10.1190/geo2022-0472.1 is OK
- 10.1016/j.jocm.2023.100418 is OK
- 10.2514/6.2022-0631 is OK
- PhysRevE.106.055311 is OK
- 10.1038/s41562-021-01282-7 is OK
- 10.20982/tqmp.16.2.p120 is OK
- 10.1007/s13349-022-00638-5 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot 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:

osorensen commented 1 year ago

@editorialbot commands

editorialbot commented 1 year ago

Hello @osorensen, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Add to this issue's reviewers list
@editorialbot add @username as reviewer

# Remove from this issue's reviewers list
@editorialbot remove @username from reviewers

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Assign a user as the editor of this submission
@editorialbot assign @username as editor

# Remove the editor assigned to this submission
@editorialbot remove editor

# Remind an author, a reviewer or the editor to return to a review after a 
# certain period of time (supported units days and weeks)
@editorialbot remind @reviewer in 2 weeks

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for version
@editorialbot set v1.0.0 as version

# Set a value for branch
@editorialbot set joss-paper as branch

# Set a value for repository
@editorialbot set https://github.com/organization/repo as repository

# Set a value for the archive DOI
@editorialbot set set 10.5281/zenodo.6861996 as archive

# Mention the EiCs for the correct track
@editorialbot ping track-eic

# Generates the pdf paper
@editorialbot generate pdf

# Recommends the submission for acceptance
@editorialbot recommend-accept

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Flag submission with questionable scope
@editorialbot query scope

# Get a link to the complete list of reviewers
@editorialbot list reviewers

# Creates a post-review checklist with editor and authors tasks
@editorialbot create post-review checklist

# Open the review issue
@editorialbot start review

osorensen commented 1 year ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

[ ] Double check authors and affiliations (including ORCIDs)
[ ] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
[ ] Archive the release on Zenodo/figshare/etc and post the DOI here.
[ ] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[ ] Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[x] Read the text of the paper and offer comments/corrections (as either a list or a PR)
[x] Check the references in the paper for corrections (e.g. capitalization)
[ ] Check that the archive title, author list, version tag, and the license are correct
[ ] Set archive DOI with @editorialbot set <DOI here> as archive
[ ] Set version with @editorialbot set <version here> as version
[ ] Double check rendering of paper with @editorialbot generate pdf
[ ] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[ ] Recommend acceptance with @editorialbot recommend-accept

osorensen commented 1 year ago

@marvinschmitt, the paper is really well written and I have no particular comments. However, could you please go through your .bib source file so that the words "Bayes" and "Bayesian" are protected with an extra set of curly braces? Currently there are several places in the reference list where they appear with lowercase first. Please report back here when done.

marvinschmitt commented 1 year ago

Thank you very much for the kind feedback @osorensen. Also thank you @LoryPack and @sandeshkatakam for your reviews. We appreciate it!

@osorensen thanks for catching those issues, I have updated the .bib source accordingly in https://github.com/stefanradev93/BayesFlow/commit/f3196e4b5140923d4db5f6535acb839828761d8f

osorensen commented 1 year ago

@editorialbot generate pdf

osorensen commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.18637/jss.v100.i07 is OK
- 10.21468/SciPostPhys.10.6.126 is OK
- 10.1007/s42113-023-00167-4 is OK
- 10.3390/s22145408 is OK
- 10.1109/TNNLS.2021.3124052 is OK
- 10.1371/journal.pcbi.1009472 is OK
- 10.1109/TNNLS.2020.3042395 is OK
- 10.1007/s11222-022-10090-6 is OK
- 10.7717/peerj-cs.55 is OK
- 10.21105/joss.04304 is OK
- 10.1016/j.jedc.2021.104082 is OK
- 10.1190/geo2022-0472.1 is OK
- 10.1016/j.jocm.2023.100418 is OK
- 10.2514/6.2022-0631 is OK
- PhysRevE.106.055311 is OK
- 10.1038/s41562-021-01282-7 is OK
- 10.20982/tqmp.16.2.p120 is OK
- 10.1007/s13349-022-00638-5 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot 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:

osorensen commented 1 year ago

@marvinschmitt

At this point could you:

[ ] Make a tagged release of your software, and list the version tag of the archived version here.
[ ] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[ ] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[ ] Please list the DOI of the archived version here.

I can then move forward with recommending acceptance of the submission.

osorensen commented 1 year ago

@marvinschmitt, how is it going with the final steps outlined in my previous post?

marvinschmitt commented 1 year ago

@osorensen Thanks for checking in.

We are currently double-checking large parts of the package and making quality-of-life improvements such as unifying keywords across functions and modules for the tagged release.

We expect to complete the final steps within the week. Does that work for you?

osorensen commented 1 year ago

Thanks for responding @marvinschmitt, that works very well. No need to rush :-)

marvinschmitt commented 1 year ago

@osorensen Here we go, thanks for your patience :-)

Tagged release: JOSS (v1.1.4) [Link]
DOI: 10.5281/zenodo.8346393 [Link]

osorensen commented 1 year ago

@editorialbot set v1.1.4 as version

editorialbot commented 1 year ago

Done! version is now v1.1.4

osorensen commented 1 year ago

@editorialbot set 10.5281/zenodo.8346393 as archive

editorialbot commented 1 year ago

Done! archive is now 10.5281/zenodo.8346393

osorensen commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.18637/jss.v100.i07 is OK
- 10.21468/SciPostPhys.10.6.126 is OK
- 10.1007/s42113-023-00167-4 is OK
- 10.3390/s22145408 is OK
- 10.1109/TNNLS.2021.3124052 is OK
- 10.1371/journal.pcbi.1009472 is OK
- 10.1109/TNNLS.2020.3042395 is OK
- 10.1007/s11222-022-10090-6 is OK
- 10.7717/peerj-cs.55 is OK
- 10.21105/joss.04304 is OK
- 10.1016/j.jedc.2021.104082 is OK
- 10.1190/geo2022-0472.1 is OK
- 10.1016/j.jocm.2023.100418 is OK
- 10.2514/6.2022-0631 is OK
- PhysRevE.106.055311 is OK
- 10.1038/s41562-021-01282-7 is OK
- 10.20982/tqmp.16.2.p120 is OK
- 10.1007/s13349-022-00638-5 is OK
- 10.1038/s41598-023-40278-3 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.

Element doi: [facet 'pattern'] The value 'PhysRevE.106.055311' is not accepted by the pattern '10\.[0-9]{4,9}/.{1,200}'.

osorensen commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.18637/jss.v100.i07 is OK
- 10.21468/SciPostPhys.10.6.126 is OK
- 10.1007/s42113-023-00167-4 is OK
- 10.3390/s22145408 is OK
- 10.1109/TNNLS.2021.3124052 is OK
- 10.1371/journal.pcbi.1009472 is OK
- 10.1109/TNNLS.2020.3042395 is OK
- 10.1007/s11222-022-10090-6 is OK
- 10.7717/peerj-cs.55 is OK
- 10.21105/joss.04304 is OK
- 10.1016/j.jedc.2021.104082 is OK
- 10.1190/geo2022-0472.1 is OK
- 10.1016/j.jocm.2023.100418 is OK
- 10.2514/6.2022-0631 is OK
- PhysRevE.106.055311 is OK
- 10.1038/s41562-021-01282-7 is OK
- 10.20982/tqmp.16.2.p120 is OK
- 10.1007/s13349-022-00638-5 is OK
- 10.1038/s41598-023-40278-3 is OK

MISSING DOIs

- None

INVALID DOIs

- None

osorensen commented 1 year ago

@openjournals/dev, could you please help with the error message I get when recommending acceptance?

danielskatz commented 1 year ago

The doi field should be 10.1103/PhysRevE.106.055311 - not just PhysRevE.106.055311

osorensen commented 1 year ago

Thanks @danielskatz. @marvinschmitt could you please update the doi field in your bib file?

marvinschmitt commented 1 year ago

@osorensen @danielskatz thank you for tracking down that issue, we appreciate it. I have updated the doi field of that bib entry.

osorensen commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.18637/jss.v100.i07 is OK
- 10.21468/SciPostPhys.10.6.126 is OK
- 10.1007/s42113-023-00167-4 is OK
- 10.3390/s22145408 is OK
- 10.1109/TNNLS.2021.3124052 is OK
- 10.1371/journal.pcbi.1009472 is OK
- 10.1109/TNNLS.2020.3042395 is OK
- 10.1007/s11222-022-10090-6 is OK
- 10.7717/peerj-cs.55 is OK
- 10.21105/joss.04304 is OK
- 10.1016/j.jedc.2021.104082 is OK
- 10.1190/geo2022-0472.1 is OK
- 10.1016/j.jocm.2023.100418 is OK
- 10.2514/6.2022-0631 is OK
- 10.1103/PhysRevE.106.055311 is OK
- 10.1038/s41562-021-01282-7 is OK
- 10.20982/tqmp.16.2.p120 is OK
- 10.1007/s13349-022-00638-5 is OK
- 10.1038/s41598-023-40278-3 is OK

MISSING DOIs

- None

INVALID DOIs

- None

osorensen commented 1 year ago

@editorialbot recommend-accept

openjournals / joss-reviews

[REVIEW]: BayesFlow: Amortized Bayesian Workflows With Neural Networks #5702

Status

Reviewer instructions & questions

Checklists

Review checklist for @sandeshkatakam

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @LoryPack

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance