[REVIEW]: pyABC: Efficient and robust easy-to-use approximate Bayesian computation

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@yannikschaelte@osorensen<!--end-editor-- Reviewers: @mattpitkin, @hpesonen, @blakeaw Archive: 10.5281/zenodo.6677826

Status

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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

@mattpitkin & @hpesonen, 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 @mattpitkin

📝 Checklist for @blakeaw

📝 Checklist for @hpesonen

editorialbot commented 2 years ago

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editorialbot commented 2 years ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.66 s (420.1 files/s, 79949.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         174           5425           8799          18305
Jupyter Notebook                23              0          10743           2310
SVG                             11              6              6           1831
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TeX                              1             50              0            562
YAML                             6             75             16            339
HTML                             7             33              0            288
INI                              2             38              0            221
make                             1             29              6            181
XML                              1              1              1            152
Markdown                         4             31              0            124
Bourne Shell                     2             19             22             99
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Mako                             1              7              0             17
TOML                             1              3              3             14
-------------------------------------------------------------------------------
SUM:                           277           6638          20000          26073
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gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

Wordcount for paper.md is 1329

editorialbot commented 2 years ago

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

OK DOIs

- 10.1126/science.1069492 is OK
- 10.1093/genetics/145.2.505 is OK
- 10.1038/nrg2509 is OK
- 10.1016/j.cels.2016.12.002 is OK
- 10.1214/07-AOS574 is OK
- 10.1002/jae.3950080507 is OK
- 10.1080/10618600.2017.1302882 is OK
- 10.1093/oxfordjournals.molbev.a026091 is OK
- 10.1093/genetics/162.4.2025 is OK
- 10.1073/pnas.0607208104 is OK
- 10.1111/j.1467-9868.2006.00553.x is OK
- 10.1145/3093172.3093233 is OK
- 10.1093/bioinformatics/btaa078 is OK
- 10.1111/2041-210X.12050 is OK
- 10.1093/bioinformatics/bty361 is OK
- 10.1515/sagmb-2012-0069 is OK
- 10.1007/978-3-319-67471-1_8 is OK
- 10.1038/s41467-019-09879-3 is OK
- 10.1371/journal.pcbi.1009149 is OK
- 10.7554/eLife.56265 is OK
- 10.1038/s41586-021-03965-7 is OK
- 10.1063/5.0010764 is OK
- 10.1101/2022.02.10.479738 is OK
- 10.7554/eLife.55665 is OK
- 10.1088/1475-7516/2021/08/027 is OK
- 10.1016/j.compbiomed.2018.10.015 is OK
- 10.1002/eap.2442 is OK
- 10.1101/2021.07.29.454327 is OK
- 10.1214/16-BA1002 is OK
- 10.1214/12-STS406 is OK
- 10.1111/j.1467-9868.2011.01010.x is OK
- 10.5705/ss.202015.0340 is OK
- 10.1016/j.jcp.2020.109999 is OK
- 10.1101/2022.03.18.484896 is OK
- 10.1515/sagmb-2013-0010 is OK
- 10.1093/bioinformatics/btaa397 is OK
- 10.1111/rssb.12312 is OK
- 10.1515/sagmb-2012-0043 is OK
- 10.1111/j.1541-0420.2010.01410.x is OK
- 10.1137/141000671 is OK
- 10.1093/bioinformatics/btl485 is OK
- 10.1371/journal.pcbi.1008646 is OK
- 10.1093/bioinformatics/btab227 is OK
- 10.1093/bioinformatics/btp619 is OK

MISSING DOIs

- 10.1137/1.9780898717921 may be a valid DOI for title: Inverse Problem Theory and Methods for Model Parameter Estimation

INVALID DOIs

- None

editorialbot 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:

mattpitkin commented 2 years ago

Review checklist for @mattpitkin

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/icb-dcm/pyabc?
[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 (@yannikschaelte) 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

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 and who the target audience is?
[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 2 years ago

@editorialbot add @blakeaw as reviewer

editorialbot commented 2 years ago

@blakeaw added to the reviewers list!

blakeaw commented 2 years ago

Review checklist for @blakeaw

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/icb-dcm/pyabc?
[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 (@yannikschaelte) 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

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 and who the target audience is?
[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?

mattpitkin commented 2 years ago

I have reviewed the paper, documentation and examples and it all looks good to me. I'm happy to sign-off the review from me.

osorensen commented 2 years ago

Thanks for your review @mattpitkin!

osorensen commented 2 years ago

@hpesonen and @blakeaw, could you please update us on how it is going with your reviews? Please let me know if you have any questions, and I'll do my best to help.

blakeaw commented 2 years ago

Hi @osorensen, sorry for the delay. I'm pretty close to finishing up my review, so I'll try to go ahead and complete it today.

hpesonen commented 2 years ago

@osorensen I should be done by tomorrow.

osorensen commented 2 years ago

Thanks for the quick reply both of you!

blakeaw commented 2 years ago

Hi @osorensen, I have completed my review.

Overall, I think the submission looks good and can proceed with minor revisions. I raised one issue regarding the automated tests and I had one minor comment about the Software paper:

hpesonen commented 2 years ago

Review checklist for @hpesonen

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/icb-dcm/pyabc?
[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 (@yannikschaelte) 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

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 and who the target audience is?
[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?

hpesonen commented 2 years ago

@osorensen Hi! I've finished the review. Submissions looks good, I've asked for only minor revisions in https://github.com/ICB-DCM/pyABC/issues/570

I also agree with https://github.com/ICB-DCM/pyABC/issues/566

osorensen commented 2 years ago

Thanks @hpesonen!

@yannikschaelte, please let us know when you have addressed the issues raised by the reviewer.

yannikschaelte commented 2 years ago

Hi @osorensen , I am currently off for two more weeks. I would address the issues as soon as I'm back then, if that's fine? Thanks all already for the very constructive feedback!

osorensen commented 2 years ago

Yes @yannikschaelte, that's fine. And thanks a lot for notifying

osorensen commented 2 years ago

@yannikschaelte, could you please update us on how it is going addressing the points raised by the reviewers?

yannikschaelte commented 2 years ago

Hi, yes! Sorry, I have been off + finishing my PhD, but will work on the revision now!

yannikschaelte commented 2 years ago

Dear all, I have now addressed the raised issues https://github.com/ICB-DCM/pyABC/issues/565 and https://github.com/ICB-DCM/pyABC/issues/566 (the latter so far only as a pull request in https://github.com/ICB-DCM/pyABC/pull/577).

osorensen commented 2 years ago

Thanks @yannikschaelte! If this addresses your points, please update your review checklists @blakeaw and @hpesonen.

hpesonen commented 2 years ago

Hi @osorensen and @yannikschaelte! I've updated my checklist and I've checked the State of the field box based on https://github.com/ICB-DCM/pyABC/pull/577

I also had few minor comments on https://github.com/ICB-DCM/pyABC/issues/570 that I hope would be addressed before checking the final box.

yannikschaelte commented 2 years ago

Hi @hpesonen , thanks for your further very useful feedback. I hope to have addressed these comments in https://github.com/ICB-DCM/pyABC/pull/578 now!

hpesonen commented 2 years ago

Hi @yannikschaelte and @osorensen - I've reviewed the latest changes and I'm happy to check all the boxes on the checklist!

p.s. The comment above links to the issue 578 on JOSS-reviews

yannikschaelte commented 2 years ago

p.s. The comment above links to the issue 578 on JOSS-reviews

Ah, of course. Changed it!

yannikschaelte commented 2 years ago

@editorialbot generate pdf

editorialbot 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:

osorensen commented 2 years ago

Thanks a lot for your quick responses @hpesonen and @yannikschaelte

blakeaw commented 2 years ago

Hi, @osorensen and @yannikschaelte. I have also reviewed the latest changes now and have completed my checklist. Thanks!

osorensen commented 2 years ago

Thanks @blakeaw!

osorensen commented 2 years ago

@yannikschaelte I will now read through the paper once more and get back to you if I have any suggested edits.

In the meantime, could you:

[x] Make a tagged release of your software, and list the version tag of the archived version here.
[x] 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.
[x] Please list the DOI of the archived version here.

yannikschaelte commented 2 years ago

Hi @osorensen , I should have addressed all points:

Tagged version: https://github.com/ICB-DCM/pyABC/releases/tag/0.12.5
ZENODO archive: https://doi.org/10.5281/zenodo.6677826

osorensen commented 2 years ago

@editorialbot help

editorialbot commented 2 years ago

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


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@editorialbot check references

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@editorialbot set v1.0.0 as version

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osorensen commented 2 years ago

@editorialbot set 10.5281/zenodo.6677826 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.6677826

osorensen commented 2 years ago

@editorialbot set 0.12.5 as version

editorialbot commented 2 years ago

Done! version is now 0.12.5

osorensen commented 2 years ago

@editorialbot generate pdf

editorialbot 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:

osorensen commented 2 years ago

@yannikschaelte can you please update the Zenodo archive so its title exactly matches the paper title? That is, remove the prefix "Supplementary code to" so it becomes only "pyABC: Efficient and robust easy-to-use approximate Bayesian computation".

osorensen commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.1126/science.1069492 is OK
- 10.1093/genetics/145.2.505 is OK
- 10.1038/nrg2509 is OK
- 10.1016/j.cels.2016.12.002 is OK
- 10.1214/07-AOS574 is OK
- 10.1002/jae.3950080507 is OK
- 10.1080/10618600.2017.1302882 is OK
- 10.1093/oxfordjournals.molbev.a026091 is OK
- 10.1093/genetics/162.4.2025 is OK
- 10.1073/pnas.0607208104 is OK
- 10.1111/j.1467-9868.2006.00553.x is OK
- 10.1145/3093172.3093233 is OK
- 10.1093/bioinformatics/btaa078 is OK
- 10.1111/2041-210X.12050 is OK
- 10.1093/bioinformatics/bty361 is OK
- 10.1515/sagmb-2012-0069 is OK
- 10.1007/978-3-319-67471-1_8 is OK
- 10.1038/s41467-019-09879-3 is OK
- 10.1371/journal.pcbi.1009149 is OK
- 10.7554/eLife.56265 is OK
- 10.1038/s41586-021-03965-7 is OK
- 10.1063/5.0010764 is OK
- 10.1101/2022.02.10.479738 is OK
- 10.7554/eLife.55665 is OK
- 10.1088/1475-7516/2021/08/027 is OK
- 10.1016/j.compbiomed.2018.10.015 is OK
- 10.1002/eap.2442 is OK
- 10.1101/2021.07.29.454327 is OK
- 10.1214/16-BA1002 is OK
- 10.1214/12-STS406 is OK
- 10.1111/j.1467-9868.2011.01010.x is OK
- 10.5705/ss.202015.0340 is OK
- 10.1016/j.jcp.2020.109999 is OK
- 10.1101/2022.03.18.484896 is OK
- 10.1515/sagmb-2013-0010 is OK
- 10.1093/bioinformatics/btaa397 is OK
- 10.1111/rssb.12312 is OK
- 10.1515/sagmb-2012-0043 is OK
- 10.1111/j.1541-0420.2010.01410.x is OK
- 10.1137/141000671 is OK
- 10.1093/bioinformatics/btl485 is OK
- 10.1371/journal.pcbi.1008646 is OK
- 10.1093/bioinformatics/btab227 is OK
- 10.1093/bioinformatics/btp619 is OK

MISSING DOIs

- None

INVALID DOIs

- None

yannikschaelte commented 2 years ago

@yannikschaelte can you please update the Zenodo archive so its title exactly matches the paper title? That is, remove the prefix "Supplementary code to" so it becomes only "pyABC: Efficient and robust easy-to-use approximate Bayesian computation".

Sure, changed it!

osorensen commented 2 years ago

@yannikschaelte please also make sure that Scott A Sisson's name is spelled consistently in the references:

yannikschaelte commented 2 years ago

@editorialbot generate pdf

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