[REVIEW]: The Basic Model Interface 2.0: A standard interface for coupling numerical models in the geosciences

whedon commented 4 years ago

Submitting author: @mdpiper (MARK PIPER) Repository: https://github.com/csdms/bmi Version: v2.0 Editor: @diehlpk Reviewer: @yangbai90, @teuben Archive: 10.5281/zenodo.3955010

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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

@yangbai90 & @teuben, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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

✨ Please try and complete your review in the next six weeks ✨

Review checklist for @yangbai90

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 repository url?
[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 (@mdpiper) 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 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: Do the authors clearly state 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?

Review checklist for @teuben

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 repository url?
[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 (@mdpiper) 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 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: Do the authors clearly state 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?

whedon commented 4 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @yangbai90, @teuben it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

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whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.1029/2018JF004757 is OK

MISSING DOIs

- https://doi.org/10.1177/1094342011414036 may be missing for title: High-performance language interoperability for scientific computing through Babel
- https://doi.org/10.5194/nhess-19-1723-2019 may be missing for title: Evaluating the impact of model complexity on flood wave propagation and inundation extent with a hydrologic-hydrodynamic model coupling framework
- https://doi.org/10.1016/j.cageo.2012.04.002 may be missing for title: A component-based approach to integrated modeling in the geosciences: The design of CSDMS

INVALID DOIs

- None

whedon commented 4 years ago

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

mdpiper commented 4 years ago

A quick note: in a pre-submission issue, editors suggested this submission be reviewed in the context of the language specifications and examples derived from the interface defined in the main repository.

yangbai90 commented 4 years ago

Hi @mdpiper , I checked your repository. It seems the source code of bmi can't be download via git clone, instead, one can only get the source code from the release page. Is it correct?

mdpiper commented 4 years ago

Hi @yangbai90 -- All source is on GitHub, and can be cloned. Note that the only contents of the main repo are documentation and an interface definition file. Source for language specifications derived from the interface are in separate repos listed in the README.

diehlpk commented 4 years ago

@mdpiper Are these listed in the JOSS paper as well? If, not would it be possible to add them?

mdpiper commented 4 years ago

@diehlpk Yup! See Table 1 in the paper.

diehlpk commented 4 years ago

@yangbai90 Can you please confirm that you finished your review? It seems that you have ticked all boxes.

yangbai90 commented 4 years ago

Hi @diehlpk, on my side, the paper is ready for publishing.

diehlpk commented 4 years ago

Hi @yangbai90 thanks for your effort supporting JOSS :)

diehlpk commented 4 years ago

@teuben How is your review going?

teuben commented 4 years ago

I hope to finish this by tomorrow.

On Fri, Jun 26, 2020, 16:32 Patrick Diehl notifications@github.com wrote:

@teuben https://github.com/teuben How is your review going?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/2317#issuecomment-650386756, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAZ4MGODFTEDJ4YX46BLLRTRYUAVLANCNFSM4NZRAPUA .

diehlpk commented 4 years ago

@teuben Thanks for the update.

mdpiper commented 4 years ago

Hi @teuben, I think we've addressed your comments in https://github.com/csdms/bmi/issues/68, https://github.com/csdms/bmi/issues/69, and https://github.com/csdms/bmi/issues/70. When you have time, would you please check the open PRs listed under each issue? If they pass muster, I'll merge the PRs and close the issues.

teuben commented 4 years ago

so done! I am finished with my review (with my apologies as google decided to count all my joss emails as spam)

diehlpk commented 4 years ago

@teuben Thanks.

diehlpk commented 4 years ago

@mdpiper I will do the final review on the paper by the end of this week. After that

When a submission is ready to be accepted, we ask that the authors issue a new tagged release of the software (if changed), and archive it (on Zenodo, figshare, or other). The authors then post the version number and archive DOI in the REVIEW issue.

diehlpk commented 4 years ago

@mdpiper

State of the field: Do the authors describe how this software compares to other commonly-used packages?

The reviewers agreed on this, however, I am as not as deeply in the topic would prefer if you can highlight this point in the paper a little more. So a broader audience can see this point.

Everything else is fine. After this point is improved, you can start to generate the archive and update the version including the two new pull requests.

mdpiper commented 4 years ago

@diehlpk Thanks for your editorial review. I'll add some text to this point. And another thank you--this a good point to make considering model coupling is decades old in, e.g., atmospheric sciences, but still relatively new in the geosciences.

diehlpk commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

mdpiper commented 4 years ago

@diehlpk Waiting on my coauthors to review my changes...

diehlpk commented 4 years ago

@mdpiper Any news from your crew?

mdpiper commented 4 years ago

@diehlpk Waiting on one. We have a meeting this aft; I'll nudge him then.

mdpiper commented 4 years ago

@diehlpk Nudging successful! The updated paper text, with a broader introduction, is in the mdpiper/paper branch. If you're OK with the changes, I'll follow your instructions upthread for finalizing the submission.

mdpiper commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

mdpiper commented 4 years ago

@whedon generate pdf from branch mdpiper/paper

whedon commented 4 years ago

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

whedon commented 4 years ago

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

diehlpk commented 4 years ago

@mdpiper The addition to the paper is sufficient and I can recommend the paper for acceptance.

Next steps are:

When a submission is ready to be accepted, we ask that the authors issue a new tagged release of the software (if changed), and archive it (on Zenodo, figshare, or other). The authors then post the version number and archive DOI in the REVIEW issue.

mdpiper commented 4 years ago

@diehlpk version: v2.0, doi: 10.5281/zenodo.3955010

On Zenodo: Basic Model Interface 2.0

diehlpk commented 4 years ago

@whedon generate pdf

diehlpk commented 4 years ago

@whedon check references

whedon commented 4 years ago

PDF failed to compile for issue #2317 with the following error:

sh: 0: getcwd() failed: No such file or directory pandoc: 10.21105.joss.02317.pdf: openBinaryFile: does not exist (No such file or directory) Looks like we failed to compile the PDF

whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.1029/2018JF004757 is OK

MISSING DOIs

- https://doi.org/10.1177/1094342005056120 may be missing for title: Design and implementation of components in the Earth System Modeling Framework
- https://doi.org/10.1177/1094342011414036 may be missing for title: High-performance language interoperability for scientific computing through Babel
- https://doi.org/10.5194/nhess-19-1723-2019 may be missing for title: Evaluating the impact of model complexity on flood wave propagation and inundation extent with a hydrologic-hydrodynamic model coupling framework
- https://doi.org/10.1016/j.cageo.2012.04.002 may be missing for title: A component-based approach to integrated modeling in the geosciences: The design of CSDMS

INVALID DOIs

- None

diehlpk commented 4 years ago

@whedon set 10.5281/zenodo.3955010 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.3955010 is the archive.

diehlpk commented 4 years ago

@whedon set v2.0 as version

whedon commented 4 years ago

OK. v2.0 is the version.

diehlpk commented 4 years ago

@whedon generate pdf from branch mdpiper/paper

whedon commented 4 years ago

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

whedon commented 4 years ago

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

diehlpk commented 4 years ago

@mdpiper Can you please check this version of the paper as the final version? After you confirmed I will pass the paper to the EICs. We like to avoid to do some after publication changes.

mdpiper commented 4 years ago

@diehlpk The rendered PDF is correct; however, I merged the mdpiper/paper branch into master earlier this morning. (I'm not sure if this is important, but I want to check.)

diehlpk commented 4 years ago

@whedon accept

whedon commented 4 years ago

Attempting dry run of processing paper acceptance...

whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.1029/2018JF004757 is OK

MISSING DOIs

- https://doi.org/10.1177/1094342005056120 may be missing for title: Design and implementation of components in the Earth System Modeling Framework
- https://doi.org/10.1177/1094342011414036 may be missing for title: High-performance language interoperability for scientific computing through Babel
- https://doi.org/10.5194/nhess-19-1723-2019 may be missing for title: Evaluating the impact of model complexity on flood wave propagation and inundation extent with a hydrologic-hydrodynamic model coupling framework
- https://doi.org/10.1016/j.cageo.2012.04.002 may be missing for title: A component-based approach to integrated modeling in the geosciences: The design of CSDMS

INVALID DOIs

- None

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/1586

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1586, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

openjournals / joss-reviews