[REVIEW]: gdess: A framework for evaluating simulated atmospheric CO~2~ in Earth System Models

[editorialbot]

Submitting author: @dkauf42 (Daniel E Kaufman)
Repository: https://github.com/E3SM-Project/gdess
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @dhhagan
Reviewers: @slayoo, @simonom
Archive: 10.5281/zenodo.6981643

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/6cc7ba8d3c09f66974550161f740e176/status.svg)](https://joss.theoj.org/papers/6cc7ba8d3c09f66974550161f740e176)

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

@slayoo & @sridge & @simonom, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @dhhagan 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 @sridge

📝 Checklist for @simonom

📝 Checklist for @slayoo

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.22 s (310.2 files/s, 46353.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          53           1503           2142           4122
TeX                              1              0              0            350
Markdown                         2             88              2            294
JSON                             2              3              0            102
YAML                             2             12             23             95
Jupyter Notebook                 3              0           1157             50
Bourne Shell                     3             12             22             24
INI                              1              2              0              9
-------------------------------------------------------------------------------
SUM:                            67           1620           3346           5046
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1679

[editorialbot]

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

OK DOIs

- 10.25925/20200903 is OK
- 10.1111/gcb.15409 is OK
- 10.1029/2018MS001603 is OK
- 10.5334/jors.148 is OK
- 10.1175/BAMS-D-13-00080.1 is OK
- 10.1029/2019MS001766 is OK
- 10.5194/acp-19-14233-2019 is OK
- 10.1029/2018MS001354 is OK
- 10.3402/tellusb.v51i2.16286 is OK
- 10.5194/gmd-9-1747-2016 is OK
- 10.5194/gmd-9-1937-2016 is OK
- 10.5194/gmd-13-3383-2020 is OK
- 10.3390/atmos9050175 is OK
- 10.1175/JCLI-D-12-00589.1 is OK
- 10.5194/bg-14-1383-2017 is OK
- 10.5194/essd-6-375-2014 is OK
- 10.1002/2014JD022411 is OK
- 10.1175/amsmonographs-d-18-0018.1 is OK
- 10.1029/2019MS001629 is OK
- 10.1029/2018GB006086 is OK
- 10.1126/science.1137004 is OK
- 10.1002/2014JD022591 is OK
- 10.1029/JD094iD06p08549 is OK
- 10.5194/acp-21-9609-2021 is OK
- 10.1016/j.jhydrol.2020.125553 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.1175/1520-0469(1983)0400303:OTROTS2.0.CO2 is INVALID

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[simonom]

Review checklist for @simonom

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/E3SM-Project/gdess?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@dkauf42) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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?
• 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).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality 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

Software paper

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

[sridge]

Review checklist for @sridge

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/E3SM-Project/gdess?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@dkauf42) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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?
• 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).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality 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

Software paper

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

[slayoo]

Review checklist for @slayoo

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/E3SM-Project/gdess?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@dkauf42) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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?
• 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).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality 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

Software paper

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

[slayoo]

@dkauf42, re the following requirement:

Does the full list of paper authors seem appropriate and complete?

According to https://github.com/E3SM-Project/gdess/graphs/contributors, you are the only code contributor. I suggest thus adding to the paper an "Author contributions" section commenting on each authors' contributions. See also https://joss.readthedocs.io/en/latest/submitting.html#authorship

[slayoo]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[dkauf42]

@dkauf42, re the following requirement:

Does the full list of paper authors seem appropriate and complete?

According to https://github.com/E3SM-Project/gdess/graphs/contributors, you are the only code contributor. I suggest thus adding to the paper an "Author contributions" section commenting on each authors' contributions. See also https://joss.readthedocs.io/en/latest/submitting.html#authorship

Yes, I can see how this needs clarification. An "author contributions" section has now been added (in PR: E3SM-Project/gdess#7).

[slayoo]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[slayoo]

@dkauf42 Isn't there a naming mismatch here? JOSS paper and the GitHub repo is named gdess. The README.md mentions pip uninstall co2_diag but the setup.cfg file lists name = e3sm_co2_diag. All three names seem to be available on pypi.org. Why not to stick to one & register it and upload to PyPI (and adjust setup.cfg and README.md accordingly?

[dkauf42]

@slayoo We agree that the name discrepancies present some confusion, and these have now been resolved with PR: E3SM-Project/gdess#8.

We understand the appeal of having gdess available via PyPI, and we spent time exploring its utility through PyPI. In the end, we decided to refrain from creating a Python distribution package, because that shifts focus and utility away from the notebooks and command-line interface, which is a primary means of interacting with the software and a focus of the JOSS manuscript.

[simonom]

@dkauf42, regarding the substantial scholarly effort section of the review.

The ESMValTool is rightly referenced in the statement of need in the paper. And its overarching objective appears to be the same as gdess, which means the benefit of gdess (over ESMValTool) lies in the details (but tell me if I'm wrong on this).

The distinction between the two software packages is stated in the gdess paper (Statement of need section) as: '—but does not provide for tailored processing of varied CO2 data sources'. From this statement I cannot tell the benefit of gdess over ESMValTool.

Although I appreciate the need for concision in the JOSS paper, I recommend that the advantage of gdess over ESMValTool be expanded in the Statement of need, so that it is clearer.

[slayoo]

Here is some more feedback on the installation instructions:

• worth mentioning that the conda steps are optional, and one can use the package without conda
• the conda install --file requirements.txt seem unneeded now that setup.cfg contains the dependency info
• the "To run the tests..." subsection does not contain any information on how to run the tests - just test data retrieval
• there are two broken links in the "Examples" section (under "configuration" and "installation")

[dkauf42]

@dkauf42, regarding the substantial scholarly effort section of the review.

The ESMValTool is rightly referenced in the statement of need in the paper. And its overarching objective appears to be the same as gdess, which means the benefit of gdess (over ESMValTool) lies in the details (but tell me if I'm wrong on this).

The distinction between the two software packages is stated in the gdess paper (Statement of need section) as: '—but does not provide for tailored processing of varied CO2 data sources'. From this statement I cannot tell the benefit of gdess over ESMValTool.

Although I appreciate the need for concision in the JOSS paper, I recommend that the advantage of gdess over ESMValTool be expanded in the Statement of need, so that it is clearer.

@simonom, to help clarify the distinction between these software packages, we've revised and added text to the 2nd paragraph of the 'statement of need' section (commit 64a80ff). The revised text reads:

"For example, the ESM Evaluation Tool (ESMValTool; @Eyring2016c; @Eyring2020b) has been used to generate specific figures from the literature, and we adopted the term recipe from its use by ESMValTool. Although ESMValTool includes a comparison of column-averaged CO₂ values as performed by Gier et al. (2020), gdess was created to provide specific CO₂ diagnostic methods and graphs that are not already provided as recipes in ESMValTool. gdess uses Observation Package (Obspack; @globalview20200911; @Masarie2014b) data, which include atmospheric greenhouse gas observations from a variety of sampling platforms and data providers following the World Data Centre for Greenhouse Gases (WDCGG) protocol, so are widely used for stimulating and supporting carbon cycle modeling studies. These data have not been set up for use within ESMValTool, and as such would require additional development/configuration to work with ESMValTool."

[dkauf42]

Here is some more feedback on the installation instructions:

• (a) worth mentioning that the conda steps are optional, and one can use the package without conda
• (b) the conda install --file requirements.txt seem unneeded now that setup.cfg contains the dependency info
• (c) the "To run the tests..." subsection does not contain any information on how to run the tests - just test data retrieval
• (d) there are two broken links in the "Examples" section (under "configuration" and "installation")

@slayoo, we appreciate the detailed feedback, and here respond to each of these points:

• (a) We have repeatedly run into errors installing cartopy, one of gdess's dependencies, with just 'pip' and 'setup.cfg'. Installing dependencies via conda has enabled us to avoid this issue, and that is why we have kept the conda instructions in the readme.
• (b) We understand that this seems a bit redundant. Although we would like to reduce duplication to a minimum, we have kept this step in the README for the same reason as in point (a) above.
• (c) This is a good point. To avoid further confusion, we have created a separate "Running the code tests" section in the readme, and clarified the language in the installation section (see commit 3e8db1).
• (d) These links have been corrected with commit 8f7ec0.

[dhhagan]

@editorialbot set v1.0.0 as version

[editorialbot]

Done! version is now v1.0.0

[dhhagan]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.25925/20200903 is OK
- 10.1111/gcb.15409 is OK
- 10.1029/2018MS001603 is OK
- 10.5334/jors.148 is OK
- 10.1175/BAMS-D-13-00080.1 is OK
- 10.1029/2019MS001766 is OK
- 10.5194/acp-19-14233-2019 is OK
- 10.1029/2018MS001354 is OK
- 10.3402/tellusb.v51i2.16286 is OK
- 10.5194/gmd-9-1747-2016 is OK
- 10.5194/gmd-9-1937-2016 is OK
- 10.5194/gmd-13-3383-2020 is OK
- 10.3390/atmos9050175 is OK
- 10.1175/JCLI-D-12-00589.1 is OK
- 10.5194/bg-14-1383-2017 is OK
- 10.5194/essd-6-375-2014 is OK
- 10.1002/2014JD022411 is OK
- 10.1175/amsmonographs-d-18-0018.1 is OK
- 10.1029/2019MS001629 is OK
- 10.1029/2018GB006086 is OK
- 10.1126/science.1137004 is OK
- 10.1175/1520-0469(1983)040<0303:OTROTS>2.0.CO;2 is OK
- 10.1002/2014JD022591 is OK
- 10.1029/JD094iD06p08549 is OK
- 10.5194/acp-21-9609-2021 is OK
- 10.1016/j.jhydrol.2020.125553 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

⚠️ Error prepararing paper acceptance. The generated XML metadata file is invalid.

Element isbn: [facet 'minLength'] The value has a length of '9'; this underruns the allowed minimum length of '10'.

[dkauf42]

@dhhagan, I saw this error a few minutes ago, and I think it's because there was an ISBN listed for Sweeney et al. (2015) in the ".bib" file that shouldn't have been there. I just removed it and pushed the change to the main branch.
Can we try this process again?

[dhhagan]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.25925/20200903 is OK
- 10.1111/gcb.15409 is OK
- 10.1029/2018MS001603 is OK
- 10.5334/jors.148 is OK
- 10.1175/BAMS-D-13-00080.1 is OK
- 10.1029/2019MS001766 is OK
- 10.5194/acp-19-14233-2019 is OK
- 10.1029/2018MS001354 is OK
- 10.3402/tellusb.v51i2.16286 is OK
- 10.5194/gmd-9-1747-2016 is OK
- 10.5194/gmd-9-1937-2016 is OK
- 10.5194/gmd-13-3383-2020 is OK
- 10.3390/atmos9050175 is OK
- 10.1175/JCLI-D-12-00589.1 is OK
- 10.5194/bg-14-1383-2017 is OK
- 10.5194/essd-6-375-2014 is OK
- 10.1002/2014JD022411 is OK
- 10.1175/amsmonographs-d-18-0018.1 is OK
- 10.1029/2019MS001629 is OK
- 10.1029/2018GB006086 is OK
- 10.1126/science.1137004 is OK
- 10.1175/1520-0469(1983)040<0303:OTROTS>2.0.CO;2 is OK
- 10.1002/2014JD022591 is OK
- 10.1029/JD094iD06p08549 is OK
- 10.5194/acp-21-9609-2021 is OK
- 10.1016/j.jhydrol.2020.125553 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3482, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[arfon]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04326 joss-papers#3484
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04326
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[arfon]

@slayoo, @simonom – many thanks for your reviews here and to @dhhagan for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@dkauf42 – your paper is now accepted and published in JOSS ⚡🚀💥

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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[slayoo]

Hello, @dhhagan, @dkauf42, @arfon!
We have a problem here with the LaTeX tilde visible in the paper title on the JOSS website.

Also in "citation string":

Same in BiBTeX metadata.

And on Twitter:

[dkauf42]

I'm not sure what to suggest for this. The tildes were used to render the subscript appropriately in the paper.md markdown file.
Perhaps there needs to be additional text parsing in the automated process for generating webpage/BiBTeX/twitter text?

[arfon]

These should be fixed now.