[REVIEW]: lpjmlkit: A toolkit for operating LPJmL and model-specific data processing
editorialbot opened this issue · 89 comments
Submitting author: @jnnsbrr (Jannes Breier)
Repository: https://github.com/PIK-LPJmL/lpjmlkit
Branch with paper.md (empty if default branch): JOSS
Version: v1.7.3
Editor: @marcosvital
Reviewers: @tonyewong, @kanishkan91
Archive: 10.5281/zenodo.13884611
Status
Status badge code:
HTML: <a href="https://joss.theoj.org/papers/19419cb26456cff5450b6e3de0f90d11"><img src="https://joss.theoj.org/papers/19419cb26456cff5450b6e3de0f90d11/status.svg"></a>
Markdown: [](https://joss.theoj.org/papers/19419cb26456cff5450b6e3de0f90d11)
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
@egouldo & @tonyewong, 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 @graciellehigino 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
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
Software report:
github.com/AlDanial/cloc v 1.88 T=0.05 s (1473.5 files/s, 287131.5 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
R 57 1346 3333 7095
Markdown 5 178 0 887
JavaScript 2 21 38 502
JSON 6 0 0 423
TeX 1 17 0 268
YAML 4 19 10 151
Rmd 2 137 606 123
make 1 11 7 27
-------------------------------------------------------------------------------
SUM: 78 1729 3994 9476
-------------------------------------------------------------------------------
gitinspector failed to run statistical information for the repository
Wordcount for paper.md is 1896
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.5194/gmd-12-5029-2019 is OK
- 10.1038/s41893-019-0465-1 is OK
- 10.1016/j.jhydrol.2003.09.029 is OK
- 10.1016/j.envsoft.2018.09.004 is OK
- 10.1111/j.1365-2486.2006.01305.x is OK
- 10.5194/gmd-11-429-2018 is OK
- 10.5194/gmd-11-2789-2018 is OK
- 10.5194/gmd-12-1299-2019 is OK
- 10.5194/gmd-12-2419-2019 is OK
- 10.5194/bg-19-957-2022 is OK
- 10.5194/esd-12-1037-2021 is OK
- 10.1371/journal.pbio.1001745 is OK
- 10.1046/j.1365-2486.2003.00569.x is OK
- 10.1038/s41597-022-01710-x is OK
- 10.5194/gmd-11-1343-2018 is OK
- 10.1046/j.1365-2486.2001.00383.x is OK
MISSING DOIs
- None
INVALID DOIs
- None
Review checklist for @tonyewong
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/PIK-LPJmL/lpjmlkit?
- 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 (@jnnsbrr) 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
- 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.
- Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
- 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
- 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, who the target audience is, and its relation to other work?
- 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?
I had a read through the accompanying paper, which is well-written and helpful. I know JOSS papers are supposed to not include too much of the API descriptions, which instead should be in the software documentation on GitHub. I'm not sure but I'm curious whether some areas of the paper might be better left to more extensive documentation in GitHub? For example lines 78-89 or 93-101.
Also related to the paper -- are there other models that can be cited, beyond MAgPIE and LPJ-GUESS, that have a similar focus? Are there other similarities/differences that can be noted in the paper?
Thank you for your comments, @tonyewong !
@jnnsbrr feel free to make edits and reply to the comments anytime. [=
@egouldo did you have a chance to take a look at this submission yet? Let me know if you need anything! [=
Thanks a lot @graciellehigino and @tonyewong!
And yes, @tonyewong, you are right - it should not include too much of the API descriptions as mentioned here. I rather wanted to highlight the key features that define lpjmlkit, so one get a better understanding of what is an LPJmL kit and what is meant by that in R.
I will try to abstract that more and rather give example usages for ongoing research projects instead.
Regarding other models that can be cited - MAgPIE and LPJ-GUESS are both good examples, one from a different discipline, but same research institute (MAgPIE) and one from the same discipline but another research institute (LPJ-GUESS). Both examples have a similar story of how research has been conducted over the last decade and what tools have had to be developed to keep it state of the art. Therefore, I do not believe that adding more examples will contribute to a better understanding of this issue.
Can you also already tick the boxes that can easily be excluded from the scope of this work, such as data sharing and research on humans and animals? 🙂
Please let me know if there is anything else I can do to move this forward.
Many thanks in advance 🙏
Hello all, and apologies for the (big!) delay! We had summer interns starting over the past couple weeks so things were chaotic. But I'm back, and alive, as far as I can tell...!
I'm working on installing and running some tests. Installing goes smoothly (great!) and I see where in the GitHub repository there is a tests directory with relevant output directories too. Are these what the vignettes are referring to in their relative file paths? Can some further instructions be added about how to run some example cases and benchmark tests?
It looks like everything we need is already in the GitHub repo, so this is probably pretty straightforward to do without the user needing to clone the GitHub.
Dear @tonyewong,
thank you! I rewrote the Package features part as promised earlier.
The tests directory ensures all functions work as intended via unit tests with coverage above 90%. As lpjmlkit is just an interface for the LPJmL model, I did not include any data-driven benchmarks.
As global data analysis requires large files to be exchanged this would be rather difficult, if you intended performance benchmarks?
And the vignette for LPJmLData is not written for the data in the tests/output folder but can be used for it (with different results). It instead provides exemplary paths that would be created by simulations using the LPJmL Runner.
I hope that clarifies some points.
Thanks a lot!
Thanks for clarifying!
Can the documentation be clarified to let the reader know exactly how to run some benchmark tests to verify that the software is running as expected? For example, comparing to some standard benchmark output? This does not necessarily need to be global in scale, if it would be easier to do for a reduced spatial domain.
I'm thinking specifically about these three items in the checklist:
- 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?
Thanks again!
Dear @tonyewong,
thanks! I will try to explain it in more detail:
- lpjmlkit follows the standard way of providing example usages via the vignettes, see them also automatically rendered in the r-universe repository for LPJmL Data and for LPJmL Runner - the base for these files are the Rmd files on github - they show common application examples.
- The whole documentation is also automatically rendered at r-universe - still the base for that is the roxygen documentation within each exported function of the package on github also following the standard procedure for R packages
- Automated tests are provided with the unit tests of lpjmlkit, stored in the
./testsfolder. You can run them for example viadevtools::test("<path_to_lpjmlkit>")also following common practices. The Codecov tool provides a good overview how much of the functions is covered by tests: https://app.codecov.io/gh/PIK-LPJmL/lpjmlkit/tree/master/R
Further (script-based) benchmarks are not part of the standard procedure when developing and publishing R packages, see also https://r-pkgs.org/testing-basics.html.
Still you could apply the examples described in the vignettes (mainly LPJmLData) to the data provided in the .tests/testdata/output folder (other outputs), even though these are examples for simulations with only three 0.5° cells.
Or I would have to provide additional data stored in a cloud service so you can test it on a global dataset to get a better visual impression - but I have not seen something like that as a request for a JOSS article (?).
I hope that helps!
Thanks a lot!
Sure, I understand that and that makes sense. What I'm thinking about is including guidance to readers to objectively assess whether the software works once they've installed the package. I don't see anything explicit in the software right now. But what you said as #3 there I think would satisfy the requirements I linked above, with just a mention of that in the README!
Ah - good point - thank you. Citing JOSS ...
Good: An automated test suite hooked up to continuous integration (GitHub Actions, Circle CI, or similar)
See https://github.com/PIK-LPJmL/lpjmlkit#readme > the check badge of the header: This should in theory be "passing", unfortunately the GitHub Actions pipeline (hosted/developed at my Institute) currently has a problem with encodings, which is why it fails (its not the lpjmlkit package - and it did work before). We are currently working on a solution! If you click on the badge, you see that it was passing the check already before: https://github.com/PIK-LPJmL/lpjmlkit/actions
And the check also includes the unit tests of ./tests
Short update: The automated tests are successfull again:
and the patch has just been merged into the JOSS branch 🙂
Hi @egouldo! Are you still available to review this software? Let me know if you're having any problems generating the checklist or if you need more time. [=
Hi all, this review process has gone mute for a month now, is there anything we can do to spark activity again? Or is it just on summer break? 😉
Are you available for reviewing the paper @egouldo?
Ahoy! Yes it's been a busy end to the summer here with internship programs ending, grant deadlines, family trips and so forth. I'm back in the office Monday and should be able to finish quickly! I think your last commit handles the main concern /suggestion that I had. Cheers!
Thanks, folks! I just emailed @egouldo to check in again. I'll get back to looking for other reviewers anyway - the more the merrier!
@editorialbot generate pdf
Hello! Apologies again for the delay, but I think I'm just about converged and done with my review.
The tests, functionality, documentation, etc all look like they're running great! Many thanks again for pointing out where folks can go to see the 0.5-degree small data sets they can use if one wishes to interactively run some tests or play with the code. The vignettes are all great and run smoothly.
The last comment I have is regarding this one:
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
Specifically, #2 and 3 are covered nicely, but there is not a note about #1 yet, at least not that I can see in the top-level README.md file. Can such a note be added? After that I think I can check my last box.
Well done!
I could add a sentence in Documentation & License
Sure, I think that would work. Alternatively, since you have #2 and 3 covered in the "Questions / Problems" section, you could add a statement about contributions there too. Any of these that you find aesthetically pleasing is okay from my end!
Hello! Just an update from my side: I'm looking for other reviewers as @egouldo does not seem to be getting my messages since he accepted to review this submission.
From my point of view, this is looking great and I would accept it for publication right now, but I think we can try to get another reviewer just in case. If we are not successful and it is taking way too long to get a second review, we can try to have it accepted as is. [=
Sure, I think that would work. Alternatively, since you have #2 and 3 covered in the "Questions / Problems" section, you could add a statement about contributions there too. Any of these that you find aesthetically pleasing is okay from my end!
Dear @tonyewong, I just remembered that we already have a sentence for contributions Documentation & License section:
The source code is available on GitHub at
https://github.com/PIK-LPJmL/lpjmlkit,
where users can also report issues and suggest improvements.
Maybe I did not fully understood if you mean the paper or the repository's README . Regarding the README This part of the README is auto generated by an R package software developer team at PIK and follows specific conventions (https://pik-piam.r-universe.dev). Also other iconic R packages do not explicitly mention contributiors.
Right! I saw that in the JOSS paper. What I'm thinking about is in the repository itself, that it would be useful to include guidelines about how to contribute and report problems. Since it's in the paper, maybe this is fine? I don't know whether to interpret JOSS's requirement of this information as requiring it in the repository itself, or just somewhere in either the paper or repository. I'm happy to follow @graciellehigino 's advice on this last review box :)
Hey!
@jnnsbrr the best practice overall is to have a separate document in the repo with details about how to contribute (do we fork and PR? Do we just open an issue? Do we open an issue and link a PR to it? See an example here)
If you can do that, that'd be awesome, but technically we can check that box because you say on the paper that people should refer to the repo and in the repo you have a contact info, which is something and it's useful.
I hope that helps!
Dear @graciellehigino,
after some discussions, we added a CONTRIBUTING.md to the repository to help people who want to contribute to the project. I hope that matches the requirements.
Please let me know if there is anything else standing in the way of publication.
Thanks in advance 🙂
Looks good to me, and my boxes are all checked :)
Hello! Just an update from my side: I'm looking for other reviewers as @egouldo does not seem to be getting my messages since he accepted to review this submission. From my point of view, this is looking great and I would accept it for publication right now, but I think we can try to get another reviewer just in case. If we are not successful and it is taking way too long to get a second review, we can try to have it accepted as is. [=
Dear @graciellehigino, I just wanted to check in and see if we're still working on finding a second reviewer or if you're happy to try accepting it as is now?
Hello! Yes, I'm still looking! Really hoping we could get this approved by the end of the year 🤞
Dear @graciellehigino - are there any updates on this? Is there anything we can do to speed up the final approval?
Hey @graciellehigino, any update for us? Thanks!
Hi @jnnsbrr — sorry for the delays here. I will be taking over as editor and hope to get this moving along again soon.
@editorialbot assign me as editor
Assigned! @kthyng is now the editor
Great thanks a lot!
@editorialbot assign me as editor
Assigned! @marcosvital is now the editor
Hi @jnnsbrr, we are sorry that this reviewing process is not proceeding as it should. Kristen asked me to assume your submission, and I'll try to move things asap, ok? Our priority is to find a second reviewer to take a look at your submission, so I'll focus on that.
@editorialbot remove @egouldo from reviewers
@egouldo removed from the reviewers list!
Dear @trashbirdecology, would you be willing to review this submission for JOSS?
We carry out an open checklist-driven reviews here in GitHub issues, and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html
This is an ongoing submission that already went through a first round of review, and we would like to have a second person to look into it. Let us know if you are available, ok?
Dear @skiptoniam, would you be willing to review this submission for JOSS?
We carry out an open checklist-driven reviews here in GitHub issues, and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html
This is an ongoing submission that already went through a first round of review, and we would like to have a second person to look into it. Let us know if you are available, ok?
Dear @marcosvital, thank you for pushing this forward!
Is there a plan for further action regarding a second reviewer and/or the publication? And is there anything I can do to support the process?
Dear @jnnsbrr, I'm sorry this is taking so long. I tried some email contacts, but still didn't find a reviewer. I'll keep trying. Let me know If you have any suggestions of potential reviewers to invite.
Dear @dm807cam, would you be willing to review this submission for JOSS?
We carry out an open checklist-driven reviews here in GitHub issues, and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html
This is an ongoing submission that already went through a first round of review, and we would like to have a second person to look into it. Let us know if you are available, ok?
Dear @mhesselbarth, would you be willing to review this submission for JOSS?
We carry out an open checklist-driven reviews here in GitHub issues, and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html
This is an ongoing submission that already went through a first round of review, and we would like to have a second person to look into it. Let us know if you are available, ok?
Sorry, but I am missing the background and also the time at the moment.
Sorry, but I am missing the background and also the time at the moment.
That's fine @mhesselbarth, and thank you for the quick reply.
Dear @jmp75, would you be willing to review this submission for JOSS?
We carry out an open checklist-driven reviews here in GitHub issues, and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html
This is an ongoing submission that already went through a first round of review, and we would like to have a second person to look into it. Let us know if you are available, ok?
Dear @stephendavidgregory, would you be willing to review this submission for JOSS?
We carry out an open checklist-driven reviews here in GitHub issues, and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html
This is an ongoing submission that already went through a first round of review, and we would like to have a second person to look into it. Let us know if you are available, ok?
Dear @vwmaus, would you be willing to review this submission for JOSS?
We carry out an open checklist-driven reviews here in GitHub issues, and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html
This is an ongoing submission that already went through a first round of review, and we would like to have a second person to look into it. Let us know if you are available, ok?
Dear @MoLi7, would you be willing to review this submission for JOSS?
We carry out an open checklist-driven reviews here in GitHub issues, and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html
This is an ongoing submission that already went through a first round of review, and we would like to have a second person to look into it. Let us know if you are available, ok?
@marcosvital @kthyng – incase it's useful, I've generated the most similar paper comparison here: #5314 (comment)
@editorialbot add @kanishkan91 as reviewer
@kanishkan91 added to the reviewers list!
@jnnsbrr again we are sorry that this is taking so long. @kanishkan91 is a part of our editorial team and agreed to review your submission, so we can follow up with a second review.
@kanishkan91 thank you so much for taking the time to review this submission.
@marcosvital Thanks. I'l try to get this done within the next two weeks.
Great, thanks a lot!
Review checklist for @kanishkan91
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/PIK-LPJmL/lpjmlkit?
- License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
- Contribution and authorship: Has the submitting author (@jnnsbrr) 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
- 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.
- Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
- 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
- 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, who the target audience is, and its relation to other work?
- 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?
@editorialbot generate pdf
@marcosvital , @jnnsbrr - I just completed my review of this software package. I was delayed on account of deadlines and paternity leave, so my apologies in advance. I have added my questions as issues which the authors can close with relevant pull requests. Most of the comments should be minor and easy to respond to. The two that would require a bit more clarification are the issues with the vignettes and the explanations regarding pre-installing lpjml. Once the authors respond, I am happy to recommend publication.
Dear @kanishkan91 thank you very much for the review!
I tried to solve the issues you created as requested - still parts of our README.md is automatically build by an R library that standardizes R package development at PIK.
I hope that my changes solve them :-)
@jnnsbrr Thanks for your responses. I think this should be good to go. Though I had two minor questions. I just want this to be documented in the review thread.
- If an LpJML installation is a pre-requisite for this package, how are the tests solving on GitHub actions? Is a pre-installed LpJML added somewhere? Or is LpJML being simultaneously installed by Github actions Because the tests are covering 90% of the code base, I find this a bit intriguing.
- Regarding the inability to edit the README, to be honest that is a bit unusual. I still approve publication, but can you comment on why you cant edit the README. Usually, there are pre-compiled templates that teams work with but at the end of the day, the README being a fundamental document should be able to be edited? I would also recommend you keep the above "issues" on the README open on your repo, just in case someone else had the same questions.
@marcosvital - I finished up the checklists.
Dear @kanishkan91 thanks again!
On 1. I answered already to some extent in the issue. There is currently no way on running an LPJmL instance within GitHub actions. There might a way for that in the future but currently this is not being worked on. We still try to cover as much as possible of the lpjmlkit functionality with tests to make sure there are no bugs/failures on our side of the pipeline.
On 2: Yes you are right, its a bit unusual. Still the RSE Team at PIK provides us with a lot of services, distribution on internal servers, Runiverse and more (https://pik-piam.r-universe.dev/). The pik-piam team has introduced this workflow for a lot of R packages and its quite an effort for us to branch off here. But I will try to open an issue on that soon to make it more flexible. This is the corresponding function we are talking about.
@marcosvital Can you proceed with this?
@marcosvital any update? Thanks a lot in advance!
@marcosvital or @kthyng can we get an update on the state of affairs here? Thanks!
Thanks everyone so much! Let's proceed with the post review items.
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
- Read the text of the paper and offer comments/corrections (as either a list or a pull request)
- 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 referencesand ask author(s) to update as needed - Recommend acceptance with
@editorialbot recommend-accept
@jnnsbrr Can you and your team please go through the bulleted list and let me know when you're done, reporting back the relevant items?
Dear @kthyng,
thanks a lot. We went trough the list and released the latest version (v1.7.3) that is also now featured in the paper. Here is the Zenodo link: https://doi.org/10.5281/zenodo.13884611.
Author information do match with an additional contributor that is now part as author.
@editorialbot generate pdf
@jnnsbrr Sorry for my delay! I've been traveling plus had a deadline, but I am back and ready to move this forward.
Can you change the Zenodo title to exactly match you JOSS paper title? This is not a requirement but is a nicety for consistency.
@editorialbot set v1.7.3 as version
Done! version is now v1.7.3
@editorialbot set 10.5281/zenodo.13884611 as archive
Done! archive is now 10.5281/zenodo.13884611
proposed paper edits: PIK-LPJmL/lpjmlkit#6
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
✅ OK DOIs
- 10.5194/gmd-12-5029-2019 is OK
- 10.1038/s41893-019-0465-1 is OK
- 10.1016/j.jhydrol.2003.09.029 is OK
- 10.1016/j.envsoft.2018.09.004 is OK
- 10.1111/j.1365-2486.2006.01305.x is OK
- 10.5194/gmd-11-429-2018 is OK
- 10.5194/gmd-11-2789-2018 is OK
- 10.5194/gmd-12-1299-2019 is OK
- 10.5194/gmd-12-2419-2019 is OK
- 10.5194/bg-19-957-2022 is OK
- 10.5194/esd-12-1037-2021 is OK
- 10.1371/journal.pbio.1001745 is OK
- 10.1046/j.1365-2486.2003.00569.x is OK
- 10.1038/s41597-022-01710-x is OK
- 10.5194/gmd-11-1343-2018 is OK
- 10.1046/j.1365-2486.2001.00383.x is OK
- 10.18637/jss.v059.i10 is OK
🟡 SKIP DOIs
- No DOI given, and none found for title: lpjmlkit: Toolkit for Basic LPJmL Handling
❌ MISSING DOIs
- 10.32614/cran.package.r6 may be a valid DOI for title: R6: Encapsulated Classes with Reference Semantics
❌ INVALID DOIs
- None