[REVIEW]: Emiproc: A Python package for emission inventory processing

[editorialbot]

Submitting author: @lionel42 (Lionel Constantin)
Repository: https://github.com/C2SM-RCM/emiproc
Branch with paper.md (empty if default branch): joss
Version: v2.3.1
Editor: @mengqi-z
Reviewers: @einaraz, @mikapfl
Archive: 10.5281/zenodo.14614230

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/e069625c156ca1c939cd794e8e396f25"><img src="https://joss.theoj.org/papers/e069625c156ca1c939cd794e8e396f25/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/e069625c156ca1c939cd794e8e396f25/status.svg)](https://joss.theoj.org/papers/e069625c156ca1c939cd794e8e396f25)

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

@dostuffthatmatters & @einaraz, 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 @mengqi-z 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 @einaraz

📝 Checklist for @mikapfl

[editorialbot]

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

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

@editorialbot commands

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

@editorialbot generate pdf

[editorialbot]

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

✅ OK DOIs

- 10.5194/gmd-13-2379-2020 is OK
- 10.5281/zenodo.3946761 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.2800/795737 is OK
- 10.35089/WDCC/IconRelease01 is OK
- 10.5194/gmd-12-1885-2019 is OK
- 10.5194/gmd-13-873-2020 is OK
- 10.5194/acp-24-2759-2024 is OK
- 10.5194/egusphere-egu24-3375 is OK
- 10.5194/egusphere-egu24-7420 is OK
- 10.1029/2006GB002735 is OK
- 10.5194/gmd-11-4043-2018 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: EDGAR (Emissions Database for Global Atmospheric R...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.16 s (1165.8 files/s, 183239.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         103           3303           3407          13090
Jupyter Notebook                13              0           5964           1254
CSV                             27              2              0            502
reStructuredText                21            437            224            483
YAML                            13             13             22            172
TeX                              1              9              0            170
Markdown                         4             56              0            152
TOML                             1              9              0             57
DOS Batch                        1              8              1             26
make                             1              4              7              9
JSON                             1              0              0              8
SVG                              1              0              1              3
-------------------------------------------------------------------------------
SUM:                           187           3841           9626          15926
-------------------------------------------------------------------------------

Commit count by author:

   446	coli
    81	Ochsner, David
    69	Gerrit Kuhlmann
    50	Haussaire JM
    39	Constantin, Lionel
    32	Michael Jähn
    21	efmkoene
    16	Jean-Matthieu Haussaire
    13	lionel constantin
    12	Lionel C
    11	Dominik Brunner
     4	Haussaire, Jean-Matthieu
     3	David Ochsner
     2	Jaehn, Michael
     2	dao
     2	jmhaussaire
     1	Joel Thanwerdas
     1	Kuhlmann, Gerrit
     1	Michael Steiner
     1	corink21
     1	gredvis

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1099

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: BSD 3-Clause "New" or "Revised" License (Valid open source OSI approved license)

[editorialbot]

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

[mengqi-z]

👋🏼 @lionel42 @dostuffthatmatters @einaraz - This is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/7509 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@mengqi-z) if you have any questions/concerns.

[einaraz]

Review checklist for @einaraz

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/C2SM-RCM/emiproc?
• 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 (@lionel42) 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?

[dostuffthatmatters]

Review checklist for @dostuffthatmatters

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/C2SM-RCM/emiproc?
• 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 (@lionel42) 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?

[dostuffthatmatters]

Dear @mengqi-z,

I have noticed that I have a conflict of interest with the second author of the paper (Dominik Brunner). We are both partly funded by the ICOS Cities PAUL, and he is part of the scientific advisory board of ITMS which my lab is partly funded by. Both of these grants fund hundreds of researchers in dozens of institutions, and we are working on separate working package tasks, but we do collaborate in some areas of ICOS Cities PAUL.

I am very sorry for only discovering this now. Before, I had a quick read of the paper and the codebase and a look at the lead author's lab – with which I don't have a single COI. But I overlooked the full author list. I do not have a COI with any other author.

I do think, I can make an impartial judgment on this software and the paper, as I am not working on emission inventories, my lab does not have a competing project, and my involvement with the second author totally disconnected from this effort. But the decision is, of course, up to you.

For full transparency: My lab was asked by Lionel Constantin to contribute to the project in November 2022 via a colleague of mine who is working with emission inventories. But we never contributed anything to the project: we are neither coauthors nor listed in the acknowledgement section, nor is our lab's inventory supported by emiproc. Hence, I don't see this as a COI.

Best regards,
Moritz Makowski

Doctoral Candidate
Environmental Sensing and Modeling (Prof. Jia Chen)
Technical University of Munich

[mengqi-z]

Hi @dostuffthatmatters,

Thank you for being transparent about potential conflicts of interest. After careful consideration, we believe there is a conflict of interest, particularly regarding the part "he is part of the scientific advisory board of ITMS which my lab is partly funded by".

Unfortunately, this means you won’t be able to review this paper. But I really appreciate your willingness to contribute. I’m sure there will be other great opportunities for you to review JOSS papers in the future! Thank you again!

[mengqi-z]

@editorialbot remove @dostuffthatmatters from reviewers

[editorialbot]

@dostuffthatmatters removed from the reviewers list!

[mengqi-z]

👋 @mikapfl @varsha2509 - Would any of you be interested in and able to take on this submission for JOSS?

[dostuffthatmatters]

Hi @mengqi-z,

Thank you for the swift decision. I totally understand it. Again, sorry for only noticing it after accepting the review.

Best of luck with the review process!

[varsha2509]

Hi @mengqi-z - my schedule is looking a bit tight until beginning of next year so I might have to pass on this review (though the work sounds super interesting!). Good luck with the review process.

[mengqi-z]

@dostuffthatmatters - Thank you for your understanding!

[mengqi-z]

@varsha2509 - No problem at all. Thanks for getting back to me!

[mikapfl]

@mengqi-z I'd be happy to review this submission.

[mengqi-z]

@mikapfl - Great, thank you! Just a quick note: this is the REVIEW issue for the paper. Please take a moment to read the instructions above, and feel free to reach out if you have any questions!

[mengqi-z]

@editorialbot add @mikapfl as reviewer

[editorialbot]

@mikapfl added to the reviewers list!

[mikapfl]

Review checklist for @mikapfl

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/C2SM-RCM/emiproc?
• 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 (@lionel42) 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?

[mikapfl]

I've finished the review. An impressive piece of software, well set up and with a good test coverage. Probably I'll use it if I need to regrid emissions inventories (so far, I haven't worked with spatially resolved emissions inventories, but that might change). The paper itself is also concise and easy to read, containing all the necessary information, I think.

Just an idea: You might want to consider adding issue and pull request templates on github. It's easier for users or contributors to know what information you need etc.

[mengqi-z]

@mikapfl - Wonderful! Thanks for your review and positive feedback on this submission!

@lionel42 - Both reviewers have completed their reviews. I’ll proofread the paper and ensure it meets JOSS standards, then follow up with you on the next steps. Thanks!

[mengqi-z]

@editorialbot generate pdf

[mengqi-z]

@editorialbot check references

[editorialbot]

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

✅ OK DOIs

- 10.5194/gmd-13-2379-2020 is OK
- 10.5281/zenodo.3946761 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.2800/795737 is OK
- 10.35089/WDCC/IconRelease01 is OK
- 10.5194/gmd-12-1885-2019 is OK
- 10.5194/gmd-13-873-2020 is OK
- 10.5194/acp-24-2759-2024 is OK
- 10.5194/egusphere-egu24-3375 is OK
- 10.5194/egusphere-egu24-7420 is OK
- 10.1029/2006GB002735 is OK
- 10.5194/gmd-11-4043-2018 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: EDGAR (Emissions Database for Global Atmospheric R...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

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

[mengqi-z]

@editorialbot generate pdf

[editorialbot]

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

[mengqi-z]

@lionel42 - Thanks for addressing my comments.

At this point could you:

• 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 released software on Zenodo or a similar service (e.g., figshare, an institutional repository).
• Make sure that the archive (e.g., on Zenodo) has the correct metadata. This includes the title (which should match the paper title) and the author list (ensure the list is correct and does not include people who only made minor contributions). You may also add the authors' ORCIDs.
• Make sure that the license listed for the archive is the same as the software license.
• Please post the DOI of the archived version here.

I can then move forward with accepting the submission.

[lionel42]

@editorialbot generate pdf

[editorialbot]

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

[lionel42]

Version: v2.3.1

https://github.com/C2SM-RCM/emiproc/releases/tag/v2.3.1

[lionel42]

• 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 released software on Zenodo or a similar service (e.g., figshare, an institutional repository).
• Make sure that the archive (e.g., on Zenodo) has the correct metadata. This includes the title (which should match the paper title) and the author list (ensure the list is correct and does not include people who only made minor contributions). You may also add the authors' ORCIDs.
• Make sure that the license listed for the archive is the same as the software license.
• Please post the DOI of the archived version here.

[lionel42]

The doi on zenodo:

https://doi.org/10.5281/zenodo.14614230

[lionel42]

@mengqi-z Thanks for the instructions, the publication to zenodo has worked, please check and proceed

v2.3.1

10.5281/zenodo.14614230

[mengqi-z]

@lionel42 - Thanks! I noticed a couple of discrepancies in the Zenodo archive:

• The order of authors in Zenodo doesn't match the paper. Could you please update the Zenodo author list to reflect the order in the paper?
• The version number in GitHub release is v2.3.1, but the Zenodo archive lists it as v2.3-joss. Could you update the Zenodo version to match the GitHub release (v2.3.1)?

Thanks!

[lionel42]

@mengqi-z

Thanks for finding that out and sorry for the discrepancies.

I have now fixed authors order and version.

[mengqi-z]

@editorialbot set 10.5281/zenodo.14614230 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.14614230

[mengqi-z]

@editorialbot set v2.3.1 as version

[editorialbot]

Done! version is now v2.3.1

[mengqi-z]

@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

- 10.5194/gmd-13-2379-2020 is OK
- 10.5281/zenodo.3946761 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.2800/795737 is OK
- 10.35089/WDCC/IconRelease01 is OK
- 10.5194/gmd-12-1885-2019 is OK
- 10.5194/gmd-13-873-2020 is OK
- 10.5194/acp-24-2759-2024 is OK
- 10.5194/egusphere-egu24-3375 is OK
- 10.5194/egusphere-egu24-7420 is OK
- 10.1029/2006GB002735 is OK
- 10.5194/gmd-11-4043-2018 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: EDGAR (Emissions Database for Global Atmospheric R...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

👋 @openjournals/ese-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#6321, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[mengqi-z]

@lionel42 – I’ve recommended your submission for acceptance. Thanks so much for submitting to JOSS! From here, our Editor-in-Chief will step in to do some final checks before the paper can be officially accepted and published. Congrats and great job!

@einaraz @mikapfl – Huge thanks to all of you for reviewing this paper! It’s been great working with you during this process, and I really appreciate your thoughtful feedback. I look forward to seeing your reviews for JOSS in the future!

[lionel42]

@editorialbot accept

[editorialbot]

I'm sorry @lionel42, I'm afraid I can't do that. That's something only eics are allowed to do.