[REVIEW]: ELDAM: A Python software for Life Cycle Inventory data management

[whedon]

Submitting author: @GustaveCoste (Gustave Coste)
Repository: https://framagit.org/GustaveCoste/eldam
Version: v1.0
Editor: @sjpfenninger
Reviewer: @konstantinstadler, @romainsacchi
Archive: 10.15454/6EKXJQ

⚠️ JOSS reduced service mode ⚠️

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Markdown: [![status](https://joss.theoj.org/papers/905491355d2bda381255aef7c7d39d05/status.svg)](https://joss.theoj.org/papers/905491355d2bda381255aef7c7d39d05)

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

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

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

Review checklist for @konstantinstadler

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 repository url?
• 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 (@GustaveCoste) 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: Do the authors clearly state 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?

Review checklist for @romainsacchi

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 repository url?
• 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 (@GustaveCoste) 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: Do the authors clearly state 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?

[whedon]

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

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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

@whedon commands

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

@whedon generate pdf

[whedon]

PDF failed to compile for issue #2765 with the following error:

Can't find any papers to compile :-(

[sjpfenninger]

@whedon generate pdf from branch joss

[whedon]

Attempting PDF compilation from custom branch joss. Reticulating splines etc...

[whedon]

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

[romainsacchi]

It is a very interesting tool, and will certainly be useful to the LCA community. Well done!
I have followed the instructions, tested it with a couple of dummy files and it produced the expected results.

I have nevertheless the three following issue (issues 1 and 2 being somewhat related).
While they are not of extreme importance, they would greatly improve the user experience.

Issue 1 - https://framagit.org/GustaveCoste/eldam/-/issues/291
Issue 2 - https://framagit.org/GustaveCoste/eldam/-/issues/292
Issue 3 - https://framagit.org/GustaveCoste/eldam/-/issues/293

[romainsacchi]

@whedon generate pdf from branch joss

[whedon]

Attempting PDF compilation from custom branch joss. Reticulating splines etc...

[whedon]

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

[romainsacchi]

The author has adequately answered all the issues I raised.

[konstantinstadler]

@whedon and @sjpfenninger : I can not mark the check-marks although I am logged in and accepted the invitation - can you help me or should I just describe my answers?

I believe the problem is due to that I am not assigned to the issue (only listed as participant)

[whedon]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

[konstantinstadler]

This is a very interesting tool and I believe it can be useful for LCA practioner. The envisaged workflow tightly coupled with Simapro has the potential to lift the quality of LCI data.

I am, however, not a LCA expert and do not have access to Simapro. As far as possible I tested the software and it works for me but I could not verify the integration with Simapro - I hope that this was covered by @romainsacchi . Thus, I focused my review on the documentation and code. I have some issues which I think need to be addressed and I took the opportunity to also add some recommendation for the way forward.

Issues:

• https://framagit.org/GustaveCoste/eldam/-/issues/302
• https://framagit.org/GustaveCoste/eldam/-/issues/294
• https://framagit.org/GustaveCoste/eldam/-/issues/297
• https://framagit.org/GustaveCoste/eldam/-/issues/299
• https://framagit.org/GustaveCoste/eldam/-/issues/300
• https://framagit.org/GustaveCoste/eldam/-/issues/301

Recommendations:

• https://framagit.org/GustaveCoste/eldam/-/issues/295
• https://framagit.org/GustaveCoste/eldam/-/issues/296
• https://framagit.org/GustaveCoste/eldam/-/issues/298

One other small point I am not sure how to handle (@sjpfenninger ): The repository lists one developer (in the commit history and as stated in the readme). The article, however, has multiple authors. Probably not a problem but perhaps demands a statement about roles (see also https://joss.readthedocs.io/en/latest/submitting.html#authorship )

[sjpfenninger]

@romainsacchi, @konstantinstadler Thanks for your reviews!

[sjpfenninger]

@romainsacchi Can you confirm that you have tested the integration with Simapro?

[sjpfenninger]

@konstantinstadler Can you check if you can now edit the checkboxes? And it looks like @GustaveCoste addressed your issues, can you confirm whether you are satisfied?

[sjpfenninger]

@GustaveCoste Can you clarify the role of the authors on the paper?

[romainsacchi]

@sjpfenninger @konstantinstadler no, I cannot say I have tested the integration with Simapro, as I do not have a Simapro license. I only tested the consistency between the inputs and the outputs (from Simapro-compatible CSV file to Excel and vice-versa).

[GustaveCoste]

@sjpfenninger ELDAM's code was written entirely by myself but the three other authors have helped to design substantial parts of the tool.

I did not address all @konstantinstadler's issues yet, I should have time to do it next week.

[konstantinstadler]

Hi,

1. @GustaveCoste - timeline is ok for me
2. Simapro (@sjpfenninger ): I can probably find someone in the institute using Simapro. I never used it before but perhaps that makes me a perfect guinea pig for following a tutorial. Probably need some time to catch a researcher here not working from home, but when I receive a tutorial from @GustaveCoste I should be able to do that within a week
3. I still can not click the buttons. Do I miss something here - I am just supposed to click, right? I tested on several browsers/os and it does not work. But I can make my own list and it works (test buttons konstantinstadler/pymrio_article#2 ) - wonder what is going on. Can we do it manually and I just confirm that I have checked this. Or perhaps repost the list and I try again

[sjpfenninger]

@whedon re-invite @konstantinstadler as reviewer

[whedon]

OK, the reviewer has been re-invited.

@konstantinstadler please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[whedon]

PDF failed to compile for issue #2765 with the following error:

Can't find any papers to compile :-(

[arfon]

@whedon accept from branch joss

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1016/j.jclepro.2020.124099 is INVALID because of 'https://doi.org/' prefix

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2027

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2027, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch joss 

[arfon]

@sjpfenninger - just checking that you're ready to hand off this paper for final checks by the EiC team?

@GustaveCoste - please change the DOI string for the DOI that Whedon has flagged to 10.1016/j.jclepro.2020.124099

[sjpfenninger]

@arfon yes should be good to go!

[arfon]

@whedon check references

[arfon]

@GustaveCoste - just to confirm, please change this line to: doi = "10.1016/j.jclepro.2020.124099",

[GustaveCoste]

@arfon Sorry for the delay, I just changed the line.

[arfon]

@whedon accept from branch joss

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2032

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2032, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch joss 

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2033

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2033, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch joss 

[arfon]

@whedon accept deposit=true from branch joss

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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.02765 joss-papers#2034
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02765
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]

@konstantinstadler, @romainsacchi - many thanks for your reviews here and to @sjpfenninger for editing this submission. JOSS relies upon the volunteer efforts of folks like yourselves, and we simply wouldn't be able to do it without you! ✨

@GustaveCoste - your paper is now accepted and published in JOSS ⚡🚀💥

[whedon]

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.02765/status.svg)](https://doi.org/10.21105/joss.02765)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02765">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02765/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02765/status.svg
   :target: https://doi.org/10.21105/joss.02765

This is how it will look in your documentation:

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