[REVIEW]: impedance.py: A Python package for electrochemical impedance analysis

[whedon]

Submitting author: @mdmurbach (Matthew D. Murbach)
Repository: https://github.com/ECSHackWeek/impedance.py
Version: v1.0.1
Editor: @mbobra
Reviewer: @ma-sadeghi, @EricaEgg
Archive: 10.5281/zenodo.3955199

⚠️ 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.

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/1d6e062c3098f6121227eece6ecfe342/status.svg)](https://joss.theoj.org/papers/1d6e062c3098f6121227eece6ecfe342)

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

@ma-sadeghi & @EricaEgg, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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

Review checklist for @ma-sadeghi

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 (@mdmurbach) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 @EricaEgg

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 (@mdmurbach) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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. @ma-sadeghi, @EricaEgg 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.

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[whedon]

Reference check summary:

OK DOIs

- 10.1016/0013-4686(93)85083-B is OK
- 10.1149/2.0711811jes is OK
- 10.21105/joss.01057 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1007/s40964-018-0054-2 is OK
- 10.1016/j.electacta.2014.01.034 is OK
- 10.1149/2.1021802jes is OK
- 10.1149/2.1051908jes is OK
- 10.1016/S0167-2738(02)00185-6 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1016/0013-4686(95)00440-8 is OK
- 10.1016/S0378-7753(99)00351-1 is OK
- 10.1016/j.electacta.2005.02.148 is OK
- 10.1149/1.1836485 is OK
- 10.1016/S0013-4686(98)00138-8 is OK
- 10.1114/1.1366675 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👉 Check article proof 📄 👈

[mbobra]

Thank you so much for reviewing this submission, @ma-sadeghi and @EricaEgg! If you have any questions, please feel free to ask -- I'm always here to help ☀️

[EricaEgg]

@mbobra, I have a question regarding the COI guidelines. One of the authors (Brian Gerwe) and I are both PhD students within UW ChemE, therefore "employed at the same institution". However, we are NOT in the same lab group, so is that acceptable? Just want to make sure we are within the regulations. Thanks!

[arfon]

@mbobra, I have a question regarding the COI guidelines. One of the authors (Brian Gerwe) and I are both PhD students within UW ChemE, therefore "employed at the same institution". However, we are NOT in the same lab group, so is that acceptable? Just want to make sure we are within the regulations. Thanks!

@EricaEgg - do you believe this will affect your ability to give an impartial review? If not, please proceed :-)

[EricaEgg]

@mbobra, I have a question regarding the COI guidelines. One of the authors (Brian Gerwe) and I are both PhD students within UW ChemE, therefore "employed at the same institution". However, we are NOT in the same lab group, so is that acceptable? Just want to make sure we are within the regulations. Thanks!

@EricaEgg - do you believe this will affect your ability to give an impartial review? If not, please proceed :-)

Thanks @arfon, it will not. I am happy to review.

[mbobra]

@ma-sadeghi and @EricaEgg Please let me know if you need any help with the review or have any questions!

[ma-sadeghi]

@mdmurbach From your repository, I see that there are 7 people who have contributed 1000+ lines of code, but I only see 4 people named as co-authors of the paper. Is that right?

[ma-sadeghi]

Hi @mbobra, I have a question for you: does the writing have to be strictly formal, or a few informalities here and there are acceptable?

[mdmurbach]

Hi @ma-sadeghi, thanks for your time with the review!

Yes, you're right. If you look at the timeline/content of the commits (1, 2, 3) for the 3 folks who are not listed as authors, they were in the initial setup of the repository structure during the Electrochemical Society (ECS) Hackweek and not in the actual content of the package being published. In this case, I don't think it makes sense to use LOC as a metric for contributions and the four authors were selected as they have all made substantial contributions to the work.

[ma-sadeghi]

@mdmurbach Sure, I completely understand. I just wanted to make sure this was not by mistake.

[ma-sadeghi]

Hi @mbobra, I have a question for you: does the writing have to be strictly formal, or a few informalities here and there are acceptable?

Hi @mbobra, apart from this, it should be good to go. Well done @mdmurbach!

[EricaEgg]

@mdmurbach The README references an examples/ directory, but I do not see that on the master branch. Should users just reference the readthedocs examples instead? Just want to clarify. Thanks!

[mdmurbach]

Good catch @EricaEgg! Yes, the directory was moved into docs/source, so you can find them here. These notebook files become the examples rendered in the documentation using nbsphinx.

I will update the README to fix that discrepancy as well.

[EricaEgg]

Great work everyone! I just have a few documentation recommendations, but other than that I would say it is good to go!

Doc recs:

1. In the notebook, fitting_example.ipynb, part 4a, numpy is called without an import. Import line needs to be added in this block or earlier.
2. In the notebook plotting_example.ipynb, part 3a, I am getting an error. There could be a bug in the function circuit.plot. (error attached as photo)

If the above errors are due to errors I've done, might be useful to mention in documentation for users. Since these are small things, I went ahead and marked the corresponding boxes.

[EricaEgg]

Great work everyone! I just have a few documentation recommendations, but other than that I would say it is good to go!

Doc recs:

1. In the notebook, fitting_example.ipynb, part 4a, numpy is called without an import. Import line needs to be added in this block or earlier.
2. In the notebook plotting_example.ipynb, part 3a, I am getting an error. There could be a bug in the function circuit.plot. (error attached as photo)

If the above errors are due to errors I've done, might be useful to mention in documentation for users. Since these are small things, I went ahead and marked the corresponding boxes.

Created an issue on target repo

[mdmurbach]

Awesome, thanks for taking the time to review @EricaEgg! I've added those changes as well as a few thoughts to the plotting error issue (I think it's potentially an adblocker or versioning issue rather than anything related to the package).

[EricaEgg]

Awesome, thanks for taking the time to review @EricaEgg! I've added those changes as well as a few thoughts to the plotting error issue (I think it's potentially an adblocker or versioning issue rather than anything related to the package).

Thanks again @mdmurbach! Everything looks great from my end now. Good to go!

[mdmurbach]

Great! Thanks again for your reviews @EricaEgg and @ma-sadeghi! 😄

[mbobra]

Thank you for all your hard work @EricaEgg and @ma-sadeghi! I really appreciate it.

@mdmurbach We're almost there! Can you please cut a new release (it doesn't have to be a major release, something like v1.0.1 is fine), archive your release on Zenodo to obtain a DOI, and then put that DOI in your README.md file? After that I think we're done 🎉

[mdmurbach]

Linked with Zenodo, released v1.0.1, and added our shiny new DOI to the README. Thanks for all of your time as well @mbobra! Please let me know if there is anything else you need

[mbobra]

@whedon generate pdf

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary:

OK DOIs

- 10.1016/0013-4686(93)85083-B is OK
- 10.1149/2.0711811jes is OK
- 10.21105/joss.01057 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1007/s40964-018-0054-2 is OK
- 10.1016/j.electacta.2014.01.034 is OK
- 10.1149/2.1021802jes is OK
- 10.1149/2.1051908jes is OK
- 10.1016/S0167-2738(02)00185-6 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1016/0013-4686(95)00440-8 is OK
- 10.1016/S0378-7753(99)00351-1 is OK
- 10.1016/j.electacta.2005.02.148 is OK
- 10.1149/1.1836485 is OK
- 10.1016/S0013-4686(98)00138-8 is OK
- 10.1114/1.1366675 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#1620

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1620, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[danielskatz]

@mdmurbach - I notice the zenodo software author list has more people than the JOSS paper author list - is this intentional? normally, we expect them to be the same, but this is not required.

[danielskatz]

@mdmurbach - can you also add countries to your affiliations in the author list?

[danielskatz]

@mdmurbach - in the paper:

• The journal for Hunter should be Computing in Science & Engineering (the & is missing)
• for Rodrigues et al. Should A.C. be in caps in the title?

[mdmurbach]

@danielskatz great catch on these. Thanks! 😄

• I've added the & to the Hunter paper
• a.c. is not capitalized in the original Rodrigues reference, so I left that as is
• added the countries to the author list
• Fixed the Zenodo affiliations to match

[danielskatz]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary:

OK DOIs

- 10.1016/0013-4686(93)85083-B is OK
- 10.1149/2.0711811jes is OK
- 10.21105/joss.01057 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1007/s40964-018-0054-2 is OK
- 10.1016/j.electacta.2014.01.034 is OK
- 10.1149/2.1021802jes is OK
- 10.1149/2.1051908jes is OK
- 10.1016/S0167-2738(02)00185-6 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1016/0013-4686(95)00440-8 is OK
- 10.1016/S0378-7753(99)00351-1 is OK
- 10.1016/j.electacta.2005.02.148 is OK
- 10.1149/1.1836485 is OK
- 10.1016/S0013-4686(98)00138-8 is OK
- 10.1114/1.1366675 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#1622

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1622, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[danielskatz]

@whedon accept deposit=true

[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.02349 joss-papers#1623
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02349
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...

[danielskatz]

Thanks to @ma-sadeghi, @EricaEgg for reviewing, and @mbobra for editing!

Congratulations to @mdmurbach (Matthew D. Murbach) and co-authors!!

(I will close this issue once the PDF appears, which has been taking a little longer than normal lately)

[mdmurbach]

Wonderful! Big thanks again for all of your time, @ma-sadeghi, @EricaEgg, @mbobra and @danielskatz! This was an awesome review process all around 😄

🎊 congrats @BGerwe, @nealde, and @lktsui!! 🎉

[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.02349/status.svg)](https://doi.org/10.21105/joss.02349)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02349">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02349/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02349/status.svg
   :target: https://doi.org/10.21105/joss.02349

This is how it will look in your documentation:

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