[REVIEW]: IFermi: A python library for Fermi surface generation and analysis

[whedon]

Submitting author: @utf (Alex Ganose)
Repository: https://github.com/fermisurfaces/IFermi
Version: v0.2.3
Editor: @danielskatz
Reviewer: @arosen93, @lucydot
Archive: 10.5281/zenodo.4609270

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Markdown: [![status](https://joss.theoj.org/papers/59fa1c336b832a772f30b85bfbc2efdc/status.svg)](https://joss.theoj.org/papers/59fa1c336b832a772f30b85bfbc2efdc)

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Review checklist for @arosen93

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

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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 (@utf) 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: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
• 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 @lucydot

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 (@utf) 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: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
• 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. @arosen93, @lucydot 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]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.67 s (61.2 files/s, 402029.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                              1              0              0          40230
Python                          17            915           1283           2844
reStructuredText                 9            225            221            343
SVG                              6              0              6            277
Markdown                         2             56              0            150
YAML                             3             26              0            106
Jupyter Notebook                 1              0         222685             79
CSS                              1              1              2              6
HTML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            41           1223         224197          44038
-------------------------------------------------------------------------------


Statistical information for the repository 'f4e3be367a80be13694bfb85' was
gathered on 2021/03/04.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Alex Ganose                    153          8395          18247           39.43
Amy                              3          1035            438            2.18
Amy Jade Searle                  8         25777            771           39.29
Amy Searle                      15           852            399            1.85
Katherine Inzani                 1             1              0            0.00
Matthew Horton                   8           106              9            0.17
ajsearle97                      10           136          11403           17.08

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Alex Ganose                4770           56.8          2.2                9.20
Amy                           5            0.5         18.3                0.00
Amy Jade Searle              97            0.4         15.8                9.28
Amy Searle                  105           12.3          0.2                7.62
Matthew Horton               60           56.6          5.7               20.00
ajsearle97                    5            3.7          8.8                0.00

[whedon]

PDF failed to compile for issue #3089 with the following error:

Can't find any papers to compile :-(

[danielskatz]

@arosen93 and @lucydot - Thanks for agreeing to review this submission.
This is the review thread for the paper. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

Please read the first couple of comments in this issue carefully, so that you can accept the invitation from JOSS and be able to check items, and so that you don't get overwhelmed with notifications from other activities in JOSS.

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 #3089 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 Whedon (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 (@danielskatz) if you have any questions/concerns.

[danielskatz]

@whedon generate pdf from branch paper

[whedon]

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

[whedon]

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

[Andrew-S-Rosen]

Fantastic. I plan to start my review towards the latter half of next week. Looking forward to learning about IFermi!

[lucydot]

Hello @utf, I started reviewing today.

On first impressions, the repo looks excellent. I am fairly certain I will be using this for my own research in the future so I'm happy to be reviewing it.

I had a little hiccup with install - I wouldn't call it a Bug, but to not clutter this issue thread (and to keep the review process within Github), I have raised it at fermisurfaces/IFermi#17 .

A couple of suggestions around testing: fermisurfaces/IFermi#18

On my first pass through the documentation (without actually trying anything out yet) I've noted a couple of things: fermisurfaces/IFermi#19

I'll take a closer look at the code itself in the next few days.

[Andrew-S-Rosen]

@utf: I just read through the paper. It is clearly written, has a nice introduction to the importance of Fermi surfaces, discusses prior software in this area, and makes it clear where IFermi fits within the existing software ecosystem. As such, I have no major suggestions for changes to the text.

I only have a couple very trivial comments on the paper, unrelated to the software or science underlying the work.

• In the Summary: "IFermi is Python library..." --> "IFermi is a Python library..."
• The "author" for the Plotly citation got a bit truncated (Inc., P.T. instead of Plotly Technologies Inc.).

[utf]

Thanks for catching those errors @arosen93. I've updated the manuscript accordingly.

[utf]

@whedon generate pdf from branch paper

[whedon]

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

[whedon]

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

[Andrew-S-Rosen]

@danielskatz, @utf:

I have concluded my review of IFermi. In short, IFermi is an excellent software package that I believe should be published in JOSS.

Overall, I am incredibly pleased with the detailed documentation, easy-to-follow tutorials, and accessible code layout. I believe that this will become the de facto tool for generating and analyzing Fermi surfaces for VASP users (and hopefully users of other codes once these features are added). I raised a few minor issues on the GitHub page, mainly with regards to the documentation, that have all been addressed to my satisfaction.

With regards to the accompanying paper, it clearly explains the purpose of IFermi. For comparison's sake, I tried out what I feel to be one of the closest packages to IFermi, PyProcar, to compare the two codes. Like IFermi, PyProcar has its own features for visualizing Fermi surface and allows for surface coloring based on properties. While there are many similarities, I came away from this exercise feeling that IFermi is still an important contribution to the field. As the authors aptly note in the accompanying manuscript, it is quite easy to analyze and modify the Fermi surfaces once generated with IFermi (since it's stored as a very convenient Python object). This was a clear advantage to me. The claim of novelty regarding the dimensionality determination is also accurate to the best of my knowledge. All in all, I agree with the statement of need and advertised features of IFermi.

Thank you for the opportunity to review IFermi. I am happy to recommend its acceptance in JOSS.

[danielskatz]

Thanks @arosen93!
@lucydot - how is your review coming?

[lucydot]

@danielskatz I'm in the process of working through the tutorials for my own dataset - I'll report back later today. All good so far!

[whedon]

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

[danielskatz]

@utf - this looks good, except for one minor issue that I've proposed a change for in fermisurfaces/IFermi#24

[utf]

Thanks @danielskatz. I've merged your PR.

[utf]

@whedon generate pdf from branch paper

[whedon]

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

[whedon]

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

[danielskatz]

@whedon accept from branch paper

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1080/10867651.2003.10487582 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1016/s1093-3263(99)00028-5 is OK
- 10.1109/mcse.2007.55 is OK
- 10.1088/0031-8949/91/5/053009 is OK
- 10.1088/0370-1328/80/2/316 is OK
- 10.1103/PhysRevResearch.3.013069 is OK
- 10.1103/PhysRevApplied.14.024064 is OK
- 10.1016/j.cpc.2019.107080 is OK
- 10.1016/j.cpc.2019.01.017 is OK
- 10.1016/j.cpc.2018.05.010 is OK
- 10.1088/0953-8984/14/11/301 is OK
- 10.1088/1361-648X/ab4007 is OK
- 10.1109/MCSE.2011.35 is OK
- 10.7717/peerj.453 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#2150

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2150, 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 paper 

[danielskatz]

@whedon accept deposit=true from branch paper

[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.03089 joss-papers#2151
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.03089
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]

Congratulations to @utf (Alex Ganose) and co-authors!!

And thanks to @arosen93 and @lucydot for a very quick and easy review process!

[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.03089/status.svg)](https://doi.org/10.21105/joss.03089)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03089">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03089/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03089/status.svg
   :target: https://doi.org/10.21105/joss.03089

This is how it will look in your documentation:

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[utf]

Thank you everyone!

[utf]

Hi @danielskatz, the paper pdf isn't loading on https://joss.theoj.org/papers/10.21105/joss.03089

Just checking if this is usual and I need to wait a little bit?

[Andrew-S-Rosen]

For what it's worth, it loads just fine for me. Maybe it's related to an ad-blocker or something similar?

[utf]

Strange, on Safari nothing loads but on Chrome I see:

I will see if this has fixed itself by tomorrow.

[Andrew-S-Rosen]

Very odd! Well, here's a sneak peak I guess! Works fine for me on Chrome and Edge even though you get the 404. Hopefully @danielskatz can provide some insight.

[danielskatz]

It worked for me on Safari - a check of it is the last thing I do before closing an issue. It's likely a caching problem somewhere - If you are on a wifi network, you could try on a phone network or something like that, or just wait a bit.