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[REVIEW]: IFermi: A python library for Fermi surface generation and analysis #3089

Closed whedon closed 3 years ago

whedon commented 3 years ago

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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HTML: <a href="https://joss.theoj.org/papers/59fa1c336b832a772f30b85bfbc2efdc"><img src="https://joss.theoj.org/papers/59fa1c336b832a772f30b85bfbc2efdc/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/59fa1c336b832a772f30b85bfbc2efdc/status.svg)](https://joss.theoj.org/papers/59fa1c336b832a772f30b85bfbc2efdc)

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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.)

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@arosen93 & @lucydot, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Review checklist for @arosen93

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @lucydot

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 3 years ago

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 :tada:.

:warning: JOSS reduced service mode :warning:

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whedon commented 3 years ago 
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 commented 3 years ago

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

Can't find any papers to compile :-(

danielskatz commented 3 years ago

@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 openjournals/joss-reviews#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 commented 3 years ago

@whedon generate pdf from branch paper

whedon commented 3 years ago 
Attempting PDF compilation from custom branch paper. Reticulating splines etc...
whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

Andrew-S-Rosen commented 3 years ago

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

lucydot commented 3 years ago

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 commented 3 years ago

@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.

utf commented 3 years ago

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

utf commented 3 years ago

@whedon generate pdf from branch paper

whedon commented 3 years ago 
Attempting PDF compilation from custom branch paper. Reticulating splines etc...
whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

Andrew-S-Rosen commented 3 years ago

@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 commented 3 years ago

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

lucydot commented 3 years ago

@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!

lucydot commented 3 years ago

@danielskatz @utf

I finished reviewing iFermi today. I ran through the tutorial using my own dataset, so that I could compare it to the corresponding bandstructure that I have generated elsewhere. The iFermi output is consistent with what I'd expect looking at my 2D slice through reciprocal space.

To re-iterate what Andrew has already said, iFermi has easy to follow, comprehensive documentation. The CLI is intuitive to use, and installation is straight forward. There are similarities with existing packages, but these are highlighted in the JOSS paper, and the flexibility of iFermi distinguishes itself from what is already out there.

Last week I raised some minor issues regarding documentation, testing and installation. All of these have been addressed are now closed.

I'm happy to recommend iFermi for publication with JOSS. Thanks @utf @ajsearle97 for the code I'm looking forward to using it for future research

danielskatz commented 3 years ago

Thanks @lucydot!

danielskatz commented 3 years ago

@utf - since both reviewers are happy, have checked off all items, and all the issues raised are closed, I think we're ready to proceed in the acceptance process. At this point could you:

utf commented 3 years ago

Hi @danielskatz

The archived version is v0.2.3 The Zenodo doi is 10.5281/zenodo.4609270

I can confirm that I have checked the Zenodo metadata.

Thanks you @lucydot and @arosen93 for the swift reviews. The package is definitely improved after your comments.

danielskatz commented 3 years ago

@whedon set 10.5281/zenodo.4609270 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4609270 is the archive.

danielskatz commented 3 years ago

@whedon set v0.2.3 as version

whedon commented 3 years ago

OK. v0.2.3 is the version.

danielskatz commented 3 years ago

@whedon generate pdf from branch paper

whedon commented 3 years ago 
Attempting PDF compilation from custom branch paper. Reticulating splines etc...
whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

danielskatz commented 3 years ago

@utf - this looks good, except for one minor issue that I've proposed a change for in https://github.com/fermisurfaces/IFermi/pull/24

utf commented 3 years ago

Thanks @danielskatz. I've merged your PR.

utf commented 3 years ago

@whedon generate pdf from branch paper

whedon commented 3 years ago 
Attempting PDF compilation from custom branch paper. Reticulating splines etc...
whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

danielskatz commented 3 years ago

@whedon accept from branch paper

whedon commented 3 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 3 years ago 
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 commented 3 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2150

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/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 commented 3 years ago

@whedon accept deposit=true from branch paper

whedon commented 3 years ago 
Doing it live! Attempting automated processing of paper acceptance...
whedon commented 3 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 3 years ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/2151
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.03089
  3. If everything looks good, then close this review issue.

  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

    Any issues? Notify your editorial technical team...

danielskatz commented 3 years ago

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

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

whedon commented 3 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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:

DOI

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utf commented 3 years ago

Thank you everyone!

utf commented 3 years ago

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 commented 3 years ago

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

utf commented 3 years ago

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

Screenshot 2021-03-16 at 18 51 51

I will see if this has fixed itself by tomorrow.

Andrew-S-Rosen commented 3 years ago

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.

image

danielskatz commented 3 years ago

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.