[REVIEW]: py-sc-fermi: self-consistent Fermi energies and defect concentrations from electronic structure calculations

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@alexsquires@rkurchin<!--end-editor-- Reviewers: @hongzhouye, @ajgoyal Archive: 10.5281/zenodo.7567782

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/2fa8b3d80281c36371472485adbc83e7"><img src="https://joss.theoj.org/papers/2fa8b3d80281c36371472485adbc83e7/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/2fa8b3d80281c36371472485adbc83e7/status.svg)](https://joss.theoj.org/papers/2fa8b3d80281c36371472485adbc83e7)

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

@hongzhouye & @agoyal06, 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 @rkurchin 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 @hongzhouye

📝 Checklist for @ajgoyal

editorialbot commented 2 years ago

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 commented 2 years ago

Software report:

github.com/AlDanial/cloc v 1.88  T=1.32 s (27.2 files/s, 194865.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                              1              0              0         252860
Python                          14            377            569           1693
Jupyter Notebook                 2              0            847            260
TeX                              1             21              0            248
YAML                             6              6              6            187
reStructuredText                 7             66             53            125
Markdown                         2             28              0            105
DOS Batch                        1              8              1             26
make                             2              8             14             18
-------------------------------------------------------------------------------
SUM:                            36            514           1490         255522
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

Wordcount for paper.md is 986

editorialbot commented 2 years ago

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

editorialbot commented 2 years ago

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

OK DOIs

- None

MISSING DOIs

- 10.1039/d0ee00291g may be a valid DOI for title: Upper limit to the photovoltaic efficiency of imperfect crystals from first principles
- 10.1039/b300139n may be a valid DOI for title: Complex oxides: high temperature defect chemistry vs. low temperature defect chemistry
- 10.26434/chemrxiv-2021-1lw5t may be a valid DOI for title: Defect chemistry and doping of BiCuSeO
- 10.1021/acsenergylett.7b01313.s001 may be a valid DOI for title: Identification of Killer Defects in Kesterite Thin-Film Solar Cells
- 10.1021/acs.inorgchem.1c00278.s001 may be a valid DOI for title: Impact of Solution Chemistry on Growth and Structural Features of Mo-Substituted Spinel Iron Oxides
- 10.1039/d1tc02547c may be a valid DOI for title: Latest directions in p-type transparent conductor design
- 10.1016/j.commatsci.2022.111434 may be a valid DOI for title: DefAP: A Python code for the analysis of point defects in crystalline solids
- 10.1016/j.cpc.2019.06.017 may be a valid DOI for title: Equilibrium point defect and charge carrier concentrations in a material determined through calculation of the self-consistent Fermi energy
- 10.1038/s41524-022-00756-0 may be a valid DOI for title: An extended computational approach for point-defect equilibria in semiconductor materials
- 10.1016/j.cpc.2021.107946 may be a valid DOI for title: Spinney: Post-processing of first-principles calculations of point defects in semiconductors with Python
- 10.1021/acsenergylett.2c01961.s001 may be a valid DOI for title: Computational Prediction and Experimental Realization of Earth-Abundant Transparent Conducting Oxide Ga-Doped ZnSb_2O_6
- 10.33774/chemrxiv-2021-hhc4x may be a valid DOI for title: Computational design of thermoelectric alloys through optimization of transport and dopability
- 10.1038/s41578-022-00433-0 may be a valid DOI for title: Electronic defects in metal oxide photocatalysts
- 10.1021/acsenergylett.1c00380.s001 may be a valid DOI for title: Rapid Recombination by Cadmium Vacancies in CdTe
- 10.1038/s41578-018-0026-7 may be a valid DOI for title: Point defect engineering in thin-film solar cells
- 10.1021/acs.chemmater.8b01135.s001 may be a valid DOI for title: Defect Engineering of Earth-Abundant Solar Absorbers BiSI and BiSeI

INVALID DOIs

- None

rkurchin commented 2 years ago

@alexsquires when you have a moment, check if the DOI's suggested above are valid and add them in to your manuscript.

alexsquires commented 2 years ago

@alexsquires when you have a moment, check if the DOI's suggested above are valid and add them in to your manuscript.

Will do! Thanks all for agreeing to edit and review!

rkurchin commented 2 years ago

Reviewers @hongzhouye, @agoyal06, please let me know if you have any questions about how to get your reviews started! (Anuj, if you're still traveling, understood and no worries)

hongzhouye commented 2 years ago

Hi Rachel,

Thanks for checking in! I’m traveling this week and early next week and plan to submit my review comments after that by around Friday next week. I’ll definitely let you know if I have any questions! Thanks again for your help!

Best, Hong-Zhou

On Fri, Dec 2, 2022 at 12:49 Rachel Kurchin @.***> wrote:

Reviewers @hongzhouye https://github.com/hongzhouye, @agoyal06 https://github.com/agoyal06, please let me know if you have any questions about how to get your reviews started! (Anuj, if you're still traveling, understood and no worries)

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4962#issuecomment-1335591496, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC5HQKNZZ6BCLPDE7ZFEZILWLIZD3ANCNFSM6AAAAAASJJVS5U . You are receiving this because you were mentioned.Message ID: @.***>

-- Hong-Zhou Ye Postdoctoral Research Scientist The Berkelbach Group Department of Chemistry, Columbia University New York, NY, 10027

hongzhouye commented 1 year ago

Review checklist for @hongzhouye

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/bjmorgan/py-sc-fermi?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@alexsquires) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

hongzhouye commented 1 year ago

@rkurchin Hi Rachel, I have a very quick question about the "Contribution and authorship". Does every author need to have a recorded contribution to the code (i.e., through the commit history)? Thanks!

rkurchin commented 1 year ago

@hongzhouye thanks for the thoughtful question! I'm actually not certain if we have a formal policy about this. I've asked the rest of the editorial team and will let you know what I find out ASAP.

hongzhouye commented 1 year ago

@rkurchin Thank you! In case a bit more details would be helpful, I was particularly asking a case where someone (often a PI) helps conceptualize the work but is not actively involved in the actual coding work.

rkurchin commented 1 year ago

Okay, the answer is no, there doesn't need to be a commit history contribution – the situation you describe (as well as other conceivable ones) is perfectly fine to merit authorship. Thanks again for checking!

alexsquires commented 1 year ago

Hi both, when preparing the code for submission, I checked the authorship policy as I am aware David Scanlon is a "non-commiting" author!

The policy on the website says

Purely financial (such as being named on an award) and organizational (such as general supervision of a research group) contributions are not considered sufficient for co-authorship of JOSS submissions, but active project direction and other forms of non-code contributions are. The authors themselves assume responsibility for deciding who should be credited with co-authorship, and co-authors must always agree to be listed. In addition, co-authors agree to be accountable for all aspects of the work, and to notify JOSS if any retraction or correction of mistakes are needed after publication.

David's contributions have been scientific, and his knowledge and experience has been invaluable in identifying "edge-cases" where the code was giving numerically stable, but chemically unreasonable self-consistent Fermi energies. This led to a number changes in which the code was structured; it was my feeling from the authorship guidance that to include him would therefore be appropriate.

hongzhouye commented 1 year ago

Thank you for checking that, @rkurchin ! And thank you for the information, @alexsquires !

rkurchin commented 1 year ago

Hi again @agoyal06, just checking if you're back from traveling and able to work on the review! :)

agoyal06 commented 1 year ago

Yes, I am back. Let me go through the instructions and get back if I have any questions.

Thannks, Anuj

From: Rachel Kurchin @.> Sent: Tuesday, December 13, 2022 4:43 AM To: openjournals/joss-reviews @.> Cc: Anuj Goyal @.>; Mention @.> Subject: Re: [openjournals/joss-reviews] [REVIEW]: py-sc-fermi: self-consistent Fermi energies and defect concentrations from electronic structure calculations (Issue #4962)

Hi again @agoyal06https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fagoyal06&data=05%7C01%7C%7C7840c52859e543edf05508dadc9681b4%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C638064836228684241%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=y%2BOMWSWQvoymlaDkCyf7D6ZPc1jXdKI7sHYF1thiL4g%3D&reserved=0, just checking if you're back from traveling and able to work on the review! :)

— Reply to this email directly, view it on GitHubhttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fopenjournals%2Fjoss-reviews%2Fissues%2F4962%23issuecomment-1347475696&data=05%7C01%7C%7C7840c52859e543edf05508dadc9681b4%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C638064836228684241%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=jjGPrs7n0NfYwr2GC60sLGUSykOuUPnRQ13gSDwabyM%3D&reserved=0, or unsubscribehttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FADLVA2EHA3HYYIMYBBI3LKDWM6WSHANCNFSM6AAAAAASJJVS5U&data=05%7C01%7C%7C7840c52859e543edf05508dadc9681b4%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C638064836228684241%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=CSkpFOG4cgmM3L1ZN%2B0d3tY2oN5T6oENBs2iw3PhBCg%3D&reserved=0. You are receiving this because you were mentioned.Message ID: @.***>

rkurchin commented 1 year ago

Hey @agoyal06, any questions on this?

Also, @hongzhouye, I see your checklist is done – are you happy to recommend publication at this point?

hongzhouye commented 1 year ago

Hi @rkurchin, thanks for checking in! I just submitted my last issue (which is a minor one about the API tutorial). Once that one is resolved, I will be more than happy to recommend its publication.

hongzhouye commented 1 year ago

@rkurchin The issue I mentioned above was resolved and closed. I'm now happy to recommend its publication.

@alexsquires thank you and the team for the great work!

agoyal06 commented 1 year ago

Hi Rachel,

Sincere apologies for the delay on my side. I joined my new institute past week and it was difficult for me to get the review done.

Is anything still needed from me?

Regards, Anuj

Get Outlook for Androidhttps://aka.ms/AAb9ysg

From: Rachel Kurchin @.> Sent: Monday, December 19, 2022, 8:58 PM To: openjournals/joss-reviews @.> Cc: Anuj Goyal @.>; Mention @.> Subject: Re: [openjournals/joss-reviews] [REVIEW]: py-sc-fermi: self-consistent Fermi energies and defect concentrations from electronic structure calculations (Issue #4962)

Hey @agoyal06https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fagoyal06&data=05%7C01%7C%7C4d41291de4b943a4bcae08dae1d59b9e%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C638070604810419864%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=8rCFzucsz5X4V26SdW3FKx5u0El9mv2YuCHcLt3lu4U%3D&reserved=0, any questions on this?

Also, @hongzhouyehttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fhongzhouye&data=05%7C01%7C%7C4d41291de4b943a4bcae08dae1d59b9e%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C638070604810419864%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=sqWVyOw%2FH6uyEXGo1eztq3X3J3%2ByivRIF0IZuVYRBMQ%3D&reserved=0, I see your checklist is done – are you happy to recommend publication at this point?

— Reply to this email directly, view it on GitHubhttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fopenjournals%2Fjoss-reviews%2Fissues%2F4962%23issuecomment-1357843019&data=05%7C01%7C%7C4d41291de4b943a4bcae08dae1d59b9e%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C638070604810419864%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=DOaJqT1CYD2jKMJgvPHhlOMh9XRvvGHYr5ljuBe8VeQ%3D&reserved=0, or unsubscribehttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FADLVA2AV6YGCIKVRSMDGLRTWOB5H3ANCNFSM6AAAAAASJJVS5U&data=05%7C01%7C%7C4d41291de4b943a4bcae08dae1d59b9e%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C638070604810419864%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=lTQSmmcjsgh3UTN0hefDncDGokVzM7%2BvU%2B3CwvMk6q4%3D&reserved=0. You are receiving this because you were mentioned.Message ID: @.***>

rkurchin commented 1 year ago

Yes, take a look at the instructions above – you'll need to generate your review checklist and work through each aspect.

rkurchin commented 1 year ago

Hey @agoyal06, hope you had a great holiday! Just checking in again about this review. Let me know if you still have any questions.

agoyal06 commented 1 year ago

Yes, sorry for the delay. I will respond by weekend on the tasks completed.

Get Outlook for Androidhttps://aka.ms/AAb9ysg

From: Rachel Kurchin @.> Sent: Tuesday, January 3, 2023 8:59:38 PM To: openjournals/joss-reviews @.> Cc: Anuj Goyal @.>; Mention @.> Subject: Re: [openjournals/joss-reviews] [REVIEW]: py-sc-fermi: self-consistent Fermi energies and defect concentrations from electronic structure calculations (Issue #4962)

Hey @agoyal06https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fagoyal06&data=05%7C01%7C%7Ccabf0829da2c4ebe4d0608daed9f53f6%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C638083565806372834%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=VmKkrGmDmoOi8dueaaP%2BPWqlSU%2FPiobA97jjGz8qyGg%3D&reserved=0, hope you had a great holiday! Just checking in again about this review. Let me know if you still have any questions.

— Reply to this email directly, view it on GitHubhttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fopenjournals%2Fjoss-reviews%2Fissues%2F4962%23issuecomment-1369902766&data=05%7C01%7C%7Ccabf0829da2c4ebe4d0608daed9f53f6%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C638083565806372834%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ljD8yX3KNTkMJFcThmgn1ImK9mwPKYu8KkGJe%2BwTu0k%3D&reserved=0, or unsubscribehttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FADLVA2DADPWCMQ4RXR34X73WQRAWFANCNFSM6AAAAAASJJVS5U&data=05%7C01%7C%7Ccabf0829da2c4ebe4d0608daed9f53f6%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C638083565806372834%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=r1lz%2FoySpEXQcpJYm2L%2BvTHEUQknAgfx6itmbJNHzLo%3D&reserved=0. You are receiving this because you were mentioned.Message ID: @.***>

ajgoyal commented 1 year ago

@editorialbot generate my checklist

editorialbot commented 1 year ago

@ajgoyal I can't do that because you are not a reviewer

ajgoyal commented 1 year ago

@rkurchin I guess the delay from my side has stripped me of as a reviewer for this?

rkurchin commented 1 year ago

@editorialbot add @ajgoyal as reviewer

Nope! You just logged in from a different GitHub account. Fixing now...

editorialbot commented 1 year ago

@ajgoyal added to the reviewers list!

rkurchin commented 1 year ago

@editorialbot remove @agoyal06 as reviewer

editorialbot commented 1 year ago

@agoyal06 removed from the reviewers list!

rkurchin commented 1 year ago

@ajgoyal you should be able to generate your checklist now 👍

ajgoyal commented 1 year ago

Review checklist for @ajgoyal

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/bjmorgan/py-sc-fermi?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@alexsquires) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

ajgoyal commented 1 year ago

Hi @rkurchin, I have completed my checklist. I have suggested some minor checks/changes, and hopefully, authors would be able to implement them soon.

rkurchin commented 1 year ago

Thanks @ajgoyal! Just to confirm, you are happy to recommend this for publication at this point?

ajgoyal commented 1 year ago

Hi @rkurchin, Yes, once the issue is closed, I would be happy to recommend for the publication.

rkurchin commented 1 year ago

Great, thanks everyone! Authors, I'll do an editorial pass over the manuscript and send any comments shortly. In the meantime, the next steps for you are:

Merge any and all changes from this review into your main branch and issue a new version tag. (If you want to merge in the paper, you may, but it is not required that the actual manuscript live into the repo in perpetuity since JOSS will host it and you can simply add a badge link or whatever you like. But the actual changes to software and docs do need to be merged!)
Create a DOI for the contents of the repo at the same commit corresponding to that version tag, e.g. using figshare or Zenodo. Please make sure that the metadata (version number, title, author list, etc.) match those of your manuscript.
Post a comment here with the version number and DOI.

rkurchin commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

rkurchin commented 1 year ago

Minor editorial comments:

line 13: "obtained" is duplicated
line 14: you can probably remove "calculations" since you said that earlier in the sentence
lines 11 and 32-33: be consistent about hyphenation in phrase "net charge neutrality" (I would suggest either no hyphens at all, or if you read it as "the neutrality of net charge" as opposed to "charge neutrality in a net fashion" then perhaps "net-charge neutrality"...if you want a deeper dive than necessary on this distinction, check this out
37: I assume it's supposed to be "iterative" (or maybe "interactive"?) but in any case "interative" is not a word 😉
line 66: I would turn the comma into a period and break the "in addition" clause out to a new sentence

Broader conceptual comment: I think it's worth clarifying at least once that there's an underlying presumption of thermodynamic equilibrium in (most of) this. My suggestion would be simply modifying the end of the first sentence of the summary to read "...under the constraint of net charge neutrality and assumption of thermodynamic (quasi-)equilibrium" and perhaps also add "equilibrium" before "concentrations" on line 30. You could then perhaps add one more clarifying allusion to this idea in the paragraph beginning on line 68, since that's a nice bit of functionality for incorporating non-equilibrium information, if/when it is known.

Overall, this looks like a great little tool, and I'll definitely be keeping it in mind for my own work!

ajgoyal commented 1 year ago

Hi @rkurchin, thank you for the opportunity to review. I found the concept of JOSS very useful. I apologize for the delay from my side.

Congratulations to the authors!

rkurchin commented 1 year ago

Thanks for reviewing, and glad you liked it! Feel free to sign up to be on the volunteer list if you'd be interested in doing so more in the future! 😄

bjmorgan commented 1 year ago

Great, thanks everyone! Authors, I'll do an editorial pass over the manuscript and send any comments shortly. In the meantime, the next steps for you are:

Merge any and all changes from this review into your main branch and issue a new version tag. (If you want to merge in the paper, you may, but it is not required that the actual manuscript live into the repo in perpetuity since JOSS will host it and you can simply add a badge link or whatever you like. But the actual changes to software and docs do need to be merged!)

Create a DOI for the contents of the repo at the same commit corresponding to that version tag, e.g. using figshare or Zenodo. Please make sure that the metadata (version number, title, author list, etc.) match those of your manuscript.

Post a comment here with the version number and DOI.

The new version is tag number 1.0.0 → https://github.com/bjmorgan/py-sc-fermi/releases/tag/1.0.0
Version 1.0.0 is archived at Zenodo here: → 10.5281/zenodo.7567782

rkurchin commented 1 year ago

@editorialbot set 1.0.0 as version

editorialbot commented 1 year ago

Done! version is now 1.0.0

rkurchin commented 1 year ago

@editorialbot set 10.5281/zenodo.7567782 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7567782

rkurchin commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1039/d0ee00291g is OK
- 10.1039/b300139n is OK
- 10.1039/D1TA05112A is OK
- 10.1021/acs.chemmater.2c00944 is OK
- 10.1021/acsenergylett.7b01313.s001 is OK
- 10.1149/2.0011514jes is OK
- 10.1021/acs.inorgchem.1c00278 is OK
- 10.1039/d1tc02547c is OK
- 10.1016/j.commatsci.2022.111434 is OK
- 10.1016/j.cpc.2019.06.017 is OK
- 10.1038/s41524-022-00756-0 is OK
- 10.1016/j.cpc.2021.107946 is OK
- 10.1103/PhysRevMaterials.6.085401 is OK
- 10.1021/acsenergylett.2c01961 is OK
- 10.26434/chemrxiv-2021-hzrls is OK
- 10.1039/D1MH01539G is OK
- 10.1038/s41578-022-00433-0 is OK
- 10.1021/acsenergylett.1c00380.s001 is OK
- 10.1038/s41578-018-0026-7 is OK
- 10.1021/acs.chemmater.8b01135.s001 is OK
- 10.1021/acs.chemmater.9b04319 is OK

MISSING DOIs

- None

INVALID DOIs

- None

openjournals / joss-reviews