[REVIEW]: xtal2png: A Python package for representing crystal structure as PNG files #4528

editorialbot · 2022-06-29T14:34:26Z

Submitting author: @sgbaird (Sterling Baird)
Repository: https://github.com/sparks-baird/xtal2png
Branch with paper.md (empty if default branch): main
Version: 0.9.4
Editor: @rkurchin
Reviewers: @dandavies99, @PeterKraus
Archive: 10.5281/zenodo.6941663

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/0c704f6ae9739c1e97e05ae0ad57aecb/status.svg)](https://joss.theoj.org/papers/0c704f6ae9739c1e97e05ae0ad57aecb)

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

@dandavies99 & @PeterKraus, 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:

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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 @PeterKraus

📝 Checklist for @dandavies99

The text was updated successfully, but these errors were encountered:

editorialbot · 2022-06-29T14:34:28Z

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editorialbot · 2022-06-29T14:34:31Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.12 s (407.5 files/s, 86568.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          14            522            745           1799
Jupyter Notebook                 9              0           4033           1412
Markdown                        12            299              0            923
YAML                             8             34            126            278
TeX                              2             14              0            187
INI                              1             11              0             73
HTML                             1              0              0             64
Dockerfile                       1             15             23             26
make                             1              6              8             15
TOML                             1              1              3              5
-------------------------------------------------------------------------------
SUM:                            50            902           4938           4782
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2022-06-29T14:34:33Z

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

OK DOIs

- 10.48550/ARXIV.1910.00617 is OK
- 10.1038/s41467-020-19964-7 is OK
- 10.48550/ARXIV.1609.02907 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1038/s41524-021-00545-1 is OK
- 10.26434/chemrxiv.11869026.v1 is OK
- 10.48550/ARXIV.1710.10324 is OK
- 10.1103/PhysRevLett.120.145301 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-06-29T14:34:34Z

Wordcount for paper.md is 913

editorialbot · 2022-06-29T14:48:52Z

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

PeterKraus · 2022-06-29T18:45:57Z

Review checklist for @PeterKraus

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 https://github.com/sparks-baird/xtal2png?
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 (@sgbaird) 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: 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?
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?

rkurchin · 2022-07-05T16:28:17Z

@dandavies99 and @PeterKraus, let me know if you have any questions about getting your reviews started! Feel free to file issues in the project repository as you do so; please link to this issue for easy tracking.

PeterKraus · 2022-07-06T07:05:22Z

@rkurchin it's on my todo list for tomorrow.

PeterKraus · 2022-07-07T08:16:40Z

Alright, this is quite an interesting software package, and it's in a fairly good state. I've made a couple of issues on the project github, I will play around with the software over the next few days. @sgbaird, please let me know (here or in the issues) once you want me to have another look.

sgbaird · 2022-07-08T05:46:58Z

@PeterKraus thanks for your feedback! I've addressed each of your comments for the Software paper and the Documentation issues. It's ready for a second look!

(p.s. I wasn't sure if I should be marking the tasks/checkboxes as done or not, so I left them unchecked) EDIT: the ones in the xtal2png repo issues

rkurchin · 2022-07-08T14:47:20Z

(@sgbaird to clarify for you, the checklists are to be filled out by the reviewers, so leaving them unchecked was right 🙂 )

PeterKraus · 2022-07-08T17:06:15Z

I'll have a look on Monday. Have a nice weekend!

dandavies99 · 2022-07-11T07:24:50Z

Review checklist for @dandavies99

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 https://github.com/sparks-baird/xtal2png?
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 (@sgbaird) 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: 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?
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?

dandavies99 · 2022-07-11T08:29:56Z

Hi @sgbaird, this software is looking great. @PeterKraus - thanks for getting there first and carrying out such a thorough review! You've covered almost all of the main points I spotted already. I'll update comments in this thread and open specific issues as I go through the checklist. A few initial minor points from me (apologies if these are already being addressed in separate issues):

Installation

There are two conflicting sets of install instructions on the README: conda create -n xtal2png -c conda-forge xtal2png m3gnet at the top and conda env create -n xtal2png -c conda-forge xtal2png in the Installation section. The inclusion of m3gnet results in a very long (possibly infinite at the time of writing 😉) environment solving time. I understand m3gnet is optional, which is explained, but it might be worth not including this in the first installation instruction to save the user some frustration.
The Example in the README doesn't work straight away for me. I think because XtalConverter is in xtal2png.core now, not in xtal2png. Similarly example_structures is now in xtal2png.utils.data.

Docs

Are fantastic. @PeterKraus has made some excellent suggestions.
On ReadTheDocs, The "Getting Started, Output" section has the Original, Decoded and Relaxed Decoded outputs side by side regardless of page width. Could do with being one on top of the other.

Software paper

The paper is one of the longer JOSS papers I've come across, certainly within chemistry, but I like the level of detail so personally think this is fine. It hits all the criteria above in the checklist.

PeterKraus · 2022-07-11T12:52:12Z

@editorialbot generate pdf

editorialbot · 2022-07-11T12:53:27Z

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

PeterKraus · 2022-07-11T13:31:08Z

Looks really great. I'll give the paper another read, and I have a few crystal structures that I'd like to test out, but apart from that I'm more than happy.

dandavies99 · 2022-07-11T15:08:11Z

From my side, once the minor points I've mentioned above are addressed I will tick off Installation and Functionality. Other than that, I'm also happy and look forward to seeing this package in action - I'm sure it'll be very widely used.

PeterKraus · 2022-07-15T09:14:21Z

Alright, I have made two more issues, but they are not a blocker for me accepting. After you address the comments in sparks-baird/xtal2png#144, feel free to close the issue. The documentation issue, sparks-baird/xtal2png#146, can be closed already.

@rkurchin, do I need to do anything with the bot to recommend accept?

rkurchin · 2022-07-29T21:36:03Z

@editorialbot set 0.9.3 as version

editorialbot · 2022-07-29T21:36:04Z

Done! version is now 0.9.3

rkurchin · 2022-07-29T21:36:10Z

@editorialbot recommend-accept

editorialbot · 2022-07-29T21:36:11Z

Attempting dry run of processing paper acceptance...

editorialbot · 2022-07-29T21:36:17Z

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

OK DOIs

- 10.48550/ARXIV.1610.02415 is OK
- 10.1021/acscentsci.7b00572 is OK
- 10.48550/ARXIV.1910.00617 is OK
- 10.1038/s41467-020-19964-7 is OK
- 10.48550/ARXIV.1609.02907 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1016/j.matt.2021.11.032 is OK
- 10.1145/3528233.3530757 is OK
- 10.48550/ARXIV.2204.00056 is OK
- 10.1038/s41524-021-00545-1 is OK
- 10.26434/chemrxiv.11869026.v1 is OK
- 10.1021/ci00057a005 is OK
- 10.48550/ARXIV.1710.10324 is OK
- 10.1103/PhysRevLett.120.145301 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-07-29T21:37:28Z

⚠️ Error prepararing paper acceptance. The generated XML metadata file is invalid.

IDREFS attribute rid references an unknown ID "ref-sahariaPaletteImagetoImageDiffusion2022"

sgbaird · 2022-07-29T21:38:40Z

Ah... woops. I thought I had changed it back to sahariaPaletteImagetoImageDiffusion2022, but looks like it stayed as sahariaPaletteImagetoImageDiffusion2022a.

sgbaird · 2022-07-29T21:43:36Z

Version: v0.9.4
DOI: 10.5281/zenodo.6941663

sgbaird · 2022-07-29T21:44:40Z

@editorialbot check references

editorialbot · 2022-07-29T21:44:45Z

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

OK DOIs

- 10.48550/ARXIV.1610.02415 is OK
- 10.1021/acscentsci.7b00572 is OK
- 10.48550/ARXIV.1910.00617 is OK
- 10.1038/s41467-020-19964-7 is OK
- 10.48550/ARXIV.1609.02907 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1016/j.matt.2021.11.032 is OK
- 10.1145/3528233.3530757 is OK
- 10.48550/ARXIV.2204.00056 is OK
- 10.1038/s41524-021-00545-1 is OK
- 10.26434/chemrxiv.11869026.v1 is OK
- 10.1021/ci00057a005 is OK
- 10.48550/ARXIV.1710.10324 is OK
- 10.1103/PhysRevLett.120.145301 is OK

MISSING DOIs

- None

INVALID DOIs

- None

rkurchin · 2022-08-01T22:24:51Z

@editorialbot set 0.9.4 as version

editorialbot · 2022-08-01T22:24:53Z

Done! version is now 0.9.4

rkurchin · 2022-08-01T22:25:09Z

@editorialbot set 10.5281/zenodo.6941663 as archive

editorialbot · 2022-08-01T22:25:11Z

Done! Archive is now 10.5281/zenodo.6941663

rkurchin · 2022-08-01T22:25:45Z

@editorialbot recommend-accept

(my apologies for the extra delay fixing this very tiny thing 😆 )

editorialbot · 2022-08-01T22:25:46Z

Attempting dry run of processing paper acceptance...

editorialbot · 2022-08-01T22:25:52Z

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

OK DOIs

- 10.48550/ARXIV.1610.02415 is OK
- 10.1021/acscentsci.7b00572 is OK
- 10.48550/ARXIV.1910.00617 is OK
- 10.1038/s41467-020-19964-7 is OK
- 10.48550/ARXIV.1609.02907 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1016/j.matt.2021.11.032 is OK
- 10.1145/3528233.3530757 is OK
- 10.48550/ARXIV.2204.00056 is OK
- 10.1038/s41524-021-00545-1 is OK
- 10.26434/chemrxiv.11869026.v1 is OK
- 10.1021/ci00057a005 is OK
- 10.48550/ARXIV.1710.10324 is OK
- 10.1103/PhysRevLett.120.145301 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-08-01T22:27:06Z

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3409, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

arfon · 2022-08-03T05:32:38Z

@editorialbot accept

editorialbot · 2022-08-03T05:32:39Z

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

editorialbot · 2022-08-03T05:35:23Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2022-08-03T05:35:23Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04528 joss-papers#3410
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04528
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon · 2022-08-03T05:51:49Z

@dandavies99, @PeterKraus – many thanks for your reviews here and to @rkurchin for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@sgbaird – your paper is now accepted and published in JOSS ⚡🚀💥

editorialbot · 2022-08-03T05:51:52Z

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

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editorialbot added Dockerfile Mathematica Python review labels Jun 29, 2022

editorialbot assigned rkurchin Jun 29, 2022

editorialbot mentioned this issue Jun 29, 2022

[PRE REVIEW]: xtal2png: A Python package for representing crystal structure as PNG files #4465

Closed

editorialbot added the TeX label Jun 29, 2022

This was referenced Jul 7, 2022

JOSS paper review - Software paper sparks-baird/xtal2png#144

Closed

JOSS paper review - Documentation sparks-baird/xtal2png#146

Closed

This was referenced Jul 15, 2022

Suggestion: Add CLI parameter for max_sites sparks-baird/xtal2png#179

Closed

Bug: xtal2png error with fractional occupancy sparks-baird/xtal2png#180

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Aug 1, 2022

editorialbot added accepted published Papers published in JOSS labels Aug 3, 2022

arfon closed this as completed Aug 3, 2022

editorialbot mentioned this issue Aug 8, 2024

[PRE REVIEW]: reflectorch: a deep learning package for X-ray and neutron reflectometry #7089

Open

editorialbot mentioned this issue Sep 5, 2024

[PRE REVIEW]: cifkit: A user-friendly Python package for high-throughput CIF Analysis #7184

Closed

[REVIEW]: xtal2png: A Python package for representing crystal structure as PNG files #4528

[REVIEW]: xtal2png: A Python package for representing crystal structure as PNG files #4528

Comments

editorialbot commented Jun 29, 2022 • edited Loading

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Reviewer instructions & questions

Checklists

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PeterKraus commented Jun 29, 2022 • edited Loading

Review checklist for @PeterKraus

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

rkurchin commented Jul 5, 2022

PeterKraus commented Jul 6, 2022

PeterKraus commented Jul 7, 2022 • edited Loading

sgbaird commented Jul 8, 2022 • edited Loading

rkurchin commented Jul 8, 2022

PeterKraus commented Jul 8, 2022

dandavies99 commented Jul 11, 2022 • edited Loading

Review checklist for @dandavies99

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

dandavies99 commented Jul 11, 2022 • edited Loading

Installation

Docs

Software paper

PeterKraus commented Jul 11, 2022

editorialbot commented Jul 11, 2022

PeterKraus commented Jul 11, 2022

dandavies99 commented Jul 11, 2022

PeterKraus commented Jul 15, 2022

rkurchin commented Jul 29, 2022

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