[REVIEW]: Kanapy: A Python package for generating complex synthetic polycrystalline microstructures.

whedon commented 5 years ago

Submitting author: @mrgprasad (Mahesh R. G. Prasad) Repository: https://github.com/mrgprasad/kanapy Version: v1.0.0 Editor: @Kevin-Mattheus-Moerman Reviewer: @heprom, @KedoKudo, @chennachaos Archive: 10.5281/zenodo.3529591

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/6975adc753930bdd05326479e5ca2790"><img src="https://joss.theoj.org/papers/6975adc753930bdd05326479e5ca2790/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/6975adc753930bdd05326479e5ca2790/status.svg)](https://joss.theoj.org/papers/6975adc753930bdd05326479e5ca2790)

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

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

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @Kevin-Mattheus-Moerman know.

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

Review checklist for @heprom

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[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?

Review checklist for @KedoKudo

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[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?

Review checklist for @chennachaos

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[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?

whedon commented 5 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @heprom, @KedoKudo, @chennachaos it looks like you're currently assigned to review this paper :tada:.

:star: Important :star:

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

Kevin-Mattheus-Moerman commented 5 years ago

@mrgprasad @heprom, @KedoKudo, @chennachaos :wave: this is where the review will take place. The instructions and the checklists at the top will guide you through the process. Let me know if you have questions. Let the reviewing begin :tada:

Kevin-Mattheus-Moerman commented 5 years ago

@putanowr now that I have 3 reviewers it is okay if you are not able to join us. The review has now started. However if you are keen to help and the review process is still ongoing mid-October (which is when you said you might have time over at https://github.com/openjournals/joss-reviews/issues/1634), I can still add you here.

putanowr commented 5 years ago

Well, if you add me as sort of backu-reviewer I understand I will be notified about the raised issues. This might be helpful as I can get more familiar with the whole issue and will have more incentive to look how the journal operates. Of course if that not disturb the normal process in any way.

Regard,

Roman

September 16, 2019 10:57 AM, "Kevin Mattheus Moerman" <notifications@github.com (mailto:%22Kevin%20Mattheus%20Moerman%22%20notifications@github.com)> wrote: @putanowr (https://github.com/putanowr) now that I have 3 reviewers it is okay if you are not able to join us. The review has now started. However if you are keen to help and the review process is still ongoing mid-October (which is when you said you might have time over at #1634 (https://github.com/openjournals/joss-reviews/issues/1634)), I can still add you here.

—

You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub (https://github.com/openjournals/joss-reviews/issues/1732?email_source=notifications&email_token=ABWCIO3Z25LRXMFHUG7QEATQJ5C7LA5CNFSM4IW7PCZ2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6YQA3I#issuecomment-531693677), or mute the thread (https://github.com/notifications/unsubscribe-auth/ABWCIO67KOTECC2TG4553HDQJ5C7LANCNFSM4IW7PCZQ).

Roman Putanowicz, PhD <Roman.Putanowicz@L5.pk.edu.pl (mailto:Roman.Putanowicz@L5.pk.edu.pl)> Institute for Computational Civil Engng (L-5) Dept. of Civil Engng, Cracow Univ. of Technology www.l5.pk.edu.pl, tel. +48 12 628 2569, fax 2034

KedoKudo commented 5 years ago

@Kevin-Mattheus-Moerman After carefully reviewing kanapy, I think the following aspects of kanapy could be improved:

Add a CLI to allow easy integration into existing workflow on a high performance computing environment (https://github.com/mrgprasad/kanapy/issues/2).
The documentation can benefit from the features laid out in https://github.com/mrgprasad/kanapy/issues/3
Some other minor improvements detailed in https://github.com/mrgprasad/kanapy/issues/4

The writing of the summary is adequate, but I hope the author could add a few sentences to compare kanapy with existing synthetic microstructure construction softwares (Dream.3D for example) to highlight the innovative aspect of kanapy. Also, I noticed that the acknowledge part of paper.md is empty, which I am not sure whether this is intentional or not.

mrgprasad commented 5 years ago

@KedoKudo Thank you for taking time and reviewing the repo and the paper. I will make the necessary changes and get back to you soon.

chennachaos commented 5 years ago

Hi @mrgprasad. I have started the review for Kanapy. I have a remark related to State of the field in the Software paper section.

The paper discusses the issues with a couple of techniques used for generating synthetic microstructures, and then presents algorithms used in Kanapy, which is good. But, it does not mention anything about the need for Kanapy package. To convince the reader about Kanapy, it is important to address the following questions. 1.) What is motivation behind developing Kanapy? 2.) What are the advantages of Kanapy over other software libraries used for the generation of microstructures, for example, Dream.3D and Neper? 3.) Does Kanapy address any limitations of the existing libraries? 4.) Are there any specific features in Kanapy that are not available in other libraries? If so, what are they?

mrgprasad commented 5 years ago

@chennachaos Thank you for the paper review and pointing out that I have skipped over the actual motivation for developing Kanapy. I will address this and the related questions and push a new version of the paper soon.

mrgprasad commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

mrgprasad commented 5 years ago

@Kevin-Mattheus-Moerman, @KedoKudo, @chennachaos and @heprom I have pushed an update to the Kanapy repo based on KedoKudo's review.

mrgprasad commented 5 years ago

@KedoKudo I have updated the software paper based on your comments. Do let me know if you have any further suggestions. Also, I have removed the acknowledgement section.

@chennachaos With this update I have also tried to address our queries. I hope the motivation for Kanapy's development, its design and unique features and how it addresses the limitations of other software libraries is clear now.

KedoKudo commented 5 years ago

@mrgprasad @Kevin-Mattheus-Moerman I am happy with the current state of kanapy, and I would like to recommend this package for publication.

Kevin-Mattheus-Moerman commented 5 years ago

@KedoKudo thanks for your help here :tada:

Kevin-Mattheus-Moerman commented 5 years ago

@heprom can you give us an indication as to when you will be able to complete this review?

chennachaos commented 5 years ago

Hi @mrgprasad. The automated tests work. However, there are some warning messages at the end (see the attached image) that has the potential to confuse the users.

I suggesting fixing this issue.

tests-warning-messages

chennachaos commented 5 years ago

@mrgprasad A statement of need for Documentation is missing.

Consider adding a paragraph on 'motivation' behind Kanapy in the Overview section of the documentation.

I will open these two as issues in your Github repo so we can track them.

mrgprasad commented 5 years ago

@chennachaos I have pushed an update to Kanapy's repo based on your review. I have also updated the issues you have opened on Kanapy's repo. Do let me know if additional changes are necessary.

chennachaos commented 5 years ago

Hi @mrgprasad. Thank you for the updates.

chennachaos commented 5 years ago

Hi @Kevin-Mattheus-Moerman, I have completed the review. @mrgprasad has been prompt in responding to my questions and remarks. I am happy with the current state of the Kanapy package.

I recommend the Kanapy software package for publication in the JOSS.

Thank you for the opportunity.

heprom commented 5 years ago

Yes I'm doing it today.

On Thu, Oct 10, 2019 at 9:06 AM Kevin Mattheus Moerman < notifications@github.com> wrote:

@heprom https://github.com/heprom can you give us an indication as to when you will be able to complete this review?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/1732?email_source=notifications&email_token=AFRG4L6V2NCDE5HJ4NMXVM3QN3H6PA5CNFSM4IW7PCZ2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEA3DA3Y#issuecomment-540422255, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFRG4L2NYGGQAUMWHX3N3WDQN3H6PANCNFSM4IW7PCZQ .

heprom commented 5 years ago

Hi @Kevin-Mattheus-Moerman I have done a first pass at reading the paper and testing the code. There is a small bug in the examples (I thing after moving to json input files): the input file in ellipsoid_pack.py has not been changed which result in an error when running the example.

heprom commented 5 years ago

A comment on the paper: first it is concise and well written. I recommend changing from "With the advent of additive manufacturing, the processing steps usually result in rather complex microstructures with elongated grains and strong crystallographic textures in metals." to something less reductive like: "Metallic material processing (including additive manufacturing) often result in complex microstructures with elongated grains and strong crystallographic textures."

mrgprasad commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

mrgprasad commented 5 years ago

@heprom Thank you for the software and paper review. I have pushed an update to Kanapy's repo. With this update I have fixed the bug in ellipsoid_pack.py file and the corrected the above mentioned sentence in the JOSS paper.

Kevin-Mattheus-Moerman commented 5 years ago

@heprom thanks for your review comments! Do you feel @mrgprasad has addressed the issues you raised?

heprom commented 5 years ago

yes I'm happy with the software now.

On Sat, Oct 19, 2019 at 10:13 PM Kevin Mattheus Moerman < notifications@github.com> wrote:

@heprom https://github.com/heprom thanks for your review comments! Do you feel @mrgprasad https://github.com/mrgprasad has addressed the issues you raised?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/1732?email_source=notifications&email_token=AFRG4L4SXKLXDL6EJTTN7UTQPNS6XA5CNFSM4IW7PCZ2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEBX3ZPY#issuecomment-544193727, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFRG4L25AC7JBWEHYQ3BGN3QPNS6XANCNFSM4IW7PCZQ .

Kevin-Mattheus-Moerman commented 5 years ago

@heprom thanks. In that case are you able to tick the last box (example usage)?

heprom commented 5 years ago

another small detail in the examples (both): shouldn't the path to the input file be defined as

inputFile = os.path.join(os.getcwd(), 'stat_input.json')

so that it is plateform independent. I'm running linux so it works for me as is but I guess this will not work on windows.

mrgprasad commented 5 years ago

@heprom Currently we intend to provide Kanapy for Linux & MAC OS platforms only. In the future, with additional functionalities (that is still under development) we may release it for Windows too.

heprom commented 5 years ago

ok good then.

mrgprasad commented 5 years ago

@Kevin-Mattheus-Moerman Please let me know if anything more is required from my side.

For a future release of Kanapy, we are planning to include functionalities for modeling crystallographic texture. This would be a major update for the software. In this regard:

Is it possible to submit the software for review again?
If not, can we update the JOSS paper somehow?

mrgprasad commented 5 years ago

@Kevin-Mattheus-Moerman Since the review process is complete, could you please give an update of the status of this submission?

Kevin-Mattheus-Moerman commented 5 years ago

@mrgprasad thanks for the reminder. I'll review your paper now and will get back with comments.

Kevin-Mattheus-Moerman commented 5 years ago

@whedon check references

whedon commented 5 years ago

Attempting to check references...

whedon commented 5 years ago


OK DOIs

- 10.1186/2193-9772-3-5 is OK

MISSING DOIs

- https://doi.org/10.1016/j.cma.2011.01.002 may be missing for title: Large-scale 3D random polycrystals for the finite element method: Generation, meshing and remeshing
- https://doi.org/10.1016/j.commatsci.2014.04.011 may be missing for title: The modeling scheme to evaluate the influence of microstructure features on microcrack formation of DP-steel: The artificial microstructure model and its application to predict the strain hardening behavior
- https://doi.org/10.1103/physreve.88.053312 may be missing for title: Precise algorithm to generate random sequential addition of hard hyperspheres at saturation.
- https://doi.org/10.1016/s0167-8396(01)00049-8 may be missing for title: An algebraic condition for the separation of two ellipsoids

INVALID DOIs

- None

Kevin-Mattheus-Moerman commented 5 years ago

@mrgprasad

[x] Your paper is about to be processed for acceptance. Please double check your paper and ensure you are happy with the author list and acknowledgements as well.
[x] Can you work on those missing DOI's?
[x] Can you check this citation: (Groeber & Jackson, 2014, p. @Vajragupta2014)? The p. seems you indicate your citing a page but the number is missing?
[x] Check citation syntax for: Wang et al. (Wang, Wang, & Kim, 2001), see also: https://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html#citation_syntax
[x] I suggest removal of the space in workflows in ...to create individual work flows for generating....
[x] Can you add citations to SciPy and NumPy? in ...from the Scipy package together with various Numpy array operations...

mrgprasad commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

mrgprasad commented 5 years ago

@whedon check references

whedon commented 5 years ago

Attempting to check references...

whedon commented 5 years ago


OK DOIs

- 10.1186/2193-9772-3-5 is OK
- 10.1016/j.cma.2011.01.002 is OK
- 10.1016/j.commatsci.2014.04.011 is OK
- 10.1016/S0167-8396(01)00049-8 is OK
- 10.1103/PhysRevE.88.053312 is OK

MISSING DOIs

- None

INVALID DOIs

- None

mrgprasad commented 5 years ago

@Kevin-Mattheus-Moerman With the latest push to the repo, I have made the necessary changes for the paper. DOI's don't exist for scipy, numpy, pybind11 and eigen libraries. Please let me know if additional changes are required.

openjournals / joss-reviews