[REVIEW]: UPOsHam: A Python package for computing unstable periodic orbits in two degrees of freedom Hamiltonian systems

whedon commented 5 years ago

Submitting author: @WyLyu (WenYang Lyu) Repository: https://github.com/WyLyu/UPOsHam Version: v0.1.0 Editor: @kthyng Reviewer: @dpsanders, @JoshKarpel Archive: 10.5281/zenodo.3606676

Status

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Markdown: [![status](https://joss.theoj.org/papers/bc6d9d9b9254ef94543016a4c40fafd0/status.svg)](https://joss.theoj.org/papers/bc6d9d9b9254ef94543016a4c40fafd0)

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

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

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

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

Review checklist for @dpsanders

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 (@WyLyu) 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 @JoshKarpel

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 (@WyLyu) 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?

Shibabrat commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

dpsanders commented 4 years ago

There are a few typos and English issues (mainly singular / plural) in the paper that should be checked.

I think somewhere it needs to be made clearer exactly what is shown in the figures -- presumably contours of the Hamiltonian (which is not stated anywhere as far as I can see) and the periodic orbits computed by the code.

Other than that everything looks good and I recommend acceptance.

kthyng commented 4 years ago

@Shibabrat let us know when you've finished with @dpsanders comment!

Shibabrat commented 4 years ago

@kthyng @dpsanders we've made the corrections.

Shibabrat commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

dpsanders commented 4 years ago

Thanks, LGTM!

Shibabrat commented 4 years ago

@kthyng we are finished with the final changes.

kthyng commented 4 years ago

@Shibabrat Great! I see that the version is listed as 1.0.0. Is this still correct? I encourage you to set up a release of your code at the version you want, also: https://help.github.com/en/github/administering-a-repository/creating-releases

kthyng commented 4 years ago

After that, please archive your code at something like Zenodo, then report the DOI here.

kthyng commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

kthyng commented 4 years ago

@whedon check references

whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.1016/S0010-4655(97)00131-8 is OK
- 10.1063/1.166509 is OK
- 10.1103/PhysRevE.98.052214 is OK
- 10.1016/j.cnsns.2016.10.021 is OK
- 10.1103/PhysRevE.100.022204 is OK
- 10.1134/S1560354716060034 is OK
- 10.1063/1.439276 is OK
- 10.1063/1.442459 is OK
- 10.1063/1.456915 is OK
- 10.1063/1.456914 is OK

MISSING DOIs

- https://doi.org/10.1142/9789812792617_0222 may be missing for title: Dynamical systems, the three-body problem and space mission  design
- https://doi.org/10.1007/978-1-4612-3486-9 may be missing for title: Practical Numerical Algorithms for Chaotic Systems

INVALID DOIs

- None

kthyng commented 4 years ago

I am editing your paper now and I don't know how to fix this sentence, but it is grammatically incorrect with "the dynamics":

"In two degree of freedom systems, the phase space is four dimensional and the dynamics is on the three dimensional energy surface..."

labarba commented 4 years ago

Hi @kthyng ... it looks fine to me, but perhaps a verb change would help. Also, add hyphens to the compound modifiers:

"In two-degree-of-freedom systems, the phase space is four dimensional and the dynamics takes place on the three-dimensional energy surface…"

kthyng commented 4 years ago

Also, you go between using and not using your acronym UPO frequently through the paper — seems a little odd but is ok.

I've made more small grammar changes in PR #60 that you can merge if you agree with the changes.

kthyng commented 4 years ago

Here's another PR for your references: #61

Shibabrat commented 4 years ago

@kthyng

@Shibabrat Great! I see that the version is listed as 1.0.0. Is this still correct? I encourage you to set up a release of your code at the version you want, also: https://help.github.com/en/github/administering-a-repository/creating-releases

I think it will be better to say version = 0.1.0. Ok, let me do those merges and changes now.

@labarba

Hi @kthyng ... it looks fine to me, but perhaps a verb change would help. Also, add hyphens to the compound modifiers:

"In two-degree-of-freedom systems, the phase space is four dimensional and the dynamics takes place on the three-dimensional energy surface…"

so should I change all occurrences of degree of freedom to degree-of-freedom?

Shibabrat commented 4 years ago

@kthyng http://doi.org/10.5281/zenodo.3601504 which I've tagged as v0.1.0 release. Please note that at the moment doi on the readme links to the JOSS submitted version.

kthyng commented 4 years ago

@whedon set v0.1.0 as version

whedon commented 4 years ago

OK. v0.1.0 is the version.

kthyng commented 4 years ago

@whedon set 10.5281/zenodo.3601504 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.3601504 is the archive.

kthyng commented 4 years ago

so should I change all occurrences of degree of freedom to degree-of-freedom?

I think so, yes.

kthyng commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

kthyng commented 4 years ago

so should I change all occurrences of degree of freedom to degree-of-freedom?

I think so, yes.

@Shibabrat Sorry I should add that the "two-" at the beginning is important. Without that, it is two of the systems, not specifying the degree of the systems.

kthyng commented 4 years ago

Let me know when you're finished

Shibabrat commented 4 years ago

@kthyng ok. I've added the "two-" to the title and other occurrences in the paper. For consistency, I've also updated the zenodo archive and here is the doi: 10.5281/zenodo.3606676

kthyng commented 4 years ago

@whedon set 10.5281/zenodo.3606676 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.3606676 is the archive.

kthyng commented 4 years ago

Ok I think we're good to go!!

kthyng commented 4 years ago

@whedon accept

whedon commented 4 years ago

Attempting dry run of processing paper acceptance...

whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.1142/9789812792617_0222 is OK
- 10.1007/978-1-4612-3486-9 is OK
- 10.1016/S0010-4655(97)00131-8 is OK
- 10.1063/1.166509 is OK
- 10.1103/PhysRevE.98.052214 is OK
- 10.1016/j.cnsns.2016.10.021 is OK
- 10.1103/PhysRevE.100.022204 is OK
- 10.1134/S1560354716060034 is OK
- 10.1063/1.439276 is OK
- 10.1063/1.442459 is OK
- 10.1063/1.456915 is OK
- 10.1063/1.456914 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 4 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1212

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1212, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

kthyng commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

kthyng commented 4 years ago

@Shibabrat I think something that you changed in your last commit altered the ability of the paper to be processed correctly. Maybe it's the line breaks, like in the title?

Shibabrat commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

PDF failed to compile for issue #1684 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon.rb:145:in check_fields': Paper YAML header is missing expected fields: date (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon.rb:87:ininitialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon/processor.rb:36:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon/processor.rb:36:inset_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/bin/whedon:55:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/bin/whedon:116:in<top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

Shibabrat commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

PDF failed to compile for issue #1684 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon.rb:145:in check_fields': Paper YAML header is missing expected fields: date (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon.rb:87:ininitialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon/processor.rb:36:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon/processor.rb:36:inset_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/bin/whedon:55:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/bin/whedon:116:in<top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

Shibabrat commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

PDF failed to compile for issue #1684 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon.rb:145:in check_fields': Paper YAML header is missing expected fields: date (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon.rb:87:ininitialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon/processor.rb:36:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon/processor.rb:36:inset_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/bin/whedon:55:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/bin/whedon:116:in<top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

Shibabrat commented 4 years ago

@kthyng not sure what happened but I made sure the markdown and pdf file looks ok on my end. Is whedon using the zenodo link to build the pdf for the paper? I made sure there aren't any line breaks in the title.

Shibabrat commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

PDF failed to compile for issue #1684 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon.rb:145:in check_fields': Paper YAML header is missing expected fields: date (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon.rb:87:ininitialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon/processor.rb:36:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon/processor.rb:36:inset_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/bin/whedon:55:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/bin/whedon:116:in<top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

openjournals / joss-reviews