[REVIEW]: MCycle: A Python package for 1D sizing and analysis of thermodynamic power cycles

whedon commented 6 years ago

Submitting author: @momargoh (Momar Hughes) Repository: https://github.com/momargoh/MCycle Version: v0.1.2 Editor: @katyhuff Reviewers: @Tabeel, @puncan Archive: 10.5281/zenodo.1324221

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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) 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

@puncan, 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.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @katyhuff know.

Review checklist for @puncan

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] Version: Does the release version given match the GitHub release (v0.1.2)?
[x] Authorship: Has the submitting author (@momargoh) 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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
[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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @Tabeel

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] Version: Does the release version given match the GitHub release (v0.1.2)?
[x] Authorship: Has the submitting author (@momargoh) 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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
[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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

whedon commented 6 years ago

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @puncan it looks like you're currently assigned as the reviewer for 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:

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

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

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whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

--> Check article proof :page_facing_up: <--

katyhuff commented 6 years ago

@whedon assign @Tabeel as reviewer

whedon commented 6 years ago

OK, the reviewer is @Tabeel

katyhuff commented 6 years ago

@whedon add @puncan as reviewer

whedon commented 6 years ago

OK, @puncan is now a reviewer

katyhuff commented 6 years ago

Ok, both @puncan and @Tabeel will be reviewers for this submission. Each of you has a review checklist above. Please use the one with your name on it.

ghost commented 6 years ago

Hi @katyhuff, I am unable to make changes to the review checklist. Am I am missing something?

katyhuff commented 6 years ago

@Tabeel there's a little note about this up at the top of the issue, but it's easy to miss.

It says:

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

ghost commented 6 years ago

Thank you

arfon commented 6 years ago

@puncan - it looks like you're only part way through your review here. Any chance you could complete this in the next week or so?

puncan commented 6 years ago

Yes, my apologies. It got away from me. Certainly within a week.

-Paul

On Fri, Jun 15, 2018 at 1:02 PM Arfon Smith notifications@github.com wrote:

@puncan https://github.com/puncan - it looks like you're only part way through your review here. Any chance you could complete this in the next week or so?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/710#issuecomment-397727647, or mute the thread https://github.com/notifications/unsubscribe-auth/AgSGWflCfQTf2ml09aHLVdk6IpmSBo2Nks5t9BLagaJpZM4TuU9R .

puncan commented 6 years ago

There were a couple I checked off after creating new issues. Am I doing this right?

momargoh commented 6 years ago

Thanks @puncan I'll fix up the issues you've raised now.

momargoh commented 6 years ago

Also, there is a newer version of MCycle that uses Cython; it has a different build and different directory structure. At the moment it's just in the cython fork, I haven't pulled it to master yet. Could I update my joss submission to consider this version?

puncan commented 6 years ago

I don’t see why not.

Sent from my iPhone

On Jun 21, 2018, at 7:20 PM, Momar Hughes notifications@github.com wrote:

Also, there is a newer version of MCycle that uses Cython; it has a different build and different directory structure. At the moment it's just in the cython fork, I haven't pulled it to master yet. Could I update my joss submission to consider this version?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

katyhuff commented 6 years ago

Yes, go right ahead and update to the new version. Sorry for the delay in responding. It looks like all of the issues raised by the reviewers have now been handled. Is that correct @puncan @Tabeel @momargoh ?

If so, then @momargoh at this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

puncan commented 6 years ago

Sounds good to me.

On Mon, Jul 23, 2018 at 6:22 AM Katy Huff notifications@github.com wrote:

Yes, go right ahead and update to the new version. Sorry for the delay in responding. It looks like all of the issues raised by the reviewers have now been handled. Is that correct @puncan https://github.com/puncan @Tabeel https://github.com/Tabeel @momargoh https://github.com/momargoh ?

If so, then @momargoh https://github.com/momargoh at this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/710#issuecomment-407055895, or mute the thread https://github.com/notifications/unsubscribe-auth/AgSGWeaUTRLBzznfPMjqGC8DolRscKqiks5uJc4QgaJpZM4TuU9R .

momargoh commented 6 years ago

No, I haven't handled all the issues raised by @puncan yet, doing so now. I'm having trouble committing the new Cython-based version to pip due to problems creating a cross-platform dist wheel. The package can be built from the source using python3 setup.py install and similarly the docs will not be hosted properly until the package is on pip, so at the moment they can just be built from the source using Sphinx3 make html. Is this OK: the package needing to be built from source instead of available from pip?

momargoh commented 6 years ago

OK, the docs are building OK https://mcycle.readthedocs.io/index.html. For now the source has to be installed from source as opposed to from pip. I have updated my JOSS submission to v1.0.0: the latest version of the source code.

momargoh commented 6 years ago

Zenodo is ready to go. I will wait for @puncan 's approval, regarding the issues he raised, before creating the DOI

katyhuff commented 6 years ago

It looks to me like @puncan approved this a few comments ago. (https://github.com/openjournals/joss-reviews/issues/710#issuecomment-407145425)

It seems you can go ahead and make the DOI whenever you're ready.

momargoh commented 6 years ago

doi:10.5281/zenodo.1324221 https://zenodo.org/record/1324222#.W2BdfxiuY5k

katyhuff commented 6 years ago

Excellent!

katyhuff commented 6 years ago

@whedon set 10.5281/zenodo.1324221 as archive

whedon commented 6 years ago

OK. 10.5281/zenodo.1324221 is the archive.

katyhuff commented 6 years ago

@arfon This submission is ready for acceptance! Congratulations @momargoh , and thank you for your reviews @Tabeel and @puncan !

arfon commented 6 years ago

@Tabeel, @puncan - many thanks for your reviews here and to @katyhuff for editing this submission ✨

@momargoh - your paper is now accepted and your DOI is https://doi.org/10.21105/joss.00710 :zap: :rocket: :boom:

whedon commented 6 years ago

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