Joss-reviews: [REVIEW]: PYCV: a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python

[whedon]

Submitting author: @tonigi (Toni Giorgino)
Repository: https://github.com/giorginolab/plumed2-pycv/
Version: v1.1
Editor: @arfon
Reviewer: @amritagos, @carlocamilloni
Archive: 10.5281/zenodo.3480171

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/8fe944dca9a4c5c45dd778f8518b0251"><img src="https://joss.theoj.org/papers/8fe944dca9a4c5c45dd778f8518b0251/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/8fe944dca9a4c5c45dd778f8518b0251/status.svg)](https://joss.theoj.org/papers/8fe944dca9a4c5c45dd778f8518b0251)

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

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

1. Make sure you're logged in to your GitHub account
2. 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 @arfon know.

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

Review checklist for @amritagos

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 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 (@tonigi) 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?
• [ ] 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?
• [ ] 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 @carlocamilloni

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 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 (@tonigi) 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]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @amritagos, @carlocamilloni 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:

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

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

Attempting PDF compilation. Reticulating splines etc...

[arfon]

@amritagos, @carlocamilloni - please carry out your review in this issue by updating the checklist above and giving feedback in this issue. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Any questions/concerns please let me know.

[arfon]

@whedon generate pdf from branch joss-paper

[whedon]

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...

[whedon]

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

[amritagos]

@whedon check references

[whedon]

Attempting to check references...

[tonigi]

Perhaps stuck because the paper is not in the default branch? Re-committed there and retrying.

[tonigi]

@whedon check references

[whedon]

Attempting to check references...

[arfon]

@whedon check references from branch joss-paper

[whedon]

Attempting to check references... from custom branch joss-paper

[whedon]

```Reference check summary:

OK DOIs

• 10.1016/j.cpc.2013.09.018 is OK
• 10.1038/s41592-019-0506-8 is OK
• 10.1016/j.cpc.2018.02.017 is OK
• 10.1073/pnas.202427399 is OK
• 10.1002/wcms.31 is OK
• 10.1063/1.2432340 is OK
• 10.1093/bioinformatics/btx529 is OK
• 10.1103/PhysRevLett.119.245701 is OK
• 10.1016/0021-9991(77)90121-8 is OK

MISSING DOIs

• None

INVALID DOIs

• http://dx.doi.org/DOI: 10.1016/0010-4655(95)00053-I is INVALID because of 'https://doi.org/' prefix
  ```

[whedon]

```Reference check summary:

OK DOIs

• 10.1016/j.cpc.2013.09.018 is OK
• 10.1038/s41592-019-0506-8 is OK
• 10.1016/j.cpc.2018.02.017 is OK
• 10.1073/pnas.202427399 is OK
• 10.1002/wcms.31 is OK
• 10.1063/1.2432340 is OK
• 10.1093/bioinformatics/btx529 is OK
• 10.1103/PhysRevLett.119.245701 is OK
• 10.1016/0021-9991(77)90121-8 is OK

MISSING DOIs

• None

INVALID DOIs

• http://dx.doi.org/DOI: 10.1016/0010-4655(95)00053-I is INVALID because of 'https://doi.org/' prefix
  ```

[whedon]

```Reference check summary:

OK DOIs

• 10.1016/j.cpc.2013.09.018 is OK
• 10.1038/s41592-019-0506-8 is OK
• 10.1016/j.cpc.2018.02.017 is OK
• 10.1073/pnas.202427399 is OK
• 10.1002/wcms.31 is OK
• 10.1063/1.2432340 is OK
• 10.1093/bioinformatics/btx529 is OK
• 10.1103/PhysRevLett.119.245701 is OK
• 10.1016/0021-9991(77)90121-8 is OK

MISSING DOIs

• None

INVALID DOIs

• http://dx.doi.org/DOI: 10.1016/0010-4655(95)00053-I is INVALID because of 'https://doi.org/' prefix
  ```

[tonigi]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

```Reference check summary:

OK DOIs

• 10.1016/j.cpc.2013.09.018 is OK
• 10.1038/s41592-019-0506-8 is OK
• 10.1016/j.cpc.2018.02.017 is OK
• 10.1016/0010-4655(95)00053-I is OK
• 10.1073/pnas.202427399 is OK
• 10.1002/wcms.31 is OK
• 10.1063/1.2432340 is OK
• 10.1093/bioinformatics/btx529 is OK
• 10.1103/PhysRevLett.119.245701 is OK
• 10.1016/0021-9991(77)90121-8 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[tonigi]

@amritagos Regarding the missing checkboxes, do they mean that you would like them amended, or just not assessed yet? Thanks!

[amritagos]

Sorry, have been dragging my feet on this a little. Will have my review completed today. Not assessed them fully yet, will have more detailed input (issues) if amendments are needed.

[amritagos]

@tonigi The commit style is not clear at all.

However it is too late to change that so do keep it in mind for future work. Once the issues have been resolved I will be happy to complete my review.

[tonigi]

Thanks for the review! The paper should now be amended. In particular, I rewrote the 2nd paragraph. The development history could be rebased in the future (not now, to avoid confusion).

[tonigi]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[amritagos]

A rebase in the future would be great @tonigi, especially if there are to be subsequent releases.
That said, with my issues being addressed satisfactorily, I have completed my review and am pleased to recommend this for publication, @arfon. This work fills an important niche for the community and furthermore is well documented and in keeping with the standards of JOSS.

[tonigi]

What next? Should I send to Zenodo? Thanks

[arfon]

@carlocamilloni - I don't see any comments from you on this thread but the checkboxes are marked. Can you provide a short high-level summary of your recommendation for this paper?

[carlocamilloni]

@arfon - @tonigi contribution is well coded and documented and provide a smart tool for prototyping new code for plumed. Python is definitely the way to go. The paper is self-contained and provides all what one needs to immediately use it.

[arfon]

@whedon generate pdf from branch joss-paper

[whedon]

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...

[tonigi]

moved to the default branch for simplicity

@whedon generate pdf

[arfon]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[arfon]

@tonigi - At this point could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

• The title of the archive is the same as the JOSS paper title
• That the authors of the archive are the same as the JOSS paper authors

I can then move forward with accepting the submission.

[tonigi]

Should be done - thanks!

[arfon]

@whedon set 10.5281/zenodo.3480171 as archive

[whedon]

OK. 10.5281/zenodo.3480171 is the archive.

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

```Reference check summary:

OK DOIs

• 10.1016/j.cpc.2013.09.018 is OK
• 10.1038/s41592-019-0506-8 is OK
• 10.1016/j.cpc.2018.02.017 is OK
• 10.1016/0010-4655(95)00053-I is OK
• 10.1073/pnas.202427399 is OK
• 10.1002/wcms.31 is OK
• 10.1063/1.2432340 is OK
• 10.1093/bioinformatics/btx529 is OK
• 10.1103/PhysRevLett.119.245701 is OK
• 10.1016/0021-9991(77)90121-8 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1021

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1021, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[arfon]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

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

Here's what you must now do:

1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1022
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01773
3. If everything looks good, then close this review issue.

4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

   Any issues? notify your editorial technical team...

[arfon]

@amritagos, @carlocamilloni - many thanks for your reviews here ✨

@tonigi - your paper is now accepted into JOSS :zap::rocket::boom:

[whedon]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.01773/status.svg)](https://doi.org/10.21105/joss.01773)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01773">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01773/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01773/status.svg
   :target: https://doi.org/10.21105/joss.01773

This is how it will look in your documentation:

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