[REVIEW]: CHAMP is an HPC Access and Metadata Portal

[whedon]

Submitting author: @cc-a (Christopher Cave-Ayland)
Repository: https://github.com/ImperialCollegeLondon/champ
Version: v2.1.0
Editor: @crvernon
Reviewer: @thurber, @acrlakshman
Archive: 10.5281/zenodo.6026417

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/5439f73b03eff8700a4b573813ed369a"><img src="https://joss.theoj.org/papers/5439f73b03eff8700a4b573813ed369a/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/5439f73b03eff8700a4b573813ed369a/status.svg)](https://joss.theoj.org/papers/5439f73b03eff8700a4b573813ed369a)

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

@thurber & @acrlakshman, 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 @crvernon 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 ✨

Review checklist for @thurber

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@cc-a) 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 and who the target audience is?
• 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?

Review checklist for @acrlakshman

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@cc-a) 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 and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @thurber, @acrlakshman it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

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:

2. 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]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.09 s (934.3 files/s, 90898.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              3              0             12           2880
Python                          48            687            518           2268
HTML                            14             46             32            558
Markdown                         2            119              0            385
YAML                             8              4              1            122
Ruby                             3              9              0             26
Dockerfile                       1              5              1              9
TOML                             1              0              0              8
JavaScript                       2              0             11              2
CSS                              1              0            371              1
-------------------------------------------------------------------------------
SUM:                            83            870            946           6259
-------------------------------------------------------------------------------


Statistical information for the repository '14d546bfbf24978947c594f1' was
gathered on 2021/10/14.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Christopher Cave-Ayl            98          4065            544          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Christopher Cave-Ayl       3521           86.6          2.3                7.27

[whedon]

PDF failed to compile for issue #3824 with the following error:

 Can't find any papers to compile :-(

[crvernon]

@whedon generate pdf from branch joss

[whedon]

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

[whedon]

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

[crvernon]

👋 @cc-a @thurber @acrlakshman - the review takes place in this issue. Don't hesitate to shoot me a message in this thread if you have any questions!

❗ Please don't forget to add a link to this review issue in any issues or pull requests you may generate in the https://github.com/ImperialCollegeLondon/champ repository. This will help everyone have a single point of reference.

[crvernon]

@cc-a - While we are getting started...I noticed that you co-author several others in your paper but only you have contributed to the code. Could you simply describe (bullet points) each co-author's contributions here? Thanks!

[crvernon]

📣 Mid-week rally! Looks like @cc-a and @thurber have a good dialogue going and are keeping the review progressing.

👋 @acrlakshman - It may be good to check in on the issue @thurber has opened to make sure you don't duplicate efforts (ImperialCollegeLondon/champ#70). Also, don't hesitate to reach out if you have any questions!

❓ @cc-a Don't forget to address:

@cc-a - While we are getting started...I noticed that you co-author several others in your paper but only you have contributed to the code. Could you simply describe (bullet points) each co-author's contributions here? Thanks!

👏 Keep up the good work!

[cc-a]

@cc-a - While we are getting started...I noticed that you co-author several others in your paper but only you have contributed to the code. Could you simply describe (bullet points) each co-author's contributions here? Thanks!

Please find below:

• Henry Rzepa - Concept and overall design creation, testing and design feedback
• Charles Romain - User testing and design feedback
• Mike Bearpark - User testing and design feedback

[crvernon]

📣 Mid-week rally! Looks like @cc-a has started addressing some of the comments @thurber has made. Let's keep things rolling towards a successful review!

👋 @acrlakshman - please update me to your progress thus far and don't hesitate to reach out if you have any questions.

👏 Keep up the good work!

[whedon]

👋 @acrlakshman, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @thurber, please update us on how your review is going (this is an automated reminder).

[acrlakshman]

mega Mid-week rally! Looks like @cc-a has started addressing some of the comments @thurber has made. Let's keep things rolling towards a successful review!

wave @acrlakshman - please update me to your progress thus far and don't hesitate to reach out if you have any questions.

clap Keep up the good work!

@crvernon I didn't start my code review yet. I shall provide an update this weekend.

[crvernon]

📣 Mid-week rally! Looks like @cc-a @thurber and @acrlakshman are all participating on this issue and all is rolling along well. Let's keep pushing to get this in great shape for publication!

👏 Keep up the good work!

[crvernon]

📣 Mid-week rally!

@thurber and @acrlakshman please provide a short update in this issue thread concerning the status of your reviews. Thanks!

@cc-a are there any blockers on your side of things? I would like to keep our momentum up so we may keep pushing to get this in great shape for publication!

[acrlakshman]

mega Mid-week rally!

@thurber and @acrlakshman please provide a short update in this issue thread concerning the status of your reviews. Thanks!

@cc-a are there any blockers on your side of things? I would like to keep our momentum up so we may keep pushing to get this in great shape for publication!

I am on a different schedule last week, i shall provide my final update over the weekend.

[cc-a]

No blockers on my front. I think I have a proof of principle for running tests in a containerised demo cluster. Needs a tidy up though.

[crvernon]

@thurber and @acrlakshman please provide a short update in this issue thread concerning the status of your reviews. Thanks!

[cc-a]

Thanks for the reminder. I've archived a new release at https://doi.org/10.5281/zenodo.6026417

[crvernon]

@whedon set 10.5281/zenodo.6026417 as archive

[whedon]

OK. 10.5281/zenodo.6026417 is the archive.

[crvernon]

@whedon set v2.1.0 as version

[whedon]

OK. v2.1.0 is the version.

[crvernon]

🎉 @cc-a thanks for putting together a really nice software product! Thanks to @thurber and @acrlakshman for a constructive and timely review!

I am recommending that your submission be accepted. An EIC will review this shortly and confirm final publication if all goes well.

[crvernon]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

PDF failed to compile for issue #3824 with the following error:

 Can't find any papers to compile :-(

[crvernon]

@whedon recommend-accept from branch joss

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1021/ci500302p is OK
- 10.21105/joss.00622 is OK
- 10.14454/FXWS-0523 is OK
- 10.1186/s13321-017-0190-6 is OK
- 10.17487/RFC6749 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2936

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2936, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch joss 

[kthyng]

Hi @cc-a! Looks ready to go!!

[kthyng]

@whedon accept deposit=true from branch joss

[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:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03824 joss-papers#2937
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03824
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[kthyng]

Congratulations on your new publication @cc-a!! Many thanks to editor @crvernon and reviewers @thurber and @acrlakshman for your time, hard work, and expertise!

[whedon]

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

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.03824/status.svg)](https://doi.org/10.21105/joss.03824)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03824">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03824/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03824/status.svg
   :target: https://doi.org/10.21105/joss.03824

This is how it will look in your documentation:

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