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

whedon commented 2 years ago

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

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Reviewer instructions & questions

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✨ 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

[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 (@cc-a) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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: 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?
[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 @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

[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 (@cc-a) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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: 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?
[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 2 years ago

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 :tada:.

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whedon commented 2 years ago

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 commented 2 years ago

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

 Can't find any papers to compile :-(

crvernon commented 2 years ago

@whedon generate pdf from branch joss

whedon commented 2 years ago

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

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

crvernon commented 2 years ago

:wave: @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 commented 2 years ago

@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 commented 2 years ago

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

:wave: @acrlakshman - It may be good to check in on the issue @thurber has opened to make sure you don't duplicate efforts (https://github.com/ImperialCollegeLondon/champ/issues/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 commented 2 years ago

@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 commented 2 years ago

: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.

👏 Keep up the good work!

whedon commented 2 years ago

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

whedon commented 2 years ago

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

acrlakshman commented 2 years ago

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 commented 2 years ago

:mega: 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 commented 2 years ago

: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!

acrlakshman commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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

thurber commented 2 years ago

hi @crvernon, there are a few issues still outstanding in ImperialCollegeLondon/champ#70, the blocking one being a way to test the champ interface against a mock cluster. I believe @cc-a was close to implementing a solution.

crvernon commented 2 years ago

Thanks @thurber !

@cc-a could you provide an update as to how things are going on your end?

crvernon commented 2 years ago

:mega: Mid-week rally!

:wave: @acrlakshman please provide a short update in this issue thread concerning the status of your reviews.

:wave: @cc-a please provide an update here on the status of your responses to the reviewers thus far.

Thanks!

acrlakshman commented 2 years ago

Hi @crvernon , I need to finish going through the code, on the side I am also waiting for my comments to be addressed as noted in https://github.com/ImperialCollegeLondon/champ/issues/70.

cc-a commented 2 years ago

I've managed to sort the tricky bit with the containerised cluster for testing and will address the more minor comments in short order..

thurber commented 2 years ago

@crvernon - with @cc-a's latest updates that provide an end-to-end testing environment, I am satisfied with my review. Nice work!

crvernon commented 2 years ago

:mega: Mid-week rally!

It would be good to get this one wrapped up soon @cc-a so we can free up our reviewers. How are things looking on your side of things for finishing up the remaining issues? It looks like @acrlakshman has several more items to check off and @thurber has approved all.

@acrlakshman could you also provide an update to where things stand on your side of things?

Thanks!

acrlakshman commented 2 years ago

@crvernon, my comments were addressed. I shall submit my final review before this weekend.

crvernon commented 2 years ago

Thank you @acrlakshman !

crvernon commented 2 years ago

Also @acrlakshman please don't forget to check off any remaining boxes that have been addressed in your reviewer checklist. Thanks!

acrlakshman commented 2 years ago

Also @acrlakshman please don't forget to check off any remaining boxes that have been addressed in your reviewer checklist. Thanks!

@crvernon , sure I will clear all pending items.

acrlakshman commented 2 years ago

Things look good with the current shape, but all changes are in joss-review, may I know if things will be merged into develop branch?

cc-a commented 2 years ago

@acrlakshman Sure, if there are no further comments.

crvernon commented 2 years ago

@acrlakshman - if you have finished your current review and are satisfied with the outcome, please check off your final box for Substantial scholarly effort and I'll move to conducting my portion of this process. Thanks!

acrlakshman commented 2 years ago

@acrlakshman Sure, if there are no further comments.

no further comments from my side to get that branch merged.

acrlakshman commented 2 years ago

@acrlakshman - if you have finished your current review and are satisfied with the outcome, please check off your final box for Substantial scholarly effort and I'll move to conducting my portion of this process. Thanks!

Done.

crvernon commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

 Can't find any papers to compile :-(

crvernon commented 2 years ago

@cc-a - I want to make sure I am working on what will be the branch that is targeted for release / publication. Your default branch is develop which is fine. Are you planning on bringing the joss branch into develop?

Also, you have quite a few dependabot PRs open do you mind evaluating merging these and ensuring they don't break your code? This may help prevent potential security issues for users.

cc-a commented 2 years ago

Thanks @crvernon. All dependabot PR's have been resolved and the joss-review branch implementing feedback has been merged into develop.

Is it an expectation that the paper.md should be part of the mainline development branch? If not I would prefer to keep it in its own separate branch.

crvernon commented 2 years ago

@whedon generate pdf from branch develop

whedon commented 2 years ago

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

whedon commented 2 years ago

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

 Can't find any papers to compile :-(

crvernon commented 2 years ago

@whedon generate pdf from branch joss

whedon commented 2 years ago

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

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

crvernon commented 2 years ago

@whedon check references from branch joss

whedon commented 2 years ago

Attempting to check references... from custom branch joss

whedon commented 2 years ago

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

MISSING DOIs

- None

INVALID DOIs

- None

crvernon commented 2 years ago

@cc-a - the following are some comments concerning the paper specifically:

[x] HPC and FAIR are used as an acronym before it has been described. For example: "CHAMP (CHAMP is an HPC Access and Metadata Portal)..." This could be something like "CHAMP is a high performance computing (HPC) and metadata portal which provides an easy to use workflow for FAIR (Findability, Accessibility, Interoperability, and Reusability) scientific guiding principles data generation and publication."
[x] Figures are not referred to in text. See this previous JOSS publication for how to use figure referencing: https://joss.theoj.org/papers/10.21105/joss.03221 . Please let me know if you have questions about this.
[x] On line 22. e.g. should always be followed by a comma
[x] On line 40. Open OnDemand is given an acronym here (e.g., OOD) but it has been used earlier in text.
[x] Need citation for NGINX
[x] Need acronym breakout for UIDs
[x] "CHAMP is written in Python (>3.7)..." should read "CHAMP is written for use in Python (>3.7)..." and is this supposed to be >3.7 and not >=3.7?
[x] YAML needs acronym breakout
[x] Sentence "This allows flexibility to e.g. use a job..." should read "For example, this allows flexibility to use a job..."
[x] API needs acronym breakout
[x] OAuth2 needs citation
[x] Sentence "...data repositories where desired, in the case of Imperial..." should read "...data repositories where desired, as in the case of Imperial..."
[x] Period needed after Dr in "Dr Matthew Harvey"

Thanks!

crvernon commented 2 years ago

Thanks @crvernon. All dependabot PR's have been resolved and the joss-review branch implementing feedback has been merged into develop.

Is it an expectation that the paper.md should be part of the mainline development branch? If not I would prefer to keep it in its own separate branch.

Yes, it is fine to have the paper in a separate branch.

openjournals / joss-reviews