[REVIEW]: GHEtool: An open-source tool for borefield sizing in Python

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@wouterpeere@crvernon<!--end-editor-- Reviewers: @jasondegraw, @nmstreethran Archive: 10.5281/zenodo.7004037

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Markdown: [![status](https://joss.theoj.org/papers/0ae2224874ee0139d6f28baa48fe9127/status.svg)](https://joss.theoj.org/papers/0ae2224874ee0139d6f28baa48fe9127)

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

@jasondegraw & @nmstreethran, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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 ✨

Checklists

📝 Checklist for @nmstreethran

📝 Checklist for @jasondegraw

editorialbot commented 2 years ago

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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editorialbot commented 2 years ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.34 s (73.7 files/s, 70343.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
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Python                          18            517           1552          21478
Markdown                         4             63              0            162
TeX                              1              8              0             57
YAML                             1              1              4             18
TOML                             1              0              0              6
-------------------------------------------------------------------------------
SUM:                            25            589           1556          21721
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

Wordcount for paper.md is 1101

editorialbot commented 2 years ago

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

OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1016/j.rser.2019.04.045 is INVALID because of 'https://doi.org/' prefix

editorialbot 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: @wouterpeere , @jasondegraw , and @nmstreethran This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above.

Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/4406 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

wouterpeere commented 2 years ago

@editorialbot generate pdf

editorialbot 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:

wouterpeere commented 2 years ago

@editorialbot commands

editorialbot commented 2 years ago

Hello @wouterpeere, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Get a link to the complete list of reviewers
@editorialbot list reviewers

nmstreethran commented 2 years ago

Review checklist for @nmstreethran

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 https://github.com/wouterpeere/GHEtool?
[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 (@wouterpeere) 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?

wouterpeere commented 2 years ago

@jasondegraw, did you have some time already to take a look at the repository? I'm looking forward to your comments.

wouterpeere commented 2 years ago

From the 8th of July, I will be on holiday. @jasondegraw, do you think it would be possible to review GHEtool before the 7th of July? It would be nice if I could finish this review process before going on holiday ..

wouterpeere commented 2 years ago

@crvernon There doesn't seem to be much reaction from @jasondegraw ... How do we proceed?

jasondegraw commented 2 years ago

@wouterpeere I'm aiming to get this done within the 4-6 weeks timeframe, so I'd ask you to be patient.

wouterpeere commented 2 years ago

@jasondegraw Thanks for coming back to this. I just thought that, for some reason or another, we weren't able to reach you. Sorry for the impatience, I'm looking forward to your comments!

wouterpeere commented 2 years ago

@editorialbot generate pdf

editorialbot 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:

jasondegraw commented 2 years ago

Review checklist for @jasondegraw

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 https://github.com/wouterpeere/GHEtool?
[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 (@wouterpeere) 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, who the target audience is, and its relation to other work?
[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?

crvernon commented 2 years ago

📣 Rally time!

👋 @nmstreethran - It looks like you are making good progress on your review but I do see a few boxes left unchecked. Could you update me here to anything that is remaining from your perspective?

👋 @jasondegraw - I see you have gotten started. Could you update me here to your progress? Thanks!

Keep up the good work!

jasondegraw commented 2 years ago

@crvernon Hmmm, something is wrong, I had a comment that I was sure I posted here. Maybe I didn't click "Comment" or something? I'll have to reconstitute it from my notes, I guess, because I'm not finding any old browser tabs with unsubmitted comments. Apologies for the delay.

wouterpeere commented 2 years ago

@editorialbot generate pdf

editorialbot 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:

nmstreethran commented 2 years ago

@crvernon Sorry for the delay. I need to finish going through the paper and some of the examples. I'll complete my review by the end of the week. Thanks!

crvernon commented 2 years ago

Thanks @nmstreethran !

wouterpeere commented 2 years ago

@editorialbot generate pdf

editorialbot 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:

wouterpeere commented 2 years ago

@editorialbot generate pdf

editorialbot 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:

wouterpeere commented 2 years ago

@editorialbot generate pdf

editorialbot 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:

nmstreethran commented 2 years ago

Hi @crvernon, I've completed my review. @wouterpeere has addressed all my comments in https://github.com/wouterpeere/GHEtool/issues/7, so I'm happy to recommend to accept this submission. Many thanks!

wouterpeere commented 2 years ago

@nmstreethran, thank you for your comments! I personally learned a lot and the package, for sure, is better now :)

crvernon commented 2 years ago

Much appreciated @nmstreethran ! @jasondegraw can you provide an update to your progress here? Thanks!

jasondegraw commented 2 years ago

@crvernon I need to go back and make sure of a couple things, but I plan to work on this today/tomorrow so it should be soon.

wouterpeere commented 2 years ago

@editorialbot generate pdf

editorialbot 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:

wouterpeere commented 2 years ago

Hi @jasondegraw, I noticed that you ticked off the last check boxes of the review process. Was everything related to the installation clear for you?

jasondegraw commented 2 years ago

@wouterpeere Yes, it all went as expected after dealing with some computer issues, nothing related to your package.

@crvernon Meant to post this yesterday, but my concerns are addressed.

wouterpeere commented 2 years ago

@jasondegraw thank you for your comments!

crvernon commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.1016/j.rser.2019.04.045 is OK
- 10.3390/en13236203 is OK

MISSING DOIs

- 10.26868/25222708.2021.30180 may be a valid DOI for title: Validated combined first and last year borefield sizing methodology

INVALID DOIs

- https://doi.org/10.1016/j.enconman.2014.11.009 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.energy.2017.01.097 is INVALID because of 'https://doi.org/' prefix

crvernon commented 2 years ago

@editorialbot generate pdf

editorialbot 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

@wouterpeere - this is looking great. Just a few edits from my end that need to be addressed before we move forward:

[ ] Please address the following invalid and missing DOIs:

MISSING DOIs

10.26868/25222708.2021.30180 may be a valid DOI for title: Validated combined first > and last year borefield sizing methodology

INVALID DOIs

https://doi.org/10.1016/j.enconman.2014.11.009 is INVALID because of 'https://doi.org/' > prefix

https://doi.org/10.1016/j.energy.2017.01.097 is INVALID because of 'https://doi.org/' prefix

[ ] A recommendation, not requirement. You have tests in your package that could easily be executed via continuous integration (CI) via GitHub Actions. Please consider setting CI up for your software so that on push and/or pull request your tests automatically execute.

Great progress so far. Keep up the good work!

wouterpeere commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.1016/j.rser.2019.04.045 is OK
- 10.26868/25222708.2021.30180 is OK
- 10.1016/j.enconman.2014.11.009 is OK
- 10.1016/j.energy.2017.01.097 is OK
- 10.3390/en13236203 is OK

MISSING DOIs

- Errored finding suggestions for "pygfunction: an open-source toolbox for the evalua...", please try later
- Errored finding suggestions for "2018 Global Status Report: Towards a zero-emission...", please try later
- Errored finding suggestions for "geoSIM - your freeware tool for simulating and siz...", please try later
- Errored finding suggestions for "Software - Tools to design and support your Ground...", please try later
- Errored finding suggestions for "A European Green Deal", please try later
- Errored finding suggestions for "European Green Deal: Commission proposes to boost ...", please try later
- Errored finding suggestions for "Design and Assessment of low-carbon Residential Di...", please try later

INVALID DOIs

- None

wouterpeere commented 2 years ago

Hi @crvernon the DOIs are addressed!

W.r.t. CI: I will look into this, but for now, I was (due to some administrator issues on my university laptop) not able to run the pytest-cov locally ...

crvernon commented 2 years ago

@wouterpeere - we are almost there! Next is just setting up the archive for your new release.

We want to make sure the archival has the correct metadata that JOSS requires. This includes a title that matches the paper title and a correct author list.

So here is what we have left to do:

[ ] Conduct a GitHub release of the current reviewed version of the software you now have on the main and archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[ ] Check the archival deposit (e.g., in Zenodo) to ensure it has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[ ] Please list the DOI of the archived version here

I can then move forward with accepting the submission.

wouterpeere commented 2 years ago

@crvernon the DOI of Zenodo is: 10.5281/zenodo.7004017

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