[REVIEW]: ogs6py and VTUinterface: streamlining OpenGeoSys workflows in Python

[whedon]

Submitting author: @joergbuchwald (Jörg Buchwald)
Repository: https://github.com/joergbuchwald/joss_ogs6py_VTUinterface
Version: ogs6py-v0.34/VTUinterface-v0.69
Editor: @leouieda
Reviewer: @cpgr, @TobbeTripitaka, @akaszynski
Archive: 10.5281/zenodo.5705727

⚠️ 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:

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Markdown: [![status](https://joss.theoj.org/papers/6ddcac13634c6373e6e808952fdf4abc/status.svg)](https://joss.theoj.org/papers/6ddcac13634c6373e6e808952fdf4abc)

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

@cpgr & @TobbeTripitaka & @akaszynski , 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
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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @leouieda 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 @cpgr

✨ 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 (@joergbuchwald) 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 @TobbeTripitaka

✨ 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 (@joergbuchwald) 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 @akaszynski

✨ 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 (@joergbuchwald) 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. @cpgr, @TobbeTripitaka, @akaszynski 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]

Wordcount for paper.md is 1134

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.06 s (278.5 files/s, 52846.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                              7              2             14            622
Markdown                         3            254              0            471
TeX                              2              6              0            312
Python                           2              5              1            259
Jupyter Notebook                 1              0            945            118
YAML                             1              3              5             19
-------------------------------------------------------------------------------
SUM:                            16            270            965           1801
-------------------------------------------------------------------------------


Statistical information for the repository '698969b56866e30b46a86d3e' was
gathered on 2021/08/31.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
joergbuchwald                    1           265              0          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
joergbuchwald               265          100.0          0.0                0.38

[whedon]

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

OK DOIs

- 10.1016/j.ijrmms.2021.104683 is OK
- 10.1016/b978-012387582-2/50038-1 is OK
- 10.1016/j.ijrmms.2020.104481 is OK
- 10.1016/j.ijheatmasstransfer.2021.121127 is OK
- 10.1016/j.ijrmms.2021.104662 is OK
- 10.1007/s11242-019-01310-1 is OK
- 10.5281/zenodo.4745399 is OK
- 10.1109/38.865875 is OK
- 10.21105/joss.01450 is OK
- 10.1109/mcse.2011.35 is OK
- 10.1002/nme.2579 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Failed to discover a valid open source license.

[whedon]

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

[leouieda]

👋 @cpgr, @TobbeTripitaka, @akaszynski @joergbuchwald this is the review thread for the paper. All of our communications will happen here from now on.

All reviewers have checklists at the top of this thread 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 openjournals/joss-reviews#3673 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 reviews to be completed within about 4 weeks. Please let me know if any of you require some more time, we are happy to make acomodations. We can also use @whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me here (@leouieda) or email me privately if you have any questions/concerns.

[whedon]

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

[whedon]

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

[whedon]

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

[cpgr]

Hi @leouieda - I must have missed the invite email so can't tick any of the checklist boxes at the moment. Can you please re-invite me?

[danielskatz]

@whedon re-invite @cpgr as reviewer

[whedon]

OK, the reviewer has been re-invited.

@cpgr please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[cpgr]

I notice that the paper has been updated since I first read it

[cpgr]

@whedon generate pdf

[whedon]

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

[akaszynski]

Raised an issue regarding ogs6py installation; it's not clear: joergbuchwald/ogs6py#14
Paper reads fairly well. Made minor edits here: joergbuchwald/joss_ogs6py_VTUinterface#3

[leouieda]

@cpgr let me know if you any further issues. And yes, the paper can change due to review. Please feel free to rebuild with whedon as often as you need.

[leouieda]

@akaszynski thanks for the review comments! I see a few unchecked item in your checklist and I assume they’re related to the issues you raised. Please go ahead and mark them as done things are resolved.

[leouieda]

@whedon generate pdf

[whedon]

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

[leouieda]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1016/j.ijrmms.2021.104683 is OK
- 10.1016/b978-012387582-2/50038-1 is OK
- 10.1016/j.ijrmms.2020.104481 is OK
- 10.1016/j.ijheatmasstransfer.2021.121127 is OK
- 10.1016/j.ijrmms.2021.104662 is OK
- 10.1007/s11242-019-01310-1 is OK
- 10.5281/zenodo.4745399 is OK
- 10.1109/38.865875 is OK
- 10.21105/joss.01450 is OK
- 10.1109/mcse.2011.35 is OK
- 10.1002/nme.2579 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#2758

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2758, 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]

@joergbuchwald – there are a number of software packages mentioned in the paper (e.g., Jupyter, Pandas, scipy) which aren't cited. Could you please look up the default citations for these packages and cite them in your paper?

Many thanks!

[joergbuchwald]

@whedon generate pdf

[whedon]

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

[joergbuchwald]

@whedon generate pdf

[whedon]

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

[joergbuchwald]

@arfon thanks for the hint. I added now all missing citations.

[arfon]

@whedon accept

[whedon]

To recommend a paper to be accepted use @whedon recommend-accept

[arfon]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.3233/978-1-61499-649-1-87 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.1016/j.ijrmms.2021.104683 is OK
- 10.1016/b978-012387582-2/50038-1 is OK
- 10.1016/j.ijrmms.2020.104481 is OK
- 10.1016/j.ijheatmasstransfer.2021.121127 is OK
- 10.1016/j.ijrmms.2021.104662 is OK
- 10.1007/s11242-019-01310-1 is OK
- 10.5281/zenodo.4745399 is OK
- 10.1109/38.865875 is OK
- 10.21105/joss.01450 is OK
- 10.1109/mcse.2011.35 is OK
- 10.1002/nme.2579 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#2759

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2759, 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:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03673 joss-papers#2760
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03673
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...

[arfon]

@cpgr, @TobbeTripitaka, @akaszynski – many thanks for your reviews here and to @leouieda for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@joergbuchwald – your paper is now accepted and published in JOSS ⚡🚀💥

[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.03673/status.svg)](https://doi.org/10.21105/joss.03673)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03673">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03673/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03673/status.svg
   :target: https://doi.org/10.21105/joss.03673

This is how it will look in your documentation:

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