@jsta the review ticklist above is complete. When I have access to add issues to the author repository (seems to require manual approval.) I'll add my comments there and edit this post with links. Nothing major, just a few bits that could do with changing.

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I'm heading out on vacation starting tomorrow through the holidays. If you still need someone in early January I could do it.

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@joboog , I tried signing in with my GitHub user name to the GitLab repo (to start a Review issue), but it's waiting on approval. I'm guessing it's not a great time during the holidays and all, but also wanted to make sure that's the way to get access to creating issues. Let me know if there's something else I would need to do.

Probably, the responsible gitlab admin is still on holidays.
I will migrate r2ogs6 to github.com to allow free access.

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Until the r2ogs6 package can handle vtk 9.3.0 which is the version that is linked from the doc (https://pypi.org/project/vtk/), I don't think I can review the package functionality

@joboog Is this something you can do? Other potential users may have this issue too.

@kthyng Yes, I am working on it.

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IT WORKED! 🎉
The installation on a Windows computer using reticulate worked following the instructions on the README. Thank you for adding those! As a Windows R user with limited admin access to my own computer (which...is not uncommon for a government worker, or some industries), that is not uncommon.

The response to the original review sounds great!

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

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.11 s (1573.4 files/s, 233058.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                              118           2903           2379          10071
XML                             39             12             61           6240
HTML                             3            100              6           1263
Markdown                         4            167              0            642
Rmd                              3            265            372            340
CMake                            1             21             23            295
TeX                              1             21              5            171
YAML                             2              2              9             54
Python                           1             14              5             36
-------------------------------------------------------------------------------
SUM:                           172           3505           2860          19112
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 1551

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

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

OK DOIs

- 10.1007/s11242-019-01310-1 is OK
- 10.1007/978-3-642-27177-9 is OK
- 10.5281/zenodo.5387765 is OK
- 10.18637/jss.v064.i12 is OK
- 10.5194/adgeo-56-33-2021 is OK
- 10.21105/joss.02412 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1111/gwat.12413 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1111/gwat.13017 is INVALID because of 'https://doi.org/' prefix

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Hello @jmp75 and @waternumbers! Thanks so much for agreeing to review. Links to reviewing information are in the top message. You can generate your checklist with @editorialbot generate my checklist. Please let me know if you have questions.

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Review checklist for @waternumbers

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 https://gitlab.opengeosys.org/ogs/tools/r2ogs6?
• 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 (@joboog) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
• 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?

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Hey @waternumbers, @jmp75! Checking in. Do either of you need any help getting started?

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@jsta as you can see I started! I've got further then the tick boxes above suggest. Will finish by Friday. Am I correct in thinking I can give feedback to the authors via github issues?

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@waternumbers Ah yes, I'm sorry, my mistake. Yes, opening GitHub issues on the authors repository would be ideal. If something doesn't quite fit the issue format, leaving a note in the checklist box is an alternative. Thanks for your work on the review.

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@waternumbers Thanks so much! I take a look at those links when they're up.

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@waternumbers Thanks for your review. I have also a push mirror at https://github.com/joboog/r2ogs6 where you could open an issue if that would be ok with the JOSS guidelines (@jsta ).

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@joboog its OK I have access now - delay is me being in a different place to the PC with the review notes on...

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Links to review comments:
Paper comments: https://gitlab.opengeosys.org/ogs/tools/r2ogs6/-/issues/86
Functionality/Documentation: https://gitlab.opengeosys.org/ogs/tools/r2ogs6/-/issues/87

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Hello @jmp75 ! Just checking in, have you had a chance to start your review?

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@joboog Since this review seems to have stalled. I've begun searching for a reviewer to replace @jmp75. Do you have any suggestions?

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What about @rchlumsk or @ldecicco-USGS ?

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@jsta – I've generated a list of possible reviewers by looking at the most similar previous papers over here: #5067 (comment) – if any of these suggestions look good, please approach previous authors before tagging historical reviewers.

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I am sorry for the extreme delay here.

@waternumbers I see you have most of your boxes checked and then went into issues to bring up a few more items. Were these finished?

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Hi @ldecicco-USGS and @rchlumsk! Are you interested in reviewing this submission? We had a reviewer disappear and would love to have your expert eyes on this software. We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

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@kthyng sorry was in normal journal mode, viewed these as minor corrections so didn't expect to see the changes....
I see @joboog has replied to one set of issues I raised but will presume both sets are fixed are revise review as though they are

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@waternumbers Ok great! Please be sure to check off the review boxes as tasks are finished.

@ldecicco-USGS I will take you up on this! Many people won't be working for the next few weeks so that will be pretty consistent across the board. I'll add you as a reviewer and edit this page accordingly, but let me know if you have any permissions issues.

Thank you @rchlumsk!

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@editorialbot remove @jmp75 from reviewers

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@jmp75 removed from the reviewers list!

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@editorialbot add @ldecicco-USGS as reviewer

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@ldecicco-USGS added to the reviewers list!

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Review checklist for @ldecicco-USGS

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 https://gitlab.opengeosys.org/ogs/tools/r2ogs6?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@joboog) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
• 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?

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@joboog , I tried signing in with my GitHub user name to the GitLab repo (to start a Review issue), but it's waiting on approval. I'm guessing it's not a great time during the holidays and all, but also wanted to make sure that's the way to get access to creating issues. Let me know if there's something else I would need to do.

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Please note the JOSS submission requirements include:

The software must be hosted at a location where users can open issues and propose code changes without manual approval of (or payment for) accounts.

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Good to know @danielskatz , hopefully that's an easy fix.

My first issue is figuring out where the "your_ogs6_bin_path" is. I installed in my Terminal:

python -m venv .venv
pip install ogs

I do not see a bin path anywhere in the ogs folder. Are there additional instructions for finding that? I'm on Windows, and I don't have administrative access to my computer. I'll need to file an IT ticket to install OGS if it's more complicated than the pip installation.

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@joboog Please comment on your updates and respond to comments above when possible.

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Good to know @danielskatz , hopefully that's an easy fix.

My first issue is figuring out where the "your_ogs6_bin_path" is. I installed in my Terminal:

python -m venv .venv
pip install ogs

I do not see a bin path anywhere in the ogs folder. Are there additional instructions for finding that? I'm on Windows, and I don't have administrative access to my computer. I'll need to file an IT ticket to install OGS if it's more complicated than the pip installation.

On Windows, the ogs executable is located in the Scripts sub directory of your installation directory (see instructions for Windows here).

The other option is just to download the zip files including ogs binaries for Windows from the release page. Works without admin rights.

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In case there's a question, we're debugging installation questions here:
joboog/r2ogs6#1

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I'm taking over as editor!

@ldecicco-USGS Thank you for the update! Yes it's hard to tell exactly where any conversation is occurring...

@joboog Did you migrate to github? If so I can update the repo address in this issue.

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@editorialbot assign me as editor

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Assigned! @kthyng is now the editor

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I'm taking over as editor!

@ldecicco-USGS Thank you for the update! Yes it's hard to tell exactly where any conversation is occurring...

@joboog Did you migrate to github? If so I can update the repo address in this issue.

@kthyng Yes, the package is available on github despite not fully migrated yet.

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@waternumbers can you check off all the boxes from your review that are indeed finished?

@ldecicco-USGS and @joboog looks like you have an on-going conversation and @ldecicco-USGS perhaps some more checkboxes to go!

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Package feedback

At this point I'm still unable to install the proper version of vtk (8.2). Until the r2ogs6 package can handle vtk 9.3.0 which is the version that is linked from the doc (https://pypi.org/project/vtk/), I don't think I can review the package functionality. All of the functions that are used to create the ogs6_obj work perfectly. I therefore assume ogs6_run_simulation and ogs6_read_output_files would work - but they require the older vtk library.

Since this package is for R users, it will be important to include detailed instructions on how to install the mandatory Python libraries. The reason I would choose this package over the Python ogs6py package is because I'm much more comfortable in R. The reason I'm more comfortable in R is because installing things in Python gives me a headache 😂

##########

Paper feedback:

The paper nicely outlines why someone would be interested in this package, and gives a nice example of how to use it. I would recommend cleaning up the final paragraph.

"Please, check the following package vignettes for more information: a) a further guide on how to create ensemble runs (link), b) a tutorial to set up a single simulation of a hydro-mechanics benchmark with the package functions (link), and c) a guide how to start to further develop the package (link)."

Would it be possible to create a GitLab page using pkgdown, and link to a rendered version of the Rmd? I'd also suggest removing the "Please, " to just read:

"Check the following package vignettes...."

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Until the r2ogs6 package can handle vtk 9.3.0 which is the version that is linked from the doc (https://pypi.org/project/vtk/), I don't think I can review the package functionality

@joboog Is this something you can do? Other potential users may have this issue too.

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@joboog Ok I'll check back in in a few weeks.

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@joboog How are things going? I would suggest that I "pause" this issue so that I stop bothering you about it every few weeks. Alternatively, if it looks like the revisions necessary will take more than 1-2 months it may be better to withdraw the submission with the intention of resubmitting, so as to not keep this review issue open for too too long. Let me know what you would like to do.

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@joboog I am going to pause this issue but I would like to hear back from you in the next 2 weeks, say by April 22nd, about the time frame you'll need for the revisions. Thanks.

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@kthyng Sorry, I have been sick the last two weeks and did not check this issue recently. I think will be done with the revision by end of April. Would that be ok for you?

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@joboog Yes let's aim for that, thanks! Hope you feel better.

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Package feedback

At this point I'm still unable to install the proper version of vtk (8.2). Until the r2ogs6 package can handle vtk 9.3.0 which is the version that is linked from the doc (https://pypi.org/project/vtk/), I don't think I can review the package functionality. All of the functions that are used to create the ogs6_obj work perfectly. I therefore assume ogs6_run_simulation and ogs6_read_output_files would work - but they require the older vtk library.

Since this package is for R users, it will be important to include detailed instructions on how to install the mandatory Python libraries. The reason I would choose this package over the Python ogs6py package is because I'm much more comfortable in R. The reason I'm more comfortable in R is because installing things in Python gives me a headache 😂

##########

Paper feedback:

The paper nicely outlines why someone would be interested in this package, and gives a nice example of how to use it. I would recommend cleaning up the final paragraph.

"Please, check the following package vignettes for more information: a) a further guide on how to create ensemble runs (link), b) a tutorial to set up a single simulation of a hydro-mechanics benchmark with the package functions (link), and c) a guide how to start to further develop the package (link)."

Would it be possible to create a GitLab page using pkgdown, and link to a rendered version of the Rmd? I'd also suggest removing the "Please, " to just read:

"Check the following package vignettes...."

I updated the package and the paper accordingly.

@Package Feedback

• Added support to use VTK v9.0.3
• There is now also a function to install OpenGeoSys 6 as python module (install_ogs())
• The section r2ogs6-installation was revised accordingly.

@paper Feedback

• The paragraph was revised to

  "Check the following package vignettes for more information:

  • a guide to set up a single simulation of a hydro-mechanics benchmark (link)
  • a guide to create ensemble runs (link)
  • a development guide (link)"

• Gitlab page with vignettes was created link

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@ldecicco-USGS It looks like this would be a good time for you to check back to see if you can finish your review, if possible.

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The reticulate instructions are great! As an R user, that seemed a lot more streamlined for setting up the environments.

That being said, I'm still seeing:

Error in ogs6_read_output_files(ogs6_obj = ogs6_obj) : 
  Output file not written out correctly.
                    Unable to import *.pvd

When I look at the r2ogs6 CI tests, the pipeline is failing in the same way:

https://gitlab.opengeosys.org/ogs/tools/r2ogs6/-/jobs/434727

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@joboog Can you address this comment?

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@ldecicco-USGS sometimes reticulate is not pointing to the created virtual python environment where the ogs package is installed. Then the simulations are actually not run.
I did some bugfixes (on master branch).
Please try again using the updated instructions in the README of the actual master branch.

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@ldecicco-USGS Can you try with the updated instructions please?

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Hi @ldecicco-USGS! I know it's hard having this draw out over a long period of time like this, plus you might be traveling like I have been lately. When might you be able to get back to this? Thanks.

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Ack sorry! I'll look at it now!

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@ldecicco-USGS Where does that leave us with your review then? I see a few checkboxes unchecked — are those finished or are there outstanding issues yet?

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Those are now good (I just edited the review to check them off) - I was able to verify the remaining examples and installation, so I think we can move on to the next phase.

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Woohoo!!! Thank you SO MUCH @ldecicco-USGS! You really saved the day... or year as the case may be.

@joboog I went back and found these issues opened by reviewer @waternumbers https://gitlab.opengeosys.org/ogs/tools/r2ogs6/-/issues/86, https://gitlab.opengeosys.org/ogs/tools/r2ogs6/-/issues/87. The first looks like you addressed it, but not the second. Can you update me on the status?

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