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[REVIEW]: r2ogs6: An R wrapper of the OpenGeoSys 6 Multiphysics Simulator #5360

Open editorialbot opened 1 year ago

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@joboog<!--end-author-handle-- (Johannes Boog) Repository: https://gitlab.opengeosys.org/ogs/tools/r2ogs6 Branch with paper.md (empty if default branch): 40-joss-submission Version: 0.4.643 Editor: !--editor-->@kthyng<!--end-editor-- Reviewers: @waternumbers, @ldecicco-USGS Archive: Pending

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Markdown: [![status](https://joss.theoj.org/papers/08cb661c22ca8553e418acafeb9e7cb5/status.svg)](https://joss.theoj.org/papers/08cb661c22ca8553e418acafeb9e7cb5)

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

@ldecicco-USGS & @waternumbers, 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 @jsta 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 @waternumbers

📝 Checklist for @ldecicco-USGS

editorialbot commented 1 year ago

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
editorialbot commented 1 year ago 
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
editorialbot commented 1 year ago

Wordcount for paper.md is 1551

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago 
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
jsta commented 1 year ago

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.

waternumbers commented 1 year ago

Review checklist for @waternumbers

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

jsta commented 1 year ago

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

waternumbers commented 1 year ago

@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?

jsta commented 1 year ago

@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.

waternumbers commented 1 year ago

@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.

jsta commented 1 year ago

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

joboog commented 1 year ago

@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 ).

waternumbers commented 1 year ago

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

waternumbers commented 1 year ago

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

jsta commented 1 year ago

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

jsta commented 1 year ago

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

joboog commented 1 year ago

What about @rchlumsk or @ldecicco-USGS ?

arfon commented 1 year ago

@jsta – I've generated a list of possible reviewers by looking at the most similar previous papers over here: https://github.com/openjournals/joss-reviews/issues/5067#issuecomment-1741990601 – if any of these suggestions look good, please approach previous authors before tagging historical reviewers.

kthyng commented 9 months ago

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?

kthyng commented 9 months ago

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

ldecicco-USGS commented 9 months ago

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

waternumbers commented 9 months ago

@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

rchlumsk commented 9 months ago

Hi all

Thanks for the opportunity. I'm afraid I have to decline though, I don't have capacity for reviews at the moment.

Best of luck, Rob

Robert Chlumsky, MASc, P.Eng. (he/him) PhD Candidate, University of Waterloo President, CWRA Ontario Branch President, Heron Hydrologic Ltd.

On Thu, Dec 14, 2023 at 2:47 AM Paul Smith @.***> wrote:

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

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/5360#issuecomment-1855339920, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEUSZULO2CDUYYEMJXVDP7LYJKVHNAVCNFSM6AAAAAAW3V254GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNJVGMZTSOJSGA . You are receiving this because you were mentioned.Message ID: @.***>

kthyng commented 9 months ago

@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!

kthyng commented 9 months ago

@editorialbot remove @jmp75 from reviewers

editorialbot commented 9 months ago

@jmp75 removed from the reviewers list!

kthyng commented 9 months ago

@editorialbot add @ldecicco-USGS as reviewer

editorialbot commented 9 months ago

@ldecicco-USGS added to the reviewers list!

ldecicco-USGS commented 9 months ago

Review checklist for @ldecicco-USGS

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

ldecicco-USGS commented 9 months ago

@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.

danielskatz commented 9 months ago

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.

ldecicco-USGS commented 9 months ago

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.

kthyng commented 9 months ago

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

joboog commented 9 months ago

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.

joboog commented 9 months ago

@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.

ldecicco-USGS commented 8 months ago

In case there's a question, we're debugging installation questions here: https://github.com/joboog/r2ogs6/issues/1

kthyng commented 8 months ago

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 commented 8 months ago

@editorialbot assign me as editor

editorialbot commented 8 months ago

Assigned! @kthyng is now the editor

joboog commented 7 months ago

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.

kthyng commented 7 months ago

@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!

ldecicco-USGS commented 7 months ago

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...."

kthyng commented 7 months ago

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.

joboog commented 7 months ago

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.

kthyng commented 7 months ago

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

kthyng commented 6 months ago

@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.

kthyng commented 6 months ago

@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.

joboog commented 5 months ago

@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?

kthyng commented 5 months ago

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