[REVIEW]: OpenGeoSysUncertaintyQuantification.jl: a Julia library implementing an uncertainty quantification toolbox for OpenGeoSys #6725

editorialbot · 2024-05-06T16:00:28Z

Submitting author: @baxmittens (maximilian bittens)
Repository: https://github.com/baxmittens/OpenGeoSysUncertaintyQuantification.jl
Branch with paper.md (empty if default branch):
Version: v0.1.6
Editor: @kanishkan91
Reviewers: @ziyiyin97, @dannys4
Archive: 10.5281/zenodo.11923516

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/58a9a8e2572ccdd13f109776b92ca3bd"><img src="https://joss.theoj.org/papers/58a9a8e2572ccdd13f109776b92ca3bd/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/58a9a8e2572ccdd13f109776b92ca3bd/status.svg)](https://joss.theoj.org/papers/58a9a8e2572ccdd13f109776b92ca3bd)

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

@ziyiyin97 & @dannys4, 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 @kanishkan91 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 @ziyiyin97

📝 Checklist for @dannys4

The text was updated successfully, but these errors were encountered:

editorialbot · 2024-05-06T16:00:31Z

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 · 2024-05-06T16:00:52Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1227.2 files/s, 108476.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           17            256            546           1302
XML                             14              0              7            690
Markdown                         4            146              0            437
YAML                             4              3              4             95
TeX                              1              9              0             90
TOML                             1              2              0             37
-------------------------------------------------------------------------------
SUM:                            41            416            557           2651
-------------------------------------------------------------------------------

Commit count by author:

   379	Bittens
    18	Max Bittens
     1	baxmittens

editorialbot · 2024-05-06T16:01:00Z

Paper file info:

📄 Wordcount for paper.md is 806

✅ The paper includes a Statement of need section

editorialbot · 2024-05-06T16:01:02Z

License info:

✅ License found: MIT License (Valid open source OSI approved license)

editorialbot · 2024-05-06T16:01:39Z

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

editorialbot · 2024-05-06T16:01:44Z

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

OK DOIs

- 10.1137/100786356 is OK
- 10.1137/060663660 is OK
- 10.1016/j.jcp.2009.01.006 is OK
- 10.48550/arXiv.1509.01462 is OK
- 10.21105/joss.04300 is OK
- 10.1109/38.865875 is OK
- 10.21105/joss.05003 is OK

MISSING DOIs

- No DOI given, and none found for title: Quadrature and interpolation formulas for tensor p...
- 10.1007/s12665-012-1546-x may be a valid DOI for title: OpenGeoSys: an open-source initiative for numerica...

INVALID DOIs

- None

kanishkan91 · 2024-05-06T16:38:08Z

@baxmittens, @ziyiyin97, @dannys4, 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.

For @ziyiyin97 and @dannys4 - 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.

As you are probably already aware, 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 #6725 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.

Thanks in advance and let me know if you have any questions!!

kanishkan91 · 2024-05-06T16:41:55Z

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

OK DOIs

- 10.1137/100786356 is OK
- 10.1137/060663660 is OK
- 10.1016/j.jcp.2009.01.006 is OK
- 10.48550/arXiv.1509.01462 is OK
- 10.21105/joss.04300 is OK
- 10.1109/38.865875 is OK
- 10.21105/joss.05003 is OK

MISSING DOIs

- No DOI given, and none found for title: Quadrature and interpolation formulas for tensor p...
- 10.1007/s12665-012-1546-x may be a valid DOI for title: OpenGeoSys: an open-source initiative for numerica...

INVALID DOIs

- None

@baxmittens, in the meantime see comment above. Looks like a DOI is missing for a reference. Could you get that corrected? Thanks!

ziyiyin97 · 2024-05-06T16:44:45Z

Review checklist for @ziyiyin97

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://github.com/baxmittens/OpenGeoSysUncertaintyQuantification.jl?
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 (@baxmittens) 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?

dannys4 · 2024-05-06T19:40:59Z

Review checklist for @dannys4

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://github.com/baxmittens/OpenGeoSysUncertaintyQuantification.jl?
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 (@baxmittens) 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?

kanishkan91 · 2024-05-06T22:21:07Z

@dannys4 - When you get a chance, could you fill out this form here- https://reviewers.joss.theoj.org/reviewers/new? This would convey JOSS editors your willingness to review for JOSS in the future based on interest. Let me know what you think. Thanks!

dannys4 · 2024-05-07T12:25:01Z

@kanishkan91 - the form should be filled out. Thanks!

dannys4 · 2024-05-13T16:39:28Z

The software paper largely looks great and very clear, there's just a few (admittedly narrow) nitpicks I have:

Distributions.jl should probably be properly cited in the referencessince it is referenced in the work (citation here)
Sobol' should have the apostrophe at the end for proper method attribution.

Less a comment and more of a question for @kanishkan91 : the paper states "special attention was paid to implement allocation-free in-place variants of all necessary math operators for all output datatypes such as VTUFile or XDMF3File". Is this a "performance claim" as suggested in the checklist and, if so, how rigorously should I try to check this?

dannys4 · 2024-05-13T17:18:13Z

On the examples side, I was having trouble getting the "plug and play" provided example to work.

A minor detail is that the docs for altered_StochasticOGSModelParams.xml do not match the actual file in the test repo and I wasn't sure if I was supposed to change anything to make the mean and variance to match the documented example.
I also wasn't sure if I was supposed to be able to generate the plots provided in the documentation (and if so, how).
It only started working for me once I used the version of DistributedSparseGrids on the main branch. It seems like it was known that PlotlyJS has some issues, and this was preventing my functionality (Julia 1.10.3). This may be above my paygrade as a reviewer, but there's definitely compats missing for the dependencies that would prevent some of these issues.
Once I got that figured out, it looks like there's some pathing issue going on. I get to start!(ogsuqasg) and then I get a bunch of output like

julia> start!(ogsuqasg)
[ Info: Starting 65 simulatoin calls
      From worker 2:    1_1_1_1Progress: 100%|███████████████████████████████████████████████████████████████████████████████████████████████| Time: 0:00:00

      From worker 3:	1_2_1_1
      From worker 2:	ogs call @[0.0, 0.0]
      From worker 3:	ogs call @[0.0, -1.0]
...
ERROR: TaskFailedException

    nested task error: On worker 2:
    IOError: could not spawn `/path/to/ogs/bin/ogs -o ./Res/1_1_1_1 ./Res/1_1_1_1/point_heat_source_2D.prj`: no such file or directory (ENOENT)
    Stacktrace:
      [1] _spawn_primitive
        @ ./process.jl:128
      [2] #784
        @ ./process.jl:139 [inlined]
      [3] setup_stdios
        @ ./process.jl:223
      [4] _spawn
        @ ./process.jl:138 [inlined]
      [5] _spawn
        @ ./process.jl:166
      [6] #run#798
        @ ./process.jl:479
      [7] run
        @ ./process.jl:477 [inlined]
      [8] fun
        @ ~/.julia/dev/OpenGeoSysUncertaintyQuantification/test/ex1/user_functions.jl:46
      [9] fun
        @ ~/.julia/dev/OpenGeoSysUncertaintyQuantification/test/ex1/user_functions.jl:41
     [10] #invokelatest#2
        @ ./essentials.jl:892
     [11] invokelatest
        @ ./essentials.jl:889
     [12] #110
        @ ~/.julia/juliaup/julia-1.10.3+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Distributed/src/process_messages.jl:287
     [13] run_work_thunk
        @ ~/.julia/juliaup/julia-1.10.3+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Distributed/src/process_messages.jl:70
     [14] #109
        @ ~/.julia/juliaup/julia-1.10.3+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Distributed/src/process_messages.jl:287
    Stacktrace:
     [1] remotecall_fetch(::Function, ::Distributed.Worker, ::StaticArraysCore.SVector{…}, ::Vararg{…}; kwargs::@Kwargs{})
       @ Distributed ~/.julia/juliaup/julia-1.10.3+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Distributed/src/remotecall.jl:465
     [2] remotecall_fetch(::Function, ::Distributed.Worker, ::StaticArraysCore.SVector{2, Float64}, ::Vararg{Any})
       @ Distributed ~/.julia/juliaup/julia-1.10.3+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Distributed/src/remotecall.jl:454
     [3] remotecall_fetch(::Function, ::Int64, ::StaticArraysCore.SVector{2, Float64}, ::Vararg{Any}; kwargs::@Kwargs{})
       @ Distributed ~/.julia/juliaup/julia-1.10.3+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Distributed/src/remotecall.jl:492
     [4] remotecall_pool(::Function, ::Function, ::Distributed.WorkerPool, ::StaticArraysCore.SVector{…}, ::Vararg{…}; kwargs::@Kwargs{})
       @ Distributed ~/.julia/juliaup/julia-1.10.3+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Distributed/src/workerpool.jl:126
     [5] remotecall_pool
       @ ~/.julia/juliaup/julia-1.10.3+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Distributed/src/workerpool.jl:123 [inlined]
     [6] remotecall_fetch
       @ ~/.julia/juliaup/julia-1.10.3+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Distributed/src/workerpool.jl:232 [inlined]
     [7] (::DistributedSparseGrids.var"#41#42"{…})()
       @ DistributedSparseGrids ~/.julia/dev/DistributedSparseGrids/src/DistributedSparseGrids.jl:353

...and 64 more exceptions.

Stacktrace:
 [1] sync_end(c::Channel{Any})
   @ Base ./task.jl:448
 [2] macro expansion
   @ ./task.jl:480 [inlined]
 [3] distributed_fvals!(asg::AdaptiveHierarchicalSparseGrid{…}, cpts::Vector{…}, fun::typeof(fun), worker_ids::Vector{…})
   @ DistributedSparseGrids ~/.julia/dev/DistributedSparseGrids/src/DistributedSparseGrids.jl:344
 [4] distributed_init_weights_inplace_ops!(asg::AdaptiveHierarchicalSparseGrid{…}, cpts::Vector{…}, fun::typeof(fun), worker_ids::Vector{…})
   @ DistributedSparseGrids ~/.julia/dev/DistributedSparseGrids/src/DistributedSparseGrids.jl:423
 [5] macro expansion
   @ ./timing.jl:279 [inlined]
 [6] start!(ogsuqasg::OGSUQASG, refinetohypercube::Bool)
   @ OpenGeoSysUncertaintyQuantification ~/.julia/dev/OpenGeoSysUncertaintyQuantification/src/OpenGeoSysUncertaintyQuantification.jl:487
 [7] start!(ogsuqasg::OGSUQASG)
   @ OpenGeoSysUncertaintyQuantification ~/.julia/dev/OpenGeoSysUncertaintyQuantification/src/OpenGeoSysUncertaintyQuantification.jl:473
 [8] top-level scope
   @ REPL[18]:1
Some type information was truncated. Use `show(err)` to see complete types.

where I get

shell> ls Res/
1_1_1_1		1_5_1_10	2_1_3_1		2_4_1_2		3_1_4_1		4_1_2_1		4_2_6_3		5_1_6_1
1_2_1_1		1_5_1_12	2_2_1_1		2_4_1_4		3_2_2_1		4_1_4_1		4_2_8_1		5_1_8_1
1_2_1_3		1_5_1_14	2_2_1_3		2_4_1_6		3_2_2_3		4_1_6_1		4_2_8_3
1_3_1_2		1_5_1_16	2_2_3_1		2_4_1_8		3_2_4_1		4_1_8_1		5_1_10_1
1_3_1_4		1_5_1_2		2_2_3_3		2_4_3_2		3_2_4_3		4_2_2_1		5_1_12_1
1_4_1_2		1_5_1_4		2_3_1_2		2_4_3_4		3_3_2_2		4_2_2_3		5_1_14_1
1_4_1_4		1_5_1_6		2_3_1_4		2_4_3_6		3_3_2_4		4_2_4_1		5_1_16_1
1_4_1_6		1_5_1_8		2_3_3_2		2_4_3_8		3_3_4_2		4_2_4_3		5_1_2_1
1_4_1_8		2_1_1_1		2_3_3_4		3_1_2_1		3_3_4_4		4_2_6_1		5_1_4_1

For the record, I installed OpenGeoSysUncertaintyQuantification via Pkg.dev(...), so this is on the main branch.

baxmittens · 2024-05-14T08:22:36Z

The software paper largely looks great and very clear, there's just a few (admittedly narrow) nitpicks I have:

Distributions.jl should probably be properly cited in the referencessince it is referenced in the work (citation here)

Sobol' should have the apostrophe at the end for proper method attribution.

Less a comment and more of a question for @kanishkan91 : the paper states "special attention was paid to implement allocation-free in-place variants of all necessary math operators for all output datatypes such as VTUFile or XDMF3File". Is this a "performance claim" as suggested in the checklist and, if so, how rigorously should I try to check this?

Hello @dannys4

thank you for reviewing this software. I appreciate it.
I will go to your comments and alter my code appropriately. If I fix the things accordingly, I will write here again.

I added the citation and apostrophe you've suggested.

The performance claim can be tested likewise:

import AltInplaceOpsInterface: add!
import LinearAlgebra: mul!
using BenchmarkTools
xdmf = XDMF3File("./Res/1_1_1_1/PointHeatSource_quarter_002_2nd.xdmf");
tmp = deepcopy(xdmf);
@btime $xdmf + $xdmf;
# 878.125 μs (1472 allocations: 3.13 MiB)
@btime add!($xdmf, $tmp)
# 164.500 μs (0 allocations: 0 bytes)
@btime $xdmf * $xdmf;
# 599.958 μs (1472 allocations: 3.13 MiB)
@btime mul!($xdmf, $tmp, $tmp)
# 60.792 μs (0 allocations: 0 bytes)

At the moment, I use a nasty thing called AltInplaceOpsInterface.jl for in-place operation since Julia does not seem to support broadcasting for nested data types and may never will, see e.g. https://discourse.julialang.org/t/efficient-weighted-sum-for-arbitrary-data-types/113992

kanishkan91 · 2024-05-14T13:36:46Z

@dannys4 , @baxmittens looks like you guys are communicating through the issues, which is great!

@dannys4 On your question above, if a specific claim is made in the paper regarding processing for a specific data type, there may be two things to check-

If the test cases cover those special cases
If there are specific examples provided in the documentation and vignettes/tutorials.

But again seems like @baxmittens responded to that already!

baxmittens · 2024-05-15T13:47:53Z

@dannys4

A minor detail is that the docs for altered_StochasticOGSModelParams.xml do not match the actual file in the test repo and I wasn't sure if I was supposed to change anything to make the mean and variance to match the documented example.

I fixed that

I also wasn't sure if I was supposed to be able to generate the plots provided in the documentation (and if so, how).

I updated the ./test/ex1/start.jl

in line 22-30, you can find

# import Pkg
# Pkg.add("PlotlyJS")
# Pkg.add("DistributedSparseGridsPlotting")

using PlotlyJS
using DistributedSparseGridsPlotting
display(PlotlyJS.plot([PlotlyJS.scatter3d(ogsuqasg.asg), surface_inplace_ops(ogsuqasg.asg, 20, x->maximum(x["temperature_interpolated"]))], PlotlyJS.Layout(title="ASG-Surrogate response function ASG(x) - max. temp")))
display(PlotlyJS.plot([PlotlyJS.scatter3d(asg_expval), surface_inplace_ops(asg_expval, 50, x->maximum(x["temperature_interpolated"]))], PlotlyJS.Layout(title="ASG(x)*pdf(x) - max. temp")))
display(PlotlyJS.plot([PlotlyJS.scatter3d(asg_varval), surface_inplace_ops(asg_varval, 50, x->maximum(x["temperature_interpolated"]))], PlotlyJS.Layout(title="(ASG(x)-𝔼(x))^2*pdf(x) - max. temp")))

It only started working for me once I used the version of DistributedSparseGrids on the main branch. It seems like it was known that PlotlyJS has some issues, and this was preventing my functionality (Julia 1.10.3). This may be above my paygrade as a reviewer, but there's definitely compats missing for the dependencies that would prevent some of these issues.

I agree. Recently, PlotlyJS stopped working (at least for me) if it is included in remote workers.
I did throw PlotlyJS out since I plan to switch to Makie, and, in addition, I do not like to have these heavy graphic libraries as a dependency, anyway. I issued a new version. this should be fixed, I hope.

Once I got that figured out, it looks like there's some pathing issue going on. I get to start!(ogsuqasg) and then I get a bunch of output like

You have to change simcall from /path/to/ogs/bin/ogs to the path of you ogs installation in the altered_StochasticOGSModelParams.xml

https://www.opengeosys.org/docs/userguide/basics/introduction/

Installing OGS can be a bit cumbersome. I can provide some help if you need it.

dannys4 · 2024-05-15T16:38:45Z

Thanks for the quick response!

I'm not seeing that the file is generated/changes from what's in the github repo. In particular, I'm getting that this file/line is unchanged, so it tries to call OGS on your system when doing the example
Sorry I totally overlooked the path to the binary. I've fixed this and now the only issue seems to be the one above, at least for the time being (I'll try it from scratch again once that gets addressed)

baxmittens · 2024-05-16T12:14:37Z

@dannys4

Thanks for the quick response!

No problem. it's me who has to say thank you!

I'm not seeing that the file is generated/changes from what's in the github repo. In particular, I'm getting that this file/line is unchanged, so it tries to call OGS on your system when doing the example

Sorry I totally overlooked the path to the binary. I've fixed this and now the only issue seems to be the one above, at least for the time being (I'll try it from scratch again once that gets addressed)

With that example, I wanted to emphasize that the helper functions can generate XML templates that can be altered accordingly if the user wants to.
I figured that this was a rather bad idea.

I altered the three files generate_stoch_params_file.jl, generate_stoch_model.jl, and start.jl. But you can also just run run_ex1.jl, which calls the three files, consecutively.
I deleted this whole altered_ nonsense since it only caused confusion (sorry about that).
The needed changes are now implemented in code in the three files above and the results are stored in StochasticParameters.xml, StochasticOGSModelParams.xml, and SampleMethodParams.xml.

I updated the documentation, too. See Usage

The only things to notice is that you still have to alter the simcall in generate_stoch_model.jl (or you have to have the ogs binary in your PATH) and if you want to create the plot, you have install PlotlyJS and DistributedSparseGridsPlotting.jl

import Pkg
Pkg.add("PlotlyJS")
Pkg.add("DistributedSparseGridsPlotting")

I hope this will fix things now. If it still does not run, I will take care of it as soon as possible. But for me it does work on different systems.

You already have the dev version, so a git pull for the directory should be sufficient. If we are through here, I will fix the compats and issue new versions of OpenGeoSysUncertaintyQuantification and all the underlying packages.

Anyways thank you for your patience and efforts.

kanishkan91 · 2024-05-21T13:34:17Z

@dannys4 , @ziyiyin97 and @baxmittens - Looks like this review is moving forward. Could you give me a short update as to where things are at your end? No rush obviously! Just wanted to check in. Thanks everyone!

baxmittens · 2024-05-22T15:22:38Z

Hi @kanishkan91

I'm looking forward to receiving more input from the reviewers, but as you said, there's no need to rush.

Greetz max

ziyiyin97 · 2024-05-22T17:21:47Z

Hi, thanks for the follow up. I will take a closer look this week.

editorialbot · 2024-06-17T18:08:20Z

👋 @openjournals/ese-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5510, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

kthyng · 2024-06-17T20:03:51Z

Hi! I'll take over now as Track Associate Editor in Chief to do some final submission editing checks. After these checks are complete, I will publish your submission!

Are checklists all checked off?
Check that version was updated and make sure the version from JOSS matches github and Zenodo.
Check that software archive exists, has been input to JOSS, and title and author list match JOSS paper (or purposefully do not).
Check paper.

kthyng · 2024-06-17T20:07:29Z

@baxmittens Can you update the metadata on your Zenodo archive so the title and author list exactly match your JOSS paper? This is a request and not a requirement to make a cohesive archive with your paper publication.

kthyng · 2024-06-17T20:10:59Z

@baxmittens In your paper please check the capitalization in your references. You can preserve capitalization by placing {} around characters/words in your .bib file. For example, "julia" and "germany" are not capitalized; please check for others.

baxmittens · 2024-06-18T08:02:56Z

@editorialbot generate pdf

editorialbot · 2024-06-18T08:04:09Z

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

baxmittens · 2024-06-18T08:06:06Z

@dannys4 @ziyiyin97
Thank you for your review. The usability of my package has been greatly improved because of you guys.
Appreciate it!

baxmittens · 2024-06-18T08:08:29Z

@kthyng
I altered the Zenodo title and updated the capitalization in the references.

kthyng · 2024-06-20T14:16:06Z

Ok looks ready to go!

kthyng · 2024-06-20T14:16:16Z

@editorialbot accept

editorialbot · 2024-06-20T14:16:19Z

Doing it live! Attempting automated processing of paper acceptance...

editorialbot · 2024-06-20T14:23:25Z

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Bittens
  given-names: Maximilian
  orcid: "https://orcid.org/0000-0001-9954-294X"
doi: 10.5281/zenodo.11923516
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Bittens
    given-names: Maximilian
    orcid: "https://orcid.org/0000-0001-9954-294X"
  date-published: 2024-06-20
  doi: 10.21105/joss.06725
  issn: 2475-9066
  issue: 98
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6725
  title: "OpenGeoSysUncertaintyQuantification.jl: a Julia library
    implementing an uncertainty quantification toolbox for OpenGeoSys"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06725"
  volume: 9
title: "OpenGeoSysUncertaintyQuantification.jl: a Julia library
  implementing an uncertainty quantification toolbox for OpenGeoSys"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot · 2024-06-20T14:23:29Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-06-20T14:23:30Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06725 joss-papers#5516
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06725
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kthyng · 2024-06-20T14:28:28Z

Congratulations on your new publication @baxmittens! Many thanks to @kanishkan91 and to reviewers @ziyiyin97 and @dannys4 for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

editorialbot · 2024-06-20T14:28:30Z

🎉🎉🎉 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.06725/status.svg)](https://doi.org/10.21105/joss.06725)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06725">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06725/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06725/status.svg
   :target: https://doi.org/10.21105/joss.06725

This is how it will look in your documentation:

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://reviewers.joss.theoj.org/join
Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

kthyng · 2024-06-20T14:30:45Z

@baxmittens If you're interested in joining JOSS as a reviewer, please register at https://reviewers.joss.theoj.org/.

baxmittens · 2024-06-20T14:59:48Z

Once again, thank you all for reviewing my software project.

@kthyng I recently did a review in JOSS, and I am willing to continue doing reviews. I completed my profile. JOSS is an excellent journal!

editorialbot added Julia review TeX Track: 6 (ESE) Earth Sciences and Ecology waitlisted Submissions in the JOSS backlog due to reduced service mode. labels May 6, 2024

editorialbot assigned kanishkan91 May 6, 2024

editorialbot mentioned this issue May 6, 2024

[PRE REVIEW]: OpenGeoSysUncertaintyQuantification.jl: a Julia library implementing an uncertainty quantification toolbox for OpenGeoSys #6517

Closed

kanishkan91 removed the waitlisted Submissions in the JOSS backlog due to reduced service mode. label May 6, 2024

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Jun 17, 2024

editorialbot added accepted published Papers published in JOSS labels Jun 20, 2024

kthyng closed this as completed Jun 20, 2024

editorialbot mentioned this issue Jun 28, 2024

[PRE REVIEW]: Fortuna.jl: Structural and System Reliability Analysis in Julia #6931

Closed

editorialbot mentioned this issue Jul 24, 2024

[PRE REVIEW]: MicroFloatingPoints.jl: providing very small IEEE 754-compliant floating-point types #7030

Closed

editorialbot mentioned this issue Aug 28, 2024

[PRE REVIEW]: QuantizedSystemSolver: A discontinuous ODE system 2 solver for Julia. #7156

Closed

editorialbot mentioned this issue Sep 12, 2024

[PRE REVIEW]: UncertRadio: Software for determining characteristic limits in accordance to DIN EN ISO 11929 for radioactivity measurements #7199

Closed

editorialbot mentioned this issue Sep 23, 2024

[PRE REVIEW]: DiscreteEntropy.jl: Entropy Estimation of Discrete Random Variables with Julia #7260

Closed

This was referenced Nov 18, 2024

[PRE REVIEW]: CurvilinearGrids.jl: A Julia package for curvilinear coordinate transformations #7494

Closed

[PRE REVIEW]: NMRInversions.jl, a julia package for time-domain Nuclear Magnetic Resonance #7496

Closed

editorialbot mentioned this issue Jan 14, 2025

[PRE REVIEW]: LongMemory.jl: Generating, Estimating, and Forecasting Long Memory Models in Julia #7665

Closed

[REVIEW]: OpenGeoSysUncertaintyQuantification.jl: a Julia library implementing an uncertainty quantification toolbox for OpenGeoSys #6725

[REVIEW]: OpenGeoSysUncertaintyQuantification.jl: a Julia library implementing an uncertainty quantification toolbox for OpenGeoSys #6725

Comments

editorialbot commented May 6, 2024 • edited Loading

Status

Reviewer instructions & questions

Checklists

editorialbot commented May 6, 2024

editorialbot commented May 6, 2024

editorialbot commented May 6, 2024

editorialbot commented May 6, 2024

editorialbot commented May 6, 2024

editorialbot commented May 6, 2024

kanishkan91 commented May 6, 2024 • edited Loading

kanishkan91 commented May 6, 2024

ziyiyin97 commented May 6, 2024 • edited Loading

Review checklist for @ziyiyin97

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

dannys4 commented May 6, 2024 • edited Loading

Review checklist for @dannys4

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

kanishkan91 commented May 6, 2024

dannys4 commented May 7, 2024

dannys4 commented May 13, 2024

dannys4 commented May 13, 2024 • edited Loading

baxmittens commented May 14, 2024

kanishkan91 commented May 14, 2024

baxmittens commented May 15, 2024 • edited Loading

dannys4 commented May 15, 2024

baxmittens commented May 16, 2024

kanishkan91 commented May 21, 2024

baxmittens commented May 22, 2024

ziyiyin97 commented May 22, 2024

editorialbot commented Jun 17, 2024

kthyng commented Jun 17, 2024 • edited Loading

kthyng commented Jun 17, 2024

kthyng commented Jun 17, 2024

baxmittens commented Jun 18, 2024

editorialbot commented Jun 18, 2024

baxmittens commented Jun 18, 2024

baxmittens commented Jun 18, 2024

kthyng commented Jun 20, 2024

kthyng commented Jun 20, 2024

editorialbot commented Jun 20, 2024

editorialbot commented Jun 20, 2024

editorialbot commented Jun 20, 2024

editorialbot commented Jun 20, 2024

kthyng commented Jun 20, 2024

editorialbot commented Jun 20, 2024

kthyng commented Jun 20, 2024

baxmittens commented Jun 20, 2024

editorialbot commented May 6, 2024 •

edited

Loading

kanishkan91 commented May 6, 2024 •

edited

Loading

ziyiyin97 commented May 6, 2024 •

edited

Loading

dannys4 commented May 6, 2024 •

edited

Loading

dannys4 commented May 13, 2024 •

edited

Loading

baxmittens commented May 15, 2024 •

edited

Loading

kthyng commented Jun 17, 2024 •

edited

Loading