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[PRE REVIEW]: Pywaterflood: Well connectivity analysis through capacitance-resistance modeling #5918

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editorialbot opened this issue Oct 2, 2023 · 48 comments
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[PRE REVIEW]: Pywaterflood: Well connectivity analysis through capacitance-resistance modeling #5918

editorialbot opened this issue Oct 2, 2023 · 48 comments
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@elbeejay @amandersillinois @mgcooper
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Dockerfile pre-review Python TeX Track: 6 (ESE) Earth Sciences and Ecology waitlisted Submissions in the JOSS backlog due to reduced service mode.

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editorialbot commented Oct 2, 2023 •
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Submitting author: @frank1010111 (Frank Male)
Repository: https://github.com/frank1010111/pywaterflood
Branch with paper.md (empty if default branch):
Version: v0.3.1
Editor: @elbeejay
Reviewers: @mgcooper, @amandersillinois
Managing EiC: Kristen Thyng

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/2fdffa96e936553d289e622e5e12388c"><img src="https://joss.theoj.org/papers/2fdffa96e936553d289e622e5e12388c/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/2fdffa96e936553d289e622e5e12388c/status.svg)](https://joss.theoj.org/papers/2fdffa96e936553d289e622e5e12388c)

Author instructions

Thanks for submitting your paper to JOSS @frank1010111. Currently, there isn't a JOSS editor assigned to your paper.

@frank1010111 if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

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@editorialbot editorialbot added pre-review Track: 6 (ESE) Earth Sciences and Ecology labels Oct 2, 2023
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Hello human, 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=0.08 s (463.8 files/s, 46823.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          10            263            481           1058
Markdown                        14            177              0            428
YAML                             6             23             12            230
Rust                             2             12              2            150
Jupyter Notebook                 3              0            662            144
TeX                              1             11              0            136
TOML                             2             15              3            114
Dockerfile                       1              3              1             12
-------------------------------------------------------------------------------
SUM:                            39            504           1161           2272
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 521

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

OK DOIs

- 10.2118/83381-PA is OK
- 10.3390/en11123368 is OK
- 10.1016/j.petrol.2010.05.006 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1016/j.egypro.2013.06.290 is OK
- 10.2118/51793-PA is OK
- 10.2118/95322-PA is OK

MISSING DOIs

- None

INVALID DOIs

- None

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

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kthyng commented Oct 2, 2023

Hi @SanchitMinocha and apologies for the delay in getting this going (I've been out of office). Given that the size of this package is right at the number of lines of code where we need to check in with the editorial board, I am going to run a scope query to make sure this is in scope. Thanks for your patience.

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kthyng commented Oct 2, 2023

@editorialbot query scope

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Submission flagged for editorial review.

@editorialbot editorialbot added the query-scope Submissions of uncertain scope for JOSS label Oct 2, 2023
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Five most similar historical JOSS papers:

Capytaine: a Python-based linear potential flow solver
Submitting author: @mancellin
Handling editor: @leouieda (Retired)
Reviewers: @mikaem, @harpolea
Similarity score: 0.8258

GroundwaterDupuitPercolator: A Landlab component for groundwater flow
Submitting author: @davidlitwin
Handling editor: @kthyng (Active)
Reviewers: @dvalters, @rreinecke
Similarity score: 0.8152

PySWMM: The Python Interface to Stormwater Management Model (SWMM)
Submitting author: @katmratliff
Handling editor: @kbarnhart (Retired)
Reviewers: @nickrsan, @jrkasprzyk
Similarity score: 0.8148

Integrated hydrologic model development and postprocessing for GSFLOW using pyGSFLOW
Submitting author: @jlarsen-usgs
Handling editor: @crvernon (Active)
Reviewers: @thurber, @mdbartos, @mdbartos
Similarity score: 0.8120

Water Systems Integrated Modelling framework, WSIMOD: A Python package for integrated modelling of water quality and quantity across the water cycle
Submitting author: @barneydobson
Handling editor: @crvernon (Active)
Reviewers: @cheginit, @jlarsen-usgs
Similarity score: 0.8112

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before before considering asking the reviewers of these papers to review again for JOSS.

@frank1010111
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Hello! A few potential reviewers include Dennis Glaeser (dglaeser), Guilherme P. Castelao (castelao), wkearn, leouieda and sgrieve.

Is 1200 lines of code on the low side?

I used Tokei to calculate the lines of code, which appears to handle docstrings as code, while your tool calls them comments:

tokei 
===============================================================================
 Language            Files        Lines         Code     Comments       Blanks
===============================================================================
 Dockerfile              1           16           12            1            3
 Python                 11         1831         1614           27          190
 Rust                    2          164          150            2           12
 TOML                    2          132          114            3           15
-------------------------------------------------------------------------------
 Jupyter Notebooks       4            0            0            0            0
 |- Markdown             3           71            1           49           21
 |- Python               4          321          290            3           28
 (Total)                            392          291           52           49
-------------------------------------------------------------------------------
 Markdown               11          521            0          361          160
 |- BASH                 1            1            1            0            0
 |- Python               1           12           12            0            0
 (Total)                            534           13          361          160
===============================================================================
 Total                  31         2664         1890          394          380
===============================================================================

@kthyng
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kthyng commented Oct 2, 2023

Yes 1000 is the approximate cut off for needing to query scope: https://joss.readthedocs.io/en/latest/submitting.html#substantial-scholarly-effort

@frank1010111
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Okay, how does a scope query work?

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kthyng commented Oct 24, 2023

Hi @frank1010111! We just wait to hear back from the editorial board which has now happened. This passes the scope query!

@kthyng kthyng removed the query-scope Submissions of uncertain scope for JOSS label Oct 24, 2023
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kthyng commented Oct 24, 2023

The next step is for me to find an appropriate editor for the submission. We have an active waitlist which I will add your submission to now. Thank you for your patience!

@kthyng kthyng added the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Oct 24, 2023
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kthyng commented Nov 20, 2023

@elbeejay Could you edit this submission?

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kthyng commented Nov 20, 2023

@editorialbot invite @elbeejay as editor

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Invitation to edit this submission sent!

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@editorialbot assign me as editor

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Assigned! @elbeejay is now the editor

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@frank1010111 I took a look and the code and paper look pretty good to me, so I'll start looking for reviewers. I'll likely wait until next week to start pinging folks due to the holiday here in the US.

My one note on the paper is that you should introduce the acronym "CRM" as a parenthetical "Capacitance Resistance Models (CRM)" (maybe on line 7) as later the acronym is used (line 15).

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@DavidLitwin would you be interested in reviewing "Pywaterflood"? I know you are familiar with the JOSS review process so please take a look when you get a chance and let us know if you think you'll have the time to conduct a review.

Hope you are well,
Jay

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@mhesse do you think you or one of your students would be a good fit to review this submission, "Pywaterflood: Well connectivity analysis through capacitance-resistance modeling", for JOSS? This submission seems to take an interesting approach to estimating well connectivity, and when I think of interesting math and modeling flow through the subsurface I tend to think of you.

At JOSS we do open checklist-driven reviews; peer-review criteria can be viewed here. This issue is a "pre-review issue" which we use to find peer-reviewers. Once 3 reviewers are found, we will officially start the review in a dedicated GitHub issue. At present we are asking reviewers to complete reviews in 6 weeks, although this can be extended if needed. If you are not able to review but can recommend someone else, please mention them here (in this case please mention their GitHub handle without the "@" symbol).

If you are interested, please take a look at the journal's conflict of interest policy to ensure you do not have a conflict before agreeing to review this submission.

Please do not feel any pressure to accept this review request if you do not have the time or do not feel comfortable reviewing this software package, we appreciate and respect our peer-reviewers' time. If you cannot serve as a reviewer at this time but have a peer, collaborator, student, or colleague who might be available and would be a good fit for this submission, please let me know!

Thanks,
Jay

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elbeejay commented Dec 4, 2023

@anner-paldor would you be interested in reviewing this submission, "Pywaterflood: Well connectivity analysis through capacitance-resistance modeling", for JOSS? I assume the notion of modeling well connectivity is of interest to you. If not you, do you think anyone else at the lab might be qualified and interested in reviewing this submission?

At JOSS we do open checklist-driven reviews; peer-review criteria can be viewed here. This issue is a "pre-review issue" which we use to find peer-reviewers. Once 3 reviewers are found, we will officially start the review in a dedicated GitHub issue. At present we are asking reviewers to complete reviews in 6 weeks, although this can be extended if needed. If you are not able to review but can recommend someone else, please mention them here (in this case please mention their GitHub handle without the "@" symbol).

If you are interested, please take a look at the journal's conflict of interest policy to ensure you do not have a conflict before agreeing to review this submission.

Please do not feel any pressure to accept this review request if you do not have the time or do not feel comfortable reviewing this software package, we appreciate and respect our peer-reviewers' time. If you cannot serve as a reviewer at this time but have a peer, collaborator, student, or colleague who might be available and would be a good fit for this submission, please let me know!

Thanks and hope you are well,
Jay

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Hey @elbeejay ,
Thanks for thinking of me. Unfortunately, I don't think I can review this one. Our lab mates aren't on GitHub, as far as I know, but if that's not a problem then I can suggest Rachel Housego and/or Ryan Frederiks.
Cheers,
Anner.

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elbeejay commented Dec 5, 2023

Thanks for the reply @anner-paldor, I understand.

@frank1010111 I'm going to continue reaching out to people, I appreciate your patience.

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elbeejay commented Dec 5, 2023

@mgcooper might you be interested in conducting a review for JOSS? I'm not sure how comfortable you are with Python, but the subject area might be a good fit, the submission is titled: "Pywaterflood: Well connectivity analysis through capacitance-resistance modeling".

Please let me know if you'd be willing to review, thanks!

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elbeejay commented Dec 5, 2023

@katmratliff would you be interested in conducting a review for JOSS? The submission is titled: "Pywaterflood: Well connectivity analysis through capacitance-resistance modeling". It might be a bit outside of your typical sub-discipline, but I think you might find it interesting and tangentially related to some of your work. I know you've published with and reviewed for JOSS in the past so will skip the spiel about the review process - please just let me know if you'd like to review, thanks!

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@amandersillinois and @charman2 would either of you be interested in reviewing this submission for JOSS titled, "Pywaterflood: Well connectivity analysis through capacitance-resistance modeling"? I saw you've both been involved in groundwater modeling as well as the landlab project, which hopefully means the subject of this paper is of some interest to you, and you have the technical expertise to review the software in addition to the content of the short paper.

At JOSS we do open checklist-driven reviews; peer-review criteria can be viewed here. This issue is a "pre-review issue" which we use to find peer-reviewers. Once 3 reviewers are found, we will officially start the review in a dedicated GitHub issue. At present we are asking reviewers to complete reviews in 6 weeks, although this can be extended if needed. If you are not able to review but can recommend someone else, please mention them here (in this case please mention their GitHub handle without the "@" symbol).

If you are interested, please take a look at the journal's conflict of interest policy to ensure you do not have a conflict before agreeing to review this submission.

Please do not feel any pressure to accept this review request if you do not have the time or do not feel comfortable reviewing this software package, we appreciate and respect our peer-reviewers' time. If you cannot serve as a reviewer at this time but have a peer, collaborator, student, or colleague who might be available and would be a good fit for this submission, please let me know!

Thanks,
Jay

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@mancellin, any chance you'd be interested in reviewing this submission to JOSS titled: "Pywaterflood: Well connectivity analysis through capacitance-resistance modeling"? I think this submission falls (broadly) within your area of expertise. I know you've published with and reviewed for JOSS in the past so I thought I'd reach out. Let me know if you'd be available and interested in reviewing -- no pressure at all if not!

Thanks,
Jay

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@frank1010111 I wanted to check in and let you know I haven't forgotten about your submission. Given that we are at the very end of the year now, I am planning to stop reaching out to reviewers for now, and try again in early January.

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@mancellin, any chance you'd be interested in reviewing this submission to JOSS titled: "Pywaterflood: Well connectivity analysis through capacitance-resistance modeling"? I think this submission falls (broadly) within your area of expertise. I know you've published with and reviewed for JOSS in the past so I thought I'd reach out. Let me know if you'd be available and interested in reviewing -- no pressure at all if not!

Thanks, Jay

Thank you for the invitation. The package seems to be very domain-specific and not an application I'm very familiar with. But I can give it a try. You might need to be patient as I won't be able to start working on this before mid-January due to holidays.

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@mancellin, any chance you'd be interested in reviewing this submission to JOSS titled: "Pywaterflood: Well connectivity analysis through capacitance-resistance modeling"? I think this submission falls (broadly) within your area of expertise. I know you've published with and reviewed for JOSS in the past so I thought I'd reach out. Let me know if you'd be available and interested in reviewing -- no pressure at all if not!
Thanks, Jay

Thank you for the invitation. The package seems to be very domain-specific and not an application I'm very familiar with. But I can give it a try. You might need to be patient as I won't be able to start working on this before mid-January due to holidays.

Thanks @mancellin - no pressure. I will reach out again after the new year to see how your schedule is looking when we resume the search for other willing reviewers.

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mhesse commented Dec 21, 2023 via email

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Hi @elbeejay, sorry to be late to the game on this. I don't think I'll be able to review. It feels a little too far from my expertise.

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elbeejay commented Jan 3, 2024

@mhesse you'll need to follow the link at the bottom of that message to unsubscribe to the notifications. You are receiving emails because you've signed up to receive email notifications from GitHub when you are mentioned in an issue or pull request. I assume you are also not interested in peer-reviewing this submission?

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mgcooper commented Jan 3, 2024 •
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@mgcooper might you be interested in conducting a review for JOSS? I'm not sure how comfortable you are with Python, but the subject area might be a good fit, the submission is titled: "Pywaterflood: Well connectivity analysis through capacitance-resistance modeling".

Please let me know if you'd be willing to review, thanks!

@elbeejay In general I am happy to review for JOSS and I am comfy with python. In this particular case, I could complete the review by ~8 February. I will be unavailable from 9 Feb to 3 March. Please reach out or feel free to assign me if this timeline is acceptable.

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elbeejay commented Jan 3, 2024

@mgcooper might you be interested in conducting a review for JOSS? I'm not sure how comfortable you are with Python, but the subject area might be a good fit, the submission is titled: "Pywaterflood: Well connectivity analysis through capacitance-resistance modeling".
Please let me know if you'd be willing to review, thanks!

@elbeejay In general I am happy to review for JOSS and I am comfy with python. In this particular case, I could complete the review by ~8 February. I will be unavailable from 9 Feb to 3 March. Please reach out or feel free to assign me if this timeline is acceptable.

That'd be great and very much appreciated, thanks! The timeline works just fine.

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elbeejay commented Jan 3, 2024

@editorialbot add @mgcooper as reviewer

I am hoping to start the formal review issue by the end of next week, but feel free to go ahead and start your review whenever you are ready due to the tighter timeline you've got, and then you can always update your reviewer checklist and post comments once that review issue is available.

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@mgcooper added to the reviewers list!

@frank1010111
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@elbeejay Thank you for your persistence.

Another few reviewers who might be able and willing to look at this paper include dankusanovic, jlarsen-usgs, and leouieda.

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elbeejay commented Jan 6, 2024

@dankusanovic would you be interested in reviewing (once again) for JOSS. The submission is titled: "Pywaterflood: Well connectivity analysis through capacitance-resistance modeling" and the submitting author, @frank1010111, believes you'd be able to provide a good review.

Please let us know, thank you!

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amandersillinois commented Jan 7, 2024 via email

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elbeejay commented Jan 8, 2024

@editorialbot add @amandersillinois as reviewer

Thank you @amandersillinois!

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@amandersillinois added to the reviewers list!

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elbeejay commented Jan 8, 2024

@editorialbot start review

@mancellin, given your availability but more importantly given that you are not familiar with the application and specific domain being presented here, I've not added you to the list of reviewers for this submission. I appreciate your willingness to review for JOSS and will be sure to reach out when I see a submission that is a better fit for your expertise.

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OK, I've started the review over in #6191.

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@editorialbot generate my checklist

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Checklists can only be created once the review has started in the review issue

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