Closed editorialbot closed 10 months 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:
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Software report:
github.com/AlDanial/cloc v 1.88 T=0.21 s (1264.4 files/s, 199617.5 lines/s)
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Language files blank comment code
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HTML 86 1914 1208 16788
MATLAB 167 3142 8204 9454
JSON 4 4 0 768
PHP 1 14 26 289
Markdown 5 92 0 251
TeX 1 17 0 236
XML 4 12 82 98
CSS 1 13 0 77
YAML 2 11 41 43
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SUM: 271 5219 9561 28004
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gitinspector failed to run statistical information for the repository
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1016/j.cageo.2016.10.005 is OK
- 10.1029/WR013i003p00637 is OK
- 10.1029/97WR03068 is OK
- 10.1137/070710111 is OK
- 10.1029/2018WR022816 is OK
- 10.1029/2022WR033154 is OK
- 10.5194/hess-21-65-2017 is OK
- 10.1016/j.envsoft.2021.104983 is OK
- 10.1029/WR004i005p00973 is OK
- 10.1029/2008WR007392 is OK
- 10.5194/hess-24-1159-2020 is OK
- 10.1029/2008WR006912 is OK
- 10.1016/j.advwatres.2017.07.013 is OK
- 10.1029/2005WR004241 is OK
- 10.1029/2006WR005080 is OK
- 10.1002/wrcr.20407 is OK
MISSING DOIs
- None
INVALID DOIs
- None
Wordcount for paper.md
is 1212
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Hi @deboraydo, @aymnassar, and @alessandroamaranto,
This is the official "review" issue. @mgcooper has asked that you review the content in the joss
branch of the baseflow
repository, so please make your comments accordingly. Instructions for creating your reviewer checklist and conducting the review should be in the top comment of this issue, but please do not hesitate to reach out to me with any questions or to ask for any clarification.
Ideally we'd like to ask that you complete your reviews within 6 weeks, and I will set up reminder so the bot prods us all in 3 weeks.
Thanks, Jay
@editorialbot remind @deboraydo in three weeks
Reminder set for @deboraydo in three weeks
@editorialbot remind @aymnassar in three weeks
Reminder set for @aymnassar in three weeks
@editorialbot remind @alessandroamaranto in three weeks
Reminder set for @alessandroamaranto in three weeks
@deboraydo @aymnassar @alessandroamaranto @elbeejay I aim to push the Octave-compatibility fixes tomorrow afternoon. If anyone is reviewing the toolbox exclusively in Octave, please let me know if this is an inconvenience and I will push the update asap. Thank you, Matt
:wave: @deboraydo, please update us on how your review is going (this is an automated reminder).
:wave: @aymnassar, please update us on how your review is going (this is an automated reminder).
:wave: @alessandroamaranto, please update us on how your review is going (this is an automated reminder).
Hi @deboraydo, @aymnassar, @alessandroamaranto,
I just wanted to check in here to remind you all about this review. Feel free to reach out if you have any questions about the JOSS process.
Jay
@deboraydo and @aymnassar,
Just checking in here, please let me know if you still anticipate being able to complete your review in the next two weeks or so or if you'll need an extension.
@alessandroamaranto,
It looks like you've checked off all of the items on your review checklist. Can you please summarize your review briefly here and let us know if you have any suggestions or recommendations for the authors? Thanks!
I was going to do it this morning but got caught up in some meetings.
I will submit a brief summary soon (perhaps tomorrow).
Thanks
On Wed, Jun 21, 2023, 14:31 J. Hariharan @.***> wrote:
@deboraydo https://github.com/deboraydo and @aymnassar https://github.com/aymnassar,
Just checking in here, please let me know if you still anticipate being able to complete your review in the next two weeks or so or if you'll need an extension.
@alessandroamaranto https://github.com/alessandroamaranto,
It looks like you've checked off all of the items on your review checklist. Can you please summarize your review briefly here and let us know if you have any suggestions or recommendations for the authors? Thanks!
— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/5492#issuecomment-1600748650, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADJOC4MHCABYW4U3AMJTWRDXMLSR5ANCNFSM6AAAAAAYMG7F4Y . You are receiving this because you were mentioned.Message ID: @.***>
@deboraydo and @aymnassar,
Just trying to follow up here and make sure this review doesn't get lost - please check in with us here when you get a chance, thanks!
The package is easy to install, use and understand. It is well-documented and comes with a set of workflows to ease the users through the functionalities. Much appreciated, thanks.
@deboraydo and @aymnassar, I'm checking in here, would be great to get an update from you both on when you might be able to review this package. Please let us know and do not hesitate to reach out if you've got any questions, thanks
@deboraydo and @aymnassar, please let me know if you both are still planning on completing this review; it has been some time since we have heard from either of you. If you are unable to review, please tell us so we can begin the process of contacting and finding alternative reviewers - thanks.
cc @kthyng
@mgcooper we seem to have lost contact with two of our reviewers. Given the positive review from @alessandroamaranto I am thinking we will look for a single replacement reviewer to replace them in the hopes of keeping this process from dragging out too long. Thank you for your patience.
@mgcooper, @tianydong has agreed to step in and review your submission. He's out of the office through Aug. 6, but anticipates being able to conduct his review in the third week of August.
Thanks @mgcooper for your patience, and big thanks to @tianydong for stepping in to review!
@tianydong do you have any updates on this review? Thanks!
Overall the package is easy to install, the codes are well-commented, and demo 1 runs fine. But I am getting some errors on the other demos, for example:
Maybe a path thing? Also, I am using MATLAB 2022b, but I wonder if that's a problem. Also, there's a conflict between the .m and .mlx files for the linear theory demos. does this mean the user suppose to stick with LiveScript? Thanks again for having me as part of the review. I will provide some comments on the paper shortly
I made some minor comments, but overall the paper is well-written, and the figure is nicely made. Good luck! paper_TDedits.pdf
Thanks for the review @tianydong - please look over the marked up paper @mgcooper and make revisions and provide responses for the comments as appropriate. The error above should also be addressed, thanks!
@elbeejay @tianydong @alessandroamaranto
Thank you kindly for the review, @tianydong and @alessandroamaranto! I will formally respond to the edits and make the needed code revisions to resolve the errors, but wanted to quickly explain them. The first one occurs because the input parser allows the argument T to be either double (for datenum compatibility) or datetime. But then I have a second check (the one throwing the error, on line 180) which is requiring T to be double. So I will just add 'datetime' to that validation function. This is a newer change I pushed recently, so it did not affect @alessandroamaranto version.
The second error is because Matlab does not allow m-files (.m) to have the same name as live scripts (.mlx). To work around this, I used "demo" for the .m files and "example" for the .mlx. For example, "bfra_demo_1.m" is identical to "bfra_example_1.mlx" in terms of the content, but the former is a traditional .m file and the latter is in the newer live script format. I just completely overlooked this name shadowing for the two "theory" examples. So I'll rename them for the revisions. You could also change the name to anything other than the current one and it should work (as long as the new name doesn't shadow some other file) if you want to try running it.
I'll get these fixes pushed asap. Thanks again for the reviews and many thanks @elbeejay for managing the submission. Matt
@elbeejay @tianydong @alessandroamaranto @hydrotian
Revisions are complete and pushed to the joss branch (also main). Updates include:
Some important changes were made to the repository structure:
paper/
folder.toolbox/
folder.From a user-perspective, the reorganization only affects the tests. Instead of typing bfra.test.runtests
, just type runtests
. Overall, the new structure aligns with standard software development practices. I think it is important for the release associated with this paper.
Please see a point by point reply to reviewer comments below.
@tianydong "Overall the package is easy to install, the codes are well-commented, and demo 1 runs fine. But I am getting some errors on the other demos, for example:
todatenum
that ensures datetimes are converted to datenums. See commit 98499ac91f2987678c63ce1bb74c4c9b78662475.@tianydong "Maybe a path thing? Also, I am using MATLAB 2022b, but I wonder if that's a problem."
@tianydong "Also, there's a conflict between the .m and .mlx files for the linear theory demos."
demos/mfiles
sub-folder so they don't shadow the live script .mlx files in the demos
folder. Users with access to Matlab are encouraged to use the .mlx files, whereas Octave users can use the m-files, but the content is identical and both live scripts and m-files run in Matlab. See commit 0b9b00cee415bfececef26a2edcad53961da31a9.We believe this satisfies all requests from reviewers. Please let us know if any issues are encountered running the software. Many thanks for the review.
Matt Cooper Tian Zhou
Thank you for the revisions, @tianydong please weigh in on the responses made to your review comments when you get a chance.
All looks good! Thank you. @elbeejay
@mgcooper did you update the paper itself, by the way?
@tianydong We did update the paper, our apologies for omitting that from the response. Specifically, to address each of your comments:
As suggested, we added examples of aquifer properties to the abstract.
As suggested, we added a sentence to the first paragraph to define baseflow. We also broke the first paragraph into two. The first paragraph includes the baseflow definition, as requested, and a statement about why baseflow matters. The second paragraph addresses comment #3, specifically "how exactly recession curve can be used to infer ... aquifer properties".
We removed the phrase "geologic structures" to avoid confusion among those with a groundwater hydrology background. We also removed this phrase from the abstract. To answer your question, the geologic structures themselves cannot be inferred, rather the theory is based on an assumption that the aquifer is unconfined. To address this, we emphasize "unconfined aquifer properties" throughout the paper, and removed "geologic structures".
To address the other side of your comment: "how exactly recession curve can be used to infer ... aquifer properties", see our first two answers above. Additionally, we added a sentence to the first paragraph of the "State of the field" section that directly addresses this question: "Several well-known solutions to the one-dimensional lateral groundwater flow equation for unconfined aquifers can be written in the same form as [the recession equation]" and this forms the basis for estimating aquifer properties from the parameters obtained by curve-fitting recession sequences.
We also added a sentence immediately before "State of the field" that mentions the two theory-focused notebooks, which also provide more specific information about how recession curves can be used to infer aquifer properties.
Finally, we made various edits to improve the writing quality and/or grammar. Please see the compiled pdf in the paper/ folder at the top-level of the repo.
Thank you,
Matt Cooper Tian Zhou
Great, thanks all. I'm not going to be able to get to this until next week but will do a final check and get back to you @mgcooper with next steps then.
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1016/j.cageo.2016.10.005 is OK
- 10.1029/WR013i003p00637 is OK
- 10.1029/97WR03068 is OK
- 10.1137/070710111 is OK
- 10.1029/2018WR022816 is OK
- 10.1029/2022WR033154 is OK
- 10.5194/hess-21-65-2017 is OK
- 10.1016/j.envsoft.2021.104983 is OK
- 10.1029/WR004i005p00973 is OK
- 10.1029/2008WR007392 is OK
- 10.5194/hess-24-1159-2020 is OK
- 10.1029/2008WR006912 is OK
- 10.1016/j.advwatres.2017.07.013 is OK
- 10.1029/2005WR004241 is OK
- 10.1016/j.advwatres.2005.03.019 is OK
- 10.1029/2006WR005080 is OK
- 10.1029/92WR02087 is OK
- 10.1002/wrcr.20407 is OK
MISSING DOIs
- None
INVALID DOIs
- None
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
It looks good to me, thanks again to @alessandroamaranto and @tianydong for providing their reviews.
@mgcooper I'm going to generate a post-review checklist now that has a few last things for you to do before I can recommend this submission for publication.
@editorialbot set <DOI here> as archive
@editorialbot set <version here> as version
@editorialbot generate pdf
@editorialbot check references
and ask author(s) to update as needed@editorialbot recommend-accept
@mgcooper if you could notify me when you've done the author items on the above list that'd be great (as it's my comment so you won't be able to edit that checklist directly). Then I'll go ahead and go through the editor part of the checklist and we'll be ready to recommend this paper for publication. Thanks!
@mgcooper what's your estimated timeline for taking care of these last few items? They should be pretty quick, they exist to ensure the metadata associated with the JOSS publication is up to date.
@elbeejay My apologies for the delay. I found some Octave incompatibilities that I wanted to address for the release. I will complete these last few items today! Thank you for your attention, Matt
@elbeejay
I completed the check list. Below are my replies to action items:
Release version is v1.0.0. I made a v1.0.0-joss-branch release which used the joss branch as the target and another on main branch. Feel free to use whichever you prefer, but I wanted a v1.0.0 release to point to main for future clarity.
Please let me know if anything remains. Thank you, Matt
Hi @mgcooper - I need the title of the zenodo entry to match the title of the paper, if you could do that it'd be great.
@editorialbot set v1.0.0 as version
Done! version is now v1.0.0
@mgcooper is there a reason the license is in a file called COPYING
? as opposed to one called LICENSE
? I think the latter would be our preference as it is more standard.
Submitting author: !--author-handle-->@mgcooper<!--end-author-handle-- (Matthew Cooper) Repository: https://github.com/mgcooper/baseflow Branch with paper.md (empty if default branch): joss Version: v1.0.0 Editor: !--editor-->@elbeejay<!--end-editor-- Reviewers: @alessandroamaranto, @tianydong Archive: 10.5281/zenodo.8401301
Status
Status badge code:
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
@deboraydo & @aymnassar & @alessandroamaranto, 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:
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @elbeejay 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 ✨
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