[REVIEW]: HydroMT: Automated and reproducible model building and analysis #4897

editorialbot · 2022-10-31T22:09:49Z

Submitting author: @DirkEilander (Dirk Eilander)
Repository: https://github.com/Deltares/hydromt
Branch with paper.md (empty if default branch): joss_paper
Version: v0.7.0
Editor: @elbeejay
Reviewers: @JannisHoch, @mcflugen, ~~@LejoFlores~~
Archive: 10.5281/zenodo.7663065

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/71294ea46e6a8003db2badc551056deb"><img src="https://joss.theoj.org/papers/71294ea46e6a8003db2badc551056deb/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/71294ea46e6a8003db2badc551056deb/status.svg)](https://joss.theoj.org/papers/71294ea46e6a8003db2badc551056deb)

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

@JannisHoch & @mcflugen & @LejoFlores, 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 @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 ✨

Checklists

📝 Checklist for @JannisHoch

📝 Checklist for @mcflugen

📝 ~~Checklist for @LejoFlores~~ - dropped due to inactivity in review process

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

editorialbot · 2022-10-31T22:09:51Z

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

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editorialbot · 2022-10-31T22:10:03Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.17 s (638.5 files/s, 136004.3 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Python                           51           1707           4347           9142
YAML                             12            126             20           2230
reStructuredText                 33            963           1150           1525
TeX                               1             26              4            717
Jupyter Notebook                  4              0           1085            226
Markdown                          2             40              0            132
TOML                              1              8              1             82
DOS Batch                         1              8              1             27
JSON                              1              0              0             18
CSS                               1              7              9             16
make                              1              4              6             10
Bourne Again Shell                1              1              0              3
SVG                               2              0              0              2
--------------------------------------------------------------------------------
SUM:                            111           2890           6623          14130
--------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2022-10-31T22:10:04Z

Wordcount for paper.md is 1573

elbeejay · 2022-10-31T22:11:40Z

Thanks again @JannisHoch, @mcflugen and @LejoFlores for agreeing to review HydroMT. Instructions about how to generate your reviewer checklist as well as how to conduct a JOSS review are provided in the above comments, but please feel free to reach out to me if you have any questions. I'll be asking the bot to send out reminders about the review in 3 weeks time; note that we are currently asking our reviewers to complete their reviews within 6 weeks.

editorialbot · 2022-10-31T22:12:02Z

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

elbeejay · 2022-10-31T22:12:20Z

@editorialbot remind @JannisHoch in three weeks

editorialbot · 2022-10-31T22:12:22Z

Reminder set for @JannisHoch in three weeks

elbeejay · 2022-10-31T22:12:31Z

@editorialbot remind @mcflugen in three weeks

editorialbot · 2022-10-31T22:12:33Z

Reminder set for @mcflugen in three weeks

elbeejay · 2022-10-31T22:12:41Z

@editorialbot remind @LejoFlores in three weeks

editorialbot · 2022-10-31T22:12:42Z

Reminder set for @LejoFlores in three weeks

editorialbot · 2022-10-31T22:12:49Z

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

OK DOIs

- None

MISSING DOIs

- 10.1029/2020wr028301 may be a valid DOI for title: Estimating river channel bathymetry in large scale flood inundation models
- 10.3389/feart.2020.00050 may be a valid DOI for title: Toward reproducible environmental modeling for decision support: A worked example
- 10.31223/x58p62 may be a valid DOI for title: A hydrologist’s guide to open science
- 10.2166/hydro.2020.092 may be a valid DOI for title: Delft Dashboard: a quick set-up tool for hydrodynamic models
- 10.1111/gwat.12413 may be a valid DOI for title: Scripting MODFLOW Model Development Using Python and FloPy
- 10.5194/egusphere-egu22-5510 may be a valid DOI for title: Reproducible large-scale groundwater modelling projects using the iMOD Python package
- 10.3133/tm6a16 may be a valid DOI for title: MODFLOW-2005 : the U.S. Geological Survey modular ground-water model–the ground-water flow process
- 10.31223/osf.io/e7qzf may be a valid DOI for title: A toolbox to quickly prepare flood inundation models for LISFLOOD-FP simulations
- 10.1016/j.jhydrol.2010.03.027 may be a valid DOI for title: A simple inertial formulation of the shallow water equations for efficient two-dimensional flood inundation modelling
- 10.5194/gmd-2022-182 may be a valid DOI for title: Wflow_sbm v0.6.1, a spatially distributed hydrologic model: from global data to local applications
- 10.3389/frwa.2021.713537 may be a valid DOI for title: Estimating Regionalized Hydrological Impacts of Climate Change Over Europe by Performance-Based Weighting of CORDEX Projections
- 10.1016/j.coastaleng.2020.103796 may be a valid DOI for title: Modeling compound flooding in coastal systems using a computationally efficient reduced-physics solver: Including fluvial, pluvial, tidal, wind- and wave-driven processes
- 10.5194/egusphere-2022-149 may be a valid DOI for title: A globally-applicable framework for compound flood hazard modeling
- 10.1029/2019wr026807 may be a valid DOI for title: Scaling Point‐Scale (Pedo)transfer Functions to Seamless Large‐Domain Parameter Estimates for High‐Resolution Distributed Hydrologic Modeling: An Example for the Rhine River
- 10.5334/jors.148 may be a valid DOI for title: xarray: N-D labeled Arrays and Datasets in Python

INVALID DOIs

- None

LejoFlores · 2022-10-31T22:15:00Z

Strike-out of text by @elbeejay on Jan. 3, 2023 due to inactivity.

~~## Review checklist for @LejoFlores~~

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/Deltares/hydromt?

License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?

Contribution and authorship: Has the submitting author (@DirkEilander) 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?

JannisHoch · 2022-11-07T21:33:02Z

Review checklist for @JannisHoch

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/Deltares/hydromt?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@DirkEilander) 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?

editorialbot · 2022-11-21T22:12:23Z

👋 @JannisHoch, please update us on how your review is going (this is an automated reminder).

editorialbot · 2022-11-21T22:12:34Z

👋 @mcflugen, please update us on how your review is going (this is an automated reminder).

editorialbot · 2022-11-21T22:12:45Z

👋 @LejoFlores, please update us on how your review is going (this is an automated reminder).

elbeejay · 2022-11-23T13:11:08Z

Hi @JannisHoch, @mcflugen, and @LejoFlores - we are now 3 weeks into this review process so I just wanted to check-in and make sure this was still on your to-do lists! As a reminder we are asking our reviewers to complete their reviews within 6 weeks; to help keep us on track I'll ask the bot to send out another set of reminders in 2 weeks.

As always, let me know if you have any questions about the JOSS review process.

Thanks,
Jay

elbeejay · 2022-11-23T13:11:25Z

@editorialbot remind @JannisHoch in two weeks

editorialbot · 2022-11-23T13:11:26Z

Reminder set for @JannisHoch in two weeks

elbeejay · 2022-11-23T13:11:44Z

@editorialbot remind @mcflugen in two weeks

editorialbot · 2022-11-23T13:11:45Z

Reminder set for @mcflugen in two weeks

elbeejay · 2022-11-23T13:12:04Z

@editorialbot remind @LejoFlores in two weeks

elbeejay · 2023-02-23T19:28:52Z

@DirkEilander there is one outstanding issue you'll need to remedy.

Both the title and list of authors are inconsistent between the paper.md file (which gets rendered into the JOSS paper like above) and the Zenodo archive you provided. We need both of these to match before we can proceed.

Thanks!

DirkEilander · 2023-02-24T05:54:05Z

@elbeejay I've updated the title of the zenodo archive (it sill the same DOI). Part of the title was accidently set in the description field.

elbeejay · 2023-02-24T13:22:22Z

Thank you for doing that @DirkEilander. You and your co-authors need to make a decision on the final author list, and then amend the paper or zenodo archive as necessary to get those to match as well.

DirkEilander · 2023-02-27T08:57:49Z

@elbeejay Got it. I'll get back to you with an updated author list that matches with the zenodo archive later this week.

DirkEilander · 2023-03-07T09:53:25Z

@elbeejay I've updated the authors list (with their permissions) in the paper.md manuscript and aligned it with zenodo. As a result I also had to change the acknowledgements. Hope it's in line with the requirements now. Let me know if you have remaining questions.

elbeejay · 2023-03-07T13:53:23Z

@editorialbot generate pdf

editorialbot · 2023-03-07T13:54:49Z

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

elbeejay · 2023-03-07T13:57:13Z

This looks great, thanks @DirkEilander. I will be recommending this for publication. An editor-in-chief will look over this issue and check the paper / metadata information sometime in the next few days and will be the one to formally publish this.

Thanks again for your work to get everything finalized here.

elbeejay · 2023-03-07T13:57:40Z

@editorialbot recommend-accept

editorialbot · 2023-03-07T13:57:42Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-03-07T13:58:46Z

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

OK DOIs

- 10.1088/1748-9326/ac4d4f is OK
- 10.1029/2020wr028301 is OK
- 10.3389/feart.2020.00050 is OK
- 10.5194/hess-26-647-2022 is OK
- 10.1111/gwat.12413 is OK
- 10.5194/egusphere-egu22-5510 is OK
- 10.3133/tm6a16 is OK
- 10.1016/j.envsoft.2019.104561 is OK
- 10.1016/j.jhydrol.2010.03.027 is OK
- 10.5194/gmd-2022-182 is OK
- 10.3389/frwa.2021.713537 is OK
- 10.5194/hess-2021-605 is OK
- 10.1016/j.ejrh.2021.100911 is OK
- 10.1016/j.coastaleng.2020.103796 is OK
- 10.5194/egusphere-2022-149 is OK
- 10.1029/2019WR026807 is OK
- 10.5334/jors.148 is OK
- 10.5281/zenodo.6478182 is OK
- 10.5281/zenodo.5573592 is OK
- 10.5281/zenodo.6108034 is OK
- 10.5281/zenodo.5884351 is OK
- 10.15497/RDA00068 is OK
- 10.1016/j.envsoft.2020.104812 is OK
- 10.5281/zenodo.7344967 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-03-07T13:59:34Z

👋 @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#4021, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

kthyng · 2023-03-07T15:16:25Z

Check that version was updated
Check that software archive exists, has been input to JOSS, and title and author list look good
Check paper

kthyng · 2023-03-07T15:16:39Z

No further comments! Everything looks good!

kthyng · 2023-03-07T15:16:46Z

@editorialbot accept

editorialbot · 2023-03-07T15:16:49Z

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

editorialbot · 2023-03-07T15:19:27Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2023-03-07T15:19:28Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2023-03-07T15:19:30Z

🚨🚨🚨 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.04897 joss-papers#4024
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04897
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kthyng · 2023-03-07T15:24:47Z

Congrats on your new publication @DirkEilander! Many thanks to editor @elbeejay and reviewers @JannisHoch and @mcflugen for your time, hard work, and expertise!!

editorialbot · 2023-03-07T15:24:50Z

🎉🎉🎉 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.04897/status.svg)](https://doi.org/10.21105/joss.04897)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04897">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04897/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04897/status.svg
   :target: https://doi.org/10.21105/joss.04897

This is how it will look in your documentation:

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editorialbot added Python review Shell TeX Track: 6 (ESE) Earth Sciences and Ecology labels Oct 31, 2022

editorialbot assigned elbeejay Oct 31, 2022

editorialbot mentioned this issue Oct 31, 2022

[PRE REVIEW]: HydroMT: Automated and reproducible model building and analysis #4809

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editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Mar 7, 2023

editorialbot added accepted published Papers published in JOSS labels Mar 7, 2023

kthyng closed this as completed Mar 7, 2023

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[REVIEW]: HydroMT: Automated and reproducible model building and analysis #4897

[REVIEW]: HydroMT: Automated and reproducible model building and analysis #4897

Comments

editorialbot commented Oct 31, 2022 • edited Loading

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Reviewer instructions & questions

Checklists

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LejoFlores commented Oct 31, 2022 • edited by elbeejay Loading

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

JannisHoch commented Nov 7, 2022 • edited Loading

Review checklist for @JannisHoch

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

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elbeejay commented Feb 24, 2023

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DirkEilander commented Mar 7, 2023

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edited

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edited by elbeejay

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