[PRE REVIEW]: HexWatershed

[whedon]

Submitting author: @changliao1025 (Chang Liao) Repository: https://github.com/pnnl/hexwatershed Version: Version 1.0 Editor: @kbarnhart Reviewer: Pending Managing EiC: Daniel S. Katz

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Author instructions

Thanks for submitting your paper to JOSS @changliao1025. Currently, there isn't an JOSS editor assigned to your paper.

@changliao1025 if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

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

@whedon commands

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

For a list of things I can do to help you, just type:

@whedon commands

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

@whedon generate pdf

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=3.87 s (9.8 files/s, 58178.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                             11              0              0         218965
C++                             10            476            716           3087
C/C++ Header                     9            157            185            411
INI                              1              1              0            381
make                             1            144             79            278
CMake                            2             22              7            116
Markdown                         1             36              0             69
JSON                             1              0              0             60
Bourne Shell                     2              0              0             10
-------------------------------------------------------------------------------
SUM:                            38            836            987         223377
-------------------------------------------------------------------------------

Statistical information for the repository 'e081ee93cc6d538862d8f9fa' was
gathered on 2020/10/14.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Chang Liao                      11          4176           1221           50.28
changliao1025                   16          3068           2268           49.72

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Chang Liao                 5022          120.3         12.7               17.96
changliao1025                10            0.3         25.2                0.00

[whedon]

Failed to discover a valid open source license.

[whedon]

PDF failed to compile for issue #2751 with the following error:

Can't find any papers to compile :-(

[danielskatz]

@changliao1025 - where is your paper?

See https://joss.readthedocs.io/en/latest/submitting.html#typical-paper-submission-flow and specifically https://joss.readthedocs.io/en/latest/submitting.html#example-paper-and-bibliography

[danielskatz]

It looks like it might be in the README? But the README should be the README, and the paper should be in a different file, usually paper.md along with any needed references in a .bib file

[danielskatz]

I also notice that there is no open source license in the repo - this is another part of https://joss.readthedocs.io/en/latest/submitting.html#typical-paper-submission-flow

[danielskatz]

I'm going to mark this as paused for now - please ping us here when fixes are made

[changliao1025]

Hi, @danielskatz, I have made edits to the repository as you suggested. Please let me know your further suggestions.

[danielskatz]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #2751 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (340cee360f20054ecb6766fd/paper.md): could not find expected ':' while scanning a simple key at line 28 column 1 (Psych::SyntaxError) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:inparse_stream' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:325:in parse' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:252:inload' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:473:in block in load_file' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:inopen' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:in load_file' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon.rb:127:inload_yaml' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon.rb:87:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/processor.rb:38:innew' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/processor.rb:38:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/bin/whedon:58:inprepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:ininvoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:instart' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/bin/whedon:131:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:inload' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

[danielskatz]

@changliao1025 - The paper does not compile - please check the format of the paper against the example, and then use @whedon generate pdf - and repeat until it looks right to you.

[danielskatz]

@whedon check references

[danielskatz]

@whedon check references

[danielskatz]

👋 @openjournals/dev - Why doesn't the reference check work here?

[changliao1025]

Sure, I will test with the bot first and then get back.

[changliao1025]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #2751 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (27048a8315bbcd2e5886ca83/paper.md): could not find expected ':' while scanning a simple key at line 28 column 1 (Psych::SyntaxError) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:inparse_stream' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:325:in parse' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:252:inload' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:473:in block in load_file' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:inopen' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:in load_file' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon.rb:127:inload_yaml' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon.rb:87:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/processor.rb:38:innew' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/processor.rb:38:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/bin/whedon:58:inprepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:ininvoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:instart' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/bin/whedon:131:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:inload' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

[changliao1025]

@whedon generate pdf

[whedon]

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

[changliao1025]

@whedon generate pdf

[whedon]

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

[changliao1025]

@whedon generate pdf

[whedon]

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

[changliao1025]

@whedon generate pdf

[whedon]

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

[changliao1025]

@whedon generate pdf

[whedon]

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

[changliao1025]

@whedon generate pdf

[whedon]

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

[changliao1025]

@whedon generate pdf

[whedon]

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

[changliao1025]

@whedon check references

[whedon]

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

OK DOIs

- None

MISSING DOIs

- 10.1002/hyp.3360050107 may be a valid DOI for title: On the extraction of channel networks from digital elevation data
- 10.1109/mcise.2002.1032427 may be a valid DOI for title: Climate modeling with spherical geodesic grids
- 10.3133/tm6d1 may be a valid DOI for title: GSFLOW, Coupled Ground-Water and Surface-Water Flow Model Based on the Integration of the Precipitation-Runoff Modeling System (PRMS) and the Modular Ground-Water Flow Model (MODFLOW-2005)
- 10.3133/sir20095233 may be a valid DOI for title: Evaluation of catchment delineation methods for the medium-resolution national hydrography dataset
- 10.1175/2009mwr2917.1 may be a valid DOI for title: Voronoi, Delaunay, and block-structured mesh refinement for solution of the shallow-water equations on the sphere
- 10.1016/j.cageo.2013.04.024 may be a valid DOI for title: Priority-flood: An optimal depression-filling and watershed-labeling algorithm for digital elevation models
- 10.5194/isprs-archives-xlii-4-687-2018 may be a valid DOI for title: The comparison of drainage network extraction between square and hexagonal grid-based dem
- 10.3138/cart.54.1.2018-0022 may be a valid DOI for title: Central Place Indexing: Hierarchical Linear Indexing Systems for Mixed-Aperture Hexagonal Discrete Global Grid Systems

INVALID DOIs

- https://doi.org/10.1016/j.envsoft.2020.104702 is INVALID because of 'https://doi.org/' prefix

[changliao1025]

@whedon check references

[whedon]

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

OK DOIs

- 10.1002/hyp.3360050107 is OK
- 10.1109/mcise.2002.1032427 is OK
- 10.3133/tm6d1 is OK
- 10.3133/sir20095233 is OK
- 10.1175/2009mwr2917.1 is OK
-  10.1016/j.cageo.2013.04.024 is OK
- 10.5194/isprs-archives-xlii-4-687-2018 is OK
- 10.3138/cart.54.1.2018-0022 is OK
- 10.1016/j.envsoft.2020.104702 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[changliao1025]

@danielskatz , I have fixed the bug in the files and both paper.md and references were compiled successfully.

[danielskatz]

👋 @kbarnhart - given your volunteering in the editorial discussion, I'm going to go ahead and assign this to you - let me know if that's a problem.

[danielskatz]

@whedon assign @kbarnhart as editor

[whedon]

OK, the editor is @kbarnhart

[kbarnhart]

Sounds good @danielskatz thanks!

[kbarnhart]

@changliao1025 the first step in the JOSS submission/review process is that the topical editor (me) looks though the submission as an initial check. I have a couple of questions:

• Is there a place where documentation and example usage of HexWatershed are provided
• Is there a place providing instructions for testing that HexWatershed has been installed correctly?

[kbarnhart]

@changliao1025 after discussion with the JOSS editorial board I have decided to reject this submission for the following reasons:

1. Violation of JOSS ethics guidelines. Specifically that the submitted paper is almost entirely composed of text previously published in Liao et al. (2020).

   Liao, C., Tesfa, T., Duan, Z., & Leung, L. R. (2020). Watershed delineation on a hexagonal mesh grid. Environmental Modelling & Software, 104702. https://doi.org/10.1016/j.envsoft.2020.104702

2. Missing major elements: a. No documentation b. No examples of use c. No instructions for testing

If you have any questions or clarifications about this decision, please let me know here and I will do my best to further explain.

[kbarnhart]

@openjournals/joss-eics I've recommended that this submission be rejected.

[danielskatz]

@whedon reject

[whedon]

Paper rejected.

[changliao1025]

@changliao1025 after discussion with the JOSS editorial board I have decided to reject this submission for the following reasons:

1. Violation of JOSS ethics guidelines. Specifically that the submitted paper is almost entirely composed of text previously published in Liao et al. (2020). Liao, C., Tesfa, T., Duan, Z., & Leung, L. R. (2020). Watershed delineation on a hexagonal mesh grid. Environmental Modelling & Software, 104702. https://doi.org/10.1016/j.envsoft.2020.104702
2. Missing major elements: a. No documentation b. No examples of use c. No instructions for testing

If you have any questions or clarifications about this decision, please let me know here and I will do my best to further explain.

A user guide will be added to the repository shortly. We collected some user feedback to make sure all the necessary information are presented in the user guide. This submission is mainly focusing on the technical part of the model instead of the scientific implication, that is why lots of text are the same or similar to our other publication, which does not provide details of the software.

[kbarnhart]

@changliao1025 thanks for the comment. As indicated above, this submission has been rejected.

I'd recommend that you take a close look at the JOSS submission requirements and the review criteria. As the review criteria state, the JOSS review process has reviewers comment on the documentation (typically both API and some sort of narrative documentation are expected).

If you think you can revise your submission to meet the requirements, including revising the paper so that its text is distinct from the text of the prior publication, then consider re-submitting to JOSS. At that time the submission would be re-considered as a new submission.

If you have questions or clarifications about re-submission, I'd recommend you make a pre-submission inquiry (as described here). Feel free to tag me there.

If you have further questions or clarifications about why I decided to reject the submission, please feel free to voice those on this thread and I'll do my best to answer.

[changliao1025]

Thanks for the suggestions, I will revise the repository following the instructions and then re-submit.