[PRE REVIEW]: lidar: A Python package for terrain and hydrological analysis using digital elevation models

[whedon]

Submitting author: @giswqs (Qiusheng Wu)
Repository: https://github.com/giswqs/lidar
Version: 0.5.1
Editor: @kbarnhart
Reviewers: @laijingtao, @cheginit, @amanaster2
Managing EiC: Kevin M. Moerman

⚠️ JOSS reduced service mode ⚠️

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Author instructions

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

@giswqs 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.

⚠️ JOSS reduced service mode ⚠️

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]

Failed to discover a Statement of need section in paper

[whedon]

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

OK DOIs

- 10.1016/j.cageo.2005.11.002 is OK
- 10.1016/j.geomorph.2016.05.006 is OK
- 10.1007/s13157-015-0731-6 is OK
- 10.1080/13658816.2015.1038719 is OK
- 10.1111/1752-1688.12689 is OK
- 10.1080/13658810500433453 is OK
- 10.1080/13658816.2014.975715 is OK
- 10.1002/hyp.10648 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.09 s (420.1 files/s, 40023.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          13            288            259            986
reStructuredText                11            205            176            236
TeX                              1              7              0            124
Jupyter Notebook                 2              0            790             97
YAML                             4              9             20             96
make                             2             24              6             78
Markdown                         2             17              0             51
DOS Batch                        1              8              1             27
INI                              1              5              0             15
-------------------------------------------------------------------------------
SUM:                            37            563           1252           1710
-------------------------------------------------------------------------------


Statistical information for the repository '0c0f307b066ea03f6ad8c52b' was
gathered on 2020/12/08.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Qiusheng Wu                     59          2766           1233          100.00

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
Qiusheng Wu                1533           55.4         12.1               17.16

[whedon]

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

[Kevin-Mattheus-Moerman]

@giswqs since this submission is on the small side (in therms of number of lines of code). I have flagged this submission for an additional scope check by the editorial board. In particular our board will now discuss if it meets the substantial scholarly effort criterion for review by JOSS. We should get back to you sometime next week.

[giswqs]

@Kevin-Mattheus-Moerman No problem. Thank you for the consideration.

[giswqs]

@whedon generate pdf

[whedon]

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

[giswqs]

@Kevin-Mattheus-Moerman Just let you know that I have added more functionality to the package and expanded the source code by a few more hundreds of lines. You can rerun the statistics if needed. Thanks.

[danielskatz]

@whedon check repository

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.19 s (234.1 files/s, 29466.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          20            605            570           2370
reStructuredText                11            205            176            236
TeX                              1              7              0            124
Jupyter Notebook                 2              0            790             97
YAML                             4              9             20             96
make                             2             24              6             78
Markdown                         2             17              0             52
DOS Batch                        1              8              1             27
INI                              1              5              0             15
-------------------------------------------------------------------------------
SUM:                            44            880           1563           3095
-------------------------------------------------------------------------------


Statistical information for the repository '8015707b8d245e5870642f86' was
gathered on 2020/12/13.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Qiusheng Wu                     60          4778           1233          100.00

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
Qiusheng Wu                3545           74.2          5.3               14.22

[kthyng]

@kbarnhart are you willing to edit this submission?

[kthyng]

@whedon invite @kbarnhart as editor

[whedon]

@kbarnhart has been invited to edit this submission.

[kbarnhart]

@kthyng I can handle this starting in early Jan.

@giswqs thanks for the submission. It still has the query-scope label, which means we are still determining whether the submission fits the scope of JOSS. I may follow up with some questions/clarifications on this point in early January. Please let me know if you have questions.

[kbarnhart]

@whedon assign @kbarnhart as editor

[whedon]

OK, the editor is @kbarnhart

[giswqs]

@kbarnhart No problem. Thank you for the consideration.

[kyleniemeyer]

@kbarnhart @giswqs the editorial board voted to consider this one in scope, so please proceed! I'm removing the scope-query label.

[kbarnhart]

@giswqs I'm now back in the office and will start actively handling this submission.

A couple of clarifying questions.

1. Is there a place where API-level documentation is provided? I've looked through the readthedocs page and can't seem to find this. I would expect that all public facing functions/classes would have detailed documentation describing the format of all inputs and outputs.
2. Could you comment on the similarities/difference between the core package and the arcpy toolbox. E.g., is
   lidar/toolbox/scripts/4_Slicing.py intended as the arcpy equivalent of lidar/slicing.py?
3. It appears that the tests in lidar/tests are empty. Could you comment on how the contents of the package is tested?

A final comment: There are a number of dependencies (matplotlib, scipy, numpy, richDEM, skimage) that are used and not cited in the submitted paper.

[giswqs]

@kbarnhart Thank you for handling the submission. I have revised the repo according to your comments. Thanks.

• Added docstrings to all functions and classes (link)
• Added tests (link) and GitHub actions (link)
• Cited dependencies (link)

The lidar/toolbox/scripts/1_Extract_Sink.py and lidar/toolbox/scripts/4_Slicing.py are intended as the arcpy equivalent of lidar/filling.py and lidar/slicing.py, respectively. The other five scripts (i.e., 2_Delineate_Catchment.py, 3_Flow_Path.py, 5_Catchment_Hierarchy.py, 6_Simulate Inundation.py, 7_Play_Animation.py) are for the arcpy toolbox only as they rely on some arcpy functions, which are not available outside arcpy.

[giswqs]

@whedon generate pdf

[kbarnhart]

👋 @cheginit @juliohm @Hedrick-ARS would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

The submission is "lidar: A Python package for terrain and hydrological analysis using digital elevation models".

This submission includes an ArcGIS toolbox, as well as a python package that implements similar functionality. Thus, it is important that at least one (ideally all) reviewers have access to the proprietary environment ArcGIS and the Spatial Analyst extension. For reference, here is a link to the JOSS documentation statement regarding submissions which include proprietary languages/environments.

This is a pre-review issue which is used to find reviewers. Once 2-3 reviewers are found, I'll start the review on a dedicated GitHub issue. At present we are asking reviewers to complete reviews in 6 weeks. If you are not able to review and have someone to recommend, please mention them here (when mentioning, please place a space after the @ of a github handle, for example, you would refer to me as "@ kbarnhart").

If you are interested in reviewing, I would recommend looking over the journal's conflict of interest policy before the review process starts.

If you have any questions about the JOSS review process, please do not hesitate to reach out to me on this issue or at [email protected]

[juliohm]

Dear all, unfortunately I can't review the submission. I don't have access to the proprietary software and haven't used Python in a while. Thank you, -Júlio

…

On Thu, Jan 14, 2021, 16:10 Katy Barnhart ***@***.***> wrote: 👋 @cheginit <https://github.com/cheginit> @juliohm <https://github.com/juliohm> @Hedrick-ARS <https://github.com/Hedrick-ARS> would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html The submission is "lidar: A Python package for terrain and hydrological analysis using digital elevation models". This submission includes an ArcGIS toolbox, as well as a python package that implements similar functionality. Thus, it is important that at least one (ideally all) reviewers have access to the proprietary environment ArcGIS and the Spatial Analyst extension. For reference, here is a link <https://joss.readthedocs.io/en/latest/review_criteria.html#what-about-submissions-that-rely-upon-proprietary-languages-development-environments> to the JOSS documentation statement regarding submissions which include proprietary languages/environments. This is a pre-review issue which is used to find reviewers. Once 2-3 reviewers are found, I'll start the review on a dedicated GitHub issue. At present we are asking reviewers to complete reviews in 6 weeks. If you are not able to review and have someone to recommend, please mention them here (when mentioning, please place a space after the @ of a github handle, for example, you would refer to me as "@ kbarnhart"). If you are interested in reviewing, I would recommend looking over the journal's conflict of interest policy <https://joss.readthedocs.io/en/latest/reviewer_guidelines.html?#joss-conflict-of-interest-policy> before the review process starts. If you have any questions about the JOSS review process, please do not hesitate to reach out to me on this issue or at ***@***.*** — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2896 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAZQW3K3W4T5IZUP4KG4KRLSZ46UBANCNFSM4USUJ65Q> .

[cheginit]

@kbarnhart I am a Python developer but don't have access to ArcGIS. So I can review the non-ArcGIS parts of the submission. Please, let me know if that works.

[r-barnes]

I could take a look, but I don't have access to ArcGIS.

[kbarnhart]

@juliohm - thanks for the response

@cheginit and @r-barnes thanks for your willingness to review. Via email discussions, I think that I've now found a third reviewer with access to Arc, but am still confirming with them.

Thus only one you is needed as a reviewer. I'll add @cheginit as a reviewer because @r-barnes has done a review for me somewhat recently (thank you!) and then start the review issue once I can confirm the final reviewer.

[kbarnhart]

@whedon add @cheginit as reviewer

[whedon]

OK, @cheginit is now a reviewer

[kbarnhart]

@amanaster2 has confirmed that she is willing to review and has access to Arc so I will now add her and start the review.

[kbarnhart]

@whedon add @amanaster2 as reviewer

[whedon]

OK, @amanaster2 is now a reviewer

[kbarnhart]

@whedon start review

[whedon]

OK, I've started the review over in #2965.

[r-barnes]

@kbarnhart : I appreciate your choice of the alternate reviewer here. I should be more free to look at things again in a month or so. I hope your 2021 is off to a good start!

[kbarnhart]

Thanks @r-barnes, same to you!