[PRE REVIEW]: Omniscape.jl: Software to predict omni-directional landscape connectivity

[whedon]

Submitting author: @vlandau (Vincent Landau) Repository: https://github.com/Circuitscape/Omniscape.jl Version: v0.4.3 Editor: @melissawm Reviewers: @juliohm, @tpoisot Managing EiC: Kyle Niemeyer

: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 @vlandau. Currently, there isn't an JOSS editor assigned to your paper.

The author's suggestion for the handling editor is @karthik.

@vlandau 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]

Failed to discover a Statement of need section in paper

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.11 s (355.0 files/s, 27852.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           10            312            123           1436
Markdown                         5            129              0            299
INI                             13             55              0            272
SVG                              1              0              0            143
TeX                              1              6              0             67
YAML                             4             12              5             66
TOML                             2              3              0             24
Dockerfile                       1              5              3             14
CSS                              1              1              0              6
-------------------------------------------------------------------------------
SUM:                            38            523            131           2327
-------------------------------------------------------------------------------

Statistical information for the repository 'a2bfece65154bbf521f209ba' was
gathered on 2020/10/24.
No commited files with the specified extensions were found.

[whedon]

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

OK DOIs

- 10.21105/jcon.00058 is OK

MISSING DOIs

- 10.1137/141000671 may be a valid DOI for title: Julia: A fresh approach to numerical computing
- 10.1890/07-1861.1 may be a valid DOI for title: Using circuit theory to model connectivity in ecology, evolution, and conservation

INVALID DOIs

- None

[whedon]

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

[kyleniemeyer]

Hey @karthik, I realize a Julia package is a bit outside your usual wheelhouse, but could you edit this one?

[kyleniemeyer]

@whedon invite @karthik as editor

[whedon]

@karthik has been invited to edit this submission.

[karthik]

👋 @kyleniemeyer Thanks for the invitation. This submission is well outside my scope of expertise. I also had a very challenging time finding reviewers last time I handled a Julia submission. For these reasons I'd like to decline this one. 🙏

[vlandau]

Timothee Poisot (tpoisot) has offered to review this paper/software. From the spreadsheet of potential reviewers, arbennett, r-barnes, and juliohm look like excellent fits.

[kyleniemeyer]

@karthik understood, no worries.

Hi @melissawm, as one of our "official" Julia editors 😀, could you take this on?

[arfon]

@whedon invite @melissawm as editor

[whedon]

@melissawm has been invited to edit this submission.

[melissawm]

Hi all, I'll be happy to even though the subject is not one I'm totally familiar with.

[melissawm]

@whedon assign @melissawm as editor

[whedon]

OK, the editor is @melissawm

[vlandau]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
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@whedon list editors

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@whedon list reviewers

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# Compile the paper
@whedon generate pdf

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@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

[melissawm]

Hello @vlandau! I'll proceed with inviting reviewers, could you please check the DOI issues listed above?

[melissawm]

:wave: @tpoisot, @juliohm 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 Let me know if you have any further questions. Thank you!

[juliohm]

I would be happy to review the submission @melissawm :+1:

[melissawm]

@whedon assign @juliohm as reviewer

[whedon]

OK, @juliohm is now a reviewer

[vlandau]

@whedon generate pdf

[vlandau]

@whedon check references

[whedon]

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

OK DOIs

- 10.1111/j.0014-3820.2006.tb00500.x is OK
- 10.1137/141000671 is OK
- 10.1890/07-1861.1 is OK
- 10.1890/07-1861.1 is OK
- 10.21105/jcon.00058 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[vlandau]

@whedon check references

[whedon]

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

OK DOIs

- 10.1111/j.0014-3820.2006.tb00500.x is OK
- 10.1137/141000671 is OK
- 10.1890/07-1861.1 is OK
- 10.1111/cobi.13230 is OK
- 10.21105/jcon.00058 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[tpoisot]

grabs :microphone: to give some completely unsolicited advice

I'm happy to review this one, I used Omniscape a lot. I know that @vlucet and @glaroc also did, and would be suitable reviewers as well.

[VLucet]

Thanks @tpoisot for thinking of me! I actually have not had the chance to test Omniscape yet. I know @glaroc did and would therefore be better suited. I have used Circuitscape (Julia version) quite a bit. I'm unsure whether having this perspective fully qualifies me to be a reviewer.

[melissawm]

Thanks, @tpoisot !

With this, we'll already have two reviewers which is the minimum for the review process to go forward, but I'd be happy to add a third reviewer, too - @vlandau do you have a preference?

[melissawm]

@whedon add @tpoisot as reviewer

[whedon]

OK, @tpoisot is now a reviewer

[vlandau]

@melissawm I'm good either way. Lowest-hanging fruit may be to just go with the two we have. Thanks!

[melissawm]

Then we're good - I'll assign the reviewers and this issue will be automatically closed by whedon - we'll meet at the review issue. Thank you, all!

[melissawm]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2829.