[REVIEW]: Circuitscape in Julia: High Performance Connectivity Modelling to Support Conservation Decisions

[whedon]

Submitting author: !--author-handle-->@ranjanan<!--end-author-handle-- (Ranjan Anantharaman) Repository: https://github.com/Circuitscape/CircuitscapeJuliaPaper Branch with paper.md (empty if default branch): Version: Editor: !--editor-->@matbesancon<!--end-editor-- Reviewers: !--reviewers-list-->@vlandau<!--end-reviewers-list-- Archive:

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Reviewer instructions & questions

@vlandau, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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The reviewer guidelines are available here: https://proceedings.juliacon.org/guide/reviewers. Any questions/concerns please let @matbesancon know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @vlandau

Conflict of interest

• [x] As the reviewer I confirm that I have read the JuliaCon conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• [x] I confirm that I read and will adhere to the JuliaCon code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Authorship: Has the submitting author (@ranjanan) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• [x] 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

Paper format

• [x] Authors: Does the paper.tex file include a list of authors with their affiliations?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
• [x] Page limit: Is the page limit for full papers respected by the submitted document?

Content

• [x] Context: is the scientific context motivating the work correctly presented?
• [x] Methodology: is the approach taken in the work justified, presented with enough details and reference to reproduce it?
• [x] Results: are the results presented and compared to approaches with similar goals?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @vlandau it looks like you're currently assigned to review this paper :tada:.

: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.

:star: Important :star:

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/JuliaCon/proceedings-review) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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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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[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[whedon]

Reference check summary:

OK DOIs

- 10.5281/zenodo.1438428 is OK
- 10.5281/zenodo.2584373 is OK

MISSING DOIs

- https://doi.org/10.1038/373299a0 may be missing for title: Connecting landscape patterns to ecosystem and population processes
- https://doi.org/10.1007/s10980-016-0353-2 may be missing for title: Applying fire connectivity and centrality measures to mitigate the cheatgrass-fire cycle in the arid West, USA
- https://doi.org/10.1111/cobi.12938 may be missing for title: Connecting today’s climates to future climate analogs to facilitate movement of species under climate change
- https://doi.org/10.1016/j.landurbplan.2017.01.007 may be missing for title: Habitat suitability is a poor proxy for landscape connectivity during dispersal and mating movements
- https://doi.org/10.1111/j.1365-294x.2010.04657.x may be missing for title: Use of resistance surfaces for landscape genetic studies: considerations for parameterization and analysis
- https://doi.org/10.1007/s10980-012-9737-0 may be missing for title: Estimating landscape resistance to movement: a review
- https://doi.org/10.1007/s10980-012-9737-0 may be missing for title: Estimating landscape resistance to movement: a review
- https://doi.org/10.1890/07-1861.1 may be missing for title: Using circuit theory to model connectivity in ecology, evolution, and conservation
- https://doi.org/10.1109/mcse.2011.37 may be missing for title: The NumPy array: a structure for efficient numerical computation
- https://doi.org/10.1016/s0168-9274(01)00115-5 may be missing for title: BoomerAMG: a parallel algebraic multigrid solver and preconditioner
- https://doi.org/10.1137/141000671 may be missing for title: Julia: A fresh approach to numerical computing
- https://doi.org/10.1007/springerreference_72145 may be missing for title: Cholesky factorization
- https://doi.org/10.1371/journal.pone.0084135 may be missing for title: Applying circuit theory for corridor expansion and management at regional scales: tiling, pinch points, and omnidirectional connectivity
- https://doi.org/10.1007/bf02238511 may be missing for title: Algebraic multigrid by smoothed aggregation for second and fourth order elliptic problems
- https://doi.org/10.1016/b978-0-444-50616-0.50012-9 may be missing for title: A review of algebraic multigrid
- https://doi.org/10.1002/ecs2.1652 may be missing for title: Using nested connectivity models to resolve management conflicts of isolated water networks in the Sonoran Desert
- https://doi.org/10.1002/ecs2.2847 may be missing for title: A range‐wide model of contemporary, omnidirectional connectivity for the threatened Mojave desert tortoise

INVALID DOIs

- None

[matbesancon]

@vlandau thanks for the review and sorry for the delay, can you verify that the paper meets the criteria from the list above and check them when it applies?

[matbesancon]

@ranjanan for archiving purposes can you repost the review PDF here? Also there seems to be some DOI missing, whedon is sometimes incorrect on these so let us know if it doesn't apply

[vlandau]

@matbesancon Hmm, when I click the link to accept the invitation I am getting a 404 error that the page doesn't exist -- I haven't been able to accept an invitation so maybe that's why I'm not able to edit the checklist.

[matbesancon]

@whedon help

[whedon]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

[matbesancon]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

# Re-invite a reviewer (if they can't update checklists)
@whedon re-invite @username as reviewer

# Remove a GitHub user from the reviewers of this submission
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# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
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# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Set the software version at the top of the issue e.g.
@whedon set v1.0.1 as version

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EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Remind an author or reviewer to return to a review after a
# certain period of time (supported units days and weeks)
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EiC TASKS

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[matbesancon]

@whedon list reviewers

[whedon]

Here's the current list of reviewers: http://bit.ly/2V9GSFq

[matbesancon]

@whedon re-invite @vlandau as reviewer

[whedon]

The reviewer already has a pending invite.

@vlandau please accept the invite by clicking this link: https://github.com/JuliaCon/proceedings-review/invitations

[ranjanan]

Almost all the DOIs that whedon complained are missing exist, except for the cholesky factorization citation (https://onlinelibrary.wiley.com/doi/full/10.1002/wics.18) which has a different DOI than the one whedon detected. I'll update the paper with the DOI and generate it here.

[vlandau]

A couple of notes:

1. I'm not sure what the page limit is, so it is unchecked for now.

2. I left the references box unchecked for now until the DOI issue above is resolved. I wasn't able to see the specific DOI list. Is there a link to that somewhere? None of the citations in the References section of the paper show a DOI, so I wasn't sure where to look for those.

[matbesancon]

I'm not sure what the page limit is, so it is unchecked for now.

if I remember correctly it's 8 pages, so this paper is fine

You can verify that references are adequate, disregarding the technical DOI issue, that is, is the paper referencing appropriate references to point the reader where needed

[vlandau]

Okay -- all looks good on my end!

[ranjanan]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[ranjanan]

Updated the fautly DOI and generated the paper, like you asked.

[matbesancon]

fine grained -> fine-grained

Over the past decade Circuitscape -> Over the past decade, Circuitscape

Then, in collaboration with Tanmay Mohapatra, it was translated to Python for flexible scripting, platform independence, and released under an open-source license.

in the C programmming language --> 2 Ms

is high performance -> high-performance

our user base, and works well on every platform (comma)

Julia is an open source programming language --> open-source (multiple occurrences)

are often problem specific -> problem-specific

the choleksy factorization -> Choleksy (multiple occurrences)

backsubstitution -> back-substitution

process independently \cite{pelletier2014applying} , and (no space before and)

produce fine scale and localized -> fine-scale

switch to 64-bit integer ->integers

feedback loop with policy makers and result -> policymakers, and

Its high level mathematical -> high-level

presents upto -> up to

is open source and is available -> is open-source

[ranjanan]

@matbesancon I made the changes, but I changed the URL from the original package repo to https://github.com/Circuitscape/CircuitscapeJuliaPaper.

[matbesancon]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[matbesancon]

did it work ?

[ranjanan]

Yes, it worked. I see you edited the original comment. Nice.

[ranjanan]

@matbesancon what's next here?

[matbesancon]

this looks good on my side

[matbesancon]

@whedon check DOI

[whedon]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

[matbesancon]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

# Re-invite a reviewer (if they can't update checklists)
@whedon re-invite @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@whedon remove @username as reviewer

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Set the software version at the top of the issue e.g.
@whedon set v1.0.1 as version

# Open the review issue
@whedon start review

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Remind an author or reviewer to return to a review after a
# certain period of time (supported units days and weeks)
@whedon remind @reviewer in 2 weeks

# Ask Whedon to do a  dry run of accepting the paper and depositing with Crossref
@whedon accept

# 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

EiC TASKS

# Invite an editor to edit a submission (sending them an email)
@whedon invite @editor as editor

# Reject a paper
@whedon reject

# Withdraw a paper
@whedon withdraw

# Ask Whedon to actually accept the paper and deposit with Crossref
@whedon accept deposit=true

[matbesancon]

@whedon check references

[whedon]

Reference check summary:

OK DOIs

- 10.5281/zenodo.1438428 is OK
- 10.5281/zenodo.2584373 is OK

MISSING DOIs

- https://doi.org/10.1038/373299a0 may be missing for title: Connecting landscape patterns to ecosystem and population processes
- https://doi.org/10.1007/s10980-016-0353-2 may be missing for title: Applying fire connectivity and centrality measures to mitigate the cheatgrass-fire cycle in the arid West, USA
- https://doi.org/10.1111/cobi.12938 may be missing for title: Connecting today’s climates to future climate analogs to facilitate movement of species under climate change
- https://doi.org/10.1016/j.landurbplan.2017.01.007 may be missing for title: Habitat suitability is a poor proxy for landscape connectivity during dispersal and mating movements
- https://doi.org/10.1111/j.1365-294x.2010.04657.x may be missing for title: Use of resistance surfaces for landscape genetic studies: considerations for parameterization and analysis
- https://doi.org/10.1007/s10980-012-9737-0 may be missing for title: Estimating landscape resistance to movement: a review
- https://doi.org/10.1007/s10980-012-9737-0 may be missing for title: Estimating landscape resistance to movement: a review
- https://doi.org/10.1890/07-1861.1 may be missing for title: Using circuit theory to model connectivity in ecology, evolution, and conservation
- https://doi.org/10.1109/mcse.2011.37 may be missing for title: The NumPy array: a structure for efficient numerical computation
- https://doi.org/10.1016/s0168-9274(01)00115-5 may be missing for title: BoomerAMG: a parallel algebraic multigrid solver and preconditioner
- https://doi.org/10.1137/141000671 may be missing for title: Julia: A fresh approach to numerical computing
- https://doi.org/10.1007/springerreference_72145 may be missing for title: Cholesky factorization
- https://doi.org/10.1371/journal.pone.0084135 may be missing for title: Applying circuit theory for corridor expansion and management at regional scales: tiling, pinch points, and omnidirectional connectivity
- https://doi.org/10.1007/bf02238511 may be missing for title: Algebraic multigrid by smoothed aggregation for second and fourth order elliptic problems
- https://doi.org/10.1016/b978-0-444-50616-0.50012-9 may be missing for title: A review of algebraic multigrid
- https://doi.org/10.1002/ecs2.1652 may be missing for title: Using nested connectivity models to resolve management conflicts of isolated water networks in the Sonoran Desert
- https://doi.org/10.1002/ecs2.2847 may be missing for title: A range‐wide model of contemporary, omnidirectional connectivity for the threatened Mojave desert tortoise

INVALID DOIs

- None

[matbesancon]

@ranjanan can you check the DOIs above? Whedon is buggy so some of them might be wrong

[arfon]

@whedon accept

[whedon]

No archive DOI set. Exiting...

[matbesancon]

hey @ranjanan, can you archive your repo on Zenodo and give me the provided DOI here when done?

[ranjanan]

@matbesancon how do I do that? Can't find Circuitscape.jl on Zenodo...

[ranjanan]

Don't think I ever put it there, now that I think about it

[matbesancon]

if you go on Zenodo, you can link your github, and then register your project, this will allow you to register an archive

[ranjanan]

Yes, here's the release DOI: 10.5281/zenodo.3960829. Should I create a DOI for the paper as well, or will this do?

[matbesancon]

@whedon set10.5281/zenodo.3960829 as archive

[whedon]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

[matbesancon]

@whedon set 10.5281/zenodo.3960829 as archive

[whedon]

OK. 10.5281/zenodo.3960829 is the archive.

[matbesancon]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[matbesancon]

@whedon accept