Joss-reviews: [PRE REVIEW]: Ripserer.jl: flexible and efficient persistent homology computation in Julia

[whedon]

Submitting author: @mtsch (Matija Čufar)
Repository: https://github.com/mtsch/Ripserer.jl
Version: v0.14.7
Editor: @VivianePons
Reviewers: @juliohm, @sauln
Managing EiC: Kevin M. Moerman

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

@mtsch 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]

Reference check summary:

OK DOIs

- 10.5281/zenodo.889971 is OK

MISSING DOIs

- https://doi.org/10.1007/978-3-319-64185-0_11 may be missing for title: Topological data analysis for image tampering detection
- https://doi.org/10.1038/ncomms15396 may be missing for title: Quantifying similarity of pore-geometry in nanoporous materials
- https://doi.org/10.1137/15m1031151 may be missing for title: Biological Aggregation Driven by Social and Environmental Factors: A Nonlocal Model and Its Degenerate Cahn–Hilliard Approximation
- https://doi.org/10.1145/3350755.3400244 may be missing for title: Towards Lockfree Persistent Homology
- https://doi.org/10.21105/joss.00925 may be missing for title: Ripser. py: A lean persistent homology library for python
- https://doi.org/10.1137/141000671 may be missing for title: Julia: A fresh approach to numerical computing
- https://doi.org/10.1137/15m1020575 may be missing for title: JuMP: A modeling language for mathematical optimization

INVALID DOIs

- None

[whedon]

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

[Kevin-Mattheus-Moerman]

@whedon check repository

[whedon]

Failed to discover a Statement of need section in paper

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.67 s (95.5 files/s, 146842.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              4              1              1          91516
Julia                           42            951            363           4762
Markdown                         8            141              0            430
TeX                              1              0              0            129
YAML                             4              7              0             86
TOML                             3              4              0             61
make                             1              0              0              2
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                            64           1104            364          96987
-------------------------------------------------------------------------------


Statistical information for the repository '2603' was gathered on 2020/08/26.
No commited files with the specified extensions were found.

[Kevin-Mattheus-Moerman]

@mtsch can you work on the following:

• [ ] Can you check/fix those missing/invalid DOI's :point_up:? You can call @whedon check references to check these here
• [ ] As recommended in our guidelines can you rework/add text to have a Statement of Need section in your paper? You can call @whedon generate pdf to update the paper pdf here

[Kevin-Mattheus-Moerman]

@VivianePons @xuanxu @drvinceknight could one of you handle this submission?

[VivianePons]

I can

[VivianePons]

@whedon assign @VivianePons as editor

[whedon]

OK, the editor is @VivianePons

[mtsch]

@whedon check references

[whedon]

Reference check summary:

OK DOIs

- 10.1007/978-3-319-64185-0_11 is OK
- 10.1137/15M1031151 is OK
- 10.1038/ncomms15396 is OK
- 10.1145/3350755.3400244 is OK
- 10.4230/LIPIcs.SoCG.2016.71 is OK
- 10.21105/joss.00925 is OK
- 10.1137/141000671 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.5555/3122009.3122017 is INVALID

[mtsch]

@whedon check references

[whedon]

Reference check summary:

OK DOIs

- 10.1007/978-3-319-64185-0_11 is OK
- 10.1137/15M1031151 is OK
- 10.1038/ncomms15396 is OK
- 10.1145/3350755.3400244 is OK
- 10.4230/LIPIcs.SoCG.2016.71 is OK
- 10.21105/joss.00925 is OK
- 10.1137/141000671 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[mtsch]

@whedon generate pdf

[whedon]

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

[mtsch]

Ok, I fixed the DOIs and added a statement of need.

[VivianePons]

@mtsch thank you for fixing the DOI

do you have any recommendations for potential reviewers? You can look at our list of potential reviewers but also suggest names outside the list

[mtsch]

I looked through the list and the intersection between topological data analysis and Julia appears to be empty.

Maybe @sauln might find this project interesting? Potentially @juliohm as well?

[VivianePons]

Indeed, I have just asked them, let's see!

[mtsch]

Thank you!

[VivianePons]

@whedon assign @juliohm as reviewer

[whedon]

OK, @juliohm is now a reviewer

[juliohm]

@VivianePons I remember JOSS had a check list on each submission. Is it still available? I remember the bot was responsible for creating this checklist. The review process already started?

[VivianePons]

The checklist appear on the review issue, we are still on the "pre review". I have just confirmed a second reviewer and am about to launch the review :)

[VivianePons]

@whedon add @sauln as reviewer

[whedon]

OK, @sauln is now a reviewer

[VivianePons]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2614.