[PRE REVIEW]: Ripser.py: A Lean Persistent Homology Library for Python

[whedon]

Submitting author: @sauln (Nathaniel Saul)
Repository: https://github.com/scikit-tda/ripser.py
Version: 0.2.4
Editor: @arokem
Reviewers: lmcinnes

Author instructions

Thanks for submitting your paper to JOSS @sauln. The JOSS editor (shown at the top of this issue) will work with you on this issue to find a reviewer for your submission before creating the main review issue.

@sauln if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.

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. @arokem it looks like you're currently assigned as the editor for this paper 🎉

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

@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #901 with the following error:

Can't find any papers to compile :-(

[arfon]

@sauln - please review the submission guidelines for JOSS. Your project doesn't seem to have a paper.

[sauln]

Hi @arfon, sorry the paper was hiding in the Joss branch. I’ve merged it into master now.

[sauln]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

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

🚧 🚧 🚧 Experimental Whedon features 🚧 🚧 🚧

# Compile the paper
@whedon generate pdf

[sauln]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #901 with the following error:

/app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:379:in parse': (tmp/901/paper.md): did not find expected '-' indicator while parsing a block collection at line 8 column 2 (Psych::SyntaxError) from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:379:in parse_stream'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:327:in parse' from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:254:in load'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:475:in block in load_file' from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:474:in open'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:474:in load_file' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon.rb:68:in initialize'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon/processor.rb:32:in new' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon/processor.rb:32:in set_paper'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/bin/whedon:37:in prepare' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/command.rb:27:in run'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor.rb:387:in dispatch'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/bin/whedon:99:in <top (required)>'
from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in load' from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in

'

[arfon]

@sauln - this PR should fix the paper build error: scikit-tda/ripser.py#45

[sauln]

Thank you! It's merged.

[sauln]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof 📄 <--

[sauln]

@arfon, thanks for taking the time to work on this review. I look forward to learning more about this process and helping it along however I can.

[sauln]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof 📄 <--

[arfon]

@arfon, thanks for taking the time to work on this review. I look forward to learning more about this process and helping it along however I can.

👍 NP. Next we need to wait for an editor to pick this up (hopefully this will be @arokem). In the meantime, feel free to suggest some potential reviewers from this list of volunteers

[sauln]

That is an impressive list of volunteers!

I think @sealhuang, @sssomani, @abuccts, @ThomasA, and @arokem have interests and skills that could be relevant.

[ThomasA]

It sounds interesting, but I have no experience with TDA. I do not know how much that matters? Anyway, due to several reviews lately I still have one pending for JOSE (openjournals/jose-reviews#25), so I should probably not add more to the back log for now.

[sauln]

I think perspectives from outside the field of TDA would be beneficial. We hope that the library will be accessible to anyone with just an interest in TDA, so understanding how someone without previous background approaches the library would be helpful for us. That being said, a JOSS review might not be the best forum for that.

[arokem]

@whedon assign arokem as editor

[whedon]

OK, the editor is arokem

[arokem]

👋 @lmcinnes: would you be willing to review this paper for JOSS?

[arokem]

👋 @maxrousseau: would you be willing to review this paper for JOSS?

[maxrousseau]

Given my current workload, I don't think I would be able to thoroughly review this package in a timely manner. My apologies, good luck with your paper.

[lmcinnes]

@arokem , I would be willing to review this, but may need a little assistance, having never reviewed for JOSS before.

[arokem]

Thanks @lmcinnes! There is documentation that explains the principles and process here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Let me know if you have questions. Don't be alarmed if it takes me a few days to get to your questions, though. For the time being, I will start the review, which will start another issue with a check-list for you to check the software against.

[arokem]

@whedon assign lmcinnes as reviewer

[whedon]

OK, the reviewer is lmcinnes

[arokem]

@whedon start review

[whedon]

OK, I've started the review over in #925. Feel free to close this issue now!

[arokem]

@lmcinnes : the check list and more guidance should now be available for you on #925. I'm closing this one.