Joss-reviews: [REVIEW]: hankel: A Python library for performing simple and accurate Hankel transformations

Created on 22 Apr 2019 · 89Comments · Source: openjournals/joss-reviews

Submitting author: @steven-murray (Steven Murray)
Repository: https://github.com/steven-murray/hankel
Version: v0.3.9
Editor: @xuanxu
Reviewer: @melissawm
Archive: 10.5281/zenodo.3235680

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/db4645a0737759932c07c250decf72b7"><img src="http://joss.theoj.org/papers/db4645a0737759932c07c250decf72b7/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/db4645a0737759932c07c250decf72b7/status.svg)](http://joss.theoj.org/papers/db4645a0737759932c07c250decf72b7)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

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

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @xuanxu know.

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

Review checklist for @melissawm

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS 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 JOSS 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] Version: v0.3.9
[x] Authorship: Has the submitting author (@steven-murray) 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

Software paper

[x] Authors: Does the paper.md 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)?

accepted published recommend-accept review

Source

whedon

Most helpful comment

Congrats @steven-murray on your paper's acceptance in JOSS! Thanks to @melissawm for reviewing and @xuanxu for editing!

kyleniemeyer on 1 Jun 2019

🎉2

All 89 comments

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @melissawm it looks like you're currently assigned as the reviewer for this paper :tada:.

:star: Important :star:

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) 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:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

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

@whedon commands

whedon on 22 Apr 2019

Attempting PDF compilation. Reticulating splines etc...

whedon on 22 Apr 2019

PDF failed to compile for issue #1397 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/1397 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:incollect!'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/processor.rb:57:infind_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:50:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:116:in from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

whedon on 22 Apr 2019

@whedon generate pdf from branch joss-paper

xuanxu on 22 Apr 2019

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...

whedon on 22 Apr 2019

PDF failed to compile for issue #1397 with the following error:

sh: 1: cd: can't cd to tmp/1397
/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/1397 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:incollect!'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/processor.rb:57:infind_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:50:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:116:in from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

whedon on 22 Apr 2019

Git repo address updated from https://github.com/steven-murray/hankel/tree/joss-paper to https://github.com/steven-murray/hankel so whedon can clone it.

xuanxu on 22 Apr 2019

@whedon generate pdf from branch joss-paper

xuanxu on 22 Apr 2019

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...

whedon on 22 Apr 2019

PDF failed to compile for issue #1397 with the following error:

whedon on 22 Apr 2019

@arfon could you do your magic so we can get the pdf paper? (it compiled in the pre-review issue but I can't replicate it here)

xuanxu on 22 Apr 2019

@whedon generate pdf from branch joss-paper

labarba on 12 May 2019

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...

whedon on 12 May 2019

PDF failed to compile for issue #1397 with the following error:

fatal: not a git repository (or any parent up to mount point /)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
Can't find any papers to compile :-(

whedon on 12 May 2019

@arfon — This is failing to compile. Can you find the problem?

labarba on 12 May 2019

@whedon generate pdf from branch joss-paper

arfon on 12 May 2019

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...

whedon on 12 May 2019

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

whedon on 12 May 2019

OK, @melissawm — the proof has compiled. Please start your review. Feel free to ask questions here, and to open issues in the submission repository, as needed. 🙏

labarba on 12 May 2019

:wave: @melissawm - friendly reminder to take a look at this review when you get a chance.

xuanxu on 21 May 2019

Hello, @xuanxu , maybe I didn't understand the workflow for the review process. I'm doing the review, however there are some issues that I'm waiting to be solved before I can check all of the boxes and finish the review. I've opened these issues in the source repository as instructed. Should I not wait for that?

melissawm on 21 May 2019

👍1

Hi @melissawm! I didn't see the issues you opened in the hankel repository, sorry. The workflow you are following is OK.
Just a detail: as the central place for the review process, it'd be ideal if you could add a short comment in this issue whenever the status changes or to keep track of the actions being taken (for example, something like "I've opened some issues in the target repo with a couple problems that need to be addressed" in this case). That way this issue works as a log of the review.

xuanxu on 21 May 2019

Hi @melissawm, I think I have now responded to all the issues you've created so far. Thanks for some great suggestions. Let me know if there's anything else!

steven-murray on 22 May 2019

Hello all. @xuanxu the review has been finalized. @steven-murray has answered to all the issues that I've opened (adding the DOI for the references; adding a document/guide for contributors and those seeking support, including how to test the software). As far as I'm concerned this is approved.

melissawm on 23 May 2019

Great, thanks @melissawm!

xuanxu on 23 May 2019

@steven-murray can you merge the changes into master?

xuanxu on 23 May 2019

@xuanxu it is now merged.

steven-murray on 23 May 2019

@whedon generate pdf

xuanxu on 24 May 2019

Attempting PDF compilation. Reticulating splines etc...

whedon on 24 May 2019

PDF failed to compile for issue #1397 with the following error:

Error reading bibliography ./paper.bib (line 9, column 11):
unexpected "."
expecting letter, digit, white space, "#", "," or "}"
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

whedon on 24 May 2019

@steven-murray the paper compilation failed because there's a couple of missing braces. I've issued a PR in your repo to fix that.

xuanxu on 24 May 2019

@whedon generate pdf

xuanxu on 24 May 2019

Attempting PDF compilation. Reticulating splines etc...

whedon on 24 May 2019

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

whedon on 24 May 2019

@whedon check references

xuanxu on 25 May 2019

Attempting to check references...

whedon on 25 May 2019

```Reference check summary:

OK DOIs

10.2977/prims/1145474602 is OK
10.1086/496971 is OK
10.1016/S0377-0427(99)00223-X is OK
10.5281/zenodo.1336791 is OK

MISSING DOIs

https://doi.org/10.1017/cbo9781139107136.003 may be missing for title: Highly Oscillatory Quadrature

INVALID DOIs

None
```

whedon on 25 May 2019

@steven-murray Whedon suggests https://doi.org/10.1017/cbo9781139107136.003 as a posible DOI for the Highly Oscillatory Quadrature citation. Do you think it's the right one? If so I have issued a PR in the hankel repo updating it.

xuanxu on 25 May 2019

Yes, that seems right, I've merged it, thanks!

steven-murray on 28 May 2019

@whedon generate pdf

xuanxu on 28 May 2019

Attempting PDF compilation. Reticulating splines etc...

whedon on 28 May 2019

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

whedon on 28 May 2019

The source code for hankel has been archived to Zenodo with the linked DOI: [@zenodo]

@steven-murray The Zenodo archive will be linked on the first page of the paper, so we ask that you don't add an additional link in the text or references. Can you edit that citation out?

xuanxu on 28 May 2019

I have removed it now, thanks.

On Tue, May 28, 2019 at 11:27 AM Juanjo Bazán notifications@github.com
wrote:

The source code for hankel has been archived to Zenodo with the linked
DOI: [@zenodo]

The Zenodo archive will be linked on the first page of the paper, so we
ask that you don't add an additional link in the text or references. Can
you edit that citation out?

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
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steven-murray on 28 May 2019

@whedon generate pdf

xuanxu on 28 May 2019

Attempting PDF compilation. Reticulating splines etc...

whedon on 28 May 2019

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

whedon on 28 May 2019

@whedon check references

xuanxu on 28 May 2019

Attempting to check references...

whedon on 28 May 2019

```Reference check summary:

OK DOIs

10.2977/prims/1145474602 is OK
10.1086/496971 is OK
10.1017/CBO9781139107136.003 is OK
10.1016/S0377-0427(99)00223-X is OK
10.5281/zenodo.1336791 is OK

MISSING DOIs

None

INVALID DOIs

None
```

whedon on 28 May 2019

I have removed it now, thanks.

It is still in the paper and bib files, maybe forgot to push?

xuanxu on 28 May 2019

From the summary:
In this single sentence:

Highly oscillatory integrals are a topic of much interest in applied mathematics, and there does not exist a general optimal solution to numerically evaluate them double-exponential variable transformation based on the zeros of the Bessel function [@Ooura1999] has the property that the numerical integral converges with many fewer divisions compared to naively computing the transform integral.

I guess there's a missing dot somewhere.

xuanxu on 28 May 2019

Hmm, this seems to have been a line added in the wrong place in the
previous PR. Fixed now!

On Tue, May 28, 2019 at 1:53 PM Juanjo Bazán notifications@github.com
wrote:

From the summary:
In this single sentence:

Highly oscillatory integrals are a topic of much interest in applied
mathematics, and there does not exist a general optimal solution to
numerically evaluate them double-exponential variable transformation based
on the zeros of the Bessel function [@Ooura1999] has the property that the
numerical integral converges with many fewer divisions compared to naively
computing the transform integral.

I guess there's a missing dot somewhere.

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steven-murray on 28 May 2019

@whedon generate pdf

xuanxu on 28 May 2019

Attempting PDF compilation. Reticulating splines etc...

whedon on 28 May 2019

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

whedon on 28 May 2019

@whedon check references

xuanxu on 28 May 2019

Attempting to check references...

whedon on 28 May 2019

```Reference check summary:

OK DOIs

10.2977/prims/1145474602 is OK
10.1086/496971 is OK
10.1017/CBO9781139107136.003 is OK
10.1016/S0377-0427(99)00223-X is OK

MISSING DOIs

None

INVALID DOIs

None
```

whedon on 28 May 2019

Thanks @steven-murray, the paper looks ok to me now.

Please release a new version. It will include all the changes made during the review.
Then create a Zenodo archive of it and report the DOI here (make sure to edit the metadata so title and author are the same as in the paper).

xuanxu on 28 May 2019

Thanks @xuanxu .

I'm not too familiar with Zenodo. I already have a zenodo entry for hankel (https://zenodo.org/record/1336792). It looks like I have three options: create a release, edit the version that's already there, or create a new version. It's not clear to me which path I should take. The latter two are giving me internal server errors at the moment...

steven-murray on 30 May 2019

@steven-murray I suggest you try these steps:

Create a new release in Github: https://github.com/steven-murray/hankel/releases
If Zenodo has enough permissions (see https://zenodo.org/account/settings/github/ ) it should automatically upload the new zip file, otherwise it can be done manually here: https://zenodo.org/deposit/new
Edit the metadata of the new entry in Zenodo so title/author list match the paper.

xuanxu on 30 May 2019

OK thanks very much. This is now done and at https://zenodo.org/record/3235680

steven-murray on 30 May 2019

@whedon set v0.3.9 as version

xuanxu on 30 May 2019

OK. v0.3.9 is the version.

whedon on 30 May 2019

@steven-murray great! Please edit the title to match the paper:
hankel: A Python library for performing simple and accurate Hankel transformations
You can do so here: https://zenodo.org/deposit/3235680 (change title >> save >> publish)

xuanxu on 30 May 2019

@whedon set 10.5281/zenodo.3235680 as archive

xuanxu on 31 May 2019

OK. 10.5281/zenodo.3235680 is the archive.

whedon on 31 May 2019

@openjournals/joss-eics, I think we are good to go!

xuanxu on 31 May 2019

OK cool, done that.

On Thu, May 30, 2019 at 1:09 PM Juanjo Bazán notifications@github.com
wrote:

@steven-murray https://github.com/steven-murray great! Please edit the
title to match the paper:
hankel: A Python library for performing simple and accurate Hankel
transformations
You can do so here: https://zenodo.org/deposit/3235680
https://secure-web.cisco.com/1F7TYK4WmghACn4SBF_FTXPWI2ZxZXa3QGa1q2IMmm6YHObR47unS4jTzc0L2RmVz-QjDDHtv4McUQaFV-LNwuQsDXeAAEBfZT1X1KZb5SzqG33QoGLoMuQGVx6mCNRSK6oZi65aoKlfYssKOjevFchnVb_SC_Q7NaxrM0Qy_5gBA3ryXLTLrHcOcH25HD1R03TiEM-Oj0280r6tJie_lUKdSvZ0IFRK3GoL6Wp-2DmwaXYhWtZmtQj47-0unVgqSIdBf11rhI0yojxNVFICVaNK8P3_nHP6dIKTmFxqKmFygBIVL65X-4iPOgFnvPKVAMysA8EmSEKQGupfOB4hfm48IINvo9Y6ijwRgj-UruNss_aH-faXRZX4K2iB6Yr7hEfM_wVNQrTyO8v9JfrJaAIWAScVKAHW8jYYGQ3pHS1FPXBDDAw1DDq-3F5jxve9s0Uq9ivJzB3hJ9NnMy1S1M_loPT4T5ODXbwKpjHWOuEs/https%3A%2F%2Fzenodo.org%2Fdeposit%2F3235680

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Arizona State University.

steven-murray on 31 May 2019

@whedon generate pdf

kyleniemeyer on 31 May 2019

Attempting PDF compilation. Reticulating splines etc...

whedon on 31 May 2019

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

whedon on 31 May 2019

Hi @steven-murray, nearly ready to accept—I just submitted a small PR to your paper which fixes the formatting of some in-text references: https://github.com/steven-murray/hankel/pull/28

kyleniemeyer on 31 May 2019

Awesome, thanks! That's now merged.

On Fri, May 31, 2019 at 2:44 PM Kyle Niemeyer notifications@github.com
wrote:

Hi @steven-murray https://github.com/steven-murray, nearly ready to
accept—I just submitted a small PR to your paper which fixes the formatting
of some in-text references: steven-murray/hankel#28
https://github.com/steven-murray/hankel/pull/28

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Arizona State University.

steven-murray on 1 Jun 2019

@whedon generate pdf

kyleniemeyer on 1 Jun 2019

Attempting PDF compilation. Reticulating splines etc...

whedon on 1 Jun 2019

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

whedon on 1 Jun 2019

@whedon accept

kyleniemeyer on 1 Jun 2019

Attempting dry run of processing paper acceptance...

whedon on 1 Jun 2019

```Reference check summary:

OK DOIs

10.2977/prims/1145474602 is OK
10.1086/496971 is OK
10.1017/CBO9781139107136.003 is OK
10.1016/S0377-0427(99)00223-X is OK

MISSING DOIs

None

INVALID DOIs

None
```

whedon on 1 Jun 2019

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/726

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/726, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

whedon on 1 Jun 2019

@whedon accept deposit=true

kyleniemeyer on 1 Jun 2019

Doing it live! Attempting automated processing of paper acceptance...

whedon on 1 Jun 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon on 1 Jun 2019

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/727
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01397
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

whedon on 1 Jun 2019

Congrats @steven-murray on your paper's acceptance in JOSS! Thanks to @melissawm for reviewing and @xuanxu for editing!

kyleniemeyer on 1 Jun 2019

🎉2

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](http://joss.theoj.org/papers/10.21105/joss.01397/status.svg)](https://doi.org/10.21105/joss.01397)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01397">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01397/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01397/status.svg
   :target: https://doi.org/10.21105/joss.01397

This is how it will look in your documentation:

We need your help!

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whedon on 1 Jun 2019

Thanks a bunch @xuanxu, @kyleniemeyer and @melissawm!

steven-murray on 3 Jun 2019

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