Joss-reviews: [REVIEW]: IDTxl: The Information Dynamics Toolkit xl: a Python package for the efficient analysis of multivariate information dynamics in networks

Created on 15 Nov 2018  ·  78Comments  ·  Source: openjournals/joss-reviews

Submitting author: @pwollstadt (Patricia Wollstadt)
Repository: https://github.com/pwollstadt/IDTxl
Version: 1.0
Editor: @cMadan
Reviewer: @danielemarinazzo, @Autoplectic
Archive: 10.5281/zenodo.2554339

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/121584f956839529d509ecbf1bce1376"><img src="http://joss.theoj.org/papers/121584f956839529d509ecbf1bce1376/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/121584f956839529d509ecbf1bce1376/status.svg)](http://joss.theoj.org/papers/121584f956839529d509ecbf1bce1376)

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) 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

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

  1. Make sure you're logged in to your GitHub account
  2. 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 @cMadan know.

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

Review checklist for @danielemarinazzo

Conflict of interest

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: 1.0
  • [x] Authorship: Has the submitting author (@pwollstadt) 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)?

Review checklist for @Autoplectic

Conflict of interest

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: 1.0
  • [x] Authorship: Has the submitting author (@pwollstadt) 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
picture whedon

Most helpful comment

Hi @cMadan, I changed the file name to LICENSE in https://github.com/pwollstadt/IDTxl/commit/1d617372cca66449dd36139b3301c17391e193f7.

Thanks @danielemarinazzo for the quick review. I will look into the relevant references for the MuTE example, thanks for pointing that out.

picture pwollstadt on 25 Nov 2018
👍2

All 78 comments

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @danielemarinazzo, 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:

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

watching

  1. 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 picture whedon on 15 Nov 2018 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 15 Nov 2018

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

whedon picture whedon on 15 Nov 2018

We saw that in the paper some dois were missing and also fixed the inline citations.

@whedon generate pdf

pwollstadt picture pwollstadt on 15 Nov 2018

@whedon generate pdf

arfon picture arfon on 15 Nov 2018 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 15 Nov 2018

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

whedon picture whedon on 15 Nov 2018

@whedon generate pdf

pwollstadt picture pwollstadt on 15 Nov 2018 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 15 Nov 2018

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

whedon picture whedon on 15 Nov 2018
👍1

I have completed the checklist. Unless I have missed it, and I apologize in advance, the license file seems to be missing.

Suggestions:

  1. it would be convenient to add some running time indicators for different possible scenarios (number of time series, length of time series, etc).
  2. you call "multivariate" and "bivariate" the cases with more or two time series respectively. In other contexts "multivariate" refers to the case in which the driver, or the target, or both, are comprised of many time series. On the other hand the case in which you want to distinguish among direct and mediated influences is called "conditioned" as opposed to "pairwise". I understand that this is solely a matter of nomenclature, still a note of disambiguation could be useful.
  3. In the examples you refer to "MuTE network" or "generate.mute.example". If MuTE is a general acronym for multivariate transfer entropy, no problem. If on the other hand it refers to the examples implemented in our toolbox (https://github.com/montaltoalessandro/MuTE), I would just like to stress the benchmark model with 5 time series is not ours but is taken by other toolboxes, such as the MVGC by Barnett and Seth, and before that the work by Baccala and Sameshima. This does not mean that you should update the names or anything like that, just acknowledge the original authors of that toy dataset.

Congratulations and thanks for this nice upgrade.

d.

danielemarinazzo picture danielemarinazzo on 22 Nov 2018
👍1

It looks like the license is in COPYING.txt. Is there a particular reason that this is the filename, rather than LICENSE.txt?

cMadan picture cMadan on 22 Nov 2018

From memory that was to follow the GNU recommendation - is the use of LICENSE mandatory for JOSS or other options ok so long as it's following some convention such as GNU?

@danielemarinazzo thanks for the comments - all are clear, we'll get back to you on those

jlizier picture jlizier on 22 Nov 2018

JOSS doesn't have any rules about the license filename, but my impression is that LICENSE is more common of a filename than COPYING, even for GNU GPL licensed projects. The main idea is that the license should be easily found. I recommend you change the filename here, but I am not going to require it.

cMadan picture cMadan on 23 Nov 2018

Hi @cMadan, I changed the file name to LICENSE in https://github.com/pwollstadt/IDTxl/commit/1d617372cca66449dd36139b3301c17391e193f7.

Thanks @danielemarinazzo for the quick review. I will look into the relevant references for the MuTE example, thanks for pointing that out.

pwollstadt picture pwollstadt on 25 Nov 2018
👍2

Everything checklist-wise looks good to me.

A few minor suggestions:

You implement and document both multiinformation as well as multivariate mutual information. It would be best to utilize a single name, and to list alternative names (this quantity is often also called the total correlation, for example). Further, it would be good to explicitly state which multivariate mutual informations it is not (co-information/integration, dual total correlation/binding information, CAEKL mutual information).

To check my sanity, the SydneyPID estimator estimates the BROJA PID, not the recent PID of Lizier and Finn, yes?

Autoplectic picture Autoplectic on 26 Nov 2018
👍1

@whedon generate pdf

pwollstadt picture pwollstadt on 12 Dec 2018 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 12 Dec 2018

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

whedon picture whedon on 12 Dec 2018

Hi all, thanks to @danielemarinazzo and @Autoplectic for the review and the suggestions, we have addressed the remaining issues:

@danielemarinazzo, we have added the original reference for the example network used in the MuTE paper. Also, theoretical and some practical results for runtimes have been added as a wiki page. I also added a sentence to the theoretical introduction pointing our that what we call multivariate TE, is sometimes also termed "conditioned" TE. The major issue regarding the license file was already fixed earlier (see https://github.com/openjournals/joss-reviews/issues/1081#issuecomment-441458997).

@Autoplectic, we do not yet implement a measure for multiinformation, only multivariate mutual information. We apologise for the confusion. We have added a note to the variable list that it contains multiinformation for future reference and is not yet implemented. We hope, this will clear up misunderstandings about the implementation.

To check my sanity, the SydneyPID estimator estimates the BROJA PID, not the recent PID of Lizier and Finn, yes?

Yes, The Sydney PID estimator estimates the BROJA PID. I added this information to the classes' docstring.

@editor, the commits also contain a fix for an issue raised independently of the JOSS review process (#20). I hope this is alright with everyone.

Thanks again to everyone for your suggestions so far!

pwollstadt picture pwollstadt on 12 Dec 2018

@pwollstadt what exactly do you mean by multivariate mutual information? There are several quantities which have been called that, and so adding a definition or utilizing a more specific name would be very helpful.

Autoplectic picture Autoplectic on 12 Dec 2018

@Autoplectic, we have added a description of our multivariate mutual information implementation to the Wiki. Thank you for your suggestion, we hope this clears up any misunderstanding about what is meant here.

pwollstadt picture pwollstadt on 19 Dec 2018

That's very good for me, I have no further comments.
Congratulations on a useful paper and piece of software.

danielemarinazzo picture danielemarinazzo on 20 Dec 2018
👍1

@Autoplectic, do you have any additional questions, or are the definitions of the terms clear now? Thank you!

cMadan picture cMadan on 14 Jan 2019

I have no further questions. With the multitude of multivariate information measures out there, it is important to have definitions as the same term is used to refer to different quantities rather often.

Autoplectic picture Autoplectic on 14 Jan 2019

@Autoplectic, of course, that completely makes sense.

@pwollstadt, it looks like we're all set to accept! Can you mint a new release that includes all of the changes from the review process, and provide a doi associated with an archived version on Zenodo or figshare?

cMadan picture cMadan on 17 Jan 2019

@cMadan, I prepared a final release containing all requested changes and linked it to Zenodo. Here is the DOI: 10.5281/zenodo.2554339. Let me know if there is anything more you need from us for the publication. Thanks again to @Autoplectic and @danielemarinazzo and everyone else for your input!

pwollstadt picture pwollstadt on 31 Jan 2019

@whedon set 1.0 as version

cMadan picture cMadan on 13 Feb 2019

OK. 1.0 is the version.

whedon picture whedon on 13 Feb 2019

@whedon set 10.5281/zenodo.2554339 as archive

cMadan picture cMadan on 13 Feb 2019

OK. 10.5281/zenodo.2554339 is the archive.

whedon picture whedon on 13 Feb 2019

@whedon accept

cMadan picture cMadan on 13 Feb 2019 
Attempting dry run of processing paper acceptance...
whedon picture whedon on 13 Feb 2019

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/488

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/488, 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 picture whedon on 13 Feb 2019

Thanks a lot! We found a minor error in the final proof, which I fixed in the repo's master (https://github.com/pwollstadt/IDTxl/commit/84e8469545402740ec5f89dc1b9dd925f955210). Is there a way to generate the final PDF from that?

pwollstadt picture pwollstadt on 13 Feb 2019

@whedon accept

arfon picture arfon on 13 Feb 2019 
Attempting dry run of processing paper acceptance...
whedon picture whedon on 13 Feb 2019

PDF failed to compile for issue #1081 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 16 0 16 0 0 255 0 --:--:-- --:--:-- --:--:-- 258

whedon picture whedon on 13 Feb 2019

@pwollstadt - the paper.md metadata is currently broken. Please make this fix: https://github.com/pwollstadt/IDTxl/pull/31

arfon picture arfon on 13 Feb 2019

Sorry about that. Thanks, I merged the fix into master (
https://github.com/pwollstadt/IDTxl/commit/a949f07857379727ddfab98c35074b0e8f580171).

pwollstadt picture pwollstadt on 14 Feb 2019

@whedon accept

jlizier picture jlizier on 14 Feb 2019

I'm sorry @jlizier, I'm afraid I can't do that. That's something only editors are allowed to do.

whedon picture whedon on 14 Feb 2019

Ah ok, I was trying to regenerate the proof / dry run after the merge, so we can verify it then give the deposit=true line. Could you do that pls @arfon ?

jlizier picture jlizier on 14 Feb 2019

@whedon accept

arfon picture arfon on 14 Feb 2019 
Attempting dry run of processing paper acceptance...
whedon picture whedon on 14 Feb 2019

@whedon check references

arfon picture arfon on 14 Feb 2019
👍1 
Attempting to check references...
whedon picture whedon on 14 Feb 2019

```Reference check summary:

OK DOIs

MISSING DOIs

INVALID DOIs

whedon picture whedon on 14 Feb 2019
👍1

```Reference check summary:

OK DOIs

MISSING DOIs

INVALID DOIs

whedon picture whedon on 14 Feb 2019

@pwollstadt - please remove http://arxiv.org/abs/1004.2515 from the DOI field in your bibtex. Something like this should work as an entry instead.

@misc{1004.2515,
Author = {Paul L. Williams and Randall D. Beer},
Title = {Nonnegative Decomposition of Multivariate Information},
Year = {2010},
Eprint = {arXiv:1004.2515},
}

Also, ignore the DOI suggestion here. Whedon does its best to suggest possible missing DOIs but sometimes it's wrong :-)

arfon picture arfon on 14 Feb 2019

```Reference check summary:

OK DOIs

MISSING DOIs

INVALID DOIs

whedon picture whedon on 14 Feb 2019

```Reference check summary:

OK DOIs

MISSING DOIs

INVALID DOIs

whedon picture whedon on 15 Feb 2019

Thanks! :) I fixed the arxiv reference and left everything else as is in
https://github.com/pwollstadt/IDTxl/commit/de4ed33770311ba566c74d2f88fcafbecefcd6f5

pwollstadt picture pwollstadt on 15 Feb 2019

@whedon check references

cMadan picture cMadan on 15 Feb 2019
👍1 
Attempting to check references...
whedon picture whedon on 15 Feb 2019

```Reference check summary:

OK DOIs

MISSING DOIs

INVALID DOIs

  • None
    ```
whedon picture whedon on 15 Feb 2019

The suggested missing DOI is for a preprint without a DOI, so I think we can proceed

jlizier picture jlizier on 18 Feb 2019

@whedon accept

cMadan picture cMadan on 19 Feb 2019 
Attempting dry run of processing paper acceptance...
whedon picture whedon on 19 Feb 2019

```Reference check summary:

OK DOIs

MISSING DOIs

INVALID DOIs

  • None
    ```
whedon picture whedon on 19 Feb 2019

@arfon, it looks like whedon isn't giving the link to the final proof here...? Otherwise I think we're set to accept.

cMadan picture cMadan on 19 Feb 2019

@whedon accept

arfon picture arfon on 19 Feb 2019 
Attempting dry run of processing paper acceptance...
whedon picture whedon on 19 Feb 2019

```Reference check summary:

OK DOIs

MISSING DOIs

INVALID DOIs

  • None
    ```
whedon picture whedon on 19 Feb 2019

@whedon generate pdf

arfon picture arfon on 19 Feb 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 19 Feb 2019

@arfon, it looks like whedon isn't giving the link to the final proof here...? Otherwise I think we're set to accept.

Not sure what's going on here. Will debug.

arfon picture arfon on 19 Feb 2019
👍1

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/505

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/505, 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 picture whedon on 19 Feb 2019

@whedon accept

arfon picture arfon on 19 Feb 2019 
Attempting dry run of processing paper acceptance...
whedon picture whedon on 19 Feb 2019

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/506

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/506, 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 picture whedon on 19 Feb 2019

```Reference check summary:

OK DOIs

MISSING DOIs

INVALID DOIs

  • None
    ```
whedon picture whedon on 19 Feb 2019

@whedon accept deposit=true

arfon picture arfon on 19 Feb 2019 
Doing it live! Attempting automated processing of paper acceptance...
whedon picture whedon on 19 Feb 2019

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/507
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01081
  3. If everything looks good, then close this review issue.

  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

    Any issues? notify your editorial technical team...

whedon picture whedon on 19 Feb 2019

@danielemarinazzo, @Autoplectic - many thanks for your reviews here and to @cMadan for editing this one ✨

@pwollstadt - your paper is now accepted into JOSS :zap::rocket::boom:

arfon picture arfon on 19 Feb 2019
🎉1

: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.01081/status.svg)](https://doi.org/10.21105/joss.01081)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01081">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01081/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01081/status.svg
   :target: https://doi.org/10.21105/joss.01081

This is how it will look in your documentation:

DOI

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

whedon picture whedon on 19 Feb 2019

Awesome - thank you very much @arfon @cMadan and @danielemarinazzo @Autoplectic for your work!

jlizier picture jlizier on 19 Feb 2019
👍1
Was this page helpful?
0 / 5 - 0 ratings

Related issues

whedon picture whedon  ·  8Comments
whedon picture whedon  ·  12Comments
whedon picture whedon  ·  11Comments
whedon picture whedon  ·  13Comments
whedon picture whedon  ·  10Comments