[PRE REVIEW]: py2lispIDyOM: A Python package for IDyOM

[editorialbot]

Submitting author: !--author-handle-->@xinyiguan<!--end-author-handle-- (Xinyi Guan) Repository: https://github.com/xinyiguan/py2lispIDyOM Branch with paper.md (empty if default branch): Version: v1.0.1 Editor: !--editor-->@faroit<!--end-editor-- Reviewers: @AoifeHughes, @hayesall Managing EiC: Arfon Smith

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Thanks for submitting your paper to JOSS @xinyiguan. Currently, there isn't an JOSS editor assigned to your paper.

@xinyiguan 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).

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.08 s (1108.5 files/s, 92484.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          11            461            333           1622
XML                              9              0              0            830
diff                             3              8             66            321
reStructuredText                46            298            255            257
Markdown                         3             70              0            164
YAML                             5             17             11            148
Jupyter Notebook                 4              0           2030            126
TeX                              1             10              0            103
make                             1              6              9             16
Lisp                             3              0              0             14
-------------------------------------------------------------------------------
SUM:                            86            870           2704           3601
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1014

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- None

MISSING DOIs

- 10.1525/mp.2006.23.5.377 may be a valid DOI for title: Expectation in melody: The influence of context and learning
- 10.1525/mp.2005.22.4.663 may be a valid DOI for title: A model of melodic expectation
- 10.1016/j.cognition.2018.12.015 may be a valid DOI for title: Statistical learning and Gestalt-like principles predict melodic expectations
- 10.1016/j.cognition.2005.11.007 may be a valid DOI for title: Are we “experienced listeners”? A review of the musical capacities that do not depend on formal musical training
- 10.1177/102986490901300203 may be a valid DOI for title: Expectancy in Sami Yoiks revisited: The role of data-driven and schema-driven knowledge in the formation of melodic expectations
- 10.1016/j.concog.2010.07.004 may be a valid DOI for title: Incidental and online learning of melodic structure
- 10.1111/j.1756-8765.2012.01214.x may be a valid DOI for title: Auditory expectation: the information dynamics of music perception and cognition
- 10.1016/j.jecp.2020.105020 may be a valid DOI for title: Melodic expectations in 5-and 6-year-old children
- 10.1111/nyas.13654 may be a valid DOI for title: Statistical learning and probabilistic prediction in music cognition: mechanisms of stylistic enculturation

INVALID DOIs

- None

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[arfon]

@editorialbot invite @faroit as editor

:wave: @faroit – would you be willing to edit this submission for JOSS?

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@editorialbot invite @faroit as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@faroit can you help edit this one?

[faroit]

@Kevin-Mattheus-Moerman @arfon I would be available to edit this but I had a brief look at the submission and I have some concerns that this is in-scope with JOSS. I am particularly worried that it doesn't pass the criteria for substantial scholarly effort as the main contribution is to provide a python wrapper for an existing Lisp-based software.

I do not have the knowledge in Lisp to provide a scope-check myself, specifically how much scholary effort is required to provide such a wrapper compared to a rewrite in python. Therefore I would suggest we find a Lisp expert here for a scope-check.

[Kevin-Mattheus-Moerman]

@xinyiguan following @faroit's recommendation I've added the query-scope label just now which means our editorial board will inspect this submission to check if it is in scope or not. As @faroit says we'll focus on determining if it conforms to our substantial scholarly effort criteria. If you'd like to help us here it would be great if you could comment on what your software functionality offers on top of a wrapper of said Lisp library. This additional scope review should take about 2 weeks to complete.

[xinyiguan]

Hi @Kevin-Mattheus-Moerman, thanks for the updates! This package serves as a unifying Python interface that simplifies and streamlines the research workflow for running the IDyOM model and analyzing output data. The Python wrapper functionality is one of the features of this package. On top of this, we provided three key functionalities: extract, export, and visualization, which are not present in the Lisp IDyOM package and significantly enhance the content of the initial toolbox. In addition, the automatic “experiment-logger” feature in this package allows a more organized workflow and data reproducibility.

Most researchers in music psychology and cognition are not familiar with the Common Lisp ecosystem, and it can be very time-consuming and discouraging to run the IDyOM model, then extract the relevant data to other formats for further analysis in a more familiar programming language.

As a matter of fact, virtually all papers that are using IDyOM include the developer of the model or direct students working with them as one of the co-authors, which speaks about the difficulty for outsiders scientists to actually use it. And such difficulty creates a bottleneck problem that hinders the development of the field.

Therefore, we built this Python-based package for IDyOM-based analysis, so that: i) it is straightforward to define the model parameters and configurations in a simple interface, ii) researchers don't need to jump back-and-forth in different programming languages, and iii) have a clear and streamlined research workflow and automatic experiment log records for every experiment. We believe this package can greatly improve researchers' efficiency in IDyOM-based analysis.

[Kevin-Mattheus-Moerman]

@xinyiguan thanks for your patience. I have just removed the query-scope label since we've determined this may be in scope for JOSS. We will now proceed to try to find a handling editor for this work. Note however that unfortunately we may need to put this on a waitlist as we have a backlog of submission to process at the moment.

[Kevin-Mattheus-Moerman]

@editorialbot assign @faroit as editor

[editorialbot]

Assigned! @faroit is now the editor

[faroit]

👋 Hi @xinyiguan, thanks for your submission to JOSS, and sorry for the delay (I was on vacation last week)! I will be serving as the editor for this. We'll use this issue to identify reviewers and resolve technical issues.

@xinyiguan, I am also interested in your input on potential reviewers, so any suggestions you have are also welcome. As this toolbox is based on lisp wrapper, it would be great to have reviewers with domain knowledge for both, python and lisp.

Before you post suggestions, please check the JOSS COI policy and only mention them with a space between the @ and their handle (so you would refer to me as "@ faroit").

[xinyiguan]

👋 Hi @faroit, thanks for serving as the editor for the submission. Here is a list of potential reviewers with a background in both python and lisp from the JOSS reviewer list: @ hayesall; @ aminorex; @ AoifeHughes.

[faroit]

👋 @hayesall @aminorex @AoifeHughes - would any of you be willing to review this submission for JOSS? The JOSS review process takes place on GitHub and focuses on the software and a short paper. We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

The software under review is py2lispIDyOM: A Python package for IDyOM.

This issue is a "pre-review" issue in which reviewers are assigned. Once sufficient reviewers are recruited we will open a dedicated review issue where the review will take place.

[AoifeHughes]

@faroit of course, been wanting to do another review for a while now 😄

[faroit]

@AoifeHughes thanks for the quick reply. Happy you can help out!

[faroit]

@editorialbot add @AoifeHughes to reviewers

[editorialbot]

@AoifeHughes added to the reviewers list!

[hayesall]

@faroit Sure, looks interesting!

[faroit]

@editorialbot add @hayesall to reviewers

[editorialbot]

@hayesall added to the reviewers list!

[faroit]

@hayesall thanks a lot!

[faroit]

@editorialbot generate pdf

[faroit]

@editorialbot check references

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- None

MISSING DOIs

- 10.1525/mp.2006.23.5.377 may be a valid DOI for title: Expectation in melody: The influence of context and learning
- 10.1525/mp.2005.22.4.663 may be a valid DOI for title: A model of melodic expectation
- 10.1016/j.cognition.2018.12.015 may be a valid DOI for title: Statistical learning and Gestalt-like principles predict melodic expectations
- 10.1016/j.cognition.2005.11.007 may be a valid DOI for title: Are we “experienced listeners”? A review of the musical capacities that do not depend on formal musical training
- 10.1177/102986490901300203 may be a valid DOI for title: Expectancy in Sami Yoiks revisited: The role of data-driven and schema-driven knowledge in the formation of melodic expectations
- 10.1016/j.concog.2010.07.004 may be a valid DOI for title: Incidental and online learning of melodic structure
- 10.1111/j.1756-8765.2012.01214.x may be a valid DOI for title: Auditory expectation: the information dynamics of music perception and cognition
- 10.1016/j.jecp.2020.105020 may be a valid DOI for title: Melodic expectations in 5-and 6-year-old children
- 10.1111/nyas.13654 may be a valid DOI for title: Statistical learning and probabilistic prediction in music cognition: mechanisms of stylistic enculturation

INVALID DOIs

- None

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[faroit]

@xinyiguan we now have the required number of reviewers and thus can start the review process. In the meantime, can you please update the DOIs in the paper (see missing DOIs above)?

[faroit]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/4738.