[REVIEW]: Metrics As Scores: A Tool- and Analysis Suite and Interactive Application for Exploring Context-Dependent Distributions #4913

editorialbot · 2022-11-07T16:52:20Z

Submitting author: @MrShoenel (Sebastian Hönel)
Repository: https://github.com/MrShoenel/metrics-as-scores
Branch with paper.md (empty if default branch): paper
Version: v2.8.0
Editor: @mikldk
Reviewers: @mdhaber, @kostiantyn-kucher
Archive: 10.5281/zenodo.8202326

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/eb549efe6c0111490395496c68717579"><img src="https://joss.theoj.org/papers/eb549efe6c0111490395496c68717579/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/eb549efe6c0111490395496c68717579/status.svg)](https://joss.theoj.org/papers/eb549efe6c0111490395496c68717579)

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

@mdhaber & @jstvssr, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @mikldk know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @mdhaber

📝 Checklist for @kostiantyn-kucher

The text was updated successfully, but these errors were encountered:

editorialbot · 2022-11-07T16:52:21Z

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

editorialbot · 2022-11-07T16:52:24Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (718.3 files/s, 80732.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          15            507            102           1864
TeX                              1             21              0            299
Markdown                         5            108              0            234
HTML                             3             13              4            123
JSON                             2              2              0             87
TOML                             1              4              0             44
CSS                              1              5              0             24
YAML                             1              1              4             21
JavaScript                       1              1              0             14
DOS Batch                        1              0              0              2
-------------------------------------------------------------------------------
SUM:                            31            662            110           2712
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2022-11-07T16:52:25Z

Wordcount for paper.md is 1396

editorialbot · 2022-11-07T16:53:44Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

editorialbot · 2022-11-07T16:53:51Z

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

OK DOIs

- 10.1109/ISSRE.2000.885858 is OK
- 10.1109/ICSM.2010.5609747 is OK
- 10.1007/s11219-021-09568-9 is OK
- 10.1109/ACCESS.2020.2990567 is OK
- 10.1145/2507288.2507314 is OK
- 10.1109/32.544352 is OK
- 10.1145/3338906.3341462 is OK
- 10.1109/ACCESS.2019.2924040 is OK
- 10.1109/32.295895 is OK
- 10.1145/3183440.3195103 is OK
- 10.1109/METRIC.2004.1357891 is OK
- 10.1080/03461238.1928.10416862 is OK
- 10.1080/01621459.1974.10480196 is OK
- 10.1214/aoms/1177704477 is OK
- 10.1080/00949658608810963 is OK
- 10.1201/9780203738535 is OK
- 10.2307/3001913 is OK

MISSING DOIs

- 10.1016/0950-5849(93)90091-g may be a valid DOI for title: Practical Software Metrics For Project Management And Process Improvement

INVALID DOIs

- None

mikldk · 2022-11-07T16:53:56Z

@mdhaber, @jstvssr: Thanks for agreeing to review. Please carry out your review in this issue by first creating a checklist (@editorialbot generate my checklist) and then updating it as the review proceeds. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. If possible create issues (and cross-reference) in the submission's repository to avoid too specific discussions in this review thread.

If you have any questions or concerns please let me know.

@jstvssr currently has a busy schedule, and the review is not expected to be completed before the end of January 2023.

mdhaber · 2022-12-16T21:03:54Z

Review checklist for @mdhaber

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/MrShoenel/metrics-as-scores?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@MrShoenel) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
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

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
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

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

mikldk · 2023-01-06T09:59:46Z

@mdhaber, @jstvssr: Can you please give a brief status of your review? This is not to rush you, merely to give me an impression of the progress and time-frame.

MrShoenel · 2023-01-06T12:01:11Z

@mdhaber raised a couple of issues (opened in the repo directly) that we will begin to address next week.

mikldk · 2023-01-31T20:24:37Z

@MrShoenel Can you please give a status of the progress of resolving the raised issues?

MrShoenel · 2023-02-01T21:11:39Z

There were some unexpected delays on my side, but I had begun work on issues #4 (automated tests) and #2 (API documentation). I will complete some of it this week and reference the changes in these issues then.
I am confident to have addressed all of @mdhaber's comments by next week :)
I will post here then, too!

MrShoenel · 2023-02-20T16:39:50Z

@editorialbot generate pdf

editorialbot · 2023-02-20T16:41:12Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

MrShoenel · 2023-02-20T16:44:08Z

Thanks for your patience. I have made substantial changes in the meantime (please check the README.md), to address all of @mdhaber's comments (thanks for these!).
I did update the paper, trying to make it more accessible.

My to-do list is now empty :) Of course, I absolutely welcome additional comments :)

MrShoenel · 2023-02-20T16:48:28Z

@editorialbot generate pdf

editorialbot · 2023-02-20T16:49:53Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

mikldk · 2023-02-21T08:03:27Z

@mdhaber, @jstvssr Can you please continue your reviews?

MrShoenel · 2023-02-22T23:05:32Z

I got some more follow-up comments and issues from @mdhaber, all of which are addressed by now (but I suppose more is coming ;) ).

MrShoenel · 2023-03-13T14:20:17Z

@jstvssr: Do you have any critical points you want me to address?

mdhaber · 2023-03-28T07:20:23Z

@mikldk You can see the status of my review at MrShoenel/metrics-as-scores#1. We've been steadily working through things since mid-December. Many individual issues have been addressed, but a few are still open.

One of the review criteria is "Is the list of references complete...?" The paper cites some of MAS's software dependencies, but not all. How should the author decide which dependencies to cite? I am a maintainer of one such dependency, SciPy, which is used throughout MAS. Compared to other tools that are cited (e.g. Pymoo, which itself relies on SciPy), it seems to be used enough to deserve a citation, but I'm not sure that I can claim to be completely objective about this, so I'd appreciate your input.

mikldk · 2023-08-01T08:23:38Z

@editorialbot check references

editorialbot · 2023-08-01T08:23:48Z

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

OK DOIs

- 10.1109/ISSRE.2000.885858 is OK
- 10.1109/ICSM.2010.5609747 is OK
- 10.1007/s11219-021-09568-9 is OK
- 10.1109/ACCESS.2020.2990567 is OK
- 10.1145/2507288.2507314 is OK
- 10.1109/32.544352 is OK
- 10.1145/3338906.3341462 is OK
- 10.1109/ACCESS.2019.2924040 is OK
- 10.1109/32.295895 is OK
- 10.1145/3183440.3195103 is OK
- 10.1109/METRIC.2004.1357891 is OK
- 10.1109/QRS57517.2022.00042 is OK
- 10.1080/03461238.1928.10416862 is OK
- 10.1080/01621459.1974.10480196 is OK
- 10.1214/aoms/1177704477 is OK
- 10.1080/00949658608810963 is OK
- 10.1201/9780203738535 is OK
- 10.2307/3001913 is OK
- 10.5281/zenodo.7633949 is OK
- 10.5281/zenodo.7633989 is OK
- 10.5281/zenodo.7647596 is OK
- 10.5281/zenodo.7669664 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1093/biomet/34.1-2.28 is OK
- 10.1080/10691898.2005.11910641 is OK
- 10.1007/s00180-008-0120-1 is OK
- 10.1109/VISSOFT.2019.00020 is OK
- 10.1109/APSEC.2010.46 is OK
- 10.1371/journal.pone.0271185 is OK

MISSING DOIs

- 10.1016/0950-5849(93)90091-g may be a valid DOI for title: Practical Software Metrics For Project Management And Process Improvement

INVALID DOIs

- None

mikldk · 2023-08-01T08:24:06Z

@editorialbot set 10.5281/zenodo.8202326 as archive

editorialbot · 2023-08-01T08:24:08Z

Done! archive is now 10.5281/zenodo.8202326

mikldk · 2023-08-01T08:25:02Z

@editorialbot set v2.8.0 as version

editorialbot · 2023-08-01T08:25:04Z

Done! version is now v2.8.0

MrShoenel · 2023-08-01T08:25:30Z

That one missing DOI came up previously. However, it is not valid, as it refers to a review of the book, not the book itself (which has no DOI).

mikldk · 2023-08-01T08:26:58Z

That one missing DOI came up previously. However, it is not valid, as it refers to a review of the book, not the book itself (which has no DOI).

I found the same.

mikldk · 2023-08-01T08:27:07Z

@editorialbot recommend-accept

editorialbot · 2023-08-01T08:27:09Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-08-01T08:27:19Z

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

OK DOIs

- 10.1109/ISSRE.2000.885858 is OK
- 10.1109/ICSM.2010.5609747 is OK
- 10.1007/s11219-021-09568-9 is OK
- 10.1109/ACCESS.2020.2990567 is OK
- 10.1145/2507288.2507314 is OK
- 10.1109/32.544352 is OK
- 10.1145/3338906.3341462 is OK
- 10.1109/ACCESS.2019.2924040 is OK
- 10.1109/32.295895 is OK
- 10.1145/3183440.3195103 is OK
- 10.1109/METRIC.2004.1357891 is OK
- 10.1109/QRS57517.2022.00042 is OK
- 10.1080/03461238.1928.10416862 is OK
- 10.1080/01621459.1974.10480196 is OK
- 10.1214/aoms/1177704477 is OK
- 10.1080/00949658608810963 is OK
- 10.1201/9780203738535 is OK
- 10.2307/3001913 is OK
- 10.5281/zenodo.7633949 is OK
- 10.5281/zenodo.7633989 is OK
- 10.5281/zenodo.7647596 is OK
- 10.5281/zenodo.7669664 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1093/biomet/34.1-2.28 is OK
- 10.1080/10691898.2005.11910641 is OK
- 10.1007/s00180-008-0120-1 is OK
- 10.1109/VISSOFT.2019.00020 is OK
- 10.1109/APSEC.2010.46 is OK
- 10.1371/journal.pone.0271185 is OK

MISSING DOIs

- 10.1016/0950-5849(93)90091-g may be a valid DOI for title: Practical Software Metrics For Project Management And Process Improvement

INVALID DOIs

- None

editorialbot · 2023-08-01T08:29:11Z

👋 @openjournals/dsais-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4443, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

mikldk · 2023-08-01T08:29:42Z

@openjournals/joss-eics Note that the missing DOI is not correct for the book (it's for a review of the book). The book does apparently not have a DOI as far as @MrShoenel and I can find.

gkthiruvathukal · 2023-08-04T17:11:01Z

@mikldk This is fine. Most books have ISBN/ISSN. I'm ready to accept here but am going to ask @arfon whether this can or should be used as the DOI.

danielskatz · 2023-08-08T17:47:35Z

If there is no DOI for the book (or any other item), you don't need to have one. This can proceed as is.

MrShoenel · 2023-08-21T20:12:58Z

Just checking, is there anything left I need to provide or address?

gkthiruvathukal · 2023-08-25T03:10:08Z

@MrShoenel No! I will proceed with acceptance.

gkthiruvathukal · 2023-08-25T03:10:15Z

@editorialbot accept

editorialbot · 2023-08-25T03:10:16Z

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

editorialbot · 2023-08-25T03:12:00Z

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Hönel
  given-names: Sebastian
  orcid: "https://orcid.org/0000-0001-7937-1645"
- family-names: Ericsson
  given-names: Morgan
  orcid: "https://orcid.org/0000-0003-1173-5187"
- family-names: Löwe
  given-names: Welf
  orcid: "https://orcid.org/0000-0002-7565-3714"
- family-names: Wingkvist
  given-names: Anna
  orcid: "https://orcid.org/0000-0002-0835-823X"
contact:
- family-names: Hönel
  given-names: Sebastian
  orcid: "https://orcid.org/0000-0001-7937-1645"
doi: 10.5281/zenodo.8202326
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Hönel
    given-names: Sebastian
    orcid: "https://orcid.org/0000-0001-7937-1645"
  - family-names: Ericsson
    given-names: Morgan
    orcid: "https://orcid.org/0000-0003-1173-5187"
  - family-names: Löwe
    given-names: Welf
    orcid: "https://orcid.org/0000-0002-7565-3714"
  - family-names: Wingkvist
    given-names: Anna
    orcid: "https://orcid.org/0000-0002-0835-823X"
  date-published: 2023-08-25
  doi: 10.21105/joss.04913
  issn: 2475-9066
  issue: 88
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 4913
  title: "Metrics As Scores: A Tool- and Analysis Suite and Interactive
    Application for Exploring Context-Dependent Distributions"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.04913"
  volume: 8
title: "Metrics As Scores: A Tool- and Analysis Suite and Interactive
  Application for Exploring Context-Dependent Distributions"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot · 2023-08-25T03:12:04Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2023-08-25T03:12:05Z

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.04913 joss-papers#4512
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04913
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

editorialbot · 2023-08-26T04:15:43Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.04913/status.svg)](https://doi.org/10.21105/joss.04913)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04913">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04913/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04913/status.svg
   :target: https://doi.org/10.21105/joss.04913

This is how it will look in your documentation:

We need your help!

The 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:

Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://reviewers.joss.theoj.org/join
Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

MrShoenel · 2023-08-26T08:10:22Z

I would like to thank all who were involved, especially the two reviewers @mdhaber and @kostiantyn-kucher, who helped me to significantly improve our work. I also want to thank @mikldk for a very efficient editing process.

editorialbot added Batchfile Python review TeX Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning waitlisted Submissions in the JOSS backlog due to reduced service mode. labels Nov 7, 2022

editorialbot assigned mikldk Nov 7, 2022

editorialbot mentioned this issue Nov 7, 2022

[PRE REVIEW]: Metrics As Scores: A Tool- and Analysis Suite and Interactive Application for Exploring Context-Dependent Distributions #4819

Closed

mdhaber mentioned this issue Dec 16, 2022

Meta-issue for mdhaber review of JOSS submission MrShoenel/metrics-as-scores#1

Closed

25 tasks

arfon removed the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Feb 1, 2023

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Aug 1, 2023

editorialbot added accepted published Papers published in JOSS labels Aug 25, 2023

gkthiruvathukal closed this as completed Aug 26, 2023

editorialbot mentioned this issue Dec 2, 2024

[PRE REVIEW]: MZsearch: A Python-Based Compound Identification Tool for GC-MS and LC-MS-Based Metabolomics #7229

Closed

editorialbot mentioned this issue Dec 17, 2024

[PRE REVIEW]: calzone: A Python package for measuring calibration of probabilistic models for classification #7598

Open

[REVIEW]: Metrics As Scores: A Tool- and Analysis Suite and Interactive Application for Exploring Context-Dependent Distributions #4913

[REVIEW]: Metrics As Scores: A Tool- and Analysis Suite and Interactive Application for Exploring Context-Dependent Distributions #4913

Comments

editorialbot commented Nov 7, 2022 • edited Loading

Status

Reviewer instructions & questions

Checklists

editorialbot commented Nov 7, 2022

editorialbot commented Nov 7, 2022

editorialbot commented Nov 7, 2022

editorialbot commented Nov 7, 2022

editorialbot commented Nov 7, 2022

mikldk commented Nov 7, 2022

mdhaber commented Dec 16, 2022 • edited Loading

Review checklist for @mdhaber

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

mikldk commented Jan 6, 2023

MrShoenel commented Jan 6, 2023

mikldk commented Jan 31, 2023

MrShoenel commented Feb 1, 2023

MrShoenel commented Feb 20, 2023

editorialbot commented Feb 20, 2023

MrShoenel commented Feb 20, 2023

MrShoenel commented Feb 20, 2023

editorialbot commented Feb 20, 2023

mikldk commented Feb 21, 2023

MrShoenel commented Feb 22, 2023

MrShoenel commented Mar 13, 2023

mdhaber commented Mar 28, 2023 • edited Loading

mikldk commented Aug 1, 2023

editorialbot commented Aug 1, 2023

mikldk commented Aug 1, 2023

editorialbot commented Aug 1, 2023

mikldk commented Aug 1, 2023

editorialbot commented Aug 1, 2023

MrShoenel commented Aug 1, 2023

mikldk commented Aug 1, 2023

mikldk commented Aug 1, 2023

editorialbot commented Aug 1, 2023

editorialbot commented Aug 1, 2023

editorialbot commented Aug 1, 2023

mikldk commented Aug 1, 2023 • edited Loading

gkthiruvathukal commented Aug 4, 2023

danielskatz commented Aug 8, 2023

MrShoenel commented Aug 21, 2023

gkthiruvathukal commented Aug 25, 2023

gkthiruvathukal commented Aug 25, 2023

editorialbot commented Aug 25, 2023

editorialbot commented Aug 25, 2023

editorialbot commented Aug 25, 2023

editorialbot commented Aug 25, 2023

editorialbot commented Aug 26, 2023

MrShoenel commented Aug 26, 2023

editorialbot commented Nov 7, 2022 •

edited

Loading

mdhaber commented Dec 16, 2022 •

edited

Loading

mdhaber commented Mar 28, 2023 •

edited

Loading

mikldk commented Aug 1, 2023 •

edited

Loading