[REVIEW]: Nominally: A Name Parser for Record Linkage

[whedon]

Submitting author: @vaneseltine (Matthew VanEseltine)
Repository: https://github.com/vaneseltine/nominally
Version: 1.1.0
Editor: @majensen
Reviewer: @sara-02, @sap218
Archive: 10.5281/zenodo.5562628

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/d340ccbed7e8775b9fc3f4d5ee137fa0"><img src="https://joss.theoj.org/papers/d340ccbed7e8775b9fc3f4d5ee137fa0/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/d340ccbed7e8775b9fc3f4d5ee137fa0/status.svg)](https://joss.theoj.org/papers/d340ccbed7e8775b9fc3f4d5ee137fa0)

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

@sara-02 & @sap218, 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.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @majensen 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 ✨

Review checklist for @sara-02

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 repository url?
• 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 (@vaneseltine) 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

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 and who the target audience is?
• 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?

Review checklist for @sap218

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 repository url?
• 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 (@vaneseltine) 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

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 and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @sara-02, @sap218 it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

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:

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

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

@whedon commands

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

@whedon generate pdf

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.05 s (928.0 files/s, 113131.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                             8              0              0           2041
Python                          21            354            194           1487
Markdown                         4             87              0            344
SVG                              2              0              0            192
reStructuredText                 5             89             47            177
TeX                              1              6              0             61
YAML                             1              1              0             40
-------------------------------------------------------------------------------
SUM:                            42            537            241           4342
-------------------------------------------------------------------------------


Statistical information for the repository 'd6946d04b232575a7ea5b349' was
gathered on 2021/07/01.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Aru Sahni                        1             1              1            0.01
Brian S. Corbin                  1            82             60            0.38
Derek                           39           935            615            4.18
Derek Gulbranson               147          6896           2543           25.47
Edward Betts                     2             3              2            0.01
Matt VanEseltine               209         11496          14237           69.45
Matthew VanEseltine              5            78             31            0.29
Peter Scott                      4            38             13            0.14
Simeon Visser                    1             3              3            0.02
TyVik                            1             6              6            0.03
abnerjacobsen                    2             4              0            0.01

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Derek Gulbranson             10            0.1         60.1               20.00
Matt VanEseltine           2021           17.6         19.8                6.68

[whedon]

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

OK DOIs

- 10.1007/978-3-642-31164-2_3 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.21987/70kd-x544 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[sap218]

1. Regarding "Contribution and authorship" - the submitting author (@vaneseltine) has made major contributions to the software and is an author on the paper. However I did notice in the whedon software report ([REVIEW]: Nominally: A Name Parser for Record Linkage #3440 (comment)) that Derek Gulbranson made ~25% of changes for Nominally - I did quickly check the commit history and noticed Derek last committed around June 2019. Just wondering if authorship should be updated? If not, I'll be happy to check that off and continue :)

2. Installation / documentation - I like the set-up of the GitHub Repo for Nominally - however there lacks installation instructions. I did find them on ReadTheDocs (https://nominally.readthedocs.io/en/stable/use.html#installation) so I think either including installation instructions in the repo README or perhaps in the repo there should be a link to the ReadTheDocs manual! Additionally, not a major issue but the examples on the repo and the ReadTheDocs are different, suggestion would be to make them the same/consistent.

3. First error I came across was Nominally parse_name() function cannot identify "miss" as a title. As soon as this is addressed (parse_name() issues with title "miss" vaneseltine/nominally#54) I will continue with the review! :)

[sap218]

@vaneseltine @majensen

Since my issue was closed (last comment (3)) I have continued with the review - I have ticked off more tasks :)

Documentation

1. A statement of need is needed in the docs (even if very brief)
2. Continuing on from my last comment (2) I think a simple line of installation instructions in the main repo would be great :)
3. Additionally, I mentioned the examples provided (2) - there are numerous source of documentation - there is the Nominally main repo, ReadTheDocs, and a nominally-examples repo - each have examples not the same as others (I am ok with this and checked this item off - but would be nice if examples were consistent across all) and I would perhaps add more examples to the examples repo README

To conclude overall: a statement of need, installation instructions, examples of use - are all needed in each types of docs you provide - I can finish off with the software paper as soon as these are addressed :)

[majensen]

Thanks @sap218 - all very relevant issues. @vaneseltine many thanks in advance for your response to each.