Group 17 Peer Review - mds_array_manipulation

Submitting Author: Name (@sean-m-mckay ) All current maintainers: (@Owl64901, @Aishwarya120111, @jokittipong) Package Name: MDS Array Manipulation One-Line Description of Package: Numpy array manipulation helper functions Repository Link: https://github.com/UBC-MDS/mds_array_manipulation Version submitted: 2.0.0 Editor: Reviewer 1: Yingzi Jin Reviewer 2: Allan Lee Reviewer 3: Sho Inagaki Reviewer 4: Sam Fo Archive: TBD JOSS DOI: TBD Version accepted: TBD Date accepted (month/day/year): TBD

Code of Conduct & Commitment to Maintain Package

[x] I agree to abide by pyOpenSci's Code of Conduct during the review process and in maintaining my package after should it be accepted.
[x] I have read and will commit to package maintenance after the review as per the pyOpenSci Policies Guidelines.

Description

Include a brief paragraph describing what your package does:

The package is intended to do array manipulations functions like Searching, Sorting, Counting non-zero elements, Finding indices of max value. This is a package developed for the group-17 project for the UBC MDS DSCI 524 (Collaborative Software Development) course.

Scope

Please indicate which category or categories. Check out our package scope page to learn more about our scope. (If you are unsure of which category you fit, we suggest you make a pre-submission inquiry):
- [ ] Data retrieval
- [ ] Data extraction
- [x] Data processing/munging
- [ ] Data deposition
- [ ] Data validation and testing
- [ ] Data visualization[^1]
- [ ] Workflow automation
- [ ] Citation management and bibliometrics
- [ ] Scientific software wrappers
- [ ] Database interoperability

Domain Specific & Community Partnerships

- [ ] Geospatial
- [ ] Education
- [ ] Pangeo

Community Partnerships

If your package is associated with an existing community please check below:

[ ] Pangeo
- [ ] My package adheres to the Pangeo standards listed in the pyOpenSci peer review guidebook

[^1]: Please fill out a pre-submission inquiry before submitting a data visualization package.

For all submissions, explain how the and why the package falls under the categories you indicated above. In your explanation, please address the following points (briefly, 1-2 sentences for each):
- Who is the target audience and what are scientific applications of this package?
- Are there other Python packages that accomplish the same thing? If so, how does yours differ?
- If you made a pre-submission enquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted:

Technical checks

For details about the pyOpenSci packaging requirements, see our packaging guide. Confirm each of the following by checking the box. This package:

[x] does not violate the Terms of Service of any service it interacts with.
[x] uses an OSI approved license.
[x] contains a README with instructions for installing the development version.
[x] includes documentation with examples for all functions.
[x] contains a tutorial with examples of its essential functions and uses.
[x] has a test suite.
[x] has continuous integration setup, such as GitHub Actions CircleCI, and/or others.

Publication Options

[ ] Do you wish to automatically submit to the Journal of Open Source Software? If so:

JOSS Checks

- [ ] The package has an **obvious research application** according to JOSS's definition in their [submission requirements][JossSubmissionRequirements]. Be aware that completing the pyOpenSci review process **does not** guarantee acceptance to JOSS. Be sure to read their submission requirements (linked above) if you are interested in submitting to JOSS. - [ ] The package is not a "minor utility" as defined by JOSS's [submission requirements][JossSubmissionRequirements]: "Minor ‘utility’ packages, including ‘thin’ API clients, are not acceptable." pyOpenSci welcomes these packages under "Data Retrieval", but JOSS has slightly different criteria. - [ ] The package contains a `paper.md` matching [JOSS's requirements][JossPaperRequirements] with a high-level description in the package root or in `inst/`. - [ ] The package is deposited in a long-term repository with the DOI: *Note: JOSS accepts our review as theirs. You will NOT need to go through another full review. JOSS will only review your paper.md file. Be sure to link to this pyOpenSci issue when a JOSS issue is opened for your package. Also be sure to tell the JOSS editor that this is a pyOpenSci reviewed package once you reach this step.*

Are you OK with Reviewers Submitting Issues and/or pull requests to your Repo Directly?

This option will allow reviewers to open smaller issues that can then be linked to PR's rather than submitting a more dense text based review. It will also allow you to demonstrate addressing the issue via PR links.

[x] Yes I am OK with reviewers submitting requested changes as issues to my repo. Reviewers will then link to the issues in their submitted review.

Confirm each of the following by checking the box.

[x] I have read the author guide.
[ ] I expect to maintain this package for at least 2 years and can help find a replacement for the maintainer (team) if needed.

Please fill out our survey

[ ] Last but not least please fill out our pre-review survey. This helps us track submission and improve our peer review process. We will also ask our reviewers and editors to fill this out.

P.S. Have feedback/comments about our review process? Leave a comment here

Editor and Review Templates

The editor template can be found here.

The review template can be found here.

Package Review

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

[x] As the reviewer I confirm that there are no conflicts of interest for me to review this work (If you are unsure whether you are in conflict, please speak to your editor before starting your review).

Documentation

The package includes all the following forms of documentation:

[ ] A statement of need clearly stating problems the software is designed to solve and its target audience in README.
[x] Installation instructions: for the development version of the package and any non-standard dependencies in README.
[x] Vignette(s) demonstrating major functionality that runs successfully locally.
[x] Function Documentation: for all user-facing functions.
[x] Examples for all user-facing functions.
[x] Community guidelines including contribution guidelines in the README or CONTRIBUTING.
[ ] Metadata including author(s), author e-mail(s), a url, and any other relevant metadata e.g., in a pyproject.toml file or elsewhere.

Readme file requirements The package meets the readme requirements below:

[x] Package has a README.md file in the root directory.

The README should include, from top to bottom:

[x] The package name
[ ] Badges for:
- [ ] Continuous integration and test coverage,
- [x] Docs building (if you have a documentation website),
- [ ] A repostatus.org badge,
- [ ] Python versions supported,
- [ ] Current package version (on PyPI / Conda).

NOTE: If the README has many more badges, you might want to consider using a table for badges: see this example. Such a table should be more wide than high. (Note that the a badge for pyOpenSci peer-review will be provided upon acceptance.)

[x] Short description of package goals.
[x] Package installation instructions
[x] Any additional setup required to use the package (authentication tokens, etc.)
[ ] Descriptive links to all vignettes. If the package is small, there may only be a need for one vignette which could be placed in the README.md file.
- [x] Brief demonstration of package usage (as it makes sense - links to vignettes could also suffice here if package description is clear)
[x] Link to your documentation website.
[ ] If applicable, how the package compares to other similar packages and/or how it relates to other packages in the scientific ecosystem.
[ ] Citation information

Usability

Reviewers are encouraged to submit suggestions (or pull requests) that will improve the usability of the package as a whole. Package structure should follow general community best-practices. In general please consider whether:

[x] Package documentation is clear and easy to find and use.
[ ] The need for the package is clear
[x] All functions have documentation and associated examples for use
[x] The package is easy to install

Functionality

[x] Installation: Installation succeeds as documented.
[x] Functionality: Any functional claims of the software been confirmed.
[x] Performance: Any performance claims of the software been confirmed.
[x] Automated tests:
- [x] All tests pass on the reviewer's local machine for the package version submitted by the author. Ideally this should be a tagged version making it easy for reviewers to install.
- [x] Tests cover essential functions of the package and a reasonable range of inputs and conditions.
[x] Continuous Integration: Has continuous integration setup (We suggest using Github actions but any CI platform is acceptable for review)
[x] Packaging guidelines: The package conforms to the pyOpenSci packaging guidelines. A few notable highlights to look at:
- [x] Package supports modern versions of Python and not End of life versions.
- [ ] Code format is standard throughout package and follows PEP 8 guidelines (CI tests for linting pass)

For packages also submitting to JOSS

[ ] The package has an obvious research application according to JOSS's definition in their submission requirements.

Note: Be sure to check this carefully, as JOSS's submission requirements and scope differ from pyOpenSci's in terms of what types of packages are accepted.

The package contains a paper.md matching JOSS's requirements with:

[ ] A short summary describing the high-level functionality of the software
[ ] Authors: A list of authors with their affiliations
[ ] A statement of need clearly stating problems the software is designed to solve and its target audience.
[ ] References: With DOIs for all those that have one (e.g. papers, datasets, software).

Final approval (post-review)

[ ] The author has responded to my review and made changes to my satisfaction. I recommend approving this package.

Estimated hours spent reviewing: 1.5

Review Comments

Adding a statement in README to state problems the software is designed to solve and its target audience would be more clear.
Including metadata such as author(s), author e-mail(s), a URL, and any other relevant metadata e.g., in a pyproject.toml file or elsewhere would be better.
More badges for Continuous integration and test coverage, A repostatus.org badge, Python versions supported, and the current package version (on PyPI / Conda) would be better.
It would be more clear to state how the package compares to other similar packages and/or how it relates to other packages in the scientific ecosystem, and why we need this package
It would be better to add citation information.
A table about "Load Housing Prices Data" in the vignette has popped out, it would be better to adjust it.

Package Review

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

[x] As the reviewer I confirm that there are no conflicts of interest for me to review this work (If you are unsure whether you are in conflict, please speak to your editor before starting your review).

Documentation

The package includes all the following forms of documentation:

[x] A statement of need clearly stating problems the software is designed to solve and its target audience in README.
[x] Installation instructions: for the development version of the package and any non-standard dependencies in README.
[x] Vignette(s) demonstrating major functionality that runs successfully locally.
[x] Function Documentation: for all user-facing functions.
[x] Examples for all user-facing functions.
[x] Community guidelines including contribution guidelines in the README or CONTRIBUTING.
[x] Metadata including author(s), author e-mail(s), a url, and any other relevant metadata e.g., in a pyproject.toml file or elsewhere.

Readme file requirements The package meets the readme requirements below:

[x] Package has a README.md file in the root directory.

The README should include, from top to bottom:

[x] The package name
[ ] Badges for:
- [ ] Continuous integration and test coverage,
- [x] Docs building (if you have a documentation website),
- [ ] A repostatus.org badge,
- [ ] Python versions supported,
- [ ] Current package version (on PyPI / Conda).

[x] Short description of package goals.
[x] Package installation instructions
[x] Any additional setup required to use the package (authentication tokens, etc.)
[ ] Descriptive links to all vignettes. If the package is small, there may only be a need for one vignette which could be placed in the README.md file.
- [x] Brief demonstration of package usage (as it makes sense - links to vignettes could also suffice here if package description is clear)
[x] Link to your documentation website.
[x] If applicable, how the package compares to other similar packages and/or how it relates to other packages in the scientific ecosystem.
[x] Citation information

Usability

[x] Package documentation is clear and easy to find and use.
[x] The need for the package is clear
[x] All functions have documentation and associated examples for use
[x] The package is easy to install

Functionality

[x] Installation: Installation succeeds as documented.
[x] Functionality: Any functional claims of the software been confirmed.
[x] Performance: Any performance claims of the software been confirmed.
[x] Automated tests:
- [x] All tests pass on the reviewer's local machine for the package version submitted by the author. Ideally this should be a tagged version making it easy for reviewers to install.
- [x] Tests cover essential functions of the package and a reasonable range of inputs and conditions.
[x] Continuous Integration: Has continuous integration setup (We suggest using Github actions but any CI platform is acceptable for review)
[x] Packaging guidelines: The package conforms to the pyOpenSci packaging guidelines. A few notable highlights to look at:
- [x] Package supports modern versions of Python and not End of life versions.
- [ ] Code format is standard throughout package and follows PEP 8 guidelines (CI tests for linting pass)

For packages also submitting to JOSS

[ ] The package has an obvious research application according to JOSS's definition in their submission requirements.

Note: Be sure to check this carefully, as JOSS's submission requirements and scope differ from pyOpenSci's in terms of what types of packages are accepted.

The package contains a paper.md matching JOSS's requirements with:

[ ] A short summary describing the high-level functionality of the software
[ ] Authors: A list of authors with their affiliations
[ ] A statement of need clearly stating problems the software is designed to solve and its target audience.
[ ] References: With DOIs for all those that have one (e.g. papers, datasets, software).

Final approval (post-review)

[ ] The author has responded to my review and made changes to my satisfaction. I recommend approving this package.

Estimated hours spent reviewing:

Review Comments

I did not check the box where it is saying your package follows PEP 8 guidlines as I do not think you have linting set up and I am not able to tell.
I think it is best to provide a link to your read the docs page as well as Vignette even if you can access them through the badge.
Add more badges to indicate the status of all CI-CD services as well as their status.
I think adding PEP 8 type hint (type annotation) to function input and output will be useful. A lot of modern IDE rely on type annotation to provide code suggestions and make developers' lives easier.

Package Review

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

[x] As the reviewer I confirm that there are no conflicts of interest for me to review this work (If you are unsure whether you are in conflict, please speak to your editor before starting your review).

Documentation

The package includes all the following forms of documentation:

[ ] A statement of need clearly stating problems the software is designed to solve and its target audience in README.
[x] Installation instructions: for the development version of the package and any non-standard dependencies in README.
[x] Vignette(s) demonstrating major functionality that runs successfully locally.
[x] Function Documentation: for all user-facing functions.
[x] Examples for all user-facing functions.
[x] Community guidelines including contribution guidelines in the README or CONTRIBUTING.
[x] Metadata including author(s), author e-mail(s), a url, and any other relevant metadata e.g., in a pyproject.toml file or elsewhere.

Readme file requirements The package meets the readme requirements below:

[x] Package has a README.md file in the root directory.

The README should include, from top to bottom:

[x] The package name
[x] Badges for:
- [ ] Continuous integration and test coverage,
- [x] Docs building (if you have a documentation website),
- [ ] A repostatus.org badge,
- [ ] Python versions supported,
- [ ] Current package version (on PyPI / Conda).

[x] Short description of package goals.
[x] Package installation instructions
[x] Any additional setup required to use the package (authentication tokens, etc.)
[x] Descriptive links to all vignettes. If the package is small, there may only be a need for one vignette which could be placed in the README.md file.
- [x] Brief demonstration of package usage (as it makes sense - links to vignettes could also suffice here if package description is clear)
[x] Link to your documentation website.
[ ] If applicable, how the package compares to other similar packages and/or how it relates to other packages in the scientific ecosystem.
[x] Citation information

Usability

[x] Package documentation is clear and easy to find and use.
[x] The need for the package is clear
[x] All functions have documentation and associated examples for use
[x] The package is easy to install

Functionality

[x] Installation: Installation succeeds as documented.
[x] Functionality: Any functional claims of the software been confirmed.
[x] Performance: Any performance claims of the software been confirmed.
[x] Automated tests:
- [x] All tests pass on the reviewer's local machine for the package version submitted by the author. Ideally this should be a tagged version making it easy for reviewers to install.
- [x] Tests cover essential functions of the package and a reasonable range of inputs and conditions.
[x] Continuous Integration: Has continuous integration setup (We suggest using Github actions but any CI platform is acceptable for review)
[x] Packaging guidelines: The package conforms to the pyOpenSci packaging guidelines. A few notable highlights to look at:
- [x] Package supports modern versions of Python and not End of life versions.
- [x] Code format is standard throughout package and follows PEP 8 guidelines (CI tests for linting pass)

For packages also submitting to JOSS

[ ] The package has an obvious research application according to JOSS's definition in their submission requirements.

Note: Be sure to check this carefully, as JOSS's submission requirements and scope differ from pyOpenSci's in terms of what types of packages are accepted.

The package contains a paper.md matching JOSS's requirements with:

[ ] A short summary describing the high-level functionality of the software
[ ] Authors: A list of authors with their affiliations
[ ] A statement of need clearly stating problems the software is designed to solve and its target audience.
[ ] References: With DOIs for all those that have one (e.g. papers, datasets, software).

Final approval (post-review)

[ ] The author has responded to my review and made changes to my satisfaction. I recommend approving this package.

Estimated hours spent reviewing:

Review Comments

Instructions are easy to follow and the functions performs as expected.
count_nonzero_elements() returning a dictionary seems unnecessary to me. Returning a value similar to search_array() and argmax() should be sufficient and more consistent.
The functions are written defensively against unexpected inputs, which is great.
Putting more badges on the README would be a clear way to provide information about development.
Stating the target audience in the README might be a good idea, e.g. "for those who are interested in a different implementation of some array operations"

Package Review

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

[x] As the reviewer I confirm that there are no conflicts of interest for me to review this work (If you are unsure whether you are in conflict, please speak to your editor before starting your review).

Documentation

The package includes all the following forms of documentation:

[ ] A statement of need clearly stating problems the software is designed to solve and its target audience in README.
[x] Installation instructions: for the development version of the package and any non-standard dependencies in README.
[x] Vignette(s) demonstrating major functionality that runs successfully locally.
[x] Function Documentation: for all user-facing functions.
[x] Examples for all user-facing functions.
[x] Community guidelines including contribution guidelines in the README or CONTRIBUTING.
[x] Metadata including author(s), author e-mail(s), a url, and any other relevant metadata e.g., in a pyproject.toml file or elsewhere.

Readme file requirements The package meets the readme requirements below:

[x] Package has a README.md file in the root directory.

The README should include, from top to bottom:

[x] The package name
[ ] Badges for:
- [ ] Continuous integration and test coverage,
- [x] Docs building (if you have a documentation website),
- [ ] A repostatus.org badge,
- [ ] Python versions supported,
- [ ] Current package version (on PyPI / Conda).

[x] Short description of package goals.
[x] Package installation instructions
[ ] Any additional setup required to use the package (authentication tokens, etc.)
[x] Descriptive links to all vignettes. If the package is small, there may only be a need for one vignette which could be placed in the README.md file.
[x] Brief demonstration of package usage (as it makes sense - links to vignettes could also suffice here if package description is clear)
[x] Link to your documentation website.
[x] If applicable, how the package compares to other similar packages and/or how it relates to other packages in the scientific ecosystem.
[ ] Citation information

Usability

[x] Package documentation is clear and easy to find and use.
[ ] The need for the package is clear
[x] All functions have documentation and associated examples for use
[x] The package is easy to install

Functionality

[x] Installation: Installation succeeds as documented.
[x] Functionality: Any functional claims of the software been confirmed.
[x] Performance: Any performance claims of the software been confirmed.
[x] Automated tests:
- [x] All tests pass on the reviewer's local machine for the package version submitted by the author. Ideally this should be a tagged version making it easy for reviewers to install.
- [x] Tests cover essential functions of the package and a reasonable range of inputs and conditions.
[x] Continuous Integration: Has continuous integration setup (We suggest using Github actions but any CI platform is acceptable for review)
[x] Packaging guidelines: The package conforms to the pyOpenSci packaging guidelines. A few notable highlights to look at:
- [x] Package supports modern versions of Python and not End of life versions.
- [x] Code format is standard throughout package and follows PEP 8 guidelines (CI tests for linting pass)

For packages also submitting to JOSS

[x] The package has an obvious research application according to JOSS's definition in their submission requirements.

Note: Be sure to check this carefully, as JOSS's submission requirements and scope differ from pyOpenSci's in terms of what types of packages are accepted.

The package contains a paper.md matching JOSS's requirements with:

[x] A short summary describing the high-level functionality of the software
[x] Authors: A list of authors with their affiliations
[ ] A statement of need clearly stating problems the software is designed to solve and its target audience.
[x] References: With DOIs for all those that have one (e.g. papers, datasets, software).

Final approval (post-review)

[ ] The author has responded to my review and made changes to my satisfaction. I recommend approving this package.

Estimated hours spent reviewing:

Review Comments

The file organization is very clear and clean, easy to navigate and follow usage for the first-time user as well.
The function is written very defensively, and in a way to catch any unexpected inputs.
The objective of the function is a little unclear, as to why this package is more suitable for certain group of people over NumPy or any other Python manipulation package.
Badges are missing in the README file
Some of the metadata, such as email address was missing

UBC-MDS / software-review-2024