Mathdistops - Group 20

[czwcandy]

Submitting Author: Ziwei Chen (@czwcandy) All current maintainers: Oak Chong, Kun Ya, Sandra Gross( @sivakornchong, @carinaya, @sandygross) Package Name: mathdistops One-Line Description of Package: This package provides statistical functions for normal and exponential distributions, including pnorm, qnorm, pexp, and qexp. Each function not only performs the respective statistical calculation but also generates the corresponding plot of the distribution, offering both numerical results and visual outputs. Repository Link: https://github.com/UBC-MDS/mathdistops Version submitted: 2.0.0 (Milestone 3) Editor: @ttimbers Reviewer 1: Anu Banga Reviewer 2: Scout McKee Reviewer 3: Sean McKay Reviewer 4: Ruocong Sun

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:

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.

[AnuBanga]

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:
  • [x] Continuous integration and test coverage,
  • [x] Docs building (if you have a documentation website),
  • [ ] A repostatus.org badge,
  • [x] 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.)
• [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.
• [x] 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.
• [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.
• [ ] Automated tests:
  • [ ] 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.
  • [ ] 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: 1.5

---

Review Comments

Overall it is good package, with neatly organized project repository and clear installation guidelines. Certainly, a couple of review points require attention. Review points:-

1. There is an issue with the test case in tests\test_pexp.py, where it fails due to an assertion error related to the mismatch in PDF title. The error message states: "Expected: 'Probability Density Function for q = 1.5, rate = 1".
2. Ensure that the README contains usage examples for all functions, similar to what is provided for pnorm.
3. It is advisable to assign milestone labels to each GitHub issue for better organization and tracking.
4. Consider adding hyperlinks to the Code of Conduct and contributing guidelines within the contributing section of the README.

[sean-m-mckay]

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.
• [ ] 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:
  • [x] 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.
  • [ ] 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

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.
• [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

• Overall, great package with very useful and relevant functions, a good way of testing statistical knowledge
• Vignettes are interesting and easy to follow
• Since packages are installed through poetry, having a conda environment is probably not necessary, especially since it's empty
• Separation of concerns: Probably better to have plotting functions for PDF and CDF be a separate function in your package, this makes it clearer what the function's return type would be
• Having an issue running the package by using from mathdistops import pnorm - Will check with the package authors and update this review once I've got the functions running

Minor issues/suggestions:

• Minor performance: If you keep the functionality for graphs and return value in the same function - if the user passes graph=False, it might be better to just not generate the graph at all
• README could list examples for each function - and a repostatus.org indicator
• The Docstrings could have a "Raises" section to list errors they may raise

• Docstrings for qnorm and pnorm do not pass the "graph" argument, but since the default is "graph=True", the return type should have a matplotlib object 1

  • Sidenote / General stats question: In the vignette for the pexp/qexp function it mentions "Based on the output from the pexp function, we find that the cumulative probability of survival up to the median survival time (255.5 days) is approximately 0.567 or 56.7%" - Why isn't it 50%? Isn't the median

[scout-mckee]

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

• [ ] 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). The authors of this package are my classmates.

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:
  • [x] Continuous integration and test coverage,
  • [x] Docs building (if you have a documentation website),
  • [ ] A repostatus.org badge,
  • [x] 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.
• [x] 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.
• [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

• [ ] Installation: Installation succeeds as documented. poetry needs to be added to the environment
• [x] Functionality: Any functional claims of the software been confirmed. after installing poetry, yes
• [x] Performance: Any performance claims of the software been confirmed.
• [ ] Automated tests:
  • [ ] 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. A test fails locally (AssertionError: PDF title does not match expected. Expected: 'Probability Density Function for q = 1.5, rate = 1', assert False)
  • [x] Tests cover essential functions of the package and a reasonable range of inputs and conditions.
• [ ] 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: 1 hour

---

Review Comments

The package and documentation look great! Here are some suggested changes:

• One fix to improve the ease of installation is to add poetry to your environment file, without this poetry install does not work.
• Another thing to note is that not all of the tests are passing.
• It would also be helpful to include descriptive links to your vignettes in the README.md.
• Also elaborating on how the package compares to other similar packages and/or how it relates to other packages would be helpful.
• Continuous integration needs to be set up - I know this is part of Milestone 4:) Great job!

[sungg888]

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
• [x] Badges for:
  • [x] Continuous integration and test coverage,
  • [x] Docs building (if you have a documentation website),
  • [ ] A repostatus.org badge,
  • [x] Python versions supported,
  • [x] 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.
• [x] 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.
• [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

• [ ] 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.
• [ ] Automated tests:
  • [ ] 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

1. It could be more efficient if you put the environment file to pyproject as one file. (pyproject can be the file that also functions like the environment file )
2. When I install the package, it shows 'bash: poetry: command not found'. I think it means poetry is not included in the environment or dependencies.
3. Not all tests can pass
4. It is good if includes how the package compares to other similar packages and/or how it relates to other packages in the scientific ecosystem.
5. Other things look good.