Group 1 - prelim_eda_helper

[morrismanfung]

Submitting Author: Morris Chan (@morrismanfung) All current maintainers: Mehwish (@MNBhat), Xinru Lu (@Lorraine97), Austin SHIH (@austin-shih) Package Name: prelim_eda_helper One-Line Description of Package: A preliminary exploratory data analysis tool to make useful feature EDA plots and provide relevant information to simplify an otherwise tedious EDA step of any data science project. Repository Link: https://github.com/UBC-MDS/prelim_eda_helper Version submitted: v0.1.8 Editor: Mehwish (@MNBhat) Xinru Lu (@Lorraine97) Austin SHIH (@austin-shih) Reviewer 1: Zilong Yi Reviewer 2: Peng Zhang Reviewer 3: Mohammad Reza Nabizadeh Shahrbabak Reviewer 4: Ziyi Chen Archive: TBD Version accepted: TBD Date accepted (month/day/year): TBD

Description

• Include a brief paragraph describing what your package does: This package is a preliminary exploratory data analysis (EDA) tool to make useful feature EDA plots and provide relevant information to simplify an otherwise tedious EDA step of any data science project. Specifically this package allows users to target any two features, whether they are numeric or categorical, and create visualization plots supplemented with useful summary and test statistics.

  Scope

• Please indicate which category or categories this package falls under:
  • [ ] Data retrieval
  • [ ] Data extraction
  • [ ] Data munging
  • [ ] Data deposition
  • [ ] Reproducibility
  • [ ] Geospatial
  • [ ] Education
  • [x] Data visualization*

    Please fill out a pre-submission inquiry before submitting a data visualization package. For more info, see notes on categories of our guidebook.

• 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? Researchers or analysts who have the need to constantly do explanatory analysis and statistical testing. The helper functions are designed to speed up the frequently used pipelines.
  • Are there other Python packages that accomplish the same thing? If so, how does yours differ? There are existing packages for visualizations and statistical tests. However, they usually require more complicated syntaxes. Our package combines graphic visualizations with preliminary statistical test results aiming to enable users to quickly get a sense of how the data look like.

    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] has an OSI approved license.
• [x] contains a README with instructions for installing the development version.
• [x] includes documentation with examples for all functions.
• [ ] contains a vignette with examples of its essential functions and uses.
• [x] has a test suite.
• [x] has continuous integration, such as Travis CI, AppVeyor, CircleCI, and/or others.

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.

  Code of conduct

• [x] I agree to abide by pyOpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.

Editor and Review Templates

The editor template can be found here. The review template can be found here.

[mrnabiz]

Package Review

• [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,
  • [ ] 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)

• [ ] 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: Tests cover essential functions of the package and a reasonable range of inputs and conditions. All tests pass on the local machine.
• [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)

Final approval (post-review)

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

Estimated hours spent reviewing: 2 hours.

Review Comments

Overall I enjoyed installing and playing around with your package and congrats. Great Job. There are minor fixes are suggested here:

1. Some of the examples in the readme file are not running (maybe there is a problem on my side?) and they were throwing ImportError.
2. The continuous development workflow in GitHub actions has failed recently (might be due to version 0.1.8 that has been created after 1.0.0!
3. There is a redundant folder in the src folder. Please consider deleting it and moving the included files to the main src page.
4. In the documentation folder/examples notebook please make sure you handle the warning by addressing them or surpassing them. This will increase the readability of your documentation.
5. The documentation's link could be available too.
6. The make file needs to be updated with sphinx commands.

The rest was amazing. Thanks.

[pengzh313]

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.
• [ ] 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,
  • [ ] 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
• [ ] 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)
• [ ] 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.
• [ ] Functionality: Any functional claims of the software been confirmed.
• [ ] Performance: Any performance claims of the software been confirmed.
• [ ] Automated tests: Tests cover essential functions of the package and a reasonable range of inputs and conditions. All tests pass on the local machine.
• [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)

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: 2.5 hours

---

Review Comments

The package is to boost the overall efficiency when we perform EDA as part of the data analysis. It is really a great idea and valuable helper.

There are following specific suggestions:

(1) As per the instruction from ReadMe file and the pypi documentation website, I have successfully installed the package. However, it failed when importing the functions to my local Jupyter notebook. Therefore, the performance and functionality of the Python package have not been confirmed from my end. You may consider to double check from other users to see if there is a technical issue. (2) To benefit the users, especially some new data analysts, it is better to show some example plots on the Usage section of the ReadMe file. (3) The pypi documentation website is already available for the package. It would be convenient to indicate the link on the ReadMe file. (4) You can consider to add Python version support (for example Python >=3.9, <3.12) in the ReadMe file although it is visible on the documentation website. (5) You can consider to add current package version on PyPI in the ReadMe file.

[zchen156]

Package Review

• [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,
  • [ ] 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
• [ ] 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)
• [ ] 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: Tests cover essential functions of the package and a reasonable range of inputs and conditions. All tests pass on the local machine.
• [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)

Final approval (post-review)

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

Estimated hours spent reviewing: 1 hr

---

Review Comments

• I could not find the ReadTheDocs link in the main page which is a little bit inconvenient, but I can understand the effort you put there.
• When I try to find the documentation website: https://prelim-eda-helper.readthedocs.io/en/latest/?badge=latest# which should be one of the requirements for milestone3, it cannot be found. Having the link explicitly there would help the contributors.
• It is not easy to test the package without checking it out since the documentation is missing and the examples of the usage of the function in the README.md are not completed for reproduction.
• The package does a good job in terms of visualization with a series of graphs and shows the trend of dataset, and I like how you put it together.
• Maybe adding more badges on the main page such as docs and pypi so it is easier for users to see the state of the repository and the project.

[ZilongYi]

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,
  • [ ] 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
• [ ] 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)
• [ ] 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: Tests cover essential functions of the package and a reasonable range of inputs and conditions. All tests pass on the local machine.
• [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
• [x] 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)

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

Estimated hours spent reviewing: 1.5 hours

---

Review Comments

• All functions are working without error. The parameters are well-design. Nice work! I notice that some of them might have too many parameters. Might need to consider which to keep and which could be deleted.
• Dependencies. It would be better to add dependencies in README files. This way people intuitively know what packages need to be installed and if, there is any conflict they might encounter during the installment of your package.
• I noticed that the package release version is 0.2.0. From best practice point of view, it should be at least 1.0.0 by now.
• In the docs/example file, I noticed that there are future warning that is not comming from this package. It might be confusing for user to see other packages' warning.
• I cannot seem to find the link to the docs websites. It would be much intuitive if we have one. Overall, It is very practical and interesting package! Great work!