Submission Group 4: Slimeda (Python)

name: Submit Software for Review about: Use to submit your Python package for peer review title: 'Slimeda' labels: 1/editor-checks, New Submission! assignees: ''

Submitting Authors: Simon Guo ( !--author1-->@y248guo@anthea98@khalidcawl@thayeylolu<!--end-author4--) Package Name: slimeda One-Line Description of Package: Slim package for doing exploratory data analysis (EDA) in Python Repository Link: https://github.com/UBC-MDS/slimeda Version submitted: v2.0 Editor: Simon Guo (@y248guo)
Reviewer 1: Alex Guo Reviewer 2: Nagraj Rao Reviewer 3: Adrianne Leung Reviewer 4: Rakesh Pandey Archive: TBD Version accepted: TBD

Description

Include a brief paragraph describing what your package does:

Scope

Please indicate which category or categories this package falls under:
- [X] Data retrieval
- [X] Data extraction
- [X] Data munging
- [ ] Data deposition
- [ ] Reproducibility
- [ ] Geospatial
- [ ] Education
- [ ] 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.

Explain how and why the package falls under these categories (briefly, 1-2 sentences):

The package slimeda explores the dataset by creating histograms and correlation plots, in addition to that we have functions for counting missing values and counting unique values

Who is the target audience and what are scientific applications of this package?

Researchers or data analysts who would like to work with EDA

Are there other Python packages that accomplish the same thing? If so, how does yours differ?

Yes, but our Python package aims to provide a simple straightforward modifiable objects with maximum flexibility. Also comparing many mainstream packages, our package is lighter and simpler.

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: (N/A)

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.
[X] 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.

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: Do not submit your package separately to JOSS*

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.

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

Editor and Review Templates

Editor and review templates 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:

[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 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 setup.py file or elsewhere.

Readme 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, a repostatus.org badge, and any other badges. 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 badge for pyOpenSci peer-review will be provided upon acceptance.)
[x] Short description of goals of package, with descriptive links to all vignettes (rendered, i.e. readable, cf the documentation website section) unless the package is small and there’s only one vignette repeating the README.
[x] Installation instructions
[x] Any additional setup required (authentication tokens, etc)
[x] Brief demonstration usage
[x] Direction to more detailed documentation (e.g. your documentation files or website).
[x] If applicable, how the package compares to other similar packages and/or how it relates to other packages
[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:

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

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, such as Travis CI, AppVeyor, CircleCI, and/or others.
[x] Packaging guidelines: The package conforms to the pyOpenSci packaging guidelines.

For packages co-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

Great job guys! I find slimeda a very useful package for initial EDA of any numerical analysis. It is a fairly universal package for application in many fields. The package is organized well with clear differentiation between functions so that user can pick for their own usage.

I had no issues installing the package following the instructions on Windows. Good work!
It would be useful to update the documentations on readthedocs.io as well with the example usage like in the README.
A badge for code coverage could be included in README so that users can assess how robust the scripts are.
For the cat_unique_counts function, there are additional packages such as pandas and parse that require further importing. It would be good if they could be incorporated in the function so that user can skip this step before running the function.
There is no link to the Contributing.md file in the Contributing section of the README. Adding a link could be useful from a user perspective.
Author contact details could be included in the Code of Conduct.

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 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 setup.py file or elsewhere.

Readme 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, a repostatus.org badge, and any other badges. 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 badge for pyOpenSci peer-review will be provided upon acceptance.)
[x] Short description of goals of package, with descriptive links to all vignettes (rendered, i.e. readable, cf the documentation website section) unless the package is small and there’s only one vignette repeating the README.
[x] Installation instructions
[x] Any additional setup required (authentication tokens, etc)
[x] Brief demonstration usage
[x] Direction to more detailed documentation (e.g. your documentation files or website).
[x] If applicable, how the package compares to other similar packages and/or how it relates to other packages
[x] Citation information

Usability

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

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, such as Travis CI, AppVeyor, CircleCI, and/or others.
[x] Packaging guidelines: The package conforms to the pyOpenSci packaging guidelines.

For packages co-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 hours

Review Comments

Overall, great job! This package is useful for EDA, which is the starting point for most analyses conducted by academics, students, and many data enthusiasts. Thank you for making our lives easy.

The README could include more details on how to exactly use each function. For example adding a line that says: from slimeda import histogram would make it easier for the user to load the function. Else, it requires the prior knowledge/expertise of someone downloading your package.
Similarly, providing an easy to use example would facilitate faster understanding. For example, if you had a sample data frame in your package and walked a user through it, that would make it more intuitive for a new user.
Consider adding a badge for code coverage.
I noticed a file called test_slimeda.py but its utility is not clear. Would it be worthwhile deleting, if this be the case?
Small typo in README - it is Spearman's "rank" and not "rand".
As mentioned by Adrianne, any additional dependencies (pandas for example), should be taken care of within the function.

Reviewer: Rakesh Pandey

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 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 setup.py file or elsewhere.

Readme 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, a repostatus.org badge, and any other badges. 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 badge for pyOpenSci peer-review will be provided upon acceptance.)
[x] Short description of goals of package, with descriptive links to all vignettes (rendered, i.e. readable, cf the documentation website section) unless the package is small and there’s only one vignette repeating the README.
[x] Installation instructions
[x] Any additional setup required (authentication tokens, etc)
[x] Brief demonstration usage
[x] Direction to more detailed documentation (e.g. your documentation files or website).
[x] If applicable, how the package compares to other similar packages and/or how it relates to other packages
[x] Citation information

Usability

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

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, such as Travis CI, AppVeyor, CircleCI, and/or others.
[x] Packaging guidelines: The package conforms to the pyOpenSci packaging guidelines.

For packages co-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

Excellent and practical EDA package! It encapsulates all of the code and details and provides us with a user-friendly package.

I understand that the information in the README file is extensive. However, adding example usage in the documentation, such as an example dataframe and the output for each function, would be helpful. https://slimeda.readthedocs.io/en/latest/example.html
Unused scripts such as src/sli, eda/slimeda.py, and tests/test slimeda.py should be removed.
A link to contributing in the README would be useful, particularly for users who are reading the package from readthedocs.
It would be useful to include how input and output look in the usage section. Before we use any package, we usually look at these details.
There appears to be a typo in the README for the miss_counts function, as there is no dataframe in the OUTPUT section.

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 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 setup.py file or elsewhere.

Readme 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, a repostatus.org badge, and any other badges. 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 badge for pyOpenSci peer-review will be provided upon acceptance.)
[ x ] Short description of goals of package, with descriptive links to all vignettes (rendered, i.e. readable, cf the documentation website section) unless the package is small and there’s only one vignette repeating the README.
[x] Installation instructions
[x] Any additional setup required (authentication tokens, etc)
[x] Brief demonstration usage
[x] Direction to more detailed documentation (e.g. your documentation files or website).
[x] If applicable, how the package compares to other similar packages and/or how it relates to other packages
[x] Citation information

Usability

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

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, such as Travis CI, AppVeyor, CircleCI, and/or others.
[x] Packaging guidelines: The package conforms to the pyOpenSci packaging guidelines.

For packages co-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

The installation was successful on my end and all functions worked. Good job!
It is nice to see that you are using GitHub issues, projects, milestones, etc. to organize your tasks.
There are only 3 branches other than main. Maybe it could be more systematic if all group members have a branch to make changes to the main repo.
As mentioned by other reviewers, some examples would be helpful in README to better explain the package.
There seems to be some unnecessary files/folders in the repo. It would be better to delete unused structures and make the repo more organized.

UBC-MDS / software-review-2022