Submission Group 1 - magmaviz (Python)

[miyer26]

Submitting Author: Mukund Iyer (@miyer26)
Package Name: magmaviz One-Line Description of Package: Makes EDA easy by providing functions for four common types of plots with the magma color scheme. Repository Link: https://github.com/UBC-MDS/magmaviz Version submitted: 0.3.9
Editors: Mohammed Abdul Moid (@iamMoid), Irene Yang (@shyan0903), Rubén De la Garza Macías (@ruben1dlg), Mukund Iyer (@miyer26)

Reviewer 1: Yair Guterman @gutermanyair Reviewer 2: Giang Nguyen @gn385x Reviewer 3: Daniel King @danfke

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Description

This package aims to make Exploratory Data Analysis easy by providing python plot functions based on the Altair library to plot four common types of plots with the magma color scheme. To maximize interpretability, the plots have defined color schemes (discrete, diverging, sequential) based on the kind of data they show and additional inputs for customizability.

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.

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

This package has functions with the sole objective of creating plots promptly and easily based on the 'Altair' package using the magma color scheme.

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

This package is designed to be used by data scientists who are exploring data or developing a visual dashboard. The package is versatile and can be used for most data science projects.

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

Similar packages to ours include deneb, which uses Altair, and spartan-viz, which uses Matplotlib. These also streamline the EDA process but do not use the Magma theme and functionalities that this package offers.

• 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] 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*

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• [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.

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[gutermanyair]

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
• [ ] 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:

1.5 hours

Review Comments

You have an amazing package but here are a few comments for you guys! <3

1. The codecov badge does not show the percentage of coverage, even though when I click it I can see the percent!

2. There is not much detail in comparing other similar packages in the readme, I am aware that there must be many EDA packages out there!

3. I see that your plots only display in one color scheme, if people want to use the EDA plots in their report maybe adding in an option for a choice of color scheme would be very nice!

4. If I could add more stuff to your package I would maybe want to include violin plots and heat maps and then your package, in my opinion, would cover everything needed for an EDA report

5. 82 percent is some nice coverage but as a user of your package, I would love to see that number be over 90, maybe include some more tests to make sure all your code is being tested.

I love you all especially Moid , keep up the amazing work you all!

[danfke]

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.
• [ ] 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
• [ ] 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
• [ ] 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

• [ ] Installation: Installation succeeds as documented.
• [ ] 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

1. After installing using the installation instructions and then duplicating the boxplot function example from the Usage section of the README, I get an error saying that facet is an unexpected keyword argument. This is why I kept functionality unchecked.

2. I have a feeling that the installation is for an old version of the package which is probably why the facet argument didn't work in the boxplot function. The installation instructions do refer to test PyPi.

3. Code coverage is good but getting over 90% would be great!

4. I can't seem to find the author's emails which is why I left metadata unchecked. As far as I could find by looking through the readme, license, and contributing guidelines there is single email for the whole team instead.

5. In the example usage of the hisogram function, I'm not really sure what's going on, it seems like there are overlapping bars? For example it seems like there are black bars in the foreground and lighter bars in the background at some values of horsepower. Is this a possible functionality glitch? Maybe the bins are too small? Having a bin argument in the histogram function I think would be useful to users!

Overall beautiful looking package with well-written documentation. Great job!

[gn385x]

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
• [ ] 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
• [ ] 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

• [ ] 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

An amazing package guys! A few suggestions for improvement:

1. The README is descriptive and informative. Two suggestions to improve the file:

• Under the Usage section, you could add the visual outputs of each example function so that users can grasp it more easily (similar to what you have in the R package).
• Overall, you should make the installation guide more thorough for users to follow along and use the package. For example, when I was following along the README file, I did not manage to test run your example functions given the current instructions.

2. All functions are very well documented and easy to follow. You could give users more flexibility by adding an additional function at the beginning of your package to enable importing any data sets that users are interested in (rather than using data from vega_datasets only).
3. In the future, you might want to consider allowing users to customize plots a bit more. For example, you might be able to let the users choose the color of the figures they want.
4. Echoing two reviewers above, it would be nice to increase the code coverage to be over 90%. One suggestion is to add more (sophisticated) tests so that all your functions and edge cases are tested.