VisuMorph - Group 1

[SoloSynth1]

Submitting Author: Orix Au Yeung (@SoloSynth1) All current maintainers: (@atabak-alishiri, @Marcony1, @shawnhu444) Package Name: VIsuMorph One-Line Description of Package: A package for image manipulations in Python Repository Link: https://github.com/ubc-mds/visumorph Version submitted: v2.0.0 Editor: @ttimbers Reviewer 1: Ella Hein (@ella-irene) Reviewer 2: Riya Eliza Shaju (@riyaeliza123) Reviewer 3: Dan Zhang (@wqxxzd) Reviewer 4: Charles Xu (@charlesxch)

Archive: TBD JOSS DOI: TBD Version accepted: TBD Date accepted (month/day/year): TBD

---

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[wqxxzd]

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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 hour

Review Comments

The package overall is amazing and I have a lot of fun learning it. I really enjoyed trying it out and can see myself using it more. Just a couple of quick suggestions:

• Installation Command: Maybe break up the big installation command into smaller steps? It could be easier to debug if something goes wrong.

• Examples in the README: Good job on writing the detailed examples on your documentation site! It would be awesome if you could add a few simple ones in the README for quick reference.

• Pytest Section: The pytest part in the README seems a bit isolated and simple. Maybe integrate it with other sections?

• Installation Instructions: The current setup instructions seem more developer note. How about adding a straightforward command like pip or conda for regular users?

[riyaeliza123]

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

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• [x] All functions have documentation and associated examples for use
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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
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• [ ] 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: 30 minutes

---

Review Comments:

I think this package makes image transformations more convenient. I really like the motivation behind the project. I suggest that you add some more description in "Run the test" section of the READ.ME

[ella-irene]

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:

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• [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:
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  • [x] A repostatus.org badge,
  • [ ] 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.
  • [ ] 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)

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

Estimated hours spent reviewing: 1

---

Review Comments

Overall, really great project! This is very similar to the package my group built, so it was really cool to see which functions you decided to implement, and how you wrote them. I think the structure and contents of this package are very good, and the package is well documented. Furthermore, the motivation is compelling and straight-forward. I've listed below just a few minor notes I had along the way:

• Consider some examples or links to direct people to your example files in the readme. Your example files are all very thorough and easy to follow.
• I really appreciate your "Postition in the Python Ecosystem Section" of the readme, I think it's super helpful to give context to your package, and give credit to the other libraries you are wrapping.
• Also, consider adding a bit more of a description to pytest. Even just a line with "to test the functions run this in your command line:", could be helpful.
• I ran into an issue when running pytest, may be related to some setting that I have, but it might be good to have a note on what to do with this error: ====================================== short test summary info ====================================== ERROR - PermissionError: [Errno 1] Operation not permitted: '/Users/ellahein/Library/Accounts' !!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ========================================= 1 error in 5.53s ==========================================
• Consider adding the python version requirement to the badges

[charlesxch]

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.
• [ ] Function Documentation: for all user-facing functions.
• [x] Examples for all user-facing functions.
• [x] Community guidelines including contribution guidelines in the README or CONTRIBUTING.
• [ ] Metadata including author(s), author e-mail(s), a url, and any other relevant metadata e.g., in a pyproject.toml file or elsewhere.

Readme file requirements The package meets the readme requirements below:

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

The README should include, from top to bottom:

• [x] The package name
• [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,
  • [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.
• [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)

• [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 hour

---

Review Comments

Pros:

• In general, the project is outstanding, offering valuable features for fundamental image processing tasks. The code you've authored is both tidy and comprehensively documented.
• The package's documentation, including the vignettes, exhibits a well-crafted and eloquent design. I appreciate the manner in which you showcase the practical application of your methods through examples. The illustrations seamlessly complement the corresponding code and images.
• The README.md contains all essential elements, and the package's workflow functions smoothly.

Cons:

• I recommend consolidating the vignettes for various methods into a single document. It can be cumbersome to navigate to different pages to access the examples.
• I suggest that you can incorprate the flip, rotate, scale and change_hue methods into the Image class as class methods.
• I did not find an author email of link in the repository.

[SoloSynth1]

@ella-irene Thank you for your review.

Regarding the error message you encountered, it is most likely that you did not run the pytest command under the project root folder. I was able to replicate the same error message in my environment when I run the pytest command under /Users/<username>/Library/Accounts:

(ubc-mds) ╭─solosynth1@SoloSynth1s-MacBook-Air ~/Library/Accounts
╰─$ pytest                                                                                          1 ↵
========================================= test session starts ==========================================
platform darwin -- Python 3.11.6, pytest-7.4.3, pluggy-1.3.0
rootdir: /Users/solosynth1/Library/Accounts
plugins: anyio-4.0.0
collected 0 items / 1 error

================================================ ERRORS ================================================
____________________________________ ERROR collecting test session _____________________________________
../../anaconda3/envs/ubc-mds/lib/python3.11/site-packages/_pytest/runner.py:341: in from_call
    result: Optional[TResult] = func()
../../anaconda3/envs/ubc-mds/lib/python3.11/site-packages/_pytest/runner.py:372: in <lambda>
    call = CallInfo.from_call(lambda: list(collector.collect()), "collect")
../../anaconda3/envs/ubc-mds/lib/python3.11/site-packages/_pytest/main.py:729: in collect
    for direntry in visit(argpath, self._recurse):
../../anaconda3/envs/ubc-mds/lib/python3.11/site-packages/_pytest/pathlib.py:722: in visit
    entries = scandir(path)
../../anaconda3/envs/ubc-mds/lib/python3.11/site-packages/_pytest/pathlib.py:698: in scandir
    with os.scandir(path) as s:
E   PermissionError: [Errno 1] Operation not permitted: '/Users/solosynth1/Library/Accounts'
=========================================== warnings summary ===========================================
../../anaconda3/envs/ubc-mds/lib/python3.11/site-packages/_pytest/cacheprovider.py:451
  /Users/solosynth1/anaconda3/envs/ubc-mds/lib/python3.11/site-packages/_pytest/cacheprovider.py:451: PytestCacheWarning: could not create cache path /Users/solosynth1/Library/Accounts/.pytest_cache/v/cache/nodeids: [Errno 1] Operation not permitted: '/Users/solosynth1/Library/Accounts/.pytest_cache'
    config.cache.set("cache/nodeids", sorted(self.cached_nodeids))

../../anaconda3/envs/ubc-mds/lib/python3.11/site-packages/_pytest/cacheprovider.py:405
  /Users/solosynth1/anaconda3/envs/ubc-mds/lib/python3.11/site-packages/_pytest/cacheprovider.py:405: PytestCacheWarning: could not create cache path /Users/solosynth1/Library/Accounts/.pytest_cache/v/cache/lastfailed: [Errno 1] Operation not permitted: '/Users/solosynth1/Library/Accounts/.pytest_cache'
    config.cache.set("cache/lastfailed", self.lastfailed)

../../anaconda3/envs/ubc-mds/lib/python3.11/site-packages/_pytest/stepwise.py:56
  /Users/solosynth1/anaconda3/envs/ubc-mds/lib/python3.11/site-packages/_pytest/stepwise.py:56: PytestCacheWarning: could not create cache path /Users/solosynth1/Library/Accounts/.pytest_cache/v/cache/stepwise: [Errno 1] Operation not permitted: '/Users/solosynth1/Library/Accounts/.pytest_cache'
    session.config.cache.set(STEPWISE_CACHE_DIR, [])

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
======================================= short test summary info ========================================
ERROR  - PermissionError: [Errno 1] Operation not permitted: '/Users/solosynth1/Library/Accounts'
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
===================================== 3 warnings, 1 error in 0.09s =====================================
╰─$

[SoloSynth1]

@charlesxch Thank you for your review. Adding links to our GitHub profiles in the README.md sounds like a good idea and I think we will address it in the upcoming release.

Regarding your other comments:

I recommend consolidating the vignettes for various methods into a single document. It can be cumbersome to navigate to different pages to access the examples.

Our team made the deliberate decision to create separate vignettes for each function. It is to avoid unnecessary confusion in explaining the functionalities of each function, as they are all responsible for different operations in image manipulation.

I suggest that you can incorporate the flip, rotate, scale and change_hue methods into the Image class as class methods.

I wholeheartedly agree your suggestion on this. To be honest OOP was our approach initially as these functions work on the same object and naturally fit well with this paradigm.

Unfortunately, the milestone requirements explicitly specify we need to design and implement "user-facing functions".

I do not want to be pedantic as it sounds, but based on this we decided to implement functions instead of class methods out of concerns about implementing class methods might not satisfy the grading requirements.

That being said, I think we will put simple wrappers into the class object in order to address this in the upcoming release.

[SoloSynth1]

@wqxxzd @riyaeliza123 Thank you for your reviews! The feedbacks have been incorporated in the latest release.