Support NumPy > 2.0 and Python 3.12

[lochhh]

Closes #114

This PR addresses the failing tests reported in #114 (due to deprecations in NumPy 2.0) by:

• replacing the deprecated np.string_ with np.bytes_
• replacing bool(np.all(...)) with np.array_equal in grayscale detection
• replacing np.in1d with np.isin

In addition, datetime.utcnow() is also deprecated since Python 3.12. So this has been replaced with datetime.datetime.now(datetime.timezone.utc). The alternative would be datetime.datetime.now(datetime.UTC) but this alias has only been added in version 3.11.

Despite the above changes, the tests continued to fail on CI. It turns out that on conda-forge the build package is called python-build. So I've updated this in the environment.yml as well.

Summary by CodeRabbit

• New Features

  • Updated environment configuration to allow any version of numpy, enhancing compatibility with newer features.
  • Improved timestamp generation with explicit UTC timezone for better consistency across applications.

• Bug Fixes

  • Enhanced grayscale detection logic for improved reliability in image processing.

• Tests

  • Replaced np.in1d with np.isin in test cases for better clarity and performance.

[coderabbitai]

Walkthrough

This pull request modifies the environment.yml file to support any version of NumPy, addressing compatibility issues with newer releases. It also updates the sleap_io/io/labelstudio.py file to improve timestamp handling by ensuring UTC representation. The sleap_io/io/slp.py file changes JSON encoding from strings to bytes, while the sleap_io/io/video.py file enhances grayscale detection logic. Lastly, a test assertion in tests/io/test_nwb.py is updated for improved clarity and efficiency.

Changes

Files	Change Summary
environment.yml	Removed version constraint for numpy, renamed build to python-build.
sleap_io/io/labelstudio.py, sleap_io/io/video.py	Updated timestamp handling to UTC, reorganized imports, improved grayscale detection logic.
sleap_io/io/slp.py	Changed JSON encoding from np.string_ to np.bytes_ in multiple functions.
tests/io/test_nwb.py	Replaced np.in1d with np.isin in a test assertion for better clarity and efficiency.

Assessment against linked issues

Objective	Addressed	Explanation
Support for NumPy > 2.0.0 (#114)	✅
Resolve deprecation warnings related to NumPy (#114)	✅

🐰 In the meadow, we hop with glee,
New NumPy versions, wild and free!
With timestamps bright, in UTC's embrace,
Our code now dances, a joyful race!
From strings to bytes, we cheer and play,
Hooray for changes, hip-hip-hooray! 🌼

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Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 2bc3d52 and bd9293d.

Files selected for processing (5)

• environment.yml (2 hunks)
• sleap_io/io/labelstudio.py (2 hunks)
• sleap_io/io/slp.py (4 hunks)
• sleap_io/io/video.py (1 hunks)
• tests/io/test_nwb.py (1 hunks)

Files skipped from review due to trivial changes (1)

• tests/io/test_nwb.py

Additional comments not posted (9)

environment.yml (2)

17-17: Verify the impact of removing the numpy version constraint.

Removing the version constraint for numpy may introduce compatibility issues if the codebase relies on specific features or behavior of numpy versions below 2.0.0.

To verify the impact, run the test suite and manually test the critical functionalities of the application with the latest version of numpy installed.

---

27-27: LGTM!

Renaming the build package to python-build matches the package name on conda-forge.

sleap_io/io/labelstudio.py (1)

197-202: LGTM!

The change from datetime.datetime.utcnow() to datetime.datetime.now(datetime.timezone.utc) enhances the precision of the timestamps by explicitly setting the timezone to UTC and addresses the deprecation in Python 3.12.

sleap_io/io/video.py (1)

151-151: LGTM!

The change from using a boolean expression to np.array_equal improves the clarity and reliability of the grayscale detection logic by explicitly comparing the first and last channels of the image.

sleap_io/io/slp.py (5)

437-437: Verify compatibility impact of changing JSON encoding from np.string_ to np.bytes_.

This code segment changes the data type used for encoding JSON strings from np.string_ to np.bytes_ in the write_videos function.

Altering how the JSON data is represented and stored can potentially affect compatibility with components that read this data.

Ensure that all components that consume this JSON data can handle the np.bytes_ encoding. Verify there are no issues reading or deserializing the data.

---

469-469: Verify compatibility impact of changing JSON encoding to np.bytes_.

Similar to the previous code segment, this change in the write_tracks function also switches the JSON encoding to use np.bytes_.

Please refer to the compatibility verification requested in the previous comment. Ensure there are no issues with other components consuming this data.

---

520-520: Verify compatibility impact of changing JSON encoding to np.bytes_.

Once again, this code segment in the write_suggestions function changes the JSON encoding to use np.bytes_, similar to the previous segments.

As mentioned earlier, please verify compatibility with all components that consume this JSON data to ensure there are no issues caused by this change.

---

746-746: Verify compatibility impact of changing JSON encoding to np.bytes_.

This code segment in the write_metadata function also switches the JSON encoding to use np.bytes_, consistent with the previous changes.

As requested earlier, please thoroughly verify compatibility with all components that consume this JSON data to ensure there are no issues caused by this change in encoding.

---

Line range hint 1-1000: Changes look good, pending compatibility verification.

The code changes in this file are focused on transitioning from using np.string_ to np.bytes_ for JSON serialization across multiple functions, as mentioned in the summary.

The changes are straightforward and consistently applied. No other issues are observed.

However, as highlighted in the previous comments, it's crucial to verify compatibility with all components that consume this JSON data serialized with np.bytes_ encoding. Please thoroughly test and confirm there are no issues caused by this change.

If compatibility is confirmed, these changes can be approved.

---

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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 96.01%. Comparing base (e002927) to head (bd9293d).
Report is 2 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #115   +/-   ##
=======================================
  Coverage   96.01%   96.01%           
=======================================
  Files          17       17           
  Lines        2035     2035           
=======================================
  Hits         1954     1954           
  Misses         81       81           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[talmo]

LGTM! Thanks @lochhh!!

For future reference: I also cloned this and tested it with numpy==1.26.4 and the changes here still pass all the tests, so we should be safe in terms of backwards compatibility.

Now let's just hope that all of our deps are happy with numpy 2 as well 😄