Dependency management #118
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WalkthroughThe changes involve modifications to the Changes
Sequence Diagram(s)(No sequence diagrams generated as the changes do not involve new features or complex control flow modifications.) Possibly related PRs
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pyproject.toml (1)
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1-31: Summary of changes and potential impactThe removal of the "av" dependency from
pyproject.tomlis the only change in this file, which aligns with the PR objective. This focused change is good practice. However, it's crucial to ensure that this modification doesn't negatively impact the project's functionality.Consider the following:
- Test the project thoroughly to ensure that all video processing features still work as expected without "av".
- Update the project's documentation to reflect this change in dependencies.
- If "av" was used for specific features that
imageio-ffmpegdoesn't cover, ensure that alternative solutions are implemented and documented.To maintain the project's flexibility, you might want to consider making
imageio-ffmpegan optional dependency. This would allow users who don't need video processing capabilities to install a lighter version of your package. You can achieve this by movingimageio-ffmpegto an optional dependency group inpyproject.toml, like this:[project.optional-dependencies] video = ["imageio-ffmpeg>=0.5.0"]Then, update your package's code to gracefully handle cases where
imageio-ffmpegis not installed, perhaps by raising a more informative error message suggesting the user install the 'video' extra.
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pyproject.toml (1)
31-31: Verify the impact of removing the "av" dependencyThe removal of the "av" dependency aligns with the PR objective to drop it as a hard dependency due to bugs and compatibility issues. The retention of
imageio-ffmpeg>=0.5.0suggests that it might be used as an alternative for video processing tasks.To ensure a smooth transition, please consider the following:
- Confirm that
imageio-ffmpegprovides all the necessary functionality previously handled by "av".- Update any code that previously used "av" to now use
imageio-ffmpegor other alternatives.- Review and update documentation, README files, or inline comments that might reference "av".
- Consider adding a note in the project's changelog or release notes about this dependency change.
To help verify the impact of this change, you can run the following script:
This script will help identify any remaining references to "av" in the codebase that might need to be updated or removed.
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🧹 Outside diff range and nitpick comments (1)
tests/io/test_video_backends.py (1)
78-97: LGTM with minor suggestions: pyav backend test is well-implemented.The new test case for the pyav backend is well-structured and comprehensive. The try-except block is a good approach to handle the optional dependency. However, there are a couple of minor improvements we can make:
- The
avimport is flagged as unused, but it's indirectly used to check if the library is available. To make this more explicit and avoid the linter warning, you could useimportlib.util.find_spec:import importlib.util if importlib.util.find_spec("av") is not None: # Rest of the test code
- Replace
type(backend) == MediaVideowithisinstance(backend, MediaVideo)for a more idiomatic type check.Would you like me to implement these changes?
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80-80:
avimported but unused; consider usingimportlib.util.find_specto test for availability(F401)
85-85: Use
isandis notfor type comparisons, orisinstance()for isinstance checks(E721)
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- environment.yml (1 hunks)
- pyproject.toml (1 hunks)
- tests/io/test_video_backends.py (2 hunks)
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tests/io/test_video_backends.py
80-80:
avimported but unused; consider usingimportlib.util.find_specto test for availability(F401)
85-85: Use
isandis notfor type comparisons, orisinstance()for isinstance checks(E721)
🔇 Additional comments (9)
environment.yml (3)
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1-30: LGTM: Removal ofavdependencyThe
avdependency has been successfully removed from the environment file, which aligns with the PR objective to address ongoing bugs and limited platform compatibility issues.
19-19: LGTM: Version constraint update forndx-poseThe version constraint for
ndx-posehas been correctly updated tondx-pose<0.2.0, which aligns with the PR objective to pin it to a version lower than 0.2.0 until another pull request (#104) is merged.
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1-30: Verify removal of livecov development toolThe PR objectives mention the removal of the livecov development tool, which is not visible in this
environment.ymlfile. Could you please confirm if this change has been implemented in another file or if it needs to be addressed?To help verify this, you can run the following script:
This script will help identify any remaining references to livecov in the project, allowing us to ensure its complete removal as per the PR objectives.
✅ Verification successful
To address the issues encountered with the previous script, please run the following updated script to search for any references to
livecovin the project files:
To thoroughly verify the removal of the
livecovdevelopment tool, please run the following comprehensive search script:
Verification Successful:
livecovRemoval ConfirmedThe search across all project files did not find any references to
livecov, confirming its removal as per the PR objectives.🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Search for any references to livecov in the project files # Search for livecov in Python files echo "Searching for livecov in Python files:" rg --type python 'livecov' # Search for livecov in other configuration files echo "Searching for livecov in configuration files:" rg --type yaml --type toml --type json 'livecov' # Search for livecov in requirements files echo "Searching for livecov in requirements files:" rg 'livecov' *requirements*.txtLength of output: 486
Script:
#!/bin/bash # Description: Search for any references to livecov in the project files # Search for livecov in Python files using correct type specifier echo "Searching for livecov in Python files:" rg -t py 'livecov' # Search for livecov in YAML, TOML, and JSON configuration files echo "Searching for livecov in YAML, TOML, and JSON configuration files:" rg -t yaml -t toml -t json 'livecov' # Search for livecov in requirements files with flexible pattern echo "Searching for livecov in requirements files:" rg 'livecov' --glob '*requirements*.yml' --glob '*requirements*.yaml' --glob '*requirements*.txt'Length of output: 631
Script:
#!/bin/bash # Description: Comprehensive search for any references to livecov in the project files # Search for livecov in all files echo "Searching for 'livecov' in all files:" rg 'livecov' # Additionally, search for any mentions in markdown or documentation files echo "Searching for 'livecov' in documentation files:" rg -g '*.md' -g '*.rst' 'livecov' # Confirm if any requirements files exist before searching echo "Checking for existence of requirements files..." if ls *requirements*.txt 1> /dev/null 2>&1; then echo "Searching for 'livecov' in requirements files:" rg 'livecov' *requirements*.txt else echo "No requirements.txt files found to search." fiLength of output: 474
pyproject.toml (3)
31-31: Please clarify the removal of coverage and pytest configurations.The removal of sections related to coverage and pytest configuration aligns with the PR objective of removing the livecov development tool. However, it's important to ensure that this doesn't negatively impact the project's testing and coverage capabilities.
Could you please clarify:
- Have these configurations been moved to a different file?
- If not, are they no longer needed for the project?
To ensure that testing and coverage capabilities are maintained, please run:
#!/bin/bash # Description: Check for coverage and pytest configurations in other files # Test: Search for coverage configurations rg '\[coverage:' # Test: Search for pytest configurations rg '\[tool.pytest' # Test: Check if pytest and coverage are still mentioned in dev dependencies rg 'pytest|coverage' pyproject.tomlIf these configurations are still needed but have been moved, please update the PR description to reflect this change.
31-31: LGTM: Removal of av dependency.The removal of the
avdependency aligns with the PR objectives to improve stability and platform compatibility. The retention ofimageio-ffmpegsuggests that video processing capabilities are maintained.To ensure that all functionality previously dependent on
avhas been properly addressed, please run:If any results are found, please ensure that these occurrences have been properly addressed or updated.
27-27: LGTM: Version constraint added for ndx-pose.The addition of the version constraint
"ndx-pose<0.2.0"aligns with the PR objectives and helps maintain stability until PR #104 is merged.To ensure this constraint doesn't conflict with other dependencies, please run:
✅ Verification successful
Verified: ndx-pose version constraint is appropriate and no conflicts found.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check for potential conflicts with the ndx-pose version constraint # Test: Search for ndx-pose usage in Python files rg --type python 'ndx-pose' # Test: Check if any other dependency specifications mention ndx-pose rg 'ndx-pose' pyproject.toml setup.py setup.cfg requirements*.txtLength of output: 320
Script:
#!/bin/bash # Description: Check for potential conflicts with the ndx-pose version constraint # Test: Search for ndx-pose usage in Python files with correct type specifier rg --type py 'ndx-pose' # Test: Check if any other dependency specifications mention ndx-pose, ignoring missing files rg 'ndx-pose' pyproject.toml setup.py setup.cfg requirements*.txt || trueLength of output: 486
tests/io/test_video_backends.py (3)
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62-77: LGTM: New FFMPEG backend test looks good.The new test case for the FFMPEG backend is well-structured and comprehensive. It covers important aspects such as shape, slicing, and the
keep_openbehavior. The assertions are thorough and align with the existing test patterns.
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99-114: LGTM: opencv backend test remains consistent.The opencv backend test has been retained with minor adjustments to maintain consistency with the newly added tests for FFMPEG and pyav backends. The structure and assertions remain appropriate and comprehensive.
🧰 Tools
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80-80:
avimported but unused; consider usingimportlib.util.find_specto test for availability(F401)
85-85: Use
isandis notfor type comparisons, orisinstance()for isinstance checks(E721)
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62-114: Overall: Excellent improvements to video backend testing.The changes in this file significantly enhance the test coverage for various video backends, aligning well with the PR objectives of improving dependency management. The addition of FFMPEG and pyav backend tests, along with the retained opencv test, provides a more comprehensive suite for ensuring the correct behavior of different video backend options.
The use of a try-except block for the pyav test is a smart approach to handle the optional dependency, allowing the tests to run smoothly regardless of whether
avis installed or not. This change supports the PR's goal of removingavas a hard dependency while still maintaining test coverage when it's available.These improvements will contribute to better stability and compatibility of the project across different systems and configurations.
🧰 Tools
🪛 Ruff
80-80:
avimported but unused; consider usingimportlib.util.find_specto test for availability(F401)
85-85: Use
isandis notfor type comparisons, orisinstance()for isinstance checks(E721)
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #118 +/- ##
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+ Coverage 96.01% 96.05% +0.03%
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Files 17 15 -2
Lines 2035 2000 -35
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- Hits 1954 1921 -33
+ Misses 81 79 -2 ☔ View full report in Codecov by Sentry. |
avas a dependency since it's still a little buggy and doesn't have broad enough platform compatibility.ndx-pose< 0.2.0 until Adding support for more .nwb training data to SLEAP #104 is merged in.Summary by CodeRabbit
Summary by CodeRabbit
Chores
"av"dependency from the project configuration, streamlining the dependency list."ndx-pose"dependency to specify a version constraint of<0.2.0, ensuring compatibility.0.1.8to0.1.9, indicating a new release.Tests
test_mediavideofunction, enhancing coverage for the FFMPEG backend.