Upgrade python to 3.11 #80
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WalkthroughThe changes revolve around elevating the Python version from 3.9 to 3.11 across multiple files in the Changes
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #80 +/- ##
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Coverage 75.78% 75.78%
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Files 13 13
Lines 1396 1396
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Hits 1058 1058
Misses 338 338 ☔ View full report in Codecov by Sentry. |
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Actionable comments posted: 0
Out of diff range and nitpick comments (1)
sleap_roots/__init__.py (1)
Line range hint
14-27: Remove or use the unused imports to clean up the code.- import sleap_roots.trait_pipelines - from sleap_roots.trait_pipelines import ( - DicotPipeline, - TraitDef, - YoungerMonocotPipeline, - OlderMonocotPipeline, - MultipleDicotPipeline, - ) - from sleap_roots.series import ( - Series, - find_all_h5_paths, - find_all_slp_paths, - load_series_from_h5s, - load_series_from_slps, - )
Review Details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (4)
- README.md (1 hunks)
- environment.yml (1 hunks)
- pyproject.toml (1 hunks)
- sleap_roots/init.py (1 hunks)
Files skipped from review due to trivial changes (1)
- pyproject.toml
Additional Context Used
LanguageTool (2)
README.md (2)
Near line 24: Unpaired symbol: ‘]’ seems to be missing
Context: ...ntation per pipeline is available here: [sleap-roots HackMD](https://hackmd.io/DM...
Near line 141: Possible missing comma found.
Context: ...oks`. To use them, activate your conda environment which includes JupyterLab (recommended)...
Ruff (11)
sleap_roots/__init__.py (11)
14-14:
sleap_roots.trait_pipelinesimported but unused; consider removing, adding to__all__, or using a redundant alias
16-16:
sleap_roots.trait_pipelines.DicotPipelineimported but unused; consider removing, adding to__all__, or using a redundant alias
17-17:
sleap_roots.trait_pipelines.TraitDefimported but unused; consider removing, adding to__all__, or using a redundant alias
18-18:
sleap_roots.trait_pipelines.YoungerMonocotPipelineimported but unused; consider removing, adding to__all__, or using a redundant alias
19-19:
sleap_roots.trait_pipelines.OlderMonocotPipelineimported but unused; consider removing, adding to__all__, or using a redundant alias
20-20:
sleap_roots.trait_pipelines.MultipleDicotPipelineimported but unused; consider removing, adding to__all__, or using a redundant alias
23-23:
sleap_roots.series.Seriesimported but unused; consider removing, adding to__all__, or using a redundant alias
24-24:
sleap_roots.series.find_all_h5_pathsimported but unused; consider removing, adding to__all__, or using a redundant alias
25-25:
sleap_roots.series.find_all_slp_pathsimported but unused; consider removing, adding to__all__, or using a redundant alias
26-26:
sleap_roots.series.load_series_from_h5simported but unused; consider removing, adding to__all__, or using a redundant alias
27-27:
sleap_roots.series.load_series_from_slpsimported but unused; consider removing, adding to__all__, or using a redundant alias
Additional comments not posted (3)
environment.yml (1)
8-8: Update to Python 3.11 approved.sleap_roots/__init__.py (1)
32-32: Version update to "0.1.0" approved.README.md (1)
17-17: Update to Python 3.11 in installation instructions approved.
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Actionable comments posted: 0
Review Details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (2)
- .github/workflows/build.yml (1 hunks)
- .github/workflows/ci.yml (3 hunks)
Files skipped from review due to trivial changes (1)
- .github/workflows/build.yml
Additional comments not posted (5)
.github/workflows/ci.yml (5)
41-41: Updated Python version to 3.11 in the lint job setup.Verification successful
Updated Python version to 3.11 in the lint job setup. No known incompatibilities with Python 3.11 were found in the Python files of the repository. It is recommended to perform further checks or tests to ensure full compatibility with all dependencies.
Scripts Executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify all dependencies are compatible with Python 3.11. # Test: Check for any known incompatibilities in the dependencies. rg --type py 'import' --exec cat {} | grep -E 'known_incompatibilities'Length of output: 480
Script:
#!/bin/bash # Description: Verify all dependencies are compatible with Python 3.11 by checking for any known incompatibilities. # Find Python files and check for the string 'known_incompatibilities' rg --type py 'import' | xargs grep -E 'known_incompatibilities'Length of output: 28944
Script:
#!/bin/bash # Description: Verify all dependencies are compatible with Python 3.11 by checking for any known incompatibilities. # Directly search for the string 'known_incompatibilities' within Python files rg --type py 'known_incompatibilities'Length of output: 38
61-61: Updated Python version to 3.11 in the test matrix.Verification successful
The test matrix in the CI configuration covers the following operating systems:
- Ubuntu 22.04
- Windows 2022
This setup should generally suffice for broad compatibility testing across different platforms. The Python version has been correctly updated to 3.11 as intended.
Scripts Executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the test matrix covers all necessary operating systems. # Test: Check the test matrix configuration. cat .github/workflows/ci.yml | grep 'matrix:'Length of output: 59
Script:
#!/bin/bash # Description: Extract the matrix configuration details from the ci.yml file. # Extract the matrix configuration section to check the operating systems. sed -n '/matrix:/,/^ [^ ]/p' .github/workflows/ci.ymlLength of output: 205
94-94: Updated conditional execution for tests without coverage to check for Ubuntu OS and Python 3.11.Verification successful
Several conditions in the GitHub Actions workflow are tailored to handle test executions differently based on the OS and Python version:
- General tests are excluded for Ubuntu with Python 3.11.
- Tests with coverage and coverage uploads are specifically performed for this combination.
This setup ensures that coverage-related tasks are handled appropriately for specific environments, confirming the logic behind the conditional execution as intended.
Scripts Executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the condition's logic is correct. # Test: Check the conditional execution logic. cat .github/workflows/ci.yml | grep 'if:'Length of output: 272
Script:
#!/bin/bash # Description: Examine the context of the conditional statements in the ci.yml file. # Extract the sections of the file around each 'if:' condition to understand their purpose. grep -C 3 'if:' .github/workflows/ci.ymlLength of output: 696
100-100: Updated conditional execution for tests with coverage to check for Ubuntu OS and Python 3.11.
107-107: Updated conditional execution for uploading coverage to check for Ubuntu OS and Python 3.11.Verification successful
Updated conditional execution for uploading coverage to check for Ubuntu OS and Python 3.11 is correctly implemented and serves its intended purpose without conflicts or redundancy.
- The condition to negate the test with coverage ensures that standard tests run for configurations other than Ubuntu OS with Python 3.11.
- Tests with coverage and subsequent uploading of coverage are specifically targeted for Ubuntu OS with Python 3.11, aligning with the workflow's requirements.
Scripts Executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the condition's logic is correct. # Test: Check the conditional execution logic. cat .github/workflows/ci.yml | grep 'if:'Length of output: 272
Script:
#!/bin/bash # Description: Extract the full context of each conditional statement to understand their purpose. # Extract lines around each 'if:' condition to get more context. grep -C 3 'if:' .github/workflows/ci.ymlLength of output: 696
Summary by CodeRabbit
New Features
Documentation
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