chore: unpin pybedlite dependency #98
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WalkthroughThe changes in the pull request primarily involve updates to the No new dependencies have been added or removed, and the existing development dependencies remain unchanged. The overall structure and formatting of the The build system requirements specify that 📜 Recent review detailsConfiguration used: CodeRabbit UI ⛔ Files ignored due to path filters (1)
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🧹 Outside diff range and nitpick comments (1)
pyproject.toml (1)
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38-45: Consider consistent dependency pinning strategy.Other dependencies mix pinned (fgpyo=0.7.1) and unpinned (^0.22.1, ^4.1.0) versions. Establish consistent policy.
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pyproject.toml (2)
Line range hint 3-3: Version bump looks appropriate.
2.2.0 version increment aligns with dependency changes.
38-38: Verify pybedlite compatibility across minor versions.
Unpinning to ^1.0.0 allows minor updates. Need to ensure backward compatibility.
✅ Verification successful
Unpinning pybedlite to ^1.0.0 is safe.
Limited usage shows only stable Interval and OverlapDetector imports. Version history shows steady progression (0.0.1 -> 1.0.0) with recent 1.0.0 release, indicating API stability.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check available pybedlite versions and their release dates
curl -s https://pypi.org/pypi/pybedlite/json | jq -r '.releases | keys[] as $k | "\($k)\t\(.[$k][0].upload_time)"' | sort -V
# Check for any breaking changes in pybedlite changelog
gh api repos/fulcrumgenomics/pybedlite/releases | jq -r '.[].body' | grep -i "break"
Length of output: 315
Script:
#!/bin/bash
# Check for usage of pybedlite in the codebase
rg "import.*pybedlite|from.*pybedlite" -l
# Check specific pybedlite function/class usage
rg "pybedlite\." -A 2
# Look for any test files related to pybedlite
fd "test.*\.py" --exec grep -l "pybedlite"
Length of output: 2349
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #98 +/- ##
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Coverage ? 96.66%
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Files ? 26
Lines ? 1708
Branches ? 189
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Hits ? 1651
Misses ? 31
Partials ? 26 ☔ View full report in Codecov by Sentry. |
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For post-v1 dependencies that strictly follow SemVer, I go one step further and caret pin to the minor version. So for pybedlite, I'd do |
Similar to #97 , this PR unpins the dependency on pybedlite. I am opening two separate PRs in case there is an argument for one dependency to be pinned but not the other.
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Similar to #97 , this PR unpins the dependency on pybedlite.
I am opening two separate PRs in case there is an argument for one dependency to be pinned but not the other.