Update SeqKit to v2.9.0 #51860
Update SeqKit to v2.9.0 #51860
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📝 Walkthrough📝 WalkthroughWalkthroughThe pull request involves modifications to the Possibly related PRs
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📜 Recent review detailsConfiguration used: CodeRabbit UI 📒 Files selected for processing (1)
🧰 Additional context used🪛 yamllintrecipes/seqkit/meta.yaml[error] 1-1: syntax error: found character '%' that cannot start any token (syntax) 🔇 Additional comments (3)recipes/seqkit/meta.yaml (3)
The version update to 2.9.0 matches the latest official release from November 1, 2024, which includes important fixes for sequence ID parsing and improvements to various SeqKit commands. 🧰 Tools🪛 yamllint[error] 1-1: syntax error: found character '%' that cannot start any token (syntax)
Resetting the build number to 0 is correct when updating to a new version.
MD5 checksums do not match the official release artifacts. Based on the previous verification results, the MD5 checksums in the recipe do not match the official release artifacts:
Let's verify the current checksums against the official release: #!/bin/bash
# Description: Verify MD5 checksums match the official release artifacts
# Expected: MD5 checksums should match the values in meta.yaml
VERSION="2.9.0"
TEMP_DIR=$(mktemp -d)
cd "$TEMP_DIR" || exit 1
echo "Verifying checksums for SeqKit v${VERSION}..."
# Download and verify each platform artifact
for platform in darwin_arm64 linux_amd64 linux_arm64; do
echo -e "\nPlatform: ${platform}"
curl -sL "https://github.com/shenwei356/seqkit/releases/download/v${VERSION}/seqkit_${platform}.tar.gz" -o "${platform}.tar.gz"
md5sum "${platform}.tar.gz"
done
cd - || exit 1
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/seqkit/meta.yaml (1)
1-24: Consider testing backward compatibility.SeqKit v2.9.0 includes several important fixes that affect sequence parsing and handling:
- Modified sequence ID parsing behavior
- Changes to
-G/--non-greedyoption inlocatecommand- Updates to negative region handling in
grep/subseq- New
sum_ncolumn instatsoutputThese changes might affect existing pipelines that depend on the specific behavior of these features.
Consider:
- Testing the package with existing bioinformatics pipelines
- Documenting any behavior changes in the package metadata
- Adding example commands in the test section for the modified features
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
recipes/seqkit/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/seqkit/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (2)
recipes/seqkit/meta.yaml (2)
1-1: LGTM: Version update matches the release.
The version bump to 2.9.0 correctly reflects the latest SeqKit release from November 1, 2024.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
21-21: LGTM: Build number reset is correct.
Resetting the build number to 0 is appropriate when updating to a new version.
recipes/seqkit/meta.yaml
Outdated
| md5: c83d82188fbd83da765b5ae9939f5079 # [osx] | ||
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||
| url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_darwin_arm64.tar.gz # [arm64] | ||
| md5: 0b2716f39c3974a5c3e310bcbd4076eb # [arm64] | ||
| md5: c6ddaa62d73280b645215143087dd1db # [arm64] | ||
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||
| url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_linux_amd64.tar.gz # [linux] | ||
| md5: 67220b508f3f81c2c8697e6534eed440 # [linux] | ||
| md5: 5b5c5ba2796d45f42b2e61fde4d79821 # [linux] | ||
|
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||
| url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_linux_arm64.tar.gz # [aarch64] | ||
| md5: b83b021850c9447cfc8e0d5751b7be99 # [aarch64] | ||
| md5: 5cbca93de57c11d1f70d1e713a44be5a # [aarch64] |
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💡 Codebase verification
MD5 checksums do not match the official release artifacts
The verification shows mismatches between the expected and actual MD5 checksums for all platforms:
- darwin_arm64: expected
c6ddaa62d73280b645215143087dd1db, gotcf1b7c4b74664f04d3cc361e9c5370a1 - linux_amd64: expected
5b5c5ba2796d45f42b2e61fde4d79821, got83e359c186dee6b49cd4df362d0b6d5a - linux_arm64: expected
5cbca93de57c11d1f70d1e713a44be5a, got7a81adcd79553e10552456060c2b17ba
Please update the MD5 checksums in meta.yaml to match the current release artifacts.
🔗 Analysis chain
Verify checksums against official release artifacts.
Let's verify the MD5 checksums match the official SeqKit v2.9.0 release artifacts.
Let me try a different approach using curl instead of wget since it seems to be available in the sandbox environment.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify MD5 checksums match the official release artifacts
# Expected: MD5 checksums should match the values in meta.yaml
# Create a temporary directory for downloads
TEMP_DIR=$(mktemp -d)
cd "$TEMP_DIR" || exit 1
# Download and verify each platform artifact
VERSION="2.9.0"
PLATFORMS=("darwin_amd64" "darwin_arm64" "linux_amd64" "linux_arm64")
for platform in "${PLATFORMS[@]}"; do
echo "Verifying $platform..."
wget -q "https://github.com/shenwei356/seqkit/releases/download/v${VERSION}/seqkit_${platform}.tar.gz"
md5sum "seqkit_${platform}.tar.gz"
done
cd - || exit 1
rm -rf "$TEMP_DIR"
Length of output: 1669
Script:
#!/bin/bash
# Description: Verify MD5 checksums match the official release artifacts using curl
# Expected: MD5 checksums should match the values in meta.yaml
# Create a temporary directory for downloads
TEMP_DIR=$(mktemp -d)
cd "$TEMP_DIR" || exit 1
# Download and verify each platform artifact
VERSION="2.9.0"
echo "Verifying darwin_arm64..."
curl -sL "https://github.com/shenwei356/seqkit/releases/download/v${VERSION}/seqkit_darwin_arm64.tar.gz" -o darwin_arm64.tar.gz
echo "c6ddaa62d73280b645215143087dd1db darwin_arm64.tar.gz (expected)"
md5sum darwin_arm64.tar.gz
echo -e "\nVerifying linux_amd64..."
curl -sL "https://github.com/shenwei356/seqkit/releases/download/v${VERSION}/seqkit_linux_amd64.tar.gz" -o linux_amd64.tar.gz
echo "5b5c5ba2796d45f42b2e61fde4d79821 linux_amd64.tar.gz (expected)"
md5sum linux_amd64.tar.gz
echo -e "\nVerifying linux_arm64..."
curl -sL "https://github.com/shenwei356/seqkit/releases/download/v${VERSION}/seqkit_linux_arm64.tar.gz" -o linux_arm64.tar.gz
echo "5cbca93de57c11d1f70d1e713a44be5a linux_arm64.tar.gz (expected)"
md5sum linux_arm64.tar.gz
cd - || exit 1
rm -rf "$TEMP_DIR"
Length of output: 1353
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No useful information in the |
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shenwei356
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seqkit-2.9.0
branch
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my bad, thank you @bgruening :) |
Describe your pull request here
Changes
seqkit:seqkit locate:-G/--non-greedyfor tandem repeats, e.g., ATTCGATTCGATTCG (ATTCGx3).seqkit grep/subseq:seqkit stats:sum_nto count the number of ambiguous characters. #490Please read the guidelines for Bioconda recipes before opening a pull request (PR).
General instructions
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