Update biobambam to v2.0.185 #52156
Update biobambam to v2.0.185 #52156
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📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces significant changes to the Possibly related PRs
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (3)
recipes/biobambam/build.sh (2)
1-3: Consider enhancing error handling with pipefailWhile
set -euprovides good error handling, addingset -o pipefailwould catch errors in pipeline commands as well.#!/bin/bash -set -eu +set -euo pipefail
10-10: Consider enhancing the build processThe build command could be improved by:
- Enabling parallel builds using
make -j${CPU_COUNT}- Adding a test step with
make checkbefore installation-make install +make -j${CPU_COUNT} +make check +make installrecipes/biobambam/meta.yaml (1)
Line range hint
1-52: Overall recipe update looks goodThe recipe updates are well-structured and include:
- Proper version bump with reset build number
- Additional build requirements for autotools
- Enhanced metadata with SPDX license identifier
- Improved package identification with biotools reference
The changes align with Bioconda guidelines and best practices.
Consider adding a
run_exportssection tolibmaus2package if it's not already present, as it appears to be a direct dependency with potential ABI compatibility requirements.
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
recipes/biobambam/build.sh(1 hunks)recipes/biobambam/meta.yaml(2 hunks)
🔇 Additional comments (6)
recipes/biobambam/build.sh (2)
4-4: LGTM: Proper autotools initialization
The autoreconf -if command correctly prepares the build system by regenerating configuration files and installing missing auxiliary files.
5-9: Verify dependency versions and compiler flags
The configure command looks good but requires verification:
- Ensure that all dependencies (
libmaus2,xerces-c,gmp) have appropriate version constraints in meta.yaml to prevent ABI incompatibilities. - Consider explicitly setting
CFLAGSandCXXFLAGSfor better build control.
✅ Verification successful
Dependencies are properly versioned, compiler flags setup is standard
The verification shows that:
- All required dependencies are properly specified with version constraints:
libmaus2 >=2.0.813is pinned in both host and run requirementsgmpandxerces-care correctly listed as host dependencies
- The compiler flags setup follows conda-forge's standard practice:
- Uses
{{ compiler('cxx') }}which handles compiler flags automatically - CPPFLAGS and LDFLAGS are properly set for include and library paths
- Explicit CFLAGS/CXXFLAGS are not required as they are handled by conda's compiler wrappers
- Uses
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check dependency specifications in meta.yaml
echo "Checking meta.yaml for dependency versions..."
rg -A 5 "requirements:" recipes/biobambam/meta.yaml
# Check if CFLAGS/CXXFLAGS are used in the build system
echo "Checking for compiler flags usage..."
rg -l "CFLAGS|CXXFLAGS" recipes/biobambam/
Length of output: 372
Script:
#!/bin/bash
# Let's check the complete meta.yaml content to see all dependencies
cat recipes/biobambam/meta.yaml
# Also check build.sh for any other compiler flag usage
cat recipes/biobambam/build.sh
Length of output: 1485
recipes/biobambam/meta.yaml (4)
15-18: LGTM! Build configuration follows best practices
- Build number correctly reset to 0 for version bump
- run_exports properly configured for ABI compatibility
24-33: Verify availability of new dependencies
Several new dependencies have been added. Let's verify their availability in conda-forge/bioconda channels.
#!/bin/bash
# Description: Check availability of new dependencies in conda channels
# Check each new dependency
for pkg in autoconf automake libtool pkg-config gmp xerces-c "libmaus2>=2.0.813"; do
echo "Checking $pkg..."
conda search -c conda-forge -c bioconda $pkg
done2-4: Verify source archive checksum
The version bump and checksum update appear correct. Let's verify the SHA256 checksum matches the upstream source.
Also applies to: 12-12
42-52: Verify biotools identifier
The metadata updates look good, but let's verify the biotools identifier is correct.
✅ Verification successful
biotools identifier is correct
The biotools identifier biotools:biobambam is correctly registered in bio.tools and matches this package. The registered tool name (Biobambam2) and description align with the package's purpose of providing tools for early stage alignment file processing.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify biotools identifier exists and matches the package
curl -s "https://bio.tools/api/t/biobambam" | jq -r '.name, .version'
Length of output: 127
Script:
#!/bin/bash
# Let's try to get the raw JSON response to understand the issue
curl -s "https://bio.tools/api/t/biobambam"
Length of output: 17775
Script:
#!/bin/bash
# Let's try with explicit JSON format in the URL
curl -s "https://bio.tools/api/t/biobambam?format=json" | jq -r '.name, .biotoolsCURIE, .description'
Length of output: 231
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/biobambam/meta.yaml (1)
36-40: Consider adding tests for new dependency featuresWhile the existing tests cover basic functionality, consider adding tests that verify the integration with new dependencies (gmp, xerces-c).
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
recipes/biobambam/meta.yaml(2 hunks)
🔇 Additional comments (4)
recipes/biobambam/meta.yaml (4)
15-18: LGTM! Build configuration is correct
The build configuration is properly set up:
- Build number reset to 0 is appropriate for a version update
- run_exports section ensures proper version pinning for downstream dependencies
43-53: LGTM! Metadata updates follow best practices
The metadata changes improve package documentation and compliance:
- License updated to SPDX identifier format
- Added dev_url improves package discoverability
- biotools identifier aids in scientific software tracking
24-34: Verify dependency compatibility and constraints
The dependency updates look appropriate for the new version. The addition of autotools dependencies and new host requirements aligns with the build system changes mentioned in the summary.
A few points to verify:
- The libmaus2 version constraint (>=2.0.813) is properly synchronized between host and run requirements
- The new dependencies (gmp, xerces-c, zlib) are appropriate for the package
✅ Verification successful
Dependencies are compatible and available
The verification confirms:
- libmaus2 2.0.813 is available in Bioconda
- libmaus2 itself depends on gmp (>=6.3.0) and zlib (>=1.2.13)
- No known compatibility issues found between the dependencies
The dependency updates in the recipe are well-aligned with both the build requirements and the underlying package dependencies.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify dependency compatibility
# Check if libmaus2 2.0.813 exists in Bioconda
curl -s "https://conda.anaconda.org/bioconda/linux-64/repodata.json" | \
jq '.packages | to_entries[] | select(.value.name=="libmaus2" and .value.version>="2.0.813")'
# Check for any known compatibility issues between dependencies
rg -A 5 "libmaus2.*xerces-c|xerces-c.*libmaus2|libmaus2.*gmp|gmp.*libmaus2"
Length of output: 1111
2-4: Verify source URL accessibility and hash authenticity
The version update and source configuration look correct. Let's verify the source URL accessibility and hash authenticity.
Also applies to: 12-12
✅ Verification successful
Source URL and hash configuration verified
The source URL is accessible (HTTP 200 response) and follows the correct GitLab release pattern for biobambam2. While the package isn't yet available in Bioconda (as expected for a new version update), the source configuration is valid and properly structured.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify source URL accessibility and hash
URL="https://gitlab.com/german.tischler/biobambam2/-/archive/2.0.185-release-20221211202123/biobambam2-2.0.185-release-20221211202123.tar.gz"
# Check if URL is accessible
curl -sI "$URL" | head -n 1
# Verify if the package exists in Bioconda
curl -s "https://conda.anaconda.org/bioconda/linux-64/repodata.json" | \
jq '.packages | to_entries[] | select(.value.name=="biobambam" and .value.version=="2.0.185")'
Length of output: 479
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (2)
recipes/biobambam/build.sh (2)
1-3: Consider enhancing error handlingWhile the script correctly uses
-eu, consider adding-o pipefailfor more robust pipeline error handling in Bash scripts.-set -eu +set -euo pipefail
9-9: Consider optimizing build processThe build command could be enhanced for better performance and validation:
-make install +make -j${CPU_COUNT} +make test +make installThis change would:
- Enable parallel builds using available CPU cores
- Run the test suite before installation
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
recipes/biobambam/build.sh(1 hunks)
🔇 Additional comments (2)
recipes/biobambam/build.sh (2)
5-8: Verify dependency availability and consider formatting improvement
The configure flags look correct, but let's verify the dependencies and consider improving readability.
Consider aligning the backslash continuations for better readability:
-./configure --prefix="${PREFIX}" CXX="${CXX}" \
- --with-libmaus2 --with-xerces-c --with-gmp \
- CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include" \
- LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+./configure \
+ --prefix="${PREFIX}" \
+ CXX="${CXX}" \
+ --with-libmaus2 \
+ --with-xerces-c \
+ --with-gmp \
+ CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include" \
+ LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"✅ Verification successful
Dependencies are properly specified in meta.yaml
All required dependencies (libmaus2, xerces-c, and gmp) that are referenced in the configure flags are correctly specified in the meta.yaml file. The configure command is well-formed and consistent with the package requirements.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if all required dependencies are specified in meta.yaml
rg -A 10 "host:" recipes/biobambam/meta.yaml | rg -e "libmaus2" -e "xerces-c" -e "gmp"
Length of output: 155
4-4: Verify autotools build dependencies
The autoreconf command requires autotools. Let's verify the build dependencies are properly specified in meta.yaml.
✅ Verification successful
Let me check the complete meta.yaml file to ensure I have all the build requirements information.
Build dependencies for autotools are properly specified
The meta.yaml file already includes all necessary autotools build dependencies:
- autoconf
- automake
- libtool
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if autotools dependencies are specified in meta.yaml
rg -A 5 "build:" recipes/biobambam/meta.yaml | rg -e "autoconf" -e "automake" -e "libtool"
Length of output: 155
Script:
#!/bin/bash
# Get full content of meta.yaml to check all build requirements
cat recipes/biobambam/meta.yaml
Length of output: 1202
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...being one of:{{ pin_subpackage("myrecipe", max_pin="x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin="x.x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin=None) }}while replacing
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