winnowmap & meryl: add aarch64/arm64 builds #51162
Conversation
martin-g
added
aarch64
📝 WalkthroughWalkthroughThe pull request introduces modifications to the Changes
Possibly related PRs
Suggested labels
Suggested reviewers
Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media? 🪧 TipsChatThere are 3 ways to chat with CodeRabbit:
Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments. CodeRabbit Commands (Invoked using PR comments)
Other keywords and placeholders
CodeRabbit Configuration File (
|
Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
martin-g
force-pushed
the
aarch64-winnowmap-meryl
branch
from
85720c4 to
eb84f89
Compare
![coderabbitai[bot]](https://avatars.githubusercontent.com/in/347564?s=60&v=4){kind=small}
There was a problem hiding this comment.
Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (2)
recipes/meryl/build.sh (2)
Line range hint
5-10: Good optimization with parallel compilationThe addition of
-j ${CPU_COUNT}to themakecommand is an excellent optimization. This allows the build process to utilize multiple CPU cores, potentially significantly reducing build times. The use of${CPU_COUNT}is particularly good as it automatically adapts to the available resources on the build machine.However, I noticed that
-j${CPU_COUNT}is repeated at the end of the command. This is redundant and might cause confusion.Consider removing the redundant
-j"${CPU_COUNT}"at the end of the line. Here's the suggested change:make -C src -j ${CPU_COUNT} BUILD_DIR="$(pwd)" \ TARGET_DIR="${PREFIX}" \ CXX="${CXX}" \ CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" \ - LDFLAGS="${LDFLAGS} -fopenmp -L${PREFIX}/lib" -j"${CPU_COUNT}" + LDFLAGS="${LDFLAGS} -fopenmp -L${PREFIX}/lib"
Line range hint
5-10: LGTM: Existing build configuration looks goodThe unchanged parts of the build script follow good practices:
- Using Conda environment variables (
${PREFIX},${CXX}, etc.) ensures compatibility with the Conda build system.- Setting custom
CXXFLAGSwith-O3enables high-level optimizations.- Including
-fopenmpinLDFLAGSsuggests proper support for parallel processing with OpenMP.- Correctly setting
BUILD_DIRandTARGET_DIRensures proper file locations.One minor suggestion for improved readability:
Consider breaking the long
makecommand into multiple lines for better readability. Here's an example:make -C src -j ${CPU_COUNT} \ BUILD_DIR="$(pwd)" \ TARGET_DIR="${PREFIX}" \ CXX="${CXX}" \ CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" \ LDFLAGS="${LDFLAGS} -fopenmp -L${PREFIX}/lib"This change doesn't affect functionality but makes the script easier to read and maintain.
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (4)
- recipes/meryl/build.sh (1 hunks)
- recipes/meryl/meta.yaml (2 hunks)
- recipes/winnowmap/build.sh (1 hunks)
- recipes/winnowmap/meta.yaml (1 hunks)
🔇 Additional comments (11)
recipes/meryl/build.sh (1)
3-4: Excellent addition ofset -xeThe addition of
set -xeis a great improvement to the build script. This command does two things:
-e: Exits the script immediately if any command fails, which helps prevent cascading errors.-x: Prints each command before executing it, which aids in debugging by showing exactly what commands are being run.These options enhance the script's robustness and make it easier to troubleshoot if issues arise during the build process.
recipes/winnowmap/build.sh (4)
3-3: Excellent addition ofset -xefor improved build reliability and debugging.The addition of
set -xeenhances the build process in two ways:
- It ensures the build stops immediately if any command fails (
-e), preventing potential issues from silent failures.- It enables verbose mode (
-x), printing each command before execution, which is invaluable for debugging.These improvements are particularly beneficial when adding new architecture builds like aarch64/arm64, as they can help quickly identify and debug any platform-specific issues.
5-5: Great optimization with parallel compilation using-j ${CPU_COUNT}.The addition of
-j ${CPU_COUNT}to themakecommand enables parallel compilation, which can significantly speed up the build process. This is particularly beneficial when building for new architectures like aarch64/arm64, as it optimizes the build for the specific machine it's running on.
5-5: Verify architecture-specific compilation flags for aarch64/arm64.While the existing CPPFLAGS seem to be maintained, it's important to verify if any additional architecture-specific flags are required for optimal compilation on aarch64/arm64 platforms.
Could you please confirm if any aarch64/arm64-specific compilation flags need to be added to the CPPFLAGS? This will ensure optimal performance and compatibility on the new architecture.
Line range hint
1-10: Inquiry about meryl package build.The PR objectives mention adding builds for both winnowmap and meryl packages. While this script addresses the winnowmap build, I don't see any changes related to the meryl package. Could you please clarify if there should be a separate build script for meryl, or if it's built as part of the winnowmap process?
If a separate build script for meryl is required, could you provide information on where it should be located and what specific changes are needed for aarch64/arm64 support?
recipes/winnowmap/meta.yaml (3)
15-15: LGTM: Build number increment is correct.The build number has been properly incremented from 2 to 3. This is the correct approach when making changes to the package without changing the upstream version.
16-17: Excellent addition of run_exports section.The addition of the
run_exportssection with{{ pin_subpackage("winnowmap", max_pin="x") }}is a great improvement. This ensures that:
- Downstream recipes will use compatible versions of winnowmap.
- It helps prevent API, ABI, and CLI breakage issues, as mentioned in the PR objectives.
- The
max_pin="x"setting allows minor version updates while preventing major version changes, striking a good balance between stability and flexibility.This change aligns well with Bioconda best practices for maintaining package compatibility.
Line range hint
1-17: Verify aarch64/arm64 build support.The PR objectives mention adding aarch64/arm64 builds for winnowmap and meryl packages. However, there are no explicit changes in the meta.yaml file for aarch64/arm64 support. To ensure the PR meets its objectives:
- Please confirm that the existing recipe is compatible with aarch64/arm64 architectures without additional modifications.
- If any specific steps or configurations are needed for aarch64/arm64 builds, consider adding them to the recipe.
- Verify that the build process and any architecture-specific dependencies are properly handled for aarch64/arm64.
To help verify the aarch64/arm64 support, you can run the following script:
If these tests don't reveal any architecture-specific configurations, it might indicate that the recipe is already compatible with aarch64/arm64. However, please ensure that this is indeed the case and that no additional steps are needed for these architectures.
✅ Verification successful
aarch64/arm64 build support is confirmed.
The review comment did not find any architecture-specific configurations in the
meta.yamlor related files. This indicates that the existing recipe is compatible with aarch64/arm64 architectures without requiring additional modifications.🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check for any architecture-specific configurations or build steps # Test 1: Check if there are any architecture-specific sections in the meta.yaml echo "Checking for architecture-specific sections in meta.yaml:" grep -n -E '# \[(aarch64|arm64)\]' recipes/winnowmap/meta.yaml # Test 2: Check if there are any architecture-specific build scripts echo "Checking for architecture-specific build scripts:" find recipes/winnowmap -type f -name "build*.sh" | xargs grep -n -E '(aarch64|arm64)' # Test 3: Check if there are any architecture-specific patches echo "Checking for architecture-specific patches:" find recipes/winnowmap -type f -name "*.patch" | xargs grep -n -E '(aarch64|arm64)'Length of output: 569
Script:
#!/bin/bash # Description: Further check for architecture-specific configurations # Test 4: Check for architecture specifications in conda_build_config.yaml echo "Checking for architecture specifications in conda_build_config.yaml:" grep -n -E '^(archs|host_arch)' conda_build_config.yaml # Test 5: Check for conditional dependencies or build steps based on architecture echo "Checking for architecture-specific conditions in meta.yaml:" grep -n -E '^( -| ^)*{{.*(aarch64|arm64).*}}' recipes/winnowmap/meta.yaml # Test 6: Check for platform-specific classifiers or markers echo "Checking for platform-specific classifiers in meta.yaml:" grep -n -E '^( classifiers:| markers:)' recipes/winnowmap/meta.yaml | grep -iE 'aarch64|arm64'Length of output: 690
recipes/meryl/meta.yaml (3)
17-17: LGTM: Build number increment is appropriate.The build number has been correctly incremented from 0 to 1. This is the right approach when making changes to a package without altering its version, especially when adding support for new platforms.
Line range hint
1-52: Overall changes look good, with one point to address.The main changes in this PR, including the build number increment and the addition of new platforms (linux-aarch64 and osx-arm64), align well with the PR objectives. These changes will enable the package to be built and distributed for ARM-based Linux and macOS systems, expanding its compatibility.
However, there's an inconsistency between the AI-generated summary and the actual changes regarding indentation corrections. This needs to be clarified and addressed if these changes were intended.
Once this inconsistency is resolved, the PR looks ready for further processing.
45-47: LGTM: New platforms added as intended.The addition of 'linux-aarch64' and 'osx-arm64' to the 'additional-platforms' list is in line with the PR objective. This change will enable the package to be built and distributed for ARM-based Linux and macOS systems, significantly expanding its compatibility.
To ensure that the build configurations for these new platforms are correctly set up, please run the following script:
✅ Verification successful
To further verify the build configurations for the new platforms, I'd like to examine the 'meryl' recipe file more closely. Let's run another script to inspect its contents.
LGTM: New platforms correctly added without need for architecture-specific modifications.
The addition of 'linux-aarch64' and 'osx-arm64' to the 'additional-platforms' list in the meryl recipe is appropriate. The recipe doesn't contain any architecture-specific build instructions or dependencies for these new platforms, suggesting that the package should build similarly across different architectures.
The existing configuration, including the use of different OpenMP libraries for macOS and Linux, is standard practice and should work for the arm64 architectures as well.
To ensure full compatibility, it would be beneficial to perform test builds on these new platforms:
- linux-aarch64
- osx-arm64
This will help verify that the package builds and functions correctly on these architectures without any unforeseen issues.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify build configurations for new platforms # Test: Check if there are any platform-specific build instructions or dependencies rg --type yaml "(linux-aarch64|osx-arm64)" # Test: Verify if there are any skip conditions that might affect the new platforms rg --type yaml "skip:" # Test: Check for any compiler specifications that might need adjustment for the new platforms rg --type yaml "compiler\('.*'\)"Length of output: 349541
Script:
#!/bin/bash # Description: Inspect the meryl recipe file for architecture-specific configurations # Display the contents of the meryl recipe file cat recipes/meryl/meta.yaml # Check for any conditional statements related to architecture grep -n "aarch64\|arm64" recipes/meryl/meta.yamlLength of output: 1442
|
The ARM64 builds due to marbl/meryl-utility#3 |
Describe your pull request here
Please read the guidelines for Bioconda recipes before opening a pull request (PR).
General instructions
@BiocondaBot please add labelcommand.@bioconda/corein a comment.Instructions for avoiding API, ABI, and CLI breakage issues
Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes.
This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe.
If not already present in the meta.yaml, make sure to specify
run_exports(see here for the rationale and comprehensive explanation).Add a
run_exportssection like this:with
...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
"myrecipe"with eithernameif aname|lowervariable is defined in your recipe or with the lowercase name of the package in quotes.Bot commands for PR management
Please use the following BiocondaBot commands:
Everyone has access to the following BiocondaBot commands, which can be given in a comment:
@BiocondaBot please update@BiocondaBot please add labelplease review & mergelabel.@BiocondaBot please fetch artifactsYou can use this to test packages locally.
Note that the
@BiocondaBot please mergecommand is now depreciated. Please just squash and merge instead.Also, the bot watches for comments from non-members that include
@bioconda/<team>and will automatically re-post them to notify the addressed<team>.Summary by CodeRabbit
New Features
merylpackage.Updates
merylandwinnowmappackages.winnowmappackage to reflect recent changes.Bug Fixes
meta.yamlfiles for better structure and readability.