Update kmer-db to 2.2.2 #48760
Update kmer-db to 2.2.2 #48760
Conversation
📝 Walkthrough📝 Walkthrough📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces changes to the Changes
Possibly related PRs
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 (
|
![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 (3)
recipes/kmer-db/build.sh (2)
1-1: LGTM with a minor suggestion.The updated shebang line with
-euflags improves the script's robustness by exiting on errors and treating unset variables as errors. However, the-oflag is not a valid bash option on its own.Consider changing the shebang to
#!/bin/bash -euo pipefailto enable thepipefailoption, which causes a pipeline to return the exit status of the last command that exited with a non-zero status.
6-6: LGTM with a minor suggestion.The addition of
-j "${CPU_COUNT}"to the make command enables parallel compilation, which can significantly speed up the build process by utilizing all available CPU cores.Consider adding a fallback value for CPU_COUNT in case it's not set:
-make CC="${CXX}" -j "${CPU_COUNT}" +make CC="${CXX}" -j "${CPU_COUNT:-1}"This ensures the build will work even if CPU_COUNT is not set, defaulting to single-threaded compilation in such cases.
recipes/kmer-db/meta.yaml (1)
25-27: LGTM: Test command added. Consider enhancing the test.Adding a test command is a good practice. It ensures that the
kmer-dbcommand can be executed after installation.Suggestion: Consider enhancing the test to verify the version or a specific functionality of
kmer-db. For example:test: commands: - kmer-db --version - kmer-db --helpThis would provide stronger validation of the installed package.
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
- recipes/kmer-db/build.sh (1 hunks)
- recipes/kmer-db/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/kmer-db/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (9)
recipes/kmer-db/build.sh (3)
3-3: LGTM! Proper export of CFLAGS.The CFLAGS are now correctly exported, ensuring they're available to subprocesses. The -O3 flag enables high-level optimizations, and the include path is set correctly using the PREFIX variable.
4-4: LGTM! Proper export of LDFLAGS.The LDFLAGS are now correctly exported, ensuring they're available to subprocesses. The library path is set correctly using the PREFIX variable.
1-8: Overall, these changes significantly improve the build script.The modifications enhance the script's robustness, optimize compilation, and ensure proper environment variable handling. The parallel compilation feature is particularly beneficial for speeding up the build process on multi-core systems.
A few minor suggestions were made:
- Consider adding
-o pipefailto the shebang line for improved error handling in pipelines.- Add a fallback value for CPU_COUNT in the make command to ensure it works even if the variable is not set.
These changes align well with the PR objective of updating kmer-db to version 2.0.5, as they improve the build process for the new version.
recipes/kmer-db/meta.yaml (6)
6-6: LGTM: Improved package name consistency.Using a Jinja2 variable for the package name is a good practice. It ensures consistency throughout the recipe and makes future updates easier.
13-17: LGTM: Appropriate build configuration updates.The changes in the build section look good:
- Resetting the build number to 0 is correct for a new version.
- Adding the
run_exportssection with pinning is a good practice for maintaining ABI compatibility.These changes will help ensure smooth updates and compatibility for downstream packages.
29-35: LGTM: Improved metadata in the about section.The changes in the about section are all positive:
- The license has been updated to "GPL-3.0-or-later", which provides more clarity on the allowed GPL versions.
- The license family has been correctly updated to GPL3.
- Adding the dev_url is helpful for users who want to access the source code or contribute to the project.
These changes improve the package metadata and make it easier for users to understand the licensing and find the project repository.
1-3: Note on static analysis warning: False positive.The yamllint tool reported a syntax error for the '%' character at the beginning of the file. This is a false positive as the '%' character is used for Jinja2 templating in Conda recipes and is valid in this context. No action is required to address this warning.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
1-3: Verify the version number.The PR objective mentions updating to version 2.0.5, but the
versionvariable is set to 2.2.0. Please confirm if this is the correct version to be used.The use of Jinja2 variables for the package name and the updated SHA256 checksum look good.
To verify the correct version, please run the following script:
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
18-24: Verify the removal of zlib run requirement.The
zlibrun requirement has been removed from the recipe. Please confirm that this is intentional and thatkmer-dbno longer requireszlibat runtime in the new version.If
zlibis still needed, consider re-adding it to therunrequirements.To verify if
zlibis still required, please run the following script:
Update
kmer-db: 1.11.1 → 2.2.2recipes/kmer-db(click to view/edit other files)@refresh-bioThis pull request was automatically generated (see docs).