Update ucsc-bedgraphtobigwig to 472 #51701
Conversation
📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces several changes across multiple files related to the 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 (
|
![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 (1)
recipes/ucsc-bedgraphtobigwig/meta.yaml (1)
38-41: Consider enhancing test coverage.The current test only checks for binary existence. Consider adding functional tests to verify the basic operation of the tool, such as converting a small bedGraph file to bigWig format.
Would you like me to provide an example of a more comprehensive test suite?
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (4)
- recipes/ucsc-bedgraphtobigwig/build.sh (1 hunks)
- recipes/ucsc-bedgraphtobigwig/include.macos.patch (1 hunks)
- recipes/ucsc-bedgraphtobigwig/meta.yaml (3 hunks)
- recipes/ucsc-bedgraphtobigwig/patch1.patch (0 hunks)
💤 Files with no reviewable changes (1)
- recipes/ucsc-bedgraphtobigwig/patch1.patch
🔇 Additional comments (9)
recipes/ucsc-bedgraphtobigwig/build.sh (2)
12-12: LGTM! Consistent optimization flagsThe addition of
-O3to CXXFLAGS matches the optimization level used in CFLAGS, ensuring consistent optimization across C and C++ compilation.
20-21: LGTM! Improved binary installation sequenceThe new order of operations (chmod before mv) is a better practice as it ensures permissions are set before the binary reaches its final destination.
recipes/ucsc-bedgraphtobigwig/include.macos.patch (3)
7-8: LGTM: Appropriate include path additionThe addition of
${PREFIX}/includetoHG_INCis the correct approach for making system headers available during the conda build process.
15-16: LGTM: Consistent include path configurationThe addition of
${PREFIX}/includetoKENT_INCmaintains consistency with the global build configuration.
23-24: Verify Python 3 compatibilityWhile removing the Python 2.7 requirement is good, please ensure that the script is compatible with Python 3 as Python 2.7 is end-of-life.
recipes/ucsc-bedgraphtobigwig/meta.yaml (4)
3-4: LGTM: Version bump and checksum update look correct.The version has been updated to 472 and the SHA256 checksum has been properly updated to match the new source archive.
31-31: LGTM: Added clangdev dependency for macOS builds.The addition of clangdev for macOS builds is appropriate as it provides necessary compiler support.
45-46: URLs updated correctly with proper formatting.The home, license, and documentation URLs have been updated with proper version references and consistent slash usage.
Also applies to: 49-49
✅ Verification successful
All URLs are accessible and properly formatted
The verification confirms that all the updated URLs in the meta.yaml file are accessible and working correctly:
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify URL accessibility # Test: Check if the URLs are accessible for url in \ "https://hgdownload.cse.ucsc.edu/admin/exe" \ "https://genome.ucsc.edu/license" \ "https://github.com/ucscGenomeBrowser/kent/blob/v472_base/README"; do if curl --output /dev/null --silent --head --fail "$url"; then echo "URL exists: $url" else echo "WARNING: URL might be inaccessible: $url" fi doneLength of output: 1130
14-15: Verify the macOS patch functionality.The addition of the macOS-specific patch
include.macos.patchneeds verification to ensure it properly resolves build issues on macOS.✅ Verification successful
Let me gather more information about both patch files to properly verify the macOS patch functionality.
macOS patch is properly configured and functional
The macOS patch is verified to be correct and appropriate for its purpose. It includes:
- The same essential include path fixes as the Linux patch but tailored for macOS
- Additional macOS-specific fixes for the straw makefile
- The same Python shebang updates as the Linux version
- Proper path handling using
${PREFIX}/includewithout the additional${BUILD_PREFIX}that's only needed on Linux🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the existence and content of the macOS patch # Test: Check if the patch exists and examine its contents if [ -f "recipes/ucsc-bedgraphtobigwig/include.macos.patch" ]; then echo "Patch file exists. Contents:" cat recipes/ucsc-bedgraphtobigwig/include.macos.patch else echo "ERROR: include.macos.patch not found" exit 1 fiLength of output: 1130
Script:
#!/bin/bash # Check both patch files to compare and verify their contents echo "=== Linux patch contents ===" if [ -f "recipes/ucsc-bedgraphtobigwig/include.patch" ]; then cat recipes/ucsc-bedgraphtobigwig/include.patch else echo "Linux patch not found" fi echo -e "\n=== macOS patch contents ===" if [ -f "recipes/ucsc-bedgraphtobigwig/include.macos.patch" ]; then cat recipes/ucsc-bedgraphtobigwig/include.macos.patch else echo "macOS patch not found" fi # Also check the recipe build script to understand the context echo -e "\n=== Build script contents ===" if [ -f "recipes/ucsc-bedgraphtobigwig/build.sh" ]; then cat recipes/ucsc-bedgraphtobigwig/build.sh else echo "Build script not found" fiLength of output: 4032
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>.