[biobb_flexserv] update 5.0.0 #51607
Conversation
📝 Walkthrough📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces updates 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/biobb_flexserv/meta.yaml (1)
2-2: Major version bump considerationsThe update from 4.2.0 to 5.0.0 along with the Python version requirement change and biobb_common dependency update indicates breaking changes. Please ensure that:
- Breaking changes are documented in release notes
- Users are notified about the Python version requirement change
- Migration guide is provided if necessary
Also applies to: 23-23, 29-29
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/biobb_flexserv/meta.yaml (2 hunks)
🧰 Additional context used
🔇 Additional comments (4)
recipes/biobb_flexserv/meta.yaml (4)
Line range hint
12-18: Build configuration looks goodThe build configuration is appropriate for a Python package:
- Using noarch: python for platform-independent package
- Correctly configured run_exports with x-pin for version compatibility
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
21-21: Verify Python version requirement change impactThe Python requirement has been increased from >=3.8 to >=3.9. This is a potentially breaking change that should be documented in release notes.
#!/bin/bash # Check if any other biobb packages still support Python 3.8 rg "python.*>=3.8" recipes/biobb_**/meta.yamlAlso applies to: 28-28
2-2: Verify SHA256 checksum for version 5.0.0Let's verify that the SHA256 checksum matches the source tarball for version 5.0.0.
Also applies to: 10-10
✅ Verification successful
Let me try to verify the SHA256 checksum with a different approach using the PyPI JSON API.
This script will fetch the official SHA256 checksum from PyPI's JSON API, which we can compare with the one in the meta.yaml file. This is a more reliable approach as it doesn't require downloading the package.
SHA256 checksum verification successful
The SHA256 checksum in the meta.yaml file (
90c2b03541d144026f2f6866e8fd166b0440f73a7c34c83f49b81dd826374edc) matches exactly with the official checksum from PyPI for biobb_flexserv version 5.0.0.🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Download the package and verify its checksum PACKAGE="biobb_flexserv" VERSION="5.0.0" EXPECTED_SHA="90c2b03541d144026f2f6866e8fd166b0440f73a7c34c83f49b81dd826374edc" # Create temporary directory TEMP_DIR=$(mktemp -d) cd "$TEMP_DIR" # Download the package curl -sL "https://pypi.io/packages/source/b/${PACKAGE}/${PACKAGE}-${VERSION}.tar.gz" -o package.tar.gz # Calculate and compare SHA256 ACTUAL_SHA=$(sha256sum package.tar.gz | cut -d' ' -f1) echo "Expected SHA256: $EXPECTED_SHA" echo "Actual SHA256: $ACTUAL_SHA"Length of output: 2156
Script:
#!/bin/bash # Get package info from PyPI JSON API PACKAGE="biobb_flexserv" VERSION="5.0.0" EXPECTED_SHA="90c2b03541d144026f2f6866e8fd166b0440f73a7c34c83f49b81dd826374edc" # Fetch package metadata from PyPI echo "Fetching package metadata from PyPI..." curl -s "https://pypi.org/pypi/${PACKAGE}/${VERSION}/json" | \ jq -r --arg ver "$VERSION" '.urls[] | select(.filename | endswith(".tar.gz")) | .digests.sha256'Length of output: 424
23-25: Verify dependency versions compatibilityThe biobb_common dependency has been updated to match the major version (5.0.0), but flexserv and pcasuite versions remain unchanged. Let's verify if these versions are still compatible.
Also applies to: 29-31
✅ Verification successful
Let me gather more information about the dependencies and their compatibility with biobb_common 5.0.0.
Let me try one more verification to check the build requirements and any potential version constraints in the package metadata.
Dependencies appear to be correctly configured
Based on the meta.yaml content, the package versions are intentionally set and appear to be compatible:
- The package itself is being updated to version 5.0.0
- biobb_common is updated to match at 5.0.0
- flexserv and pcasuite are maintained at their specific versions (1.0.2 and 1.0.0 respectively)
- These versions are consistently set for both host and run requirements
- The package uses noarch: python and requires Python >=3.9
The dependencies seem to be properly configured, and there's no evidence of version incompatibility issues.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Check versions of flexserv and pcasuite in other biobb packages echo "Checking flexserv versions:" rg "flexserv.*==" recipes/biobb_*/meta.yaml echo -e "\nChecking pcasuite versions:" rg "pcasuite.*==" recipes/biobb_*/meta.yamlLength of output: 2156
Script:
#!/bin/bash # Check if flexserv and pcasuite are used in biobb_flexserv's source code echo "Checking flexserv usage in biobb_flexserv:" rg -A 5 "import.*flexserv" recipes/biobb_flexserv/ echo -e "\nChecking pcasuite usage in biobb_flexserv:" rg -A 5 "import.*pcasuite" recipes/biobb_flexserv/ # Check biobb_common usage and version requirements echo -e "\nChecking biobb_common version requirements:" rg "biobb_common.*==" recipes/biobb_flexserv/Length of output: 572
Script:
#!/bin/bash # Check package metadata for version constraints and requirements echo "Checking meta.yaml content:" cat recipes/biobb_flexserv/meta.yaml # Check if there's a setup.py with dependency information echo -e "\nChecking for setup.py:" fd "setup.py" recipes/biobb_flexserv/ --exec cat {}Length of output: 2083
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>.