coderabbitai[bot]
commented
3 days ago š Walkthrough
š Walkthrough
## Walkthrough The pull request introduces a new file, `meta.yaml`, for the `corneto` package, which outlines its metadata and build configuration necessary for packaging. Key components include the package name set to "corneto" and version "1.0.0a0". The source section specifies the download URL from PyPI and includes a SHA256 checksum for integrity verification. The build section indicates that the package is architecture-independent and provides a script for installation using pip without dependencies or build isolation. The requirements section details dependencies for both host and runtime environments, specifying Python version constraints and particular versions for `numpy`, `cvxpy-base`, and `scipy`. The test section includes commands to verify the installation and confirm that the `corneto` package can be imported, with `pip` listed as a testing requirement. Additional information about the package, such as its homepage, summary, license type, and maintainers, is also included in the about section. ## Possibly related PRs - #51268: The `meta.yaml` file for the `patchify` package introduces a new package with similar structure and requirements, including the use of a `run_exports` section, which is also present in the `corneto` package's `meta.yaml`. - #51612: The `meta.yaml` for the `steamboat` package also establishes its metadata and build configuration, similar to the changes made in the `corneto` package's `meta.yaml`, including the use of a `run_exports` directive and specifying dependencies. - #51643: The `meta.yaml` for the `svtopovz` package introduces a new package with a similar structure, including a `run_exports` section and detailed dependency management, akin to the `corneto` package's configuration. ## Suggested labels `please review & merge` ## Suggested reviewers - mencianš Recent review details
**Configuration used: CodeRabbit UI** **Review profile: CHILL**š„ Commits
Files that changed from the base of the PR and between 10decf520094ee19560060e60242cd6dfc836744 and 64e89d793eecddb20132dc07f9a7952c33bcf67e.š Files selected for processing (1)
* recipes/corneto/meta.yaml (1 hunks)š§° Additional context used
šŖ yamllint
recipes/corneto/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token (syntax)š Additional comments (3)
recipes/corneto/meta.yaml (3)
`38-42`: **Verify repository and license file** Let's ensure the GitHub repository exists and contains the specified license file.ā Verification successful
The output shows that the GitHub repository exists (HTTP/2 200) and contains a GPL-3.0 license file, which matches the license specified in the meta.yaml file. Let me generate the final response: **Repository and license verification successful** The GitHub repository exists and contains the GPL-3.0 license file, matching the license declaration in meta.yaml.š Scripts executed
The following scripts were executed for the analysis: Script: ```shell #!/bin/bash # Description: Verify GitHub repository and license existence # Expected results: # 1. curl should return HTTP 200 for repository # 2. GitHub API should confirm license file presence # Check if repository exists curl -sI "https://github.com/saezlab/corneto/" | head -n1 # Check license file using GitHub API gh api repos/saezlab/corneto/contents/LICENSE ``` Length of output: 49379ā Verification successful
**Source URL and checksum verified successfully** The package source URL and SHA256 checksum in meta.yaml are correct and match the published package on PyPI: - URL pattern is correct for PyPI source distributions - SHA256 checksum `966d50762f92047ea4e5d1a136607f20ae9ec1d585530a24ad5c95e700b24180` matches exactly - Version 1.0.0a0 is confirmed to exist on PyPIš Scripts executed
The following scripts were executed for the analysis: Script: ```shell #!/bin/bash # Description: Verify package existence and checksum # Expected results: # 1. curl should return HTTP 200 # 2. Downloaded file's checksum should match # Test package URL accessibility curl -sI "https://pypi.org/packages/source/c/corneto/corneto-1.0.0a0.tar.gz" | head -n1 # Download and verify checksum curl -sL "https://pypi.org/packages/source/c/corneto/corneto-1.0.0a0.tar.gz" | sha256sum ``` Length of output: 49379 --- Script: ```shell #!/bin/bash # Let's try a different approach to verify the package and checksum # 1. Check if package exists on PyPI using their JSON API curl -s "https://pypi.org/pypi/corneto/1.0.0a0/json" | jq -r '.urls[0].url,.urls[0].digests.sha256' 2>/dev/null # 2. As fallback, check the GitHub repository for release info curl -s "https://api.github.com/repos/saezlab/corneto/releases" | jq -r '.[0].tag_name' 2>/dev/null ``` Length of output: 406 --- Script: ```shell #!/bin/bash # Let's check for the source distribution specifically since meta.yaml uses .tar.gz # 1. Get all distribution URLs and their checksums from PyPI curl -s "https://pypi.org/pypi/corneto/1.0.0a0/json" | jq -r '.urls[] | select(.packagetype=="sdist") | "\(.url)\n\(.digests.sha256)"' # 2. Also check the package metadata curl -s "https://pypi.org/pypi/corneto/1.0.0a0/json" | jq -r '.info.version' ``` Length of output: 412ā Verification successful
**The numpy version constraint is appropriate** The wide numpy version constraint `>=1.15,<2.0.0` is actually reasonable in this context. The codebase shows no direct numpy imports or usage that would require a more restrictive version range. Since numpy maintains strong backward compatibility and the package appears to use it only through its dependencies (cvxpy-base and scipy), the current constraint allows for flexibility while preventing potential issues with a future numpy 2.0 release.š Scripts executed
The following scripts were executed for the analysis: Script: ```shell #!/bin/bash # Description: Check minimum numpy versions required by dependencies # Expected results: Find numpy version requirements in dependency packages rg -A 5 "numpy.*dependency" || rg -A 5 "numpy.*requires" ``` Length of output: 49379 --- Script: ```shell #!/bin/bash # Check minimum numpy version requirements in setup files and requirements fd -e txt -e yaml -e toml -e in "requirements|setup|pyproject" -x rg -l "numpy.*[>=<]" # Check for imports and usage of numpy in the codebase rg -l "import.*numpy|from numpy" # Check for specific numpy features/functions used rg "numpy\.[a-zA-Z]+" -l ``` Length of output: 1648 --- Script: ```shell #!/bin/bash # Check the actual numpy usage in the package's source code fd -e py -x rg -l "import.*numpy|from numpy" {} \; # Check if there are any specific numpy version requirements in the package's tests fd -e py "test_.*" -x rg -l "numpy.*[>=<]" {} \; # Look for any numpy-related dependencies in setup files rg -l "numpy" pyproject.toml setup.py setup.cfg 2>/dev/null || true ``` Length of output: 164Thank 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?
bgruening
BiocondaBot
nilchia
This PR adds corneto to bioconda. required for liana+
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 arun_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.
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