Update nanovar to 1.8.1

[BiocondaBot]

Update nanovar: 1.8.0 → 1.8.1

Info	Link or Description
Recipe	recipes/nanovar (click to view/edit other files)
Summary	Structural variant caller using low-depth long reads
Home	https://github.com/cytham/nanovar
Releases	https://pypi.org/pypi/nanovar/json
Recipe Maintainer(s)	@cytham

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This pull request was automatically generated (see docs).

[coderabbitai]

📝 Walkthrough

📝 Walkthrough

Walkthrough

The pull request updates the nanovar package from version 1.8.0 to 1.8.1. This includes modifications to the meta.yaml file, specifically changing the source URL to the new version's tarball on PyPI and updating the SHA-256 checksum to correspond with the new version. Additionally, the dependency constraint for numpy has been adjusted to require a version greater than or equal to 1.17.3 but less than 2.0.0. The build section remains unchanged.

Changes

File	Change Summary
recipes/nanovar/meta.yaml	- Version updated from "1.8.0" to "1.8.1" - Source URL updated to point to version 1.8.1 - SHA256 checksum updated to match the new version - Dependency constraint for numpy updated to >=1.17.3, <2.0.0

Possibly related PRs

• Update nanovar to 1.8.0 #50993: This PR updates the nanovar package from version 1.5.1 to 1.8.0, indicating a sequential version change leading up to the current update.

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📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 2349316 and a82faea.

📒 Files selected for processing (1)

• recipes/nanovar/meta.yaml (2 hunks)

🧰 Additional context used

🪛 yamllint

recipes/nanovar/meta.yaml

[error] 1-1: syntax error: found character '%' that cannot start any token

(syntax)

🔇 Additional comments (3)

recipes/nanovar/meta.yaml (3)

1-1: Version update looks good.

The package version has been correctly updated to 1.8.1, which aligns with the PR objectives.

🧰 Tools

🪛 yamllint

[error] 1-1: syntax error: found character '%' that cannot start any token

(syntax)

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26-26: Verify the numpy version constraint.

The numpy dependency has been updated to include an upper bound: ">=1.17.3, <2.0.0". While this change might be intended to ensure compatibility with the current version of nanovar, it's important to verify a few points:

1. Is this constraint necessary for nanovar 1.8.1?
2. Does this constraint align with the requirements of other dependencies in the package?
3. Could this constraint potentially cause conflicts with other packages in the bioconda ecosystem?

To help verify this, you can run the following script to check the numpy version used in the nanovar 1.8.1 source code:

Please review the output to ensure that the version constraint aligns with the actual requirements of nanovar 1.8.1.

✅ Verification successful

To further verify the necessity of the numpy version constraint, please run the following script to check for any specified numpy version requirements in the configuration files of nanovar 1.8.1:

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Numpy version constraint verified successfully.

The numpy dependency in meta.yaml is set to ">=1.17.3, <2.0.0", and the requirements.txt specifies numpy==1.26.4. This ensures compatibility and prevents potential issues with future major releases.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check numpy version requirements in nanovar 1.8.1 source code

# Download the package
curl -L -o nanovar-1.8.1.tar.gz https://pypi.io/packages/source/n/nanovar/nanovar-1.8.1.tar.gz

# Extract the package
tar -xzf nanovar-1.8.1.tar.gz

# Search for numpy import statements and version checks
echo "Numpy import statements and version checks:"
grep -R "import numpy" nanovar-1.8.1
grep -R "numpy.__version__" nanovar-1.8.1

# Clean up
rm -rf nanovar-1.8.1 nanovar-1.8.1.tar.gz

Length of output: 1081

---

Script:

#!/bin/bash
# Description: Check for numpy version requirements in configuration files of nanovar 1.8.1

# Download the package
curl -L -o nanovar-1.8.1.tar.gz https://pypi.io/packages/source/n/nanovar/nanovar-1.8.1.tar.gz

# Extract the package
tar -xzf nanovar-1.8.1.tar.gz

# Search for numpy version specifications in setup.py and requirements.txt
echo "Numpy version specifications in setup.py and requirements.txt:"
grep -E "numpy[ <>=!~]+" nanovar-1.8.1/setup.py || echo "No numpy version specified in setup.py."
grep -E "numpy[ <>=!~]+" nanovar-1.8.1/requirements.txt || echo "No numpy version specified in requirements.txt."

# Clean up
rm -rf nanovar-1.8.1 nanovar-1.8.1.tar.gz

Length of output: 1131

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9-9: Verify the SHA256 checksum.

The SHA256 checksum has been updated for the new version. It's crucial to ensure that this checksum is correct for the nanovar-1.8.1.tar.gz package.

To verify the checksum, you can run the following script:

Please compare the calculated checksum with the one specified in the meta.yaml file to ensure they match.

---

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