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Update phanotate to 1.6.6 #51443

Merged
merged 1 commit into from
Oct 16, 2024
Merged

Update phanotate to 1.6.6 #51443

merged 1 commit into from
Oct 16, 2024

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Update phanotate: 1.6.51.6.6

install with bioconda Conda

Info Link or Description
Recipe recipes/phanotate (click to view/edit other files)
Summary Phanotate gene caller for phages
Home https://github.com/deprekate/PHANOTATE
Releases https://pypi.org/pypi/phanotate/json
Recipe Maintainer(s) @linsalrob, @deprekate

This pull request was automatically generated (see docs).

@BiocondaBot BiocondaBot added autobump Automatic Version Update new version labels Oct 16, 2024
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coderabbitai bot commented Oct 16, 2024

📝 Walkthrough

Walkthrough

The pull request introduces modifications to the meta.yaml file for the phanotate package. The key changes include an update to the package version from 1.6.5 to 1.6.6, indicating a new release. Correspondingly, the SHA256 checksum for the source tarball has been updated to ef33ec3886d9934d43e5747afc316c4229800cfce60a009fa645ff307b96e162, reflecting a change in the source package. Additionally, the build number has been altered from 1 to 0. The remainder of the meta.yaml file, which encompasses package requirements, test commands, and other metadata, has not been modified. These changes are typical for package version updates, ensuring that the package manager can correctly identify and retrieve the updated package.

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Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (1)
recipes/phanotate/meta.yaml (1)

Tag 1.6.6 Not Found in PHANOTATE Repository

The meta.yaml file specifies version 1.6.6, but this tag does not exist in the PHANOTATE repository. Available tags are:

  • 1.3.1
  • 1.5.0

Please verify the correct version number and ensure that the corresponding tag 1.6.6 is created in the repository if it is the intended version.

🔗 Analysis chain

Line range hint 1-58: Verify package metadata and dependencies for the new version.

While the version update looks good, it's important to ensure that the new version (1.6.6) doesn't require any changes to the package dependencies, build requirements, or other metadata. Please verify that all the information in the meta.yaml file is still accurate for version 1.6.6.

To assist with this verification, you can run the following script to check for any changes in the package's setup.py or requirements files:

Please review the output to ensure that the meta.yaml file accurately reflects any changes in dependencies or build requirements for version 1.6.6.


To address the issues encountered, please run the following updated script to verify the package metadata and dependencies for version 1.6.6:


Please run the following script to list all available Git tags in the PHANOTATE repository. This will help verify whether the tag 1.6.6 exists or if there's an alternative tag corresponding to version 1.6.6.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for changes in setup.py or requirements files

# Clone the repository
git clone https://github.com/deprekate/PHANOTATE.git
cd PHANOTATE

# Check out the new version tag
git checkout 1.6.6

# Display setup.py
echo "Contents of setup.py:"
cat setup.py

# Check for requirements files
echo "Requirements files:"
ls *requirements*.txt 2>/dev/null || echo "No requirements.txt found"

# Display contents of requirements files if they exist
for req_file in *requirements*.txt; do
    if [ -f "$req_file" ]; then
        echo "Contents of $req_file:"
        cat "$req_file"
    fi
done

# Clean up
cd ..
rm -rf PHANOTATE

Length of output: 1200


Script:

#!/bin/bash
# Description: Check for changes in setup.py or requirements files and verify SHA256

# Clone the repository
git clone https://github.com/deprekate/PHANOTATE.git
cd PHANOTATE

# Check out the new version tag
git checkout 1.6.6

# Display setup.py if it exists
if [ -f setup.py ]; then
  echo "Contents of setup.py:"
  cat setup.py
else
  echo "setup.py not found."
fi

# Check for requirements files
echo "Checking for requirements files..."
requirements_files=$(ls *requirements*.txt 2>/dev/null)
if [ -z "$requirements_files" ]; then
  echo "No requirements.txt files found."
else
  echo "Requirements files:"
  echo "$requirements_files"
  
  # Display contents of requirements files
  for req_file in $requirements_files; do
    echo "Contents of $req_file:"
    cat "$req_file"
  done
fi

# Verify SHA256 if possible
if command -v shasum >/dev/null 2>&1; then
  echo "Calculated SHA256:"
  shasum -a 256 phanotate-1.6.6.tar.gz
else
  echo "shasum command not found. Skipping SHA256 verification."
fi

echo "Expected SHA256:"
echo "ef33ec3886d9934d43e5747afc316c4229800cfce60a009fa645ff307b96e162"

# Clean up
cd ..
rm -rf PHANOTATE phanotate-1.6.6.tar.gz

Length of output: 2437


Script:

#!/bin/bash
# Description: List all Git tags in the PHANOTATE repository

# Clone the repository
git clone https://github.com/deprekate/PHANOTATE.git
cd PHANOTATE

# List all tags
echo "Available Git tags:"
git tag

# Clean up
cd ..
rm -rf PHANOTATE

Length of output: 257

🧰 Tools
🪛 yamllint

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

(syntax)

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 84f5b88 and 55d7027.

📒 Files selected for processing (1)
  • recipes/phanotate/meta.yaml (1 hunks)
🧰 Additional context used
🔇 Additional comments (3)
recipes/phanotate/meta.yaml (3)

2-2: Version update looks good.

The version has been correctly updated from 1.6.5 to 1.6.6, which aligns with the PR objectives.


13-13: Build number reset is correct.

The build number has been appropriately reset to 0 for the new version. This is in line with Conda packaging best practices, which recommend resetting the build number when updating to a new version of the package.


10-10: SHA256 checksum update looks correct.

The SHA256 checksum has been updated, which is necessary for the new version. However, it's crucial to verify that this checksum corresponds to the correct source package for version 1.6.6.

To verify the SHA256 checksum, you can run the following script:

#!/bin/bash
# Description: Verify the SHA256 checksum of the phanotate 1.6.6 source package

# Download the source package
curl -L "https://pypi.io/packages/source/p/phanotate/phanotate-1.6.6.tar.gz" -o phanotate-1.6.6.tar.gz

# Calculate and display the SHA256 checksum
echo "Calculated SHA256:"
sha256sum phanotate-1.6.6.tar.gz

echo "Expected SHA256:"
echo "ef33ec3886d9934d43e5747afc316c4229800cfce60a009fa645ff307b96e162"

# Clean up
rm phanotate-1.6.6.tar.gz

Please ensure that the calculated SHA256 matches the expected SHA256 in the meta.yaml file.

@mencian mencian merged commit b3d04ef into master Oct 16, 2024
7 checks passed
@mencian mencian deleted the bump/phanotate branch October 16, 2024 23:07
This was referenced Nov 9, 2024
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2 participants