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Update bactopia-py to 1.3.0 #51466

Merged
merged 2 commits into from
Oct 17, 2024
Merged

Update bactopia-py to 1.3.0 #51466

merged 2 commits into from
Oct 17, 2024

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Update bactopia-py: 1.2.11.3.0

install with bioconda Conda

Info Link or Description
Recipe recipes/bactopia-py (click to view/edit other files)
Summary A Python package for working with Bactopia
Home https://bactopia.github.io/
Releases https://pypi.org/pypi/bactopia/json
Recipe Maintainer(s) @rpetit3

This pull request was automatically generated (see docs).

@BiocondaBot BiocondaBot added autobump Automatic Version Update new version labels Oct 17, 2024
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coderabbitai bot commented Oct 17, 2024

📝 Walkthrough
📝 Walkthrough

Walkthrough

This pull request involves an update to the meta.yaml file for the bactopia-py package. The primary changes include an increment in the version number from 1.2.1 to 1.3.0 and an update to the SHA256 checksum for the source tarball, changing from bd375fcea02e5ea20c55f822a7173e70c89d30098585f4b3205bb85a94f821c1 to ac777d8338823c5709d5d4ad3af719faf7084e4c1956fb108ae3d410ad6f74e8. Additionally, a new command bactopia-datasets --version has been added to the test commands section. No other structural or content changes are present in the meta.yaml file.

Possibly related PRs

  • Update bactopia-py to 1.2.1 #51226: This PR updates the bactopia-py package from version 1.2.0 to 1.2.1, which is directly related to the main PR that updates bactopia-py from 1.2.1 to 1.3.0. Both PRs involve version increments and SHA256 checksum updates for the same package.
  • Update bactopia-py to 1.2.0 #51154: This PR updates the bactopia-py package from version 1.1.1 to 1.2.0, which is a predecessor to the version updated in the main PR. It also involves changes to the meta.yaml file for the same package.
  • Update biocode to 0.12.0 #51444: This PR adds a requirement for bactopia-py >=1.2.1 in the sizemeup package, indicating a dependency on the version of bactopia-py that is being updated in the main PR.

Suggested reviewers

  • rpetit3

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 594eb4c and 27898dc.

📒 Files selected for processing (1)
  • recipes/bactopia-py/meta.yaml (2 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
  • recipes/bactopia-py/meta.yaml

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Actionable comments posted: 1

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 6a9fb9c and 594eb4c.

📒 Files selected for processing (1)
  • recipes/bactopia-py/meta.yaml (1 hunks)
🧰 Additional context used
🔇 Additional comments (2)
recipes/bactopia-py/meta.yaml (2)

2-2: Version update looks good

The version has been correctly updated from 1.2.1 to 1.3.0, which aligns with the PR objective. This change follows semantic versioning conventions, indicating a minor release.


Line range hint 1-65: Verify dependencies and test commands

The recipe update correctly maintains the build number at 0 for the new version. However, it's important to ensure that:

  1. The package dependencies haven't changed with this new version.
  2. The test commands are still applicable and sufficient for version 1.3.0.

Consider checking the package's release notes or documentation to confirm these aspects.

To assist in this verification, you can run the following script to check for any changes in the setup.py or pyproject.toml files between versions:

This script will help identify any changes in dependencies or build requirements between the two versions.

✅ Verification successful

Dependencies and test commands are unchanged

The comparison between versions 1.2.1 and 1.3.0 shows that only the version numbers have been updated. There are no changes to the dependencies or test commands, ensuring that the update maintains consistency.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Compare setup files between versions 1.2.1 and 1.3.0

# Function to download and extract a specific version
download_and_extract() {
    version=$1
    curl -sL https://pypi.io/packages/source/b/bactopia/bactopia-${version}.tar.gz -o bactopia-${version}.tar.gz
    tar -xzf bactopia-${version}.tar.gz
}

# Download and extract both versions
download_and_extract 1.2.1
download_and_extract 1.3.0

# Compare setup.py files if they exist
if [ -f bactopia-1.2.1/setup.py ] && [ -f bactopia-1.3.0/setup.py ]; then
    echo "Differences in setup.py:"
    diff -u bactopia-1.2.1/setup.py bactopia-1.3.0/setup.py
fi

# Compare pyproject.toml files if they exist
if [ -f bactopia-1.2.1/pyproject.toml ] && [ -f bactopia-1.3.0/pyproject.toml ]; then
    echo "Differences in pyproject.toml:"
    diff -u bactopia-1.2.1/pyproject.toml bactopia-1.3.0/pyproject.toml
fi

# Clean up
rm -rf bactopia-1.2.1 bactopia-1.2.1.tar.gz bactopia-1.3.0 bactopia-1.3.0.tar.gz

Length of output: 29100

🧰 Tools
🪛 yamllint

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

(syntax)


package:
name: {{ name|lower }}
version: {{ version }}

source:
url: https://pypi.io/packages/source/{{ name[0] }}/bactopia/bactopia-{{ version }}.tar.gz
sha256: bd375fcea02e5ea20c55f822a7173e70c89d30098585f4b3205bb85a94f821c1
sha256: ac777d8338823c5709d5d4ad3af719faf7084e4c1956fb108ae3d410ad6f74e8
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💡 Codebase verification

Checksum Verification Incomplete

The SHA256 checksum verification did not complete successfully. The provided output lacks confirmation of whether the calculated checksum matches the expected value. It's essential to ensure the checksum is correct to maintain package integrity.

🔗 Analysis chain

Verify SHA256 checksum

The SHA256 checksum has been updated, which is expected with a new version. However, it's crucial to verify that this checksum is correct for the new package version.

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

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify the SHA256 checksum of the bactopia-py 1.3.0 package

# Download the package
curl -sL https://pypi.io/packages/source/b/bactopia/bactopia-1.3.0.tar.gz -o bactopia-1.3.0.tar.gz

# Calculate and compare the SHA256 checksum
calculated_checksum=$(sha256sum bactopia-1.3.0.tar.gz | cut -d ' ' -f 1)
expected_checksum="ac777d8338823c5709d5d4ad3af719faf7084e4c1956fb108ae3d410ad6f74e8"

if [ "$calculated_checksum" = "$expected_checksum" ]; then
    echo "Checksum verification passed"
else
    echo "Checksum verification failed"
    echo "Calculated: $calculated_checksum"
    echo "Expected:   $expected_checksum"
fi

# Clean up
rm bactopia-1.3.0.tar.gz

Length of output: 29100

@rpetit3 rpetit3 merged commit 5dd01ae into master Oct 17, 2024
7 checks passed
@rpetit3 rpetit3 deleted the bump/bactopia_py branch October 17, 2024 21:18
This was referenced Oct 28, 2024
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2 participants