Update biobb_cmip to 5.0.0

[BiocondaBot]

Update biobb_cmip: 4.2.0 → 5.0.0

Info	Link or Description
Recipe	recipes/biobb_cmip (click to view/edit other files)
Summary	Biobb_cmip is the Biobb module collection to compute classical molecular interaction potentials.
Home	https://github.com/bioexcel/biobb_cmip
Releases	https://pypi.org/pypi/biobb_cmip/json
Recipe Maintainer(s)	@p, @A, @U, @A, @n, @d, @r, @i, @o

---

This pull request was automatically generated (see docs).

[coderabbitai]

📝 Walkthrough

Walkthrough

The pull request involves an update to the meta.yaml file for the biobb_cmip package. The version number has been incremented from 4.2.0 to 5.0.0, reflecting a significant change in the package's release. Alongside this version change, the SHA256 checksum for the source package has been updated to 4f934f23f7826b5de97fd2ecaaa476a3842d203b6a04ef52b584fa8d81ccd610. The dependencies listed in the host and run sections, specifically for the biobb_common and cmip packages, remain unchanged, still specifying versions 4.2.0 and 2.7.0, respectively. The overall structure of the meta.yaml file has not been altered, and there are no modifications to other dependencies or sections within the file.

Possibly related PRs

• [biobb_common] update 5.0.0 #51335: Updates the biobb_common package from version 4.2.0 to 5.0.0, directly related to the version update in biobb_cmip.
• [biobb_amber] update 5.0.0 #51430: Updates the biobb_amber package from 4.2.0 to 5.0.0, aligning with the version increment in biobb_cmip.
• [biobb_analysis] update 5.0.0 #51431: Updates the biobb_analysis package from 4.2.0 to 5.0.0, consistent with the version change in biobb_cmip.
• [biobb_chemistry] update 5.0.0 #51435: Updates the biobb_chemistry package from 4.2.1 to 5.0.0, related to the version change in biobb_cmip.

Suggested reviewers

• adamhospital
• gbayarri

---

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 6b9962d and c0aaa4e.

📒 Files selected for processing (1)

• recipes/biobb_cmip/meta.yaml (1 hunks)

🧰 Additional context used

🔇 Additional comments (4)

recipes/biobb_cmip/meta.yaml (4)

Line range hint 1-54: Overall, the update looks good with some considerations.

The version update to 5.0.0 and the SHA256 checksum change have been implemented correctly. However, there are a few points to consider:

1. As this is a major version update, please verify if there are any breaking changes or significant updates that users should be aware of.
2. The SHA256 checksum should be verified to ensure it corresponds to the correct source package for version 5.0.0.
3. Consider reviewing and potentially updating the dependencies, especially 'biobb_common', to ensure compatibility with the new major version.

Once these points have been addressed, the update should be ready for merging.

🧰 Tools

🪛 yamllint

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

(syntax)

---

Line range hint 22-33: Consider updating dependencies for the new major version.

While the dependencies haven't been changed in this update, it's worth reviewing them for a major version release. In particular, the 'biobb_common' dependency is still set to version 4.2.0, which might need an update to be compatible with biobb_cmip 5.0.0.

Please review the dependencies and consider if any updates are necessary. You can use the following script to check for the latest versions of the key dependencies:

#!/bin/bash
# Description: Check for the latest versions of key dependencies

# Function to get the latest version from PyPI
get_latest_version() {
    package=$1
    latest_version=$(curl -s https://pypi.org/pypi/$package/json | jq -r .info.version)
    echo "$latest_version"
}

# Check biobb_common
current_biobb_common=$(rg 'biobb_common ==([\d.]+)' -or '$1' recipes/biobb_cmip/meta.yaml)
latest_biobb_common=$(get_latest_version biobb_common)
echo "biobb_common: Current: $current_biobb_common, Latest: $latest_biobb_common"

# Check cmip
current_cmip=$(rg 'cmip ==([\d.]+)' -or '$1' recipes/biobb_cmip/meta.yaml)
latest_cmip=$(get_latest_version cmip)
echo "cmip: Current: $current_cmip, Latest: $latest_cmip"

# Check biobb_structure_checking
current_biobb_structure_checking=$(rg 'biobb_structure_checking ==([\d.]+)' -or '$1' recipes/biobb_cmip/meta.yaml)
latest_biobb_structure_checking=$(get_latest_version biobb_structure_checking)
echo "biobb_structure_checking: Current: $current_biobb_structure_checking, Latest: $latest_biobb_structure_checking"

If any of the dependencies have newer versions available, please consider updating them to ensure compatibility with biobb_cmip 5.0.0.

🧰 Tools

🪛 yamllint

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

(syntax)

---

10-10: SHA256 checksum update looks valid, but verification is recommended.

The SHA256 checksum has been updated, which is necessary for the new version. The new checksum appears to be valid (64 characters, hexadecimal).

To ensure the integrity of the package, please verify that this checksum corresponds to the correct source package for version 5.0.0. You can use the following script to download the package and verify its checksum:

#!/bin/bash
# Description: Download the package and verify its checksum

# Extract version and checksum from meta.yaml
version=$(rg '^{% set version = "(.+)" %}' -or '$1' recipes/biobb_cmip/meta.yaml)
expected_checksum=$(rg '^ *sha256: (.+)' -or '$1' recipes/biobb_cmip/meta.yaml)

# Download the package
url="https://pypi.io/packages/source/b/biobb_cmip/biobb_cmip-${version}.tar.gz"
wget "$url" -O biobb_cmip.tar.gz

# Calculate the checksum of the downloaded file
calculated_checksum=$(sha256sum biobb_cmip.tar.gz | awk '{print $1}')

# Compare the checksums
if [ "$calculated_checksum" = "$expected_checksum" ]; then
    echo "Checksum verification successful!"
else
    echo "Checksum verification failed!"
    echo "Expected: $expected_checksum"
    echo "Calculated: $calculated_checksum"
fi

# Clean up
rm biobb_cmip.tar.gz

---

2-2: Version update looks good, but consider potential breaking changes.

The version update from 4.2.0 to 5.0.0 is correctly implemented and aligns with the PR objectives. However, as this is a major version update, it may introduce breaking changes.

To ensure compatibility, please run the following script to check if there are any documented breaking changes or significant updates in the package's changelog or release notes:

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