[biobb_amber] update 5.0.2

[PauAndrio]

Describe your pull request here

---

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[coderabbitai]

📝 Walkthrough

Walkthrough

The pull request introduces updates to the meta.yaml file for the biobb_amber package. The version number is incremented from 5.0.0 to 5.0.2, and the SHA256 checksum for the source tarball is updated to align with the new version. The Python version constraints in the requirements section have been modified, changing from >=3.8,<3.11 to >=3.9,<3.11 for both host and run requirements. The dependencies on biobb_common and ambertools remain unchanged at ==5.0.0 and ==22.5.0, respectively. No alterations were made to the build or test sections, and the about section remains unchanged, maintaining the package's metadata integrity.

Possibly related PRs

• [biobb_amber] update 5.0.0 #51430: The changes in this PR involve updating the meta.yaml file for the biobb_amber package, including version increments and Python version constraints, which are directly related to the updates made in the main PR for the biobb_amber package.
• [biobb_analysis] update 5.0.0 #51431: This PR updates the biobb_analysis package's meta.yaml, including similar version and Python requirement changes, indicating a related update to the biobb_common dependency.
• [biobb_chemistry] update 5.0.0 #51435: The biobb_chemistry package's meta.yaml is updated in this PR with changes to the version and Python requirements, which align with the modifications in the main PR regarding dependency updates.
• [biobb_dna] update 5.0.0 #51601: This PR updates the biobb_dna package's meta.yaml, reflecting similar changes in versioning and Python requirements, indicating a connection to the main PR's updates.

Suggested labels

autobump, new version

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 ea2d6d1 and eb9bedd.

📒 Files selected for processing (1)

• recipes/biobb_amber/meta.yaml (2 hunks)

🔇 Additional comments (4)

recipes/biobb_amber/meta.yaml (4)

Line range hint 12-18: Build configuration follows best practices

The build configuration is well-structured:

• Correct build number reset to 0 for new version
• Appropriate use of run_exports with pin_subpackage ensures ABI compatibility

🧰 Tools

🪛 yamllint

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

(syntax)

---

21-21: Breaking change: Dropping Python 3.8 support

The Python version constraint has been tightened from >=3.8,<3.11 to >=3.9,<3.11. This is a breaking change that could affect users still on Python 3.8. Please verify if this change is necessary and document the reason in the PR description.

#!/bin/bash
# Description: Check if dependencies require Python >=3.9
# Look for Python version requirements in biobb_common and other dependencies

echo "Checking biobb_common Python requirements..."
rg -A 5 "python" "recipes/biobb_common/meta.yaml"

echo "Checking if other biobb packages have similar Python constraints..."
fd "meta.yaml" "recipes" --exec rg -l "python.*>=3.9"

Also applies to: 26-26

---

23-24: Verify dependency versions compatibility

The fixed version pins look good:

• biobb_common ==5.0.0 matches the major version
• ambertools ==22.5.0 is maintained

#!/bin/bash
# Description: Verify dependency versions exist
# Check if specified versions of dependencies are available in bioconda

echo "Checking biobb_common availability..."
rg "version = \"5.0.0\"" "recipes/biobb_common/meta.yaml"

echo "Checking ambertools availability..."
rg "version = \"22.5.0\"" "recipes/ambertools/meta.yaml"

Also applies to: 27-28

---

2-2: Verify SHA256 checksum against PyPI source

The version bump from 5.0.0 to 5.0.2 looks good as it's a minor update. Let's verify the SHA256 checksum matches the PyPI source.

Also applies to: 10-10

✅ Verification successful

Let me try a different approach to verify the SHA256 checksum since the previous script had some issues.

---

SHA256 checksum verification successful

The SHA256 checksum (33cd128cd6b8efb66b83876f978f85447c49e35a98b95bd11e0c74960c76af50) in the meta.yaml matches exactly with the official PyPI source for biobb_amber 5.0.2.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify SHA256 checksum matches PyPI source
# Download the package from PyPI and compute its checksum
VERSION="5.0.2"
PACKAGE="biobb_amber"
EXPECTED_SHA="33cd128cd6b8efb66b83876f978f85447c49e35a98b95bd11e0c74960c76af50"

# Create temp directory
TEMP_DIR=$(mktemp -d)
cd "$TEMP_DIR"

# Download package and compute SHA256
curl -sL "https://pypi.io/packages/source/b/${PACKAGE}/${PACKAGE}-${VERSION}.tar.gz" | sha256sum | cut -d' ' -f1 | tr -d '\n' > sha256.txt

# Compare with expected SHA256
if [ "$(cat sha256.txt)" = "$EXPECTED_SHA" ]; then
    echo "SHA256 checksum verified successfully"
else
    echo "SHA256 mismatch!"
    echo "Expected: $EXPECTED_SHA"
    echo "Got: $(cat sha256.txt)"
fi

Length of output: 752

---

Script:

#!/bin/bash
# Get the SHA256 from meta.yaml
echo "Extracting SHA256 from meta.yaml..."
rg "sha256:" recipes/biobb_amber/meta.yaml

# Check if package exists on PyPI
echo "Checking package on PyPI..."
curl -s "https://pypi.org/pypi/biobb_amber/5.0.2/json" | jq -r '.urls[] | select(.packagetype=="sdist") | .digests.sha256'

Length of output: 451

---

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