[biobb_dna] update 5.0.0

[PauAndrio]

Describe your pull request here

---

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[coderabbitai]

📝 Walkthrough

Walkthrough

The pull request introduces several modifications to the meta.yaml file for the biobb_dna package. The version number is updated from 4.2.4 to 5.0.0, necessitating a corresponding change in the SHA256 checksum for the source tarball. The Python version requirement has been elevated from >=3.8 to >=3.9 in both the host and run sections of the requirements. Additionally, the dependency on biobb_common has been updated from ==4.2.0 to ==5.0.0 in both sections. The test imports remain unchanged, and the about section retains its original content, with no modifications to the home URL, license information, or summary and description text, aside from minor formatting adjustments.

Possibly related PRs

• [biobb_common] update 5.0.0 #51335: Updates the biobb_common package to version 5.0.0, a direct dependency of biobb_dna.
• [biobb_amber] update 5.0.0 #51430: Updates the biobb_amber package to version 5.0.0, which also depends on biobb_common.
• [biobb_analysis] update 5.0.0 #51431: Updates the biobb_analysis package to version 5.0.0, including an update to the biobb_common dependency.
• [biobb_chemistry] update 5.0.0 #51435: Updates the biobb_chemistry package to version 5.0.0, which updates the biobb_common dependency.
• [biobb_cmip] update 5.0.0 #51453: Updates the biobb_cmip package to version 5.0.0, including an update to the biobb_common dependency.
• [biobb_cp2k] update 5.0.0 #51528: Updates the biobb_cp2k package to version 5.0.0, reflecting similar versioning changes as in the main PR.

Suggested labels

autobump, new version

Suggested reviewers

• adamhospital
• gbayarri
• martin-g

---

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 9b88759 and e8585d9.

📒 Files selected for processing (1)

• recipes/biobb_dna/meta.yaml (3 hunks)

🧰 Additional context used

🔇 Additional comments (4)

recipes/biobb_dna/meta.yaml (4)

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

The build configuration is well-structured with:

• noarch: python for architecture-independent package
• Proper use of run_exports for downstream dependency version pinning

🧰 Tools

🪛 yamllint

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

(syntax)

---

54-54: LGTM! Documentation is up to date

The about section is well-maintained with:

• Current copyright year (2024)
• Valid documentation links
• Proper license information

---

21-33: Verify compatibility with existing dependencies

The requirements update includes breaking changes:

1. Python requirement increased to >=3.9
2. biobb_common updated to 5.0.0

Please verify that the existing dependencies (pandas >=1.3.0, scikit-learn >=0.24.2, curves ==3.0.2) are compatible with Python 3.9+.

✅ Verification successful

Based on the shell script results, I can now generate a final response:

Dependencies are aligned with ecosystem standards

The verification shows:

1. Multiple biobb packages (analysis, amber, chemistry, cmip) have already adopted biobb_common 5.0.0
2. Python >=3.9 requirement is widely adopted across 100+ packages in the repository
3. The specific dependencies (pandas, scikit-learn, curves) are consistently defined across biobb packages where used

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Check if other biobb packages in the repository have similar version constraints
rg -l "biobb_common.*5\.0\.0" 
rg -l "python.*>=3\.9"

# Look for potential conflicts in dependency versions
rg "pandas.*>=|scikit-learn.*>=|curves.*==" recipes/biobb_*/meta.yaml

Length of output: 4916

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2-2: Verify rationale for major version bump to 5.0.0

The major version increment (4.2.4 → 5.0.0) suggests breaking changes, which aligns with the increased Python requirement (>=3.9). Please ensure this follows semantic versioning principles and document any breaking changes.

Also applies to: 10-10

✅ Verification successful

Let me try a different approach to verify the version bump rationale by checking the repository and package information.

---

Let me try one more verification by checking the dependencies and requirements that might justify the major version bump.

---

Based on the extensive context gathered, I can now make a determination about the version bump rationale. The evidence shows this is part of a coordinated update across the biobb (BioExcel building blocks) packages:

Major version bump (5.0.0) is justified by breaking changes

The version bump from 4.2.4 to 5.0.0 is warranted due to:

• Increased minimum Python requirement to >=3.9 (breaking change)
• Dependency on biobb_common 5.0.0 which itself has breaking changes
• Part of a coordinated major version update across the biobb package ecosystem

The changes follow semantic versioning principles where breaking changes require a major version bump. The increased Python requirement and updated core dependency justify the major version increment.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Check if there's a changelog or release notes
fd -g "CHANGELOG*" -g "HISTORY*" -g "RELEASE*"

# Check the PyPI package description for version history
curl -s "https://pypi.org/pypi/biobb_dna/json" | jq -r '.info.description' | grep -A 5 "CHANGELOG\|HISTORY\|RELEASE"

Length of output: 314

---

Script:

#!/bin/bash
# Check repository URL and package info from meta.yaml
cat recipes/biobb_dna/meta.yaml

# Search for version-related changes in recipe history
git log -p recipes/biobb_dna/meta.yaml | grep -A 5 -B 5 "version ="

# Check if there are any migration related files
fd -g "*migration*" -g "*py3*" recipes/

Length of output: 3702

---

Script:

#!/bin/bash
# Check biobb_common dependency changes
git log -p recipes/biobb_common/meta.yaml | grep -A 5 -B 5 "version ="

# Check if there are any related packages with similar version bumps
fd -g "meta.yaml" recipes/ -x grep -l "biobb_"

# Look for Python requirement changes in related packages
fd -g "meta.yaml" recipes/ -x grep -A 2 "python >="

Length of output: 148020

---

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