Update biobb_analysis to 5.0.0

[BiocondaBot]

Update biobb_analysis: 4.2.0 → 5.0.0

Info	Link or Description
Recipe	recipes/biobb_analysis (click to view/edit other files)
Summary	Biobb_analysis is the Biobb module collection to perform analysis of molecular dynamics simulations.
Home	https://github.com/bioexcel/biobb_analysis
Releases	https://pypi.org/pypi/biobb_analysis/json
Recipe Maintainer(s)	@

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This pull request was automatically generated (see docs).

[coderabbitai]

📝 Walkthrough

Walkthrough

The pull request introduces changes to the meta.yaml file for the biobb_analysis package. The primary modification involves updating the version number from "4.2.0" to "5.0.0". In conjunction with this version change, the SHA256 checksum for the source package has been updated to ensure it corresponds with the new version, changing from e42a054bbc9c066d47443a18ee370dd97632f93de32c44aeb586a19bce85aa37 to 8bf930ecd4cff6b3ad3a97a92599913225295725056c5369bd0e7f536bb4008d. The requirements section of the file remains unchanged, indicating that the dependencies on biobb_common, gromacs, and ambertools are still aligned with their previously specified versions. The overall structure of the meta.yaml file, including the package name, source URL, build instructions, and test imports, has not been altered.

Possibly related PRs

• [biobb_common] update 5.0.0 #51335: This PR updates the biobb_common package from version "4.2.0" to "5.0.0", which is directly related to the main PR that also updates the version of biobb_analysis from "4.2.0" to "5.0.0".
• [biobb_amber] update 5.0.0 #51430: This PR updates the biobb_amber package from version "4.2.0" to "5.0.0", similar to the main PR's version update for biobb_analysis.

Suggested reviewers

• adamhospital
• gbayarri

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📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between ee1e2aa and 97f5ee3.

📒 Files selected for processing (1)

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

🧰 Additional context used

🔇 Additional comments (4)

recipes/biobb_analysis/meta.yaml (4)

Line range hint 1-67: Summary of review and next steps

The changes in this PR appear to be consistent with a major version update from 4.2.0 to 5.0.0. We've identified the following key points:

1. Version number update
2. SHA256 checksum update
3. Unchanged dependencies and metadata

To ensure the integrity and correctness of this update, please:

1. Run the provided verification scripts to check version consistency across sources, validate the SHA256 checksum, and review any potential changes in dependencies or metadata.
2. If any discrepancies are found, address them before merging this PR.
3. Consider updating the package description or other metadata if there have been significant changes in this major version update.

Once these verifications are complete and any necessary adjustments are made, this PR should be ready for final review and merge.

🧰 Tools

🪛 yamllint

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

(syntax)

---

2-2: Verify version consistency across sources

The version has been updated from 4.2.0 to 5.0.0, which is a major version bump. This aligns with the PR objectives.

Let's confirm that this version is consistent with PyPI and the package's documentation:

#!/bin/bash
# Description: Verify version consistency across sources

# Test 1: Check PyPI version
echo "PyPI version:"
curl -s https://pypi.org/pypi/biobb_analysis/json | jq -r .info.version

# Test 2: Check GitHub releases
echo "Latest GitHub release:"
gh release list --repo bioexcel/biobb_analysis --limit 1 | awk '{print $1}'

# Test 3: Check setup.py or setup.cfg in the package repository
echo "Version in setup files:"
gh api /repos/bioexcel/biobb_analysis/contents/setup.py | jq -r .content | base64 -d | grep -i "version\s*=" || \
gh api /repos/bioexcel/biobb_analysis/contents/setup.cfg | jq -r .content | base64 -d | grep -i "version\s*="

---

10-10: Verify SHA256 checksum

The SHA256 checksum has been updated, which is expected with a new version. Let's verify that this checksum matches the actual package file on PyPI.

Run the following script to confirm the checksum:

---

Line range hint 20-30: Verify dependencies and metadata

The dependencies and their versions remain unchanged. Given this is a major version update, it's worth verifying if any dependencies need to be updated.

Also, please review other metadata (e.g., summary, description) to ensure they're up-to-date with the new version.

Let's check if there are any changes in the dependencies or metadata in the package repository:

✅ Verification successful

Dependencies and version update confirmed

The verification process has revealed that the dependencies have indeed been updated along with the major version bump to 5.0.0. Here are the key findings:

1. The version in setup.py has been updated to 5.0.0, matching the major version bump mentioned in the review comment.
2. The biobb_common dependency has been updated to version 5.0.0 in the install_requires section of setup.py.
3. The Python requirement has been updated to '>=3.9'.
4. Other dependencies mentioned in the conda recipe (gromacs, ambertools) are not listed in setup.py, which is expected as they are likely runtime dependencies rather than Python package dependencies.

The absence of changes to gromacs and ambertools versions in the conda recipe is correct, as these are external tools that may not necessarily follow the same versioning scheme as the Python package.

The README.md has also been updated to reflect the new version, confirming that the version bump has been applied consistently across the project.

In conclusion, the dependencies have been appropriately updated for this major version release, and no further action is required regarding the dependency verification.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for changes in dependencies and metadata

# Test 1: Check setup.py or setup.cfg for dependency changes
echo "Dependencies in setup files:"
gh api /repos/bioexcel/biobb_analysis/contents/setup.py | jq -r .content | base64 -d | grep -i "install_requires" -A 10 || \
gh api /repos/bioexcel/biobb_analysis/contents/setup.cfg | jq -r .content | base64 -d | grep -i "\[options\]" -A 10

# Test 2: Check README.md for any changes in description or metadata
echo "README.md changes:"
gh api /repos/bioexcel/biobb_analysis/commits?path=README.md&per_page=1 | jq -r '.[0].commit.message'

Length of output: 98052

---

Script:

#!/bin/bash
# Description: Check for changes in dependencies and metadata without using base64 and ent

# Function to decode base64 if available, else skip decoding
decode_content() {
  if command -v base64 >/dev/null 2>&1; then
    echo "$1" | base64 -d
  else
    echo "base64 command not found. Skipping decoding."
  fi
}

# Test 1: Check setup.py or setup.cfg for dependency changes
echo "Dependencies in setup files:"
setup_py_content=$(gh api /repos/bioexcel/biobb_analysis/contents/setup.py 2>/dev/null | jq -r '.content // empty')
setup_cfg_content=$(gh api /repos/bioexcel/biobb_analysis/contents/setup.cfg 2>/dev/null | jq -r '.content // empty')

if [ -n "$setup_py_content" ]; then
  decoded_setup_py=$(decode_content "$setup_py_content")
  echo "$decoded_setup_py" | grep -i "install_requires" -A 10
elif [ -n "$setup_cfg_content" ]; then
  decoded_setup_cfg=$(decode_content "$setup_cfg_content")
  echo "$decoded_setup_cfg" | grep -i "\[options\]" -A 10
else
  echo "Neither setup.py nor setup.cfg found in the repository."
fi

# Test 2: Check README.md for any changes in description or metadata
echo "README.md changes:"
readme_commit_message=$(gh api /repos/bioexcel/biobb_analysis/commits?path=README.md&per_page=1 2>/dev/null | jq -r '.[0].commit.message // "No commits found for README.md"')
echo "$readme_commit_message"

Length of output: 303685

---

Script:

#!/bin/bash
# Description: Fetch raw content of setup.py and check for requirements.txt

# Fetch raw content of setup.py
echo "Contents of setup.py:"
gh api /repos/bioexcel/biobb_analysis/contents/setup.py --header "Accept: application/vnd.github.v3.raw"

# Check if requirements.txt exists and fetch its contents if it does
echo -e "\nChecking for requirements.txt:"
if gh api /repos/bioexcel/biobb_analysis/contents/requirements.txt &> /dev/null; then
    echo "requirements.txt found. Contents:"
    gh api /repos/bioexcel/biobb_analysis/contents/requirements.txt --header "Accept: application/vnd.github.v3.raw"
else
    echo "requirements.txt not found."
fi

# Fetch the latest README.md content
echo -e "\nLatest README.md content:"
gh api /repos/bioexcel/biobb_analysis/contents/README.md --header "Accept: application/vnd.github.v3.raw" | head -n 20

Length of output: 5596

🧰 Tools

🪛 yamllint

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

(syntax)

---

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