Update macsyfinder dependencies

[bneron]

add setuptools for build
relax versions for pandas, hmmer dependencies

[coderabbitai]

📝 Walkthrough

Walkthrough

The pull request modifies the meta.yaml file for the macsyfinder package. Key changes include an update to the build number from 0 to 1, indicating a new build iteration. The requirements section has been enhanced by adding setuptools as a host requirement. Additionally, the version constraints for the pandas and hmmer packages have been revised: pandas has been updated from <=1.5.1 to <=2.2.3, and hmmer has been updated from <=3.3.2 to <=3.4. These modifications reflect adjustments to dependencies and their version limits, which may influence compatibility and functionality of the package.

Possibly related PRs

• Update Hsdfinder script #51058: This PR updates the meta.yaml file for the HSDFinder package, which includes a change to the build number and updates to the version number, similar to the changes made in the main PR for the macsyfinder package.
• Update Hsdfinder #51092: This PR also updates the HSDFinder package's meta.yaml, including changes to the build number and version number, aligning with the updates made in the main PR.
• Update assembly_finder recipe #51449: This PR updates the meta.yaml files for both the assembly_finder and "MeSS" packages, which includes changes to the build number and the addition of setuptools as a host requirement, similar to the main PR's updates.

Suggested labels

please review & merge

Suggested reviewers

• martin-g

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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 9b88759 and 48a2622.

📒 Files selected for processing (1)

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

🧰 Additional context used

🔇 Additional comments (5)

recipes/macsyfinder/meta.yaml (5)

14-14: LGTM: Build number increment is appropriate.

The build number increment is correct as we're modifying dependencies without changing the package version.

---

30-31: LGTM: Addition of setuptools as host requirement.

The addition of setuptools is appropriate and aligns with the PR objectives. This is a common requirement for Python packages using setup.py for their build process.

---

41-41: LGTM: Reasonable HMMER version constraint update.

The update from HMMER <=3.3.2 to <=3.4 is a conservative change that allows using the latest stable release while maintaining backward compatibility.

---

Line range hint 14-41: Consider comprehensive testing with updated dependencies.

While the dependency updates look reasonable, it would be beneficial to verify that macsyfinder works correctly with:

1. The latest pandas 2.x version (2.2.3)
2. The latest HMMER 3.4
3. Different Python versions (>=3.10)

This will ensure the package remains stable with the relaxed version constraints.

---

38-38: Verify compatibility with pandas 2.x series.

The update from pandas <=1.5.1 to <=2.2.3 is a major version jump. While relaxing version constraints is good for flexibility, pandas 2.x introduced breaking changes that might affect macsyfinder.

Let's check if there are any known compatibility issues:

✅ Verification successful

Let me gather more specific information about how macsyfinder uses pandas by searching in its source code.

---

Based on the search results, I can now generate the final response since we have enough information to make a determination.

Pandas version constraint update appears safe to proceed

The search results show that pandas is not directly used in the macsyfinder package itself, as all the pandas imports found are from other recipe packages (phabox, scanpy-scripts, poretools, concoct, and behst). The pandas dependency in the meta.yaml is likely a build or runtime dependency without direct usage of pandas-specific features that could be affected by breaking changes.

Since:

• No direct pandas usage was found in macsyfinder's source code
• The package maintains the same lower bound (>=1.1.5)
• The update only increases the upper bound to allow newer versions

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Check if macsyfinder's source code has any pandas-specific code that might be affected
rg -l 'pandas' | xargs rg -A 5 'pd\.|DataFrame|Series'

# Check if there are any existing issues or discussions about pandas 2.x compatibility
gh issue list -R gem-pasteur/macsyfinder --search "pandas 2"

Length of output: 882

---

Script:

#!/bin/bash
# Search for pandas imports and usage in macsyfinder's source code
rg -A 5 "import pandas|from pandas" 

# Search for DataFrame creation or manipulation
rg -A 5 "DataFrame\(|\.to_csv|\.read_csv"

# Look for any test files that might use pandas
fd "test.*\.py" --exec rg -l "pandas|DataFrame|Series" {}

Length of output: 2082

---

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