Dev

[ypriverol]

Summary by CodeRabbit

• New Features

  • Updated version of the quantms-rescoring package to 0.0.2.
  • Enhanced command for rescoring with improved help instructions.

• Bug Fixes

  • Removed dependency on sdrf-pipelines to streamline the environment setup.

• Documentation

  • Updated licensing from MIT to Apache 2.0 for better compliance.

[coderabbitai]

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📥 Commits

Reviewing files that changed from the base of the PR and between 2957290 and b2825dd.

Walkthrough

The pull request introduces several modifications across multiple configuration files for the quantms-rescoring project. Key changes include the removal of the sdrf-pipelines dependency from both environment.yml and recipe/meta.yaml, and updates to version numbers across pyproject.toml, quantmsrescore/__init__.py, and recipe/meta.yaml, reflecting a new version of the project. Additionally, the Python version constraint in pyproject.toml has been changed to allow compatibility with Python 3.11, and the license type in recipe/meta.yaml has been updated from MIT to Apache 2.0.

Changes

File	Change Summary
environment.yml	Removed dependency: sdrf-pipelines>=0.0.31
pyproject.toml	Updated version: 0.0.1 to 0.0.2; changed Python version constraint: >=3.8,<3.11 to >=3.8,<3.12
quantmsrescore/init.py	Updated version: __version__ from "0.0.1" to "0.0.2"
recipe/meta.yaml	Updated version: 0.0.1 to 0.0.2; removed dependency: - sdrf-pipelines>=0.0.31; updated command; changed license from "MIT" to "Apache 2.0"

Possibly related PRs

• Minor changes.  #2: The recipe/meta.yaml file in this PR also removes the dependency on sdrf-pipelines, which is directly related to the changes made in the main PR regarding the removal of the same dependency in environment.yml.

Poem

In the garden where we play,
Dependencies have gone away!
With a hop and a skip, we cheer,
New versions bring us joy, oh dear!
From MIT to Apache's light,
Our project shines, oh what a sight! 🐇✨

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[coderabbitai]

Actionable comments posted: 2

🧹 Outside diff range and nitpick comments (2)

recipe/meta.yaml (1)

Line range hint 24-31: Consider relaxing version constraints for better compatibility

Several dependencies have strict version pins (ms2rescore=3.0.3, deepLC=2.2.38, scipy=1.13.1, protobuf=3.19.6). Consider using more flexible version constraints (e.g., >=) to allow for compatible updates and security patches.

pyproject.toml (1)

Line range hint 33-42: Consider standardizing dependency version constraints

The project uses a mix of exact pins (=) and wildcards (*) for dependencies. Consider:

1. Using consistent version constraint patterns
2. Documenting the rationale for strict pins vs flexible constraints
3. Aligning constraint patterns between pyproject.toml and meta.yaml

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between 9ef4a6a and 3f7df45.

📒 Files selected for processing (4)

• environment.yml (0 hunks)
• pyproject.toml (2 hunks)
• quantmsrescore/__init__.py (1 hunks)
• recipe/meta.yaml (2 hunks)

💤 Files with no reviewable changes (1)

• environment.yml

✅ Files skipped from review due to trivial changes (1)

• quantmsrescore/init.py

🔇 Additional comments (3)

recipe/meta.yaml (2)

4-4: LGTM: Version update is consistent

The version update to "0.0.2" aligns with changes in other project files.

---

39-39: LGTM: Additional test command

The added test command helps validate the ms2rescore subcommand functionality.

pyproject.toml (1)

6-6: LGTM: Version update is consistent

The version update to "0.0.2" matches the version in meta.yaml.