Added support for DIA-NN version 2.1.0

[ypriverol]

Summary by CodeRabbit

• New Features
  • Added support for DIA-NN version 2.1.0.
• Bug Fixes
  • Improved handling of report file formats for different DIA-NN versions, ensuring correct file type is used for all 1.x versions.
• Chores
  • Updated version number to 0.0.21.

[coderabbitai]

Walkthrough

This update increases the version number of the package from 0.0.20 to 0.0.21 in both the configuration and source files. In addition, the codebase now recognizes DIA-NN version 2.1.0 as valid. The logic for determining how to read the main report file has been refined: instead of excluding versions containing "2.0", the code now explicitly checks if the version starts with "1." to decide the file format and columns to read, ensuring more precise handling of different DIA-NN versions.

Changes

File(s)	Change Summary
pyproject.toml, quantmsutils/init.py	Incremented version from 0.0.20 to 0.0.21 in both the configuration and source files.
quantmsutils/diann/diann2mztab.py	Added support for DIA-NN version 2.1.0; refined logic for reading the main report file based on version.

Poem

Up hopped the version, a step to twenty-one,
DIA-NN grows wiser, new support has begun!
Reports now read smarter, with versions in mind,
The code checks the start, leaving old checks behind.
With numbers aligned and logic anew,
This rabbit’s release is hopping right through!
🐇✨

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📜 Recent review details

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📥 Commits

Reviewing files that changed from the base of the PR and between 467280d and f096815.

📒 Files selected for processing (3)

• pyproject.toml (1 hunks)
• quantmsutils/__init__.py (1 hunks)
• quantmsutils/diann/diann2mztab.py (2 hunks)

⏰ Context from checks skipped due to timeout of 90000ms (4)

• GitHub Check: Codacy Static Code Analysis
• GitHub Check: build (3.10)
• GitHub Check: build (3.9)
• GitHub Check: build

🔇 Additional comments (4)

pyproject.toml (1)

6-6: Version increment looks good

The version has been properly incremented from "0.0.20" to "0.0.21", which aligns with the changes made in the codebase, particularly the DIA-NN version 2.1.0 support added in the diann2mztab.py file.

quantmsutils/__init__.py (1)

1-1: Version update is consistent

The version string has been updated from "0.0.20" to "0.0.21", maintaining synchronization with the version in pyproject.toml. This consistency is important for proper package versioning.

quantmsutils/diann/diann2mztab.py (2)

375-376: Successfully added support for DIA-NN version 2.1.0

The list of supported DIA-NN versions has been extended to include version "2.1.0", which properly enables the software to recognize and work with this newer version.

---

475-480: Improved version detection logic

The logic for determining how to read the main report file has been refined to explicitly check if the version starts with "1." rather than checking if "2.0" is not contained in the version string. This change provides more precise handling of different DIA-NN versions and makes the code more maintainable.

For versions starting with "1.", it reads the report as a TSV file with specific columns plus "MS2.Scan". For all other versions (including 2.x series), it reads a parquet file with those columns plus "Decoy".

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