Add local and online PfamScan support

[ShinThomas]

Summary

Adds local and online PfamScan support to the refactor-v2 domain scanning workflow.

Changes

Local PfamScan

• Added LocalPfamScanner
• Runs local pfam_scan.pl
• Writes the protein query to a temporary FASTA file
• Uses the configured Pfam database directory
• Parses local PfamScan output into DomainRecord
• Converts Pfam coordinates to zero-based, half-open indexing

Online PfamScan

• Added OnlinePfamScanner
• Submits jobs to the EMBL-EBI PfamScan service
• Explicitly requests JSON output
• Polls job status with bounded retries
• Discovers the JSON result type
• Fetches and parses the result into DomainRecord
• Handles terminal failure and timeout states

Tests

Added focused test modules:

• tests/v2/test_local_pfam.py
• tests/v2/test_online_pfam.py

Focused local and online Pfam tests pass, and the full v2 test suite passes.

Remaining work

• PfamScan validation on SCC would be good

[Copilot]

Copilot review overview

🔵 Needs a closer look

Fix Windows temporary-file handling in the local scanner; add the missing Pfam API documentation.

Review effort: Lite
Findings: None

What changed in this PR

Adds local and online PfamScan adapters for the v2 domain-scanning workflow.

Changes:

• Added local PfamScan execution and parsing.
• Added online submission, polling, and JSON result handling.
• Added focused local and online scanner tests.

File	Summary
tests/​v2/​test_online_pfam.py	Tests online scanning behavior.
tests/​v2/​test_local_pfam.py	Tests local scanning behavior.
src/​lverage/​pfam.py	Implements both scanners. Needs Windows-safe temporary-file handling and API documentation updates.

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[AnthonyGarza124]

Awesome. So I looked at the copilot review and agreed with what it said after I reviewed. So the problem was that Windows is a pain with temporary files and can fail to run a process on a file that is currently open/being written to. So I applied a patch that makes sure the file is closed and applied a try and catch statement around just in case.

[AnthonyGarza124]

@ShinThomas If possible re-run the code and its tests to make sure they work fine with my adjustment. Then comment on the PR again and I'll look at it.

[ShinThomas]

Retested after the temporary-file handling patch.

• Local PfamScan unit tests: 5 passed.
• Online PfamScan unit tests: 6 passed.