Claude/expand test coverage - #91

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Create four new test modules to expand coverage of previously untested code:

1. test_extract_3di.py (19 test methods, ~370 lines)
   - Tests for 3Di sequence extraction from PDB/CIF files
   - Argument parsing, file filtering, FASTA output validation
   - Integration tests for full workflow
   - Covers dscript/commands/extract_3di.py (~58 lines)

2. test_par_writer.py (24 test methods, ~400 lines)
   - Tests for parallel prediction writer process
   - TSV output writing, threshold filtering, contact map storage
   - HDF5 contact map dataset handling
   - Progress tracking and data type validation
   - Covers dscript/commands/par_writer.py (~40 lines)

3. test_main.py (24 test methods, ~320 lines)
   - Tests for CLI entry point and argument parsing
   - CitationAction class testing
   - All subcommand registration and invocation
   - Version and help flag handling
   - Integration tests for command dispatch
   - Covers dscript/__main__.py (~87 lines, increasing from ~85% to ~95%)

4. test_load_worker.py (23 test methods, ~330 lines)
   - Direct unit tests for HDF5 loading worker function
   - Queue handling, data type conversion, memory sharing
   - Error handling for corrupted/missing files
   - Multi-dimensional array support
   - Covers dscript/load_worker.py (~25 lines, previously only indirect coverage)

Total additions:
- ~1,420 lines of new test code
- 90+ test methods with comprehensive assertions
- ~210 lines of source code now directly tested
- Addresses high-priority gaps identified in coverage analysis

These tests complement the existing suite and focus on command-line
interface components and parallel processing infrastructure.

Rewrote test_load_worker.py to prevent CI hangs that occurred when
tests called the blocking worker function directly. The worker function
_hdf5_load_partial_func runs in an infinite loop waiting on a queue,
which caused tests to hang indefinitely.

Changes:
- Created run_worker_with_timeout() helper that wraps worker execution
  in a daemon thread with configurable timeout (default 5 seconds)
- Modified all tests to use this helper and assert successful completion
- Changed queue operations from blocking get() to non-blocking get_nowait()
- Reduced test count from 23 to 16 focused tests
- Added documentation noting worker is primarily tested via LoadingPool

This should resolve the CI timeout issue where tests hung at 43% completion.

The original tests were calling the real language model which:
- Downloads/loads pretrained model weights (slow, can fail)
- Runs actual neural network inference (resource intensive)
- Causes test failures when model files aren't available

Changes:
- Rewrote unit tests to mock get_pretrained() function
- Mock model returns realistic tensor shapes but doesn't load weights
- Tests are now fast, reliable, and don't require model files
- Moved real model tests to TestLanguageModelIntegration class
- Marked integration tests with @pytest.mark.slow so they can be skipped
- Removed unnecessary loguru import that caused import errors
- Removed problematic setup.py install step from setup_class

This should fix the 4 failing tests reported by CI.

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

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