test: increase test coverage overall - #49
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- create new test_helpers module to centralize file handling
- Introduce reusable test templates with `rstest_reuse`. - Add new test cases to ensure CLI subcommands handle missing inputs correctly. - Enhance subcommand coverage for `reformat-plate-reader-data`.
- Remove `#[ignore]` attribute for `test_blosum62_error_handling` as it is no longer needed. - Limit `set_blosum62_to_err_for_test` function visibility to the current module by removing `pub(crate)`.
…remove internal API dependency - Introduced `EnrichrAPITrait` to abstract API interactions. - Removed internal `api` field from `Enrichment` and adjusted `run` method to accept `EnrichrAPITrait` implementations. - Simplified `EnrichrAPI` initialization by passing `background` directly. refactor(enrichment): extract gene list parsing into separate function test: add tests for enrichment module
- Replaced `#[should_panic]` in `handle_command` tests with explicit error handling checks. - Added validation for unsupported background file usage in `handle_command`. - Introduced parameterized tests for `APIFailure::to_string` with `rstest`. - Enhanced `test_enrichr_result_empty` with multithreaded async execution and result persistence checks.
…tions - Introduced `create_dual_progress_bar` to handle progress bar creation for outer and inner loops. - Extracted `calculate_single_chain_score` and `calculate_single_chain_background_score` for better modularity and reduced code duplication. - Removed redundant `height` parameter by directly retrieving it from `groups.height()`. - Optimized test coverage by parameterizing `test_downsample_vec_limits` with `rstest`. - Added helper `get_f64_col_by_idx` to streamline test code for column value extraction. test(tcr-align): enforce `cargo nextest run` for `test_blosum62_error_handling` - Added an assertion to ensure the test runs only with `cargo nextest run` due to its reliance on per-test process isolation.
…onality - Added assertions in `read_excel` tests to ensure non-empty dimensions (width and height). - Introduced `test_read_excel_from_generic` for testing Excel file parsing with generic input.
…test` - Added tests for `thread_parser` and `thread_default` with separate cases for `base_cmd` and `no_base_cmd` configurations. - Refactored `num_cpu` logic to support test-specific overrides and ensure consistency in test environments. - Updated `thread_parser` to utilize the new `num_cpu` function.
…angerTCR chore: add missing empty line in gene list file
- Update `Cargo.lock` - Added `temp_testdir` for improved test sandboxing. - Adjusted Codecov config to include `target: auto` in project status checks.
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This closes #45.