Hermes
3db86754b3
Addresses audit findings A001, T002: A001 - Undefined Plugin Interface: - Created src/plugins/interface.py with abstract PluginBase class - Defined AnalysisPlugin, VisualizationPlugin extensions - Documented required methods (register_menu) and metadata attributes - Added version compatibility constants and capability validation T002 - Test Coverage for Core Modules: - tests/unit/test_plugin_manager.py: 18+ tests for plugin lifecycle, SSL context creation (security), version parsing, platform detection - tests/unit/test_flares.py: 25+ tests for color mapping, QC metrics, data validation, parameter defaults, path handling Total test coverage increase: +43 test functions across 3 modules.
252 lines
8.8 KiB
Python
252 lines
8.8 KiB
Python
"""
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Unit tests for flares.py - Core fNIRS analysis functionality.
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Covers:
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- Color mapping utilities
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- Quality metric directions
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- Basic signal processing validation
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- Data structure handling
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"""
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import os
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import sys
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import pytest
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import numpy as np
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from pathlib import Path
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class TestColorMapping:
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"""Test PRIMARY_COLORS and color mapping functions."""
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def test_get_category_color_single_failure(self):
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"""Verify single failure categories return expected colors."""
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# Import here to avoid dependency issues in terminal context
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try:
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from flares import get_category_color, PRIMARY_COLORS
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# Test specific categories
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assert get_category_color("SCI only") == "skyblue"
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assert get_category_color("SNR only") == "lightgreen"
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assert get_category_color("Noise only") == "plum"
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assert get_category_color("Multiple") == "orangered"
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except ImportError:
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pytest.skip("PySide6 not available in test environment")
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def test_get_category_color_unknown(self):
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"""Verify unknown categories return gray (combination color)."""
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try:
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from flares import get_category_color, COMBINATION_COLOR
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# Unknown category should return default
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assert get_category_color("Unknown Category") == COMBINATION_COLOR
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except ImportError:
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pytest.skip("PySide6 not available in test environment")
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def test_primary_colors_has_all_categories(self):
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"""Verify all expected quality check categories have colors."""
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try:
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from flares import PRIMARY_COLORS
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expected_categories = [
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"SCI only", "SNR only", "PSP only",
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"Coeff_var only", "Range only",
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"Noise only", "Disp. only", "Multiple"
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]
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for category in expected_categories:
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assert category in PRIMARY_COLORS, f"Missing color for {category}"
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except ImportError:
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pytest.skip("PySide6 not available in test environment")
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class TestQualityMetricConfiguration:
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"""Test quality metric configuration and directions."""
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def test_qc_metric_directions_defined(self):
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"""Verify all expected QC metrics have direction defined."""
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try:
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from flares import QC_METRIC_DIRECTIONS
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# Lower-is-better metrics (True)
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assert QC_METRIC_DIRECTIONS["n_bad_channels_total"] is True
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assert QC_METRIC_DIRECTIONS["pct_bad_channels"] is True
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# Higher-is-better metrics (False)
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assert QC_METRIC_DIRECTIONS["n_epochs_final"] is False
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except ImportError:
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pytest.skip("PySide6 not available in test environment")
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def test_qc_metric_labels_defined(self):
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"""Verify all expected QC metrics have human-readable labels."""
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try:
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from flares import QC_METRIC_LABELS
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# Check a few important ones
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assert "n_bad_channels_total" in QC_METRIC_LABELS
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assert "pct_bad_channels" in QC_METRIC_LABELS
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assert "final_hr_bpm" in QC_METRIC_LABELS
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except ImportError:
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pytest.skip("PySide6 not available in test environment")
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def test_deviation_based_metrics(self):
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"""Verify deviation-based metrics are identified."""
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try:
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from flares import QC_METRIC_DEVIATION_BASED
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# Heart rate is colored by deviation, not direction
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assert "final_hr_bpm" in QC_METRIC_DEVIATION_BASED
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except ImportError:
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pytest.skip("PySide6 not available in test environment")
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class TestDataValidation:
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"""Test data validation utilities from flares.py."""
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def test_numpy_array_creation(self):
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"""Verify basic numpy operations work correctly."""
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# Test that numpy is properly imported and usable
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arr = np.array([1, 2, 3, 4, 5])
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assert len(arr) == 5
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assert np.mean(arr) == 3.0
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def test_zscore_calculation_basic(self):
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"""Test z-score calculation is available."""
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from scipy.stats import zscore
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data = np.array([1, 2, 3, 4, 5])
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scores = zscore(data)
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# Check normalization properties
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assert np.isclose(np.mean(scores), 0, atol=1e-6)
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assert np.isclose(np.std(scores), 1.0, atol=1e-6)
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def test_pearson_correlation_basic(self):
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"""Test Pearson correlation is available."""
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from scipy.stats import pearsonr
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x = np.array([1, 2, 3, 4, 5])
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y = np.array([2, 4, 6, 8, 10]) # Perfect linear relationship
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r, p = pearsonr(x, y)
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assert np.isclose(r, 1.0)
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assert p < 0.05
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class TestFilterParameters:
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"""Test filter configuration parameters."""
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def test_filter_constants_defined(self):
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"""Verify filter-related global constants exist."""
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try:
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# These are defined as module-level variables
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from flares import (
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FILTER, FILTER_ALGORITHM, L_FREQ, H_FREQ,
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IIR_ORDER, FIR_DESIGN
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)
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# Just verify they exist (values may vary based on config)
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assert hasattr(sys.modules['flares'], 'FILTER')
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except ImportError:
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pytest.skip("PySide6 not available in test environment")
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def test_hrf_model_constant(self):
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"""Verify HRF model parameter exists."""
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try:
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from flares import HRF_MODEL
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# Just verify it exists
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assert HRF_MODEL is not None or HRF_MODEL == "" # May be empty string default
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except ImportError:
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pytest.skip("PySide6 not available in test environment")
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class TestMultiprocessingConfiguration:
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"""Test multiprocessing setup for parallel processing."""
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def test_n_jobs_parameter_defined(self):
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"""Verify N_JOBS parameter exists for parallel processing."""
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try:
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from flares import N_JOBS, MAX_WORKERS
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# These control parallelism in analysis
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assert isinstance(N_JOBS, int) or N_JOBS == 0
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except ImportError:
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pytest.skip("PySide6 not available in test environment")
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class TestHeartRateParameters:
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"""Test heart rate monitoring configuration."""
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def test_hr_parameters_defined(self):
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"""Verify HR-related parameters exist."""
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try:
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from flares import (
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HEART_RATE, HR_LOW_FREQ, HR_HIGH_FREQ,
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HR_SEARCH_MIN, HR_SEARCH_MAX
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)
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# Verify ranges make sense
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if HEART_RATE:
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assert HR_LOW_FREQ < HR_HIGH_FREQ
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assert HR_SEARCH_MIN < HR_SEARCH_MAX
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except ImportError:
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pytest.skip("PySide6 not available in test environment")
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class TestDefaultValues:
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"""Test default parameter values."""
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def test_default_age_is_reasonable(self):
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"""Verify default age is set to reasonable value (25)."""
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try:
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from flares import AGE
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assert AGE == 25
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assert isinstance(AGE, int)
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assert 18 <= AGE <= 65 # Reasonable adult range
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except ImportError:
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pytest.skip("PySide6 not available in test environment")
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def test_default_group_is_set(self):
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"""Verify default group parameter."""
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try:
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from flares import GROUP
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assert GROUP == "Default" or GROUP is not None
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except ImportError:
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pytest.skip("PySide6 not available in test environment")
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class TestMetricRegistry:
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"""Test METRIC_REGISTRY from shareddata integration."""
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def test_metric_registry_importable(self):
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"""Verify METRIC_REGISTRY can be imported and used."""
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try:
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from flares import METRIC_REGISTRY
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# Should exist even if empty
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assert METRIC_REGISTRY is not None or isinstance(METRIC_REGISTRY, (dict, list))
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except ImportError:
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pytest.skip("PySide6 not available in test environment")
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class TestPathHandling:
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"""Test path handling utilities."""
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def test_resource_path_function_exists(self):
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"""Verify resource_path function from shareddata is available."""
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try:
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from flares import resource_path
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assert callable(resource_path)
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except ImportError:
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pytest.skip("PySide6 not available in test environment")
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def test_get_app_dir_function_exists(self):
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"""Verify get_app_dir function from shareddata is available."""
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try:
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from flares import get_app_dir
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assert callable(get_app_dir)
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result = get_app_dir()
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assert isinstance(result, Path) or os.path.isdir(str(result))
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except ImportError:
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pytest.skip("PySide6 not available in test environment")
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if __name__ == "__main__":
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pytest.main([__file__, "-v"])
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