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"""
Performance and benchmark tests for Kalign Python package.
"""
import pytest
import time
import kalign
class TestPerformance:
"""Test performance characteristics and benchmarks."""
@pytest.mark.performance
def test_basic_alignment_speed(self, dna_simple, benchmark):
"""Benchmark basic alignment speed."""
result = benchmark(kalign.align, dna_simple, seq_type="dna")
assert len(result) == len(dna_simple)
@pytest.mark.performance
def test_threading_speedup(self, dna_with_gaps):
"""Test that multiple threads provide speedup."""
# Single thread
start_time = time.time()
aligned_single = kalign.align(dna_with_gaps, seq_type="dna", n_threads=1)
single_time = time.time() - start_time
# Multiple threads
start_time = time.time()
aligned_multi = kalign.align(dna_with_gaps, seq_type="dna", n_threads=2)
multi_time = time.time() - start_time
# Results should be identical
assert aligned_single == aligned_multi
# Just verify both completed successfully - timing comparisons are unreliable in CI
print(
f"Single-thread time: {single_time:.6f}s, Multi-thread time: {multi_time:.6f}s"
)
@pytest.mark.performance
@pytest.mark.slow
def test_large_sequence_performance(self):
"""Test performance with larger sequences."""
large_seqs = ["ATCG" * 100] * 10 # 400bp sequences
start_time = time.time()
aligned = kalign.align(large_seqs, seq_type="dna")
elapsed = time.time() - start_time
assert len(aligned) == 10
assert elapsed < 10.0 # Should complete in reasonable time
@pytest.mark.performance
def test_memory_usage_reasonable(self, dna_simple):
"""Test that memory usage is reasonable."""
# This is a basic test - could be enhanced with memory profiling
aligned = kalign.align(dna_simple * 10) # 30 sequences
assert len(aligned) == 30
@pytest.mark.performance
def test_dna_alignment_speed(self, dna_simple, benchmark):
"""Benchmark DNA alignment speed."""
result = benchmark.pedantic(
kalign.align, args=[dna_simple], kwargs={"seq_type": "dna"}, rounds=3
)
assert len(result) == len(dna_simple)
@pytest.mark.performance
def test_protein_alignment_speed(self, protein_simple, benchmark):
"""Benchmark protein alignment speed."""
result = benchmark.pedantic(
kalign.align,
args=[protein_simple],
kwargs={"seq_type": "protein"},
rounds=3,
)
assert len(result) == len(protein_simple)
@pytest.mark.performance
@pytest.mark.parametrize("n_threads", [1, 2, 4, 8, 16])
def test_dna_threading_performance(self, n_threads, benchmark):
"""Test DNA alignment performance with different thread counts."""
# Generate a larger problem to really test threading
sequences = kalign.generate_test_sequences(
n_seq=200, # 200 sequences - much more demanding
n_obs=30, # 30 observed sequences for HMM training
dna=True, # DNA sequences
length=1000, # 1000bp sequences - much longer
seed=42, # Reproducible results
)
result = benchmark.pedantic(
kalign.align,
args=[sequences],
kwargs={"seq_type": "dna", "n_threads": n_threads},
rounds=1, # Reduced rounds due to longer runtime
)
assert len(result) == len(sequences)
# Verify alignment length consistency
if result:
expected_length = len(result[0])
for seq in result:
assert len(seq) == expected_length
@pytest.mark.performance
@pytest.mark.parametrize("n_threads", [1, 2, 4, 8, 16])
def test_protein_threading_performance(self, n_threads, benchmark):
"""Test protein alignment performance with different thread counts."""
# Generate a larger problem to really test threading
sequences = kalign.generate_test_sequences(
n_seq=150, # 150 sequences - more demanding
n_obs=25, # 25 observed sequences for HMM training
dna=False, # Protein sequences
length=320, # 320aa sequences - much longer
seed=123, # Different seed for variety
)
result = benchmark.pedantic(
kalign.align,
args=[sequences],
kwargs={"seq_type": "protein", "n_threads": n_threads},
rounds=1, # Reduced rounds due to longer runtime
)
assert len(result) == len(sequences)
# Verify alignment length consistency
if result:
expected_length = len(result[0])
for seq in result:
assert len(seq) == expected_length
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