test: complete migration to structured test suite

Phase 1: Removed 6 duplicate old test files (fermi, finite_size, screening,
exchange, radiative, phase_space) — their tests are now in physics/ and quality/
using shared helpers from common/.

Phase 2: Migrated remaining 7 old test files:
- test_spectrum.py → integration/test_spectrum_pipeline.py (integration tests)
- test_fitter.py → physics/test_fitter.py (fit quality tests)
- test_cw_extractor.py → physics/test_cw_extractor.py (extraction accuracy)
- test_multi_branch.py → physics/test_multi_branch.py (branching physics)
- test_detector_response.py → physics/ + quality/ (split into physics + API)
- test_nuclear_data.py → quality/test_nuclear_data.py (parsing/API)
- test_logging_utils.py → quality/test_logging_utils.py (API tests)

Removed 12 old flat files, created 4 new files.
Total: 251 tests passing (6 skipped), down from 230 → 251 (net +21
from better coverage, not duplicates).

Test structure:
- tests/common/ — shared property/API helpers (eliminates ~18 duplicates)
- tests/physics/ — 10 files, unique physics behavior tests
- tests/quality/ — 8 files, API contract + parsing tests
- tests/integration/ — 1 file, end-to-end pipeline tests
This commit is contained in:
2026-05-15 15:52:50 +03:00
parent fea151d8d7
commit c78d0655a0
15 changed files with 145 additions and 1325 deletions
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"""
API / quality tests for DetectorResponse.
Tests factory methods, repr, error handling.
"""
import numpy as np
import pytest
from beta_spectrum.components.detector_response import DetectorResponse
class TestFactoryMethods:
"""Test convenience factory methods."""
def test_from_gaussian_params(self):
"""from_gaussian_params should create correct DetectorResponse."""
resp = DetectorResponse.from_gaussian_params(
channel_energy_range=(0.0, 5.0),
n_channels=1024,
sigma_a=0.005,
sigma_b=0.01,
tail_fraction=0.2,
tau=0.01,
model="gaussian_tail",
fano_factor=0.12,
)
assert resp.n_channels == 1024
assert np.isclose(resp.channel_energies[0], 0.0)
assert np.isclose(resp.channel_energies[-1], 5.0)
assert resp._mode == "analytical"
assert resp.tail_fraction == 0.2
def test_from_mc_simulation(self):
"""from_mc_simulation should create tabulated DetectorResponse."""
channel_energies = np.linspace(0.0, 5.0, 512)
calib_energies = np.array([1.0, 2.0, 3.0])
response_matrix = np.zeros((3, 512))
for i, e in enumerate(calib_energies):
idx = np.argmin(np.abs(channel_energies - e))
response_matrix[i, idx] = 1.0
resp = DetectorResponse.from_mc_simulation(
channel_energies=channel_energies,
response_matrix=response_matrix,
calibration_energies=calib_energies,
)
assert resp._mode == "tabulated"
assert resp.n_channels == 512
assert len(resp.calibration_energies) == 3
class TestEdgeCases:
"""Test edge cases and error handling."""
def test_repr_analytical(self):
"""__repr__ should show analytical mode info."""
channel_energies = np.linspace(0.0, 5.0, 100)
resp = DetectorResponse(channel_energies, model="gaussian", sigma_a=0.01)
repr_str = repr(resp)
assert "analytical" in repr_str
assert "gaussian" in repr_str
def test_repr_tabulated(self):
"""__repr__ should show tabulated mode info."""
channel_energies = np.linspace(0.0, 5.0, 100)
calib_energies = np.array([1.0, 2.0])
response_matrix = np.zeros((2, 100))
resp = DetectorResponse(
channel_energies=channel_energies,
response_matrix=response_matrix,
calibration_energies=calib_energies,
)
repr_str = repr(resp)
assert "tabulated" in repr_str
def test_invalid_model(self):
"""Should reject unknown model names."""
channel_energies = np.linspace(0.0, 5.0, 100)
resp = DetectorResponse(channel_energies, model="unknown_model")
try:
resp.get_response(2.0)
assert False, "Should have raised ValueError"
except ValueError as e:
assert "Unknown model" in str(e)
def test_convolve_mismatched_lengths(self):
"""Should reject mismatched W and spectrum_values lengths."""
channel_energies = np.linspace(0.0, 5.0, 100)
resp = DetectorResponse(channel_energies, model="gaussian")
W = np.linspace(0.0, 5.0, 100)
spectrum = np.zeros(50)
try:
resp.convolve(W, spectrum)
assert False, "Should have raised ValueError"
except ValueError:
pass
def test_non_1d_input(self):
"""Should reject non-1D inputs."""
channel_energies = np.linspace(0.0, 5.0, 100)
resp = DetectorResponse(channel_energies, model="gaussian")
W = np.array([[0.0, 5.0]])
spectrum = np.array([[1.0, 1.0]])
try:
resp.convolve(W, spectrum)
assert False, "Should have raised ValueError"
except ValueError:
pass
def test_tabulated_validation_wrong_columns(self):
"""Should reject response matrix with wrong column count."""
channel_energies = np.linspace(0.0, 5.0, 100)
calib_energies = np.array([1.0, 2.0])
response_matrix = np.zeros((2, 200))
try:
DetectorResponse(
channel_energies=channel_energies,
response_matrix=response_matrix,
calibration_energies=calib_energies,
)
assert False, "Should have raised ValueError"
except ValueError:
pass
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"""Tests for logging infrastructure."""
import logging
import os
import pytest
from beta_spectrum.logging_utils import (
LoggingConfig,
_find_git_root,
get_git_short_hash,
get_logger,
setup_logging,
)
class TestLoggingConfig:
"""Test LoggingConfig dataclass defaults and behavior."""
def test_default_level(self):
config = LoggingConfig()
assert config.level == "WARNING"
def test_default_log_file(self):
config = LoggingConfig()
assert config.log_file is None
def test_custom_level(self):
config = LoggingConfig(level="DEBUG")
assert config.level == "DEBUG"
def test_custom_log_file(self):
config = LoggingConfig(log_file="test.log")
assert config.log_file == "test.log"
class TestSetupLogging:
"""Test logging setup and configuration."""
def test_setup_returns_logger(self):
logger = setup_logging()
assert isinstance(logger, logging.Logger)
assert logger.name == "beta_spectrum"
def test_setup_sets_level(self):
config = LoggingConfig(level="DEBUG")
logger = setup_logging(config)
assert logger.level == logging.DEBUG
def test_setup_info_level(self):
config = LoggingConfig(level="INFO")
logger = setup_logging(config)
assert logger.level == logging.INFO
def test_setup_creates_console_handler(self):
config = LoggingConfig()
logger = setup_logging(config)
handlers = [h for h in logger.handlers if isinstance(h, logging.StreamHandler)]
assert len(handlers) == 1
def test_setup_creates_file_handler(self, tmp_path):
log_file = str(tmp_path / "test.log")
config = LoggingConfig(log_file=log_file)
logger = setup_logging(config)
file_handlers = [
h for h in logger.handlers if isinstance(h, logging.FileHandler)
]
assert len(file_handlers) == 1
assert os.path.exists(log_file)
def test_setup_prevents_duplicate_handlers(self):
config = LoggingConfig()
logger1 = setup_logging(config)
logger2 = setup_logging(config)
assert logger1 is logger2
assert len(logger1.handlers) == 1 # Only console handler
def test_setup_with_file_prevents_duplicates(self, tmp_path):
log_file = str(tmp_path / "test2.log")
config = LoggingConfig(log_file=log_file)
logger1 = setup_logging(config)
setup_logging(config) # Second call should not add handlers
assert len(logger1.handlers) == 2 # Console + File
class TestGetLogger:
"""Test getting named loggers."""
def test_get_logger_creates_child(self):
setup_logging()
logger = get_logger("test_module")
assert logger.name == "beta_spectrum.test_module"
assert logger.parent is not None
def test_get_logger_nested(self):
setup_logging()
logger = get_logger("spectrum.components")
assert logger.name == "beta_spectrum.spectrum.components"
class TestGitShortHash:
"""Test git hash retrieval."""
def test_returns_short_hash(self):
result = get_git_short_hash()
assert len(result) == 7
assert all(c in "0123456789abcdef" for c in result)
def test_returns_custom_length(self):
result = get_git_short_hash(length=5)
assert len(result) == 5
def test_returns_unknown_outside_repo(self):
# Patch _find_git_root to return a non-existent path
import unittest.mock
with unittest.mock.patch(
"beta_spectrum.logging_utils._find_git_root",
return_value="/nonexistent/path",
):
result = get_git_short_hash()
assert result == "unknown"
def test_find_git_root(self):
root = _find_git_root()
assert os.path.exists(os.path.join(root, ".git"))
class TestCSVMetadataHeader:
"""Test CSV export metadata header."""
def test_header_contains_version(self):
from beta_spectrum.spectrum import (
BetaSpectrum,
BetaSpectrumAnalyzer,
SpectrumConfig,
)
config = SpectrumConfig(
Z_parent=43,
Z_daughter=44,
A_number=99,
endpoint_MeV=0.294,
transition_type="F2",
)
spectrum = BetaSpectrum.from_config(config)
analyzer = BetaSpectrumAnalyzer(spectrum, config)
import tempfile
with tempfile.NamedTemporaryFile(mode="w", suffix=".csv", delete=False) as f:
filename = f.name
analyzer.export_to_csv(filename, source_type="paceENSDF")
with open(filename, "r") as f:
lines = f.readlines()
assert any("# beta-spectrum v" in line for line in lines)
assert any("0.3.0" in line for line in lines)
os.unlink(filename)
def test_header_contains_timestamp(self):
from beta_spectrum.spectrum import (
BetaSpectrum,
BetaSpectrumAnalyzer,
SpectrumConfig,
)
config = SpectrumConfig(
Z_parent=43,
Z_daughter=44,
A_number=99,
endpoint_MeV=0.294,
transition_type="F2",
)
spectrum = BetaSpectrum.from_config(config)
analyzer = BetaSpectrumAnalyzer(spectrum, config)
import tempfile
with tempfile.NamedTemporaryFile(mode="w", suffix=".csv", delete=False) as f:
filename = f.name
analyzer.export_to_csv(filename, source_type="json")
with open(filename, "r") as f:
content = f.read()
assert "# timestamp:" in content
os.unlink(filename)
def test_header_contains_nuclide_info(self):
from beta_spectrum.spectrum import (
BetaSpectrum,
BetaSpectrumAnalyzer,
SpectrumConfig,
)
config = SpectrumConfig(
Z_parent=43,
Z_daughter=44,
A_number=99,
endpoint_MeV=0.294,
transition_type="F2",
)
spectrum = BetaSpectrum.from_config(config)
analyzer = BetaSpectrumAnalyzer(spectrum, config)
import tempfile
with tempfile.NamedTemporaryFile(mode="w", suffix=".csv", delete=False) as f:
filename = f.name
analyzer.export_to_csv(filename, source_type="paceENSDF")
with open(filename, "r") as f:
content = f.read()
assert "# nuclide: Tc99 -> Ru99" in content
assert "Z=43->44" in content
os.unlink(filename)
def test_header_contains_git_commit(self):
from beta_spectrum.spectrum import (
BetaSpectrum,
BetaSpectrumAnalyzer,
SpectrumConfig,
)
config = SpectrumConfig(
Z_parent=43,
Z_daughter=44,
A_number=99,
endpoint_MeV=0.294,
transition_type="F2",
)
spectrum = BetaSpectrum.from_config(config)
analyzer = BetaSpectrumAnalyzer(spectrum, config)
import tempfile
with tempfile.NamedTemporaryFile(mode="w", suffix=".csv", delete=False) as f:
filename = f.name
analyzer.export_to_csv(filename, source_type="cli")
with open(filename, "r") as f:
content = f.read()
assert "# git_commit:" in content
os.unlink(filename)
def test_header_contains_corrections(self):
from beta_spectrum.spectrum import (
BetaSpectrum,
BetaSpectrumAnalyzer,
SpectrumConfig,
)
config = SpectrumConfig(
Z_parent=43,
Z_daughter=44,
A_number=99,
endpoint_MeV=0.294,
transition_type="F2",
)
spectrum = BetaSpectrum.from_config(config)
analyzer = BetaSpectrumAnalyzer(spectrum, config)
import tempfile
with tempfile.NamedTemporaryFile(mode="w", suffix=".csv", delete=False) as f:
filename = f.name
analyzer.export_to_csv(filename, source_type="paceENSDF")
with open(filename, "r") as f:
content = f.read()
assert "# corrections:" in content
assert "phase_space" in content
assert "fermi" in content
os.unlink(filename)
class TestCLILogging:
"""Test CLI logging integration."""
def test_verbose_flag_sets_info(self):
"""Test that -v sets INFO level."""
from beta_spectrum.cli import _build_parser
parser = _build_parser()
args = parser.parse_args(["--nuclide", "Tc99", "--dry-run"])
assert args.verbose == 0
def test_double_verbose_flag(self):
"""Test that -vv sets DEBUG level."""
from beta_spectrum.cli import _build_parser
parser = _build_parser()
args = parser.parse_args(["--nuclide", "Tc99", "--dry-run", "-vv"])
assert args.verbose == 2
def test_quiet_flag(self, capsys):
"""Test that -q suppresses output."""
from beta_spectrum.cli import _build_parser
parser = _build_parser()
args = parser.parse_args(["--nuclide", "Tc99", "--dry-run", "-q"])
assert args.quiet is True
def test_log_file_flag(self, capsys):
"""Test that --log-file sets log file path."""
from beta_spectrum.cli import _build_parser
parser = _build_parser()
args = parser.parse_args(
["--nuclide", "Tc99", "--dry-run", "--log-file", "/tmp/test.log"]
)
assert args.log_file == "/tmp/test.log"
def test_dry_run_flag(self, capsys):
"""Test that --dry-run is recognized."""
from beta_spectrum.cli import _build_parser
parser = _build_parser()
args = parser.parse_args(["--nuclide", "Tc99", "--dry-run"])
assert args.dry_run is True
def test_version_flag(self, capsys):
"""Test that --version prints version."""
from beta_spectrum.cli import _build_parser
parser = _build_parser()
with pytest.raises(SystemExit) as exc_info:
parser.parse_args(["--version"])
assert exc_info.value.code == 0
def test_removed_mode_flag(self):
"""Test that --mode option has been removed."""
from beta_spectrum.cli import _build_parser
parser = _build_parser()
with pytest.raises(SystemExit):
parser.parse_args(["--nuclide", "Tc99", "--mode", "beta_minus"])
def test_removed_transition_type_flag(self):
"""Test that --transition-type option has been removed."""
from beta_spectrum.cli import _build_parser
parser = _build_parser()
with pytest.raises(SystemExit):
parser.parse_args(["--nuclide", "Tc99", "--transition-type", "A"])
def test_removed_decay_index_flag(self):
"""Test that --decay-index option has been removed."""
from beta_spectrum.cli import _build_parser
parser = _build_parser()
with pytest.raises(SystemExit):
parser.parse_args(["--nuclide", "Tc99", "--decay-index", "0"])
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"""Tests for nuclear_data module (paceENSDF integration and JSON input)."""
import json
import tempfile
from pathlib import Path
from typing import Any, Dict
import pytest
# ruff: noqa: E402, ANN201, ANN001
from beta_spectrum.nuclear_data import ( # noqa: E402
BranchInfo,
DecayInfo,
create_config_from_source,
decay_info_to_config,
get_decay_info_from_paceENSDF,
json_to_config,
load_json_input,
validate_json_input,
_parse_nuclide_symbol,
)
from beta_spectrum.spectrum import SpectrumConfig
def _has_paceENSDF() -> bool: # noqa: ANN201
"""Check if paceENSDF is available."""
try:
import paceENSDF # noqa: F401
return True
except ImportError:
return False
# ---------------------------------------------------------------------------
# _parse_nuclide_symbol
# ---------------------------------------------------------------------------
class TestParseNuclideSymbol:
"""Test nuclide symbol parsing."""
def test_tc99(self):
element, Z, A = _parse_nuclide_symbol("Tc99")
assert element == "Tc"
assert Z == 43
assert A == 99
def test_co60(self):
element, Z, A = _parse_nuclide_symbol("Co60")
assert element == "Co"
assert Z == 27
assert A == 60
def test_he3(self):
element, Z, A = _parse_nuclide_symbol("He3")
assert element == "He"
assert Z == 2
assert A == 3
def test_invalid_symbol(self):
with pytest.raises(ValueError, match="Cannot parse nuclide symbol"):
_parse_nuclide_symbol("99Tc")
def test_unknown_element(self):
with pytest.raises(ValueError, match="Unknown element symbol"):
_parse_nuclide_symbol("Xx99")
# ---------------------------------------------------------------------------
# validate_json_input
# ---------------------------------------------------------------------------
class TestValidateJsonInput:
"""Test JSON input validation."""
def test_valid_input(self):
data = {
"endpoint_MeV": 0.5,
"Z_parent": 43,
"Z_daughter": 44,
"A_number": 99,
}
validate_json_input(data) # should not raise
def test_missing_endpoint(self):
data = {"Z_parent": 43, "Z_daughter": 44, "A_number": 99}
with pytest.raises(ValueError, match="Missing required field"):
validate_json_input(data)
def test_negative_endpoint(self):
data = {
"endpoint_MeV": -0.5,
"Z_parent": 43,
"Z_daughter": 44,
"A_number": 99,
}
with pytest.raises(ValueError, match="endpoint_MeV must be positive"):
validate_json_input(data)
def test_invalid_transition_type(self):
data = {
"endpoint_MeV": 0.5,
"Z_parent": 43,
"Z_daughter": 44,
"A_number": 99,
"transition_type": "invalid",
}
with pytest.raises(ValueError, match="Invalid transition_type"):
validate_json_input(data)
# ---------------------------------------------------------------------------
# load_json_input / json_to_config
# ---------------------------------------------------------------------------
class TestJsonInput:
"""Test JSON file loading and conversion."""
def _write_json(self, data: Dict[str, Any]) -> Path:
"""Write data to a temp JSON file."""
tmp = tempfile.NamedTemporaryFile(mode="w", suffix=".json", delete=False)
json.dump(data, tmp)
tmp.close()
return Path(tmp.name)
def test_load_and_convert(self):
data = {
"parent_symbol": "Tc99",
"Z_parent": 43,
"Z_daughter": 44,
"A_number": 99,
"endpoint_MeV": 0.294,
"transition_type": "F2",
"e_step_MeV": 0.001,
}
path = self._write_json(data)
try:
loaded = load_json_input(str(path))
config = json_to_config(loaded)
assert isinstance(config, SpectrumConfig)
assert config.Z_parent == 43
assert config.Z_daughter == 44
assert config.A_number == 99
assert abs(config.endpoint_MeV - 0.294) < 1e-6
assert config.transition_type == "F2"
assert config.e_step_MeV == 0.001
finally:
path.unlink()
def test_defaults_filled(self):
data = {
"Z_parent": 43,
"Z_daughter": 44,
"A_number": 99,
"endpoint_MeV": 0.294,
}
path = self._write_json(data)
try:
loaded = load_json_input(str(path))
# Defaults should be filled in
assert loaded["detector_model"] == "gaussian"
assert loaded["detector_sigma_a_keV"] == 1.0
finally:
path.unlink()
def test_file_not_found(self):
with pytest.raises(FileNotFoundError):
load_json_input("/nonexistent/file.json")
# ---------------------------------------------------------------------------
# decay_info_to_config
# ---------------------------------------------------------------------------
class TestDecayInfoToConfig:
"""Test conversion from DecayInfo to SpectrumConfig."""
def test_basic_conversion(self):
info = DecayInfo(
parent_symbol="Tc99",
Z_parent=43,
Z_daughter=44,
A_number=99,
endpoint_keV=294000.0,
endpoint_MeV=0.294,
transition_type="A",
forbiddenness_code="0A",
parent_J=4.5,
parent_pi=1,
half_life="y",
branches=[],
)
config = decay_info_to_config(info)
assert isinstance(config, SpectrumConfig)
assert config.Z_parent == 43
assert config.Z_daughter == 44
assert config.A_number == 99
assert abs(config.endpoint_MeV - 0.294) < 1e-6
assert config.transition_type == "A"
def test_with_detector_response(self):
info = DecayInfo(
parent_symbol="Co60",
Z_parent=27,
Z_daughter=28,
A_number=60,
endpoint_keV=317860.0,
endpoint_MeV=0.31786,
transition_type="A",
forbiddenness_code="1A",
parent_J=0.0,
parent_pi=1,
half_life="y",
branches=[],
)
config = decay_info_to_config(
info, use_detector_response=True, e_step_MeV=0.005
)
assert config.use_detector_response is True
assert config.e_step_MeV == 0.005
# ---------------------------------------------------------------------------
# get_decay_info_from_paceENSDF
# ---------------------------------------------------------------------------
@pytest.mark.skipif(not _has_paceENSDF(), reason="paceENSDF not installed")
class TestPaceENSDFIntegration:
"""Test paceENSDF data retrieval."""
def test_tc99_beta_minus(self):
info = get_decay_info_from_paceENSDF("Tc99", "beta_minus")
assert isinstance(info, DecayInfo)
assert info.parent_symbol == "Tc99"
assert info.Z_parent == 43
assert info.Z_daughter == 44
assert info.A_number == 99
assert info.endpoint_MeV > 0
assert len(info.branches) > 0
def test_co60_beta_minus(self):
info = get_decay_info_from_paceENSDF("Co60", "beta_minus")
assert isinstance(info, DecayInfo)
assert info.parent_symbol == "Co60"
assert info.Z_parent == 27
assert info.Z_daughter == 28
assert info.A_number == 60
assert info.endpoint_MeV > 0
def test_branch_info(self):
info = get_decay_info_from_paceENSDF("Tc99", "beta_minus")
for branch in info.branches:
assert isinstance(branch, BranchInfo)
assert branch.level_index >= 0
assert branch.level_energy_keV >= 0
assert 0 < branch.intensity <= 1.0
if branch.log_ft is not None:
assert branch.log_ft > 0
def test_tc99_intensity_values(self):
"""Tc99 intensities from ENSDF: GS=99.9984%, 89.5keV=0.0016%."""
info = get_decay_info_from_paceENSDF("Tc99", "beta_minus")
gs = next(b for b in info.branches if b.level_energy_keV == 0.0)
ex = next(b for b in info.branches if b.level_energy_keV == 89.5)
assert abs(gs.intensity - 0.999984) < 1e-6
assert abs(ex.intensity - 0.000016) < 1e-6
def test_invalid_nuclide(self):
with pytest.raises(ValueError, match="Unknown element symbol"):
get_decay_info_from_paceENSDF("Xx99", "beta_minus")
def test_no_decay_data(self):
# Pb208 is stable, no beta-minus decay data
with pytest.raises(ValueError, match="No BM decay data found"):
get_decay_info_from_paceENSDF("Pb208", "beta_minus")
# ---------------------------------------------------------------------------
# create_config_from_source
# ---------------------------------------------------------------------------
class TestCreateConfigFromSource:
"""Test the unified config creation interface."""
def _write_json(self, data: Dict[str, Any]) -> Path:
tmp = tempfile.NamedTemporaryFile(mode="w", suffix=".json", delete=False)
json.dump(data, tmp)
tmp.close()
return Path(tmp.name)
def test_json_source(self):
data = {
"Z_parent": 43,
"Z_daughter": 44,
"A_number": 99,
"endpoint_MeV": 0.294,
}
path = self._write_json(data)
try:
config = create_config_from_source("json", json_path=str(path))
assert isinstance(config, SpectrumConfig)
assert config.Z_parent == 43
finally:
path.unlink()
def test_unknown_source(self):
with pytest.raises(ValueError, match="Unknown source"):
create_config_from_source("unknown", nuclide="Tc99")
def test_paceENSDF_requires_nuclide(self):
with pytest.raises(ValueError, match="nuclide parameter required"):
create_config_from_source("paceENSDF")
def test_json_requires_path(self):
with pytest.raises(ValueError, match="json_path parameter required"):
create_config_from_source("json")