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feat(cli): separate-branches rename, short aliases, clean dry-run

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- --normalize-to-one renamed to --separate-branches (no alias; the
  name now describes the output choice: total spectrum with
  intensity-normalized branches vs separate branches, each
  normalized to unit area with intensities left to the data user).
  SpectrumConfig.normalize_to_one -> separate_branches, CSV header
  word to_one -> separate.
- every long option gains a single-letter alias: -N -i -s -m -o -p
  -L -d -c -V -S -b (only -v/-q existed before)
- dry-run drops the top-level Transition: line — the per-branch
  list below already reports each branch's transition type
- version bumped to 0.4.1 (pyproject, __version__, CSV semantics
  docstring, TODO roadmap entry)
This commit is contained in:
unzhakov
2026-10-03 01:08:51 +03:00
parent 7f47a876ae
commit 2788ea0683
12 changed files with 210 additions and 53 deletions
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tests/physics/test_core_spectrum.py
+20 -18
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@@ -313,8 +313,8 @@ class TestCSVExportCoreSemantics:
assert "phase_space" in core_line[0]
assert "fermi" in core_line[0]
def test_normalize_to_one_per_branch_unit_area(self, tmp_path: Any) -> None:
config = make_multi_config(normalize_to_one=True)
def test_separate_branches_per_branch_unit_area(self, tmp_path: Any) -> None:
config = make_multi_config(separate_branches=True)
spectrum = BetaSpectrum.from_config(config)
analyzer = BetaSpectrumAnalyzer(spectrum, config)
_, df = export_and_read(analyzer, tmp_path)
@@ -334,12 +334,12 @@ class TestCSVExportCoreSemantics:
analyzer.export_to_csv(path)
assert not (tmp_path / "degenerate.csv").exists()
def test_degenerate_export_raises_in_normalize_to_one_mode(
def test_degenerate_export_raises_in_separate_branches_mode(
self, tmp_path: Any
) -> None:
"""The positive-integral guard must apply in to_one mode too:
"""The positive-integral guard must apply in separate-branches mode too:
no all-zero CSV may be written for a degenerate spectrum."""
config = make_degenerate_config(normalize_to_one=True)
config = make_degenerate_config(separate_branches=True)
spectrum = BetaSpectrum.from_config(config)
analyzer = BetaSpectrumAnalyzer(spectrum, config)
path = str(tmp_path / "degenerate_to_one.csv")
@@ -567,13 +567,13 @@ class TestAnalyzerUniversalFactor:
class TestNormalizationModeMatrix:
"""to_one and intensity modes must behave consistently across CSV
"""separate_branches and intensity modes must behave consistently across CSV
verbosity, branch count and the CSV-driven visualizer."""
def test_to_one_concise_multi_unit_area_no_total_no_components(
def test_separate_branches_concise_multi_unit_area_no_total_no_components(
self, tmp_path: Any
) -> None:
config = make_multi_config(normalize_to_one=True)
config = make_multi_config(separate_branches=True)
spectrum = BetaSpectrum.from_config(config)
analyzer = BetaSpectrumAnalyzer(spectrum, config)
path, df = export_and_read(
@@ -587,14 +587,14 @@ class TestNormalizationModeMatrix:
"branch_3",
}
header = header_lines_of(path)
assert any("branch normalization: to_one" in h for h in header)
assert any("branch normalization: separate" in h for h in header)
energies = df["energy_MeV"].to_numpy()
for col in ("branch_1", "branch_2", "branch_3"):
area = np.trapezoid(df[col].to_numpy(), energies)
assert np.isclose(area, 1.0, rtol=5e-4)
def test_to_one_single_mode_unit_area(self, tmp_path: Any) -> None:
config = make_single_config(normalize_to_one=True)
def test_separate_branches_single_mode_unit_area(self, tmp_path: Any) -> None:
config = make_single_config(separate_branches=True)
spectrum = BetaSpectrum.from_config(config)
analyzer = BetaSpectrumAnalyzer(spectrum, config)
_path, df = export_and_read(analyzer, tmp_path, "to_one_single.csv")
@@ -622,10 +622,10 @@ class TestNormalizationModeMatrix:
nonzero = total > 1e-12
assert np.all(np.abs(summed[nonzero] - total[nonzero]) <= total[nonzero] * 5e-4)
def test_plot_from_csv_to_one_plots_branches_without_total(
def test_plot_from_csv_separate_branches_plots_branches_without_total(
self, tmp_path: Any
) -> None:
config = make_multi_config(normalize_to_one=True)
config = make_multi_config(separate_branches=True)
spectrum = BetaSpectrum.from_config(config)
analyzer = BetaSpectrumAnalyzer(spectrum, config)
path, df = export_and_read(analyzer, tmp_path, "to_one_plot.csv")
@@ -633,7 +633,7 @@ class TestNormalizationModeMatrix:
fig = Visualizer.plot_from_csv(path, save_path=None, show_components=True)
assert len(fig.axes) == 4
# Panel 1 has exactly the 3 branch curves — no total spectrum
# exists in to_one mode.
# exists in separate-branches mode.
panel = fig.axes[0]
curves = [np.asarray(ln.get_xydata()) for ln in panel.lines]
assert len(curves) == 3
@@ -641,8 +641,10 @@ class TestNormalizationModeMatrix:
assert np.allclose(curves[0][:, 0], energies)
assert np.allclose(curves[0][:, 1], df["branch_1_spectrum"].to_numpy())
def test_plot_analysis_to_one_returns_figure(self, tmp_path: Any) -> None:
config = make_multi_config(normalize_to_one=True)
def test_plot_analysis_separate_branches_returns_figure(
self, tmp_path: Any
) -> None:
config = make_multi_config(separate_branches=True)
spectrum = BetaSpectrum.from_config(config)
analyzer = BetaSpectrumAnalyzer(spectrum, config)
save = str(tmp_path / "analysis.png")
@@ -650,10 +652,10 @@ class TestNormalizationModeMatrix:
assert len(fig.axes) == 4
assert (tmp_path / "analysis.png").exists()
def test_plot_from_csv_to_one_concise_warns_and_falls_back(
def test_plot_from_csv_separate_branches_concise_warns_and_falls_back(
self, tmp_path: Any, capsys: Any
) -> None:
config = make_multi_config(normalize_to_one=True)
config = make_multi_config(separate_branches=True)
spectrum = BetaSpectrum.from_config(config)
analyzer = BetaSpectrumAnalyzer(spectrum, config)
path, df = export_and_read(