pre-commit fixes

.readthedocs.yaml

@@ -10,13 +10,8 @@ build:
   jobs:
     pre_build:
       - rm -rf docs/source/api
-      - sphinx-apidoc
-        --private
-        --module-first
-        --force
-        --output-dir docs/source/api
-        src/legendoptics
-        src/legendoptics/_version.py
+      - sphinx-apidoc --private --module-first --force --output-dir
+        docs/source/api src/legendoptics src/legendoptics/_version.py
 
 python:
   install:

README.md

@@ -11,8 +11,14 @@
 ![License](https://img.shields.io/github/license/legend-exp/legend-pygeom-optics)
 [![Read the Docs](https://img.shields.io/readthedocs/legend-pygeom-optics?logo=readthedocs)](https://legend-pygeom-optics.readthedocs.io)
 
-This package contains a collection of optical properties of materials used in the LEGEND experiment.
+This package contains a collection of optical properties of materials used in
+the LEGEND experiment.
 
-As a common interface, each optical property gets its own defining function in the material's module. Those functions can be used directly to just retrieve the value(s) of the property. Most property definitions contain unit information via the `pint` package. For a full list of defined properties refer to the [package documentation](https://legend-pygeom-optics.readthedocs.io).
+As a common interface, each optical property gets its own defining function in
+the material's module. Those functions can be used directly to just retrieve the
+value(s) of the property. Most property definitions contain unit information via
+the `pint` package. For a full list of defined properties refer to the
+[package documentation](https://legend-pygeom-optics.readthedocs.io).
 
-To ease the use in Geant4-based simulations, every module also provides functions to be used with [`pyg4ometry`](https://pyg4ometry.readthedocs.io).
+To ease the use in Geant4-based simulations, every module also provides
+functions to be used with [`pyg4ometry`](https://pyg4ometry.readthedocs.io).

codecov.yml

@@ -9,7 +9,7 @@ coverage:
     patch: false
 
 github_checks:
-    annotations: false
+  annotations: false
 
 ignore:
   - tests

docs/source/conf.py

@@ -1,4 +1,5 @@
 # Configuration file for the Sphinx documentation builder.
+from __future__ import annotations
 
 import sys
 from pathlib import Path

docs/source/exts/optics_plot_extension.py

@@ -66,18 +66,16 @@ def do_plot(
         x = x.magnitude
 
     # plot all supplied data vectors
-    i = 0
-    for y in ys:
-        if isinstance(y, pint.Quantity):
-            ax.set_ylabel(y.u)
-            y = y.magnitude
+    for i, val in enumerate(ys):
+        if isinstance(val, pint.Quantity):
+            ax.set_ylabel(val.u)
+            y = val.magnitude
 
         plotoptions = {}
         if "labels" in options:
             plotoptions["label"] = options["labels"][i]
 
         plt.plot(x, y, marker=".", markersize=2, linewidth=0.5, **plotoptions)
-        i += 1
 
     if len(ys) > 1 and "labels" in options:
         plt.legend()
@@ -116,16 +114,22 @@ def do_const(obj: Callable) -> list[str]:
     elif isinstance(const, float):
         description = f":math:`{const}`"
     else:
-        raise ValueError("")
+        msg = ""
+        raise ValueError(msg)
 
     if description is None:
         return [""]
-    else:
-        return [f":returns: constant value {description}"]
+
+    return [f":returns: constant value {description}"]
 
 
 def process_docstring(
-    app: Sphinx, what: str, name: str, obj: Any, options: Any, lines: list[str]
+    app: Sphinx,
+    what: str,
+    name: str,
+    obj: Any,
+    options: Any,
+    lines: list[str],
 ) -> None:
     if inspect.isclass(obj) or what != "function":
         return
@@ -166,4 +170,4 @@ def process_docstring(
 def setup(app: Sphinx) -> dict[str, bool]:
     """Register this sphinx extension."""
     app.connect("autodoc-process-docstring", process_docstring)
-    return dict(parallel_read_safe=True)
+    return {"parallel_read_safe": True}

docs/source/index.rst

@@ -35,7 +35,7 @@ This example demonstrates how to use the :py:mod:`legendoptics.lar` submodule to
     _liquidargon = g4.Material(
         name="LiquidArgon",
         state="liquid",
-        [...]
+        # [...]
         registry=g4_registry,
     )
 

pyproject.toml

@@ -92,7 +92,7 @@ log_cli_level = "info"
 testpaths = "tests"
 
 [tool.codespell]
-ignore-words-list = "manuel"
+ignore-words-list = "manuel,tre"
 
 [tool.ruff]
 src = ["src"]
@@ -101,7 +101,6 @@ src = ["src"]
 extend-select = [
   "B",        # flake8-bugbear
   "I",        # isort
-  "ARG",      # flake8-unused-arguments
   "C4",       # flake8-comprehensions
   "EM",       # flake8-errmsg
   "ICN",      # flake8-import-conventions
@@ -126,6 +125,7 @@ ignore = [
   "PLR2004",  # Magic value used in comparison
   "ISC001",   # Conflicts with formatter
   "PT011",    # too picky pytest.raises() complaint
+  "RUF003",   # we like greek letters
 ]
 isort.required-imports = ["from __future__ import annotations"]
 

src/legendoptics/__init__.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from legendoptics._version import version as __version__
 
 __all__ = ["__version__"]

src/legendoptics/lar.py

@@ -5,7 +5,7 @@
 .. [Doke1976] Doke et al. “Estimation of Fano factors in liquid argon, krypton, xenon and
     xenon-doped liquid argon.” NIM 134 (1976)353, https://doi.org/10.1016/0029-554X(76)90292-5
 .. [Bideau-Mehu1980] Bideau-Mehu et al. “Measurement of refractive indices of neon, argon, krypton
-    and xenon in the 253.7–140.4 nm wavelength range. Dispersion relations and
+    and xenon in the 253.7-140.4 nm wavelength range. Dispersion relations and
     estimated oscillator strengths of the resonance lines.” In: Journal of Quantitative
     Spectroscopy and Radiative Transfer 25.5 (1981)).
     https://doi.org/10.1016/0022-4073(81)90057-1
@@ -19,7 +19,7 @@
 .. [Doke2002] T. Doke et al. “Absolute Scintillation Yields in Liquid Argon and Xenon for Various Particles”
     Jpn. J. Appl. Phys. 41 1538, https://doi.org/10.1143/JJAP.41.1538
 .. [Hitachi1983] A. Hitachi et al. “Effect of ionization density on the time dependence of luminescence
-    from liquid argon and xenon.” In: Phys. Rev. B 27 (9 May 1983), pp. 5279–5285,
+    from liquid argon and xenon.” In: Phys. Rev. B 27 (9 May 1983), pp. 5279-5285,
     https://doi.org/10.1103/PhysRevB.27.5279
 """
 
@@ -59,10 +59,12 @@ def lar_dielectric_constant_bideau_mehu(
     .. optics-plot:: {'call_x': True}
     """
     if not λ.check("[length]"):
-        raise ValueError("input does not look like a wavelength")
+        msg = "input does not look like a wavelength"
+        raise ValueError(msg)
 
     if np.any(λ < 110 * u.nm):
-        raise ValueError(f"this parametrization is not meaningful below {110*u.nm}")
+        msg = f"this parametrization is not meaningful below {110*u.nm}"
+        raise ValueError(msg)
 
     # equation for n-1
     ϵ = 1.2055e-2 * (
@@ -87,15 +89,15 @@ def lar_dielectric_constant_cern2020(
     .. optics-plot:: {'call_x': True}
     """
     if not λ.check("[length]"):
-        raise ValueError("input does not look like a wavelength")
+        msg = "input does not look like a wavelength"
+        raise ValueError(msg)
 
     λ_uv = 106.6 * u.nm
     λ_ir = 908.3 * u.nm
 
     if np.any(λ < λ_uv + 1 * u.nm) or np.any(λ > λ_ir - 1 * u.nm):
-        raise ValueError(
-            f"this parametrization holds only between {λ_uv+1*u.nm} and {λ_ir-1*u.nm}"
-        )
+        msg = f"this parametrization holds only between {λ_uv+1*u.nm} and {λ_ir-1*u.nm}"
+        raise ValueError(msg)
 
     x = 0.334 + ((0.100 * λ**2) / (λ**2 - λ_uv**2) + (0.008 * λ**2) / (λ**2 - λ_ir**2))
 
@@ -112,9 +114,10 @@ def lar_dielectric_constant(λ: Quantity, method: str = "cern2020") -> Quantity:
     """
     if method == "bideau-mehu":
         return lar_dielectric_constant_bideau_mehu(λ)
-    elif method == "cern2020":
+    if method == "cern2020":
         return lar_dielectric_constant_cern2020(λ)
-    raise ValueError(f"Unknown LAr dielectric constant method {method}")
+    msg = f"Unknown LAr dielectric constant method {method}"
+    raise ValueError(msg)
 
 
 def lar_refractive_index(λ: Quantity, method: str = "cern2020") -> Quantity:
@@ -138,14 +141,12 @@ def lar_emission_spectrum(λ: Quantity) -> Quantity:
     heindl = readdatafile("lar_emission_heindl2010.dat")
 
     # sample the measured emission spectrum and avoid the fluctuations below 115 nm.
-    scint_em = InterpolatingGraph(
+    return InterpolatingGraph(
         *heindl,
         min_idx=115 * u.nm,
         max_idx=150 * u.nm,
     )(λ)
 
-    return scint_em
-
 
 def lar_fano_factor() -> float:
     """Fano factor.
@@ -175,7 +176,8 @@ def lar_rayleigh(
     .. optics-plot:: {'call_x': True}
     """
     if not temperature.check("[temperature]"):
-        raise ValueError("input does not look like a temperature")
+        msg = "input does not look like a temperature"
+        raise ValueError(msg)
 
     dyne = 1.0e-5 * u.newton
     κ = 2.18e-10 * u.cm**2 / dyne  # LAr isothermal compressibility
@@ -189,9 +191,8 @@ def lar_rayleigh(
     inv_l /= λ**4
     inv_l *= (2 / 3 * np.pi) ** 3
 
-    assert not np.any(inv_l < 1 / (10.0 * u.km)) and not np.any(
-        inv_l > 1 / (0.1 * u.nm)
-    )
+    assert not np.any(inv_l < 1 / (10.0 * u.km))
+    assert not np.any(inv_l > 1 / (0.1 * u.nm))
 
     return (1 / inv_l).to("cm")  # simplify units
 
@@ -219,11 +220,12 @@ def lar_peak_attenuation_length(
     if isinstance(attenuation_method, str):
         if attenuation_method == "legend200-llama":
             return 30 * u.cm
-        else:
-            raise ValueError(f"unknown attenuation_method {attenuation_method}")
-    else:
-        assert attenuation_method.check("[length]")
-        return attenuation_method
+
+        msg = f"unknown attenuation_method {attenuation_method}"
+        raise ValueError(msg)
+
+    assert attenuation_method.check("[length]")
+    return attenuation_method
 
 
 def lar_lifetimes(
@@ -238,9 +240,8 @@ def lar_lifetimes(
         if triplet_lifetime_method == "legend200-llama":
             triplet = 1.3 * u.us
         else:
-            raise ValueError(
-                f"unknown triplet_lifetime_method {triplet_lifetime_method}"
-            )
+            msg = f"unknown triplet_lifetime_method {triplet_lifetime_method}"
+            raise ValueError(msg)
     else:
         triplet = triplet_lifetime_method * u.us
 

src/legendoptics/pen.py

@@ -3,12 +3,12 @@
 .. [Manzanillas2022] L. Manzanillas et al. “Optical properties of low background PEN structural components
     for the LEGEND-200 experiment”. In: JINST 17 P09007 (2022), https://doi.org/10.1088/1748-0221/17/09/P09007
 .. [Hong2017] N. Hong et al. “Mueller matrix characterization of flexible plastic substrates”.
-    In: Applied Surface Science, 421:518–528 (2017), https://doi.org/10.1016/j.apsusc.2017.01.276
+    In: Applied Surface Science, 421:518-528 (2017), https://doi.org/10.1016/j.apsusc.2017.01.276
 .. [Mary1997] D. Mary et al. “Understanding optical emissions from electrically stressed insulating polymers:
     electroluminescence in poly(ethylene terephthalate) and poly(ethylene 2,6-naphthalate) films”
     In: J. Phys. D: Appl. Phys. 30 171 (1997), https://doi.org/10.1088/0022-3727/30/2/004
 .. [Ouchi2006] I. Ouchi et al. “Features of Fluorescence Spectra of Polyethylene 2,6-Naphthalate Films”
-    In: Journal of Applied Polymer Science, Vol. 105, 114–121 (2007), https://doi.org/10.1002/app.26085
+    In: Journal of Applied Polymer Science, Vol. 105, 114-121 (2007), https://doi.org/10.1002/app.26085
 """
 
 from __future__ import annotations

src/legendoptics/plot.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from typing import Callable
 
 import matplotlib.pyplot as plt

src/legendoptics/pyg4utils.py

@@ -91,7 +91,8 @@ def _val_pint_to_gdml(v):
 
         unit = f"{base_unit:~gdml}"
         assert unit == f"{base_unit:~}".replace(" ", "").replace("µ", "u")
-        log.debug(f"Unit pint->gdml: {unit} - {base_unit}")
+        msg = f"Unit pint->gdml: {unit} - {base_unit}"
+        log.debug(msg)
 
         v = v.m_as(base_unit)
         return unit, v
@@ -107,7 +108,7 @@ def _val_pint_to_gdml(v):
     ]
     length_props = ["ABSLENGTH", "WLSABSLENGTH", "RAYLEIGH"]
 
-    def addVecPropertyPint(self, name, e, v):  # noqa: N802
+    def addVecPropertyPint(self, name, e, v):
         vunit, v = _val_pint_to_gdml(v)
         eunit, e = _val_pint_to_gdml(e)
         v = np.array(v)
@@ -130,7 +131,7 @@ def addVecPropertyPint(self, name, e, v):  # noqa: N802
     g4.Material.addVecPropertyPint = addVecPropertyPint
     g4.solid.OpticalSurface.addVecPropertyPint = addVecPropertyPint
 
-    def addConstPropertyPint(self, name, value):  # noqa: N802
+    def addConstPropertyPint(self, name, value):
         vunit, value = _val_pint_to_gdml(value)
 
         if name in ["SCINTILLATIONYIELD"]:

src/legendoptics/tpb.py

@@ -133,7 +133,8 @@ def pyg4_tpb_attach_wls(
     from legendoptics.pyg4utils import pyg4_sample_λ
 
     if emission_spectrum not in ["default", "polystyrene_matrix"]:
-        raise ValueError("invalid parameter value of emission_spectrum")
+        msg = "invalid parameter value of emission_spectrum"
+        raise ValueError(msg)
 
     emission_fn = tpb_wls_emission
     if emission_spectrum == "polystyrene_matrix":

src/legendoptics/utils.py

@@ -30,9 +30,8 @@ def readdatafile(filename: str) -> tuple[Quantity, Quantity]:
     # parse header
     header = lines[0].lstrip()
     if header[0] != "#":
-        raise RuntimeError(
-            "input data file does not seem to contain header with (pint) units"
-        )
+        msg = "input data file does not seem to contain header with (pint) units"
+        raise RuntimeError(msg)
 
     units = header.lstrip("#").split()
 
@@ -44,7 +43,8 @@ def readdatafile(filename: str) -> tuple[Quantity, Quantity]:
 
         val = line.split()
         if len(val) < 2:
-            raise RuntimeError(f"could not parse line {lineno}: '{line}'")
+            msg = f"could not parse line {lineno}: '{line}'"
+            raise RuntimeError(msg)
 
         x.append(float(val[0]))
         y.append(float(val[1]))

tests/test_data_file_read.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from legendoptics.utils import readdatafile
 
 

tests/test_import.py

@@ -1,11 +1,13 @@
+from __future__ import annotations
+
 import numpy as np
 import pint
 
 u = pint.get_application_registry()
 
 
 def test_import():
-    import legendoptics  # noqa: F401
+    import legendoptics
     import legendoptics.copper
     import legendoptics.fibers
     import legendoptics.germanium