fix glossary generator

Author: jlogan-cfs

cfspopcon/variables.yaml

@@ -1078,7 +1078,8 @@ n_points_for_confined_region_profiles:
   - calc_1D_plasma_profiles
 n_sep_ratio:
   default_units: dimensionless
-  description: Ratio of separatrix density to pedestal density.
+  description:
+  - Ratio of separatrix density to pedestal density.
   set_by: []
   used_by:
   - calc_peaked_profiles
@@ -1378,7 +1379,8 @@ peak_pressure:
   used_by: []
 pedestal_width:
   default_units: dimensionless
-  description: Width of the edge pedestal in normalized rho space.
+  description:
+  - Width of the edge pedestal in normalized rho space.
   set_by: []
   used_by:
   - calc_peaked_profiles
@@ -1626,7 +1628,8 @@ reference_ne_tau:
   - calc_edge_impurity_concentration
 required_H98:
   default_units: dimensionless
-  description: Required H98 factor to maintain power balance with a specified P_aux.
+  description:
+  - Required H98 factor to maintain power balance with a specified P_aux.
   set_by:
   - solve_energy_confinement_scaling_for_input_power
   - calc_power_balance_from_input_P_aux
@@ -1883,7 +1886,8 @@ sustainment_power_in_ion_channel:
   used_by: []
 t_sep:
   default_units: kiloelectron_volt
-  description: Electron temperature at the separatrix.
+  description:
+  - Electron temperature at the separatrix.
   set_by: []
   used_by:
   - calc_peaked_profiles

docs/doc_sources/physics_glossary.rst

@@ -300,54 +300,7 @@ Physics Glossary
     The number of points to use for the confined region profiles.
 
   n_sep_ratio
-    R
-    a
-    t
-    i
-    o
-     
-    o
-    f
-     
-    s
-    e
-    p
-    a
-    r
-    a
-    t
-    r
-    i
-    x
-     
-    d
-    e
-    n
-    s
-    i
-    t
-    y
-     
-    t
-    o
-     
-    p
-    e
-    d
-    e
-    s
-    t
-    a
-    l
-     
-    d
-    e
-    n
-    s
-    i
-    t
-    y
-    .
+    Ratio of separatrix density to pedestal density.
 
   neoclassical_loop_resistivity
     Plasma loop neoclassical resistivity.
@@ -446,57 +399,7 @@ Physics Glossary
     Peak total pressure in the core.
 
   pedestal_width
-    W
-    i
-    d
-    t
-    h
-     
-    o
-    f
-     
-    t
-    h
-    e
-     
-    e
-    d
-    g
-    e
-     
-    p
-    e
-    d
-    e
-    s
-    t
-    a
-    l
-     
-    i
-    n
-     
-    n
-    o
-    r
-    m
-    a
-    l
-    i
-    z
-    e
-    d
-     
-    r
-    h
-    o
-     
-    s
-    p
-    a
-    c
-    e
-    .
+    Width of the edge pedestal in normalized rho space.
 
   plasma_current
     Current carried by the plasma :math:`I_p`.
@@ -568,75 +471,7 @@ Physics Glossary
     A constant :math:`n_e\tau` (upstream electron density times impurity residence time) used when evaluating the :math:`L_Z` impurity radiation curve.
 
   required_H98
-    R
-    e
-    q
-    u
-    i
-    r
-    e
-    d
-     
-    H
-    9
-    8
-     
-    f
-    a
-    c
-    t
-    o
-    r
-     
-    t
-    o
-     
-    m
-    a
-    i
-    n
-    t
-    a
-    i
-    n
-     
-    p
-    o
-    w
-    e
-    r
-     
-    b
-    a
-    l
-    a
-    n
-    c
-    e
-     
-    w
-    i
-    t
-    h
-     
-    a
-     
-    s
-    p
-    e
-    c
-    i
-    f
-    i
-    e
-    d
-     
-    P
-    _
-    a
-    u
-    x
-    .
+    Required H98 factor to maintain power balance with a specified P_aux.
 
   resistive_flux
     Usually this is the magnetic flux induced by the resistance of the plasma. However, given that POPCON calculates this with the empirical :math:`C_E`, it may also hold information about flux induced coupling with the wall. :math:`\psi_{res} = C_E\mu_0R_0I_p`.
@@ -711,45 +546,7 @@ Physics Glossary
     The power in the ion channel required to maintain the ion temperature gradient at the separatrix.
 
   t_sep
-    E
-    l
-    e
-    c
-    t
-    r
-    o
-    n
-     
-    t
-    e
-    m
-    p
-    e
-    r
-    a
-    t
-    u
-    r
-    e
-     
-    a
-    t
-     
-    t
-    h
-    e
-     
-    s
-    e
-    p
-    a
-    r
-    a
-    t
-    r
-    i
-    x
-    .
+    Electron temperature at the separatrix.
 
   target_angle_of_incidence
     Angle of incidence between magnetic field vector and surface normal vector at divertor target.

tests/test_helpers.py

@@ -1,6 +1,7 @@
 import numpy as np
 import pytest
 import xarray as xr
+from utils.variable_consistency_checker import VariableConsistencyChecker
 
 from cfspopcon import named_options
 from cfspopcon.formulas.impurities.impurity_array_helpers import (
@@ -65,3 +66,9 @@ def test_impurity_array_helpers():
 
     assert np.isclose(ds["array2"].sel(dim_species=AtomicSpecies.Helium).isel(a=0, b=1).item(), 0.1)
     assert np.isclose(ds["array2"].sel(dim_species=AtomicSpecies.Tungsten).isel(a=1, b=1).item(), 0.4)
+
+
+def test_variable_consistency_checker_normalize_description():
+    assert VariableConsistencyChecker.normalize_description("single line") == ["single line"]
+    assert VariableConsistencyChecker.normalize_description("first line\nsecond line") == ["first line", "second line"]
+    assert VariableConsistencyChecker.normalize_description(["first line", "second line"]) == ["first line", "second line"]

tests/utils/variable_consistency_checker.py

@@ -39,8 +39,8 @@ def read_physics_glossary(self) -> tuple[dict[str, list[str]], set[str]]:
 
         # Define patterns for identifying blank lines, keys and descriptions.
         pattern_for_key = re.compile(r"^\s{2}\S+\s*$")
-        pattern_for_description = re.compile(r"^\s{4}\S.+")
-        pattern_for_blank = re.compile(r"^\s*$")
+        pattern_for_description = re.compile(r"^\s{4}.*$")
+        pattern_for_blank = re.compile(r"^$")
 
         # Store the results in a dictionary
         glossary: dict[str, list[str]] = dict()
@@ -98,6 +98,24 @@ def read_variables_dict(self) -> tuple[dict[str, dict[str, Any]], set[str]]:
 
         return variables_dict, set(variables_dict.keys())
 
+    @staticmethod
+    def normalize_description(description: str | list[str]) -> list[str]:
+        """Normalize a variable description into a list of glossary lines.
+
+        ``variables.yaml`` historically contains a mix of plain strings and
+        explicit line lists. The glossary writer expects a list, so string
+        descriptions must be wrapped as single entries rather than iterated
+        character-by-character.
+        """
+        if isinstance(description, str):
+            return description.splitlines() or [description]
+
+        normalized_description: list[str] = []
+        for line in description:
+            normalized_description.extend(line.splitlines() or [line])
+
+        return normalized_description
+
     def run(self, apply_changes: bool = True) -> None:  # noqa: PLR0912, PLR0915
         """Check the files and, if apply_changes = True, modify the files in place."""
         success = True
@@ -153,7 +171,7 @@ def run(self, apply_changes: bool = True) -> None:  # noqa: PLR0912, PLR0915
                 default_units = self.variables_dict[key]["default_units"]
                 if default_units is not None:
                     default_units = str(Quantity(1.0, default_units).units)
-                description = self.variables_dict[key]["description"]
+                description = self.normalize_description(self.variables_dict[key]["description"])
                 if key not in self.glossary:
                     print(f"Adding description for '{key}'.{linebreak}New: '{description}'.{linebreak}")
                 elif not (description == self.glossary[key]):
@@ -204,8 +222,8 @@ def run(self, apply_changes: bool = True) -> None:  # noqa: PLR0912, PLR0915
                 for line in description:
                     glossary_text += [f"    {line}"]
 
-                with as_file(files("cfspopcon").parents[0] / "docs" / "doc_sources" / "physics_glossary.rst") as filepath:  # type:ignore[attr-defined]
-                    filepath.write_text("\n".join(glossary_text))
+            with as_file(files("cfspopcon").parents[0] / "docs" / "doc_sources" / "physics_glossary.rst") as filepath:  # type:ignore[attr-defined]
+                filepath.write_text("\n".join(glossary_text))
 
         exit(0) if success else exit(1)