Follow up PR#866 ♻️ - 👌Minor cosmetic changes

benchmark/pytest/analysis/test_optimization_group.py

@@ -32,7 +32,7 @@
     np.ones((TEST_AXIS_GLOBAL_SIZE, TEST_AXIS_MODEL_SIZE)),
     coords=(("global", TEST_AXIS_GLOBAL.data), ("test", TEST_AXIS_MODEL.data)),
 )
-TEST_PARAMETER = ParameterGroup.from_list([])
+TEST_PARAMETERS = ParameterGroup.from_list([])
 
 
 @megacomplex(dimension="test", properties={"is_index_dependent": bool})
@@ -74,7 +74,7 @@ def setup_model(index_dependent, link_clp):
 def setup_scheme(model):
     return Scheme(
         model=model,
-        parameters=TEST_PARAMETER,
+        parameters=TEST_PARAMETERS,
         data={
             "dataset1": TEST_DATA,
             "dataset2": TEST_DATA,

glotaran/builtin/io/yml/test/test_save_scheme.py

@@ -12,7 +12,7 @@
 from glotaran.project import Scheme
 from glotaran.testing.simulated_data.sequential_spectral_decay import DATASET
 from glotaran.testing.simulated_data.sequential_spectral_decay import MODEL
-from glotaran.testing.simulated_data.sequential_spectral_decay import PARAMETER
+from glotaran.testing.simulated_data.sequential_spectral_decay import PARAMETERS
 
 if TYPE_CHECKING:
     from pathlib import Path
@@ -36,11 +36,11 @@
 
 def test_save_scheme(tmp_path: Path):
     save_model(MODEL, tmp_path / "m.yml")
-    save_parameters(PARAMETER, tmp_path / "p.csv")
+    save_parameters(PARAMETERS, tmp_path / "p.csv")
     save_dataset(DATASET, tmp_path / "d.nc")
     scheme = Scheme(
         MODEL,
-        PARAMETER,
+        PARAMETERS,
         {"dataset_1": DATASET},
     )
     scheme_path = tmp_path / "testscheme.yml"

glotaran/deprecation/deprecation_utils.py

@@ -611,9 +611,8 @@ def deprecate_module_attribute(
         Version the support for this usage will be removed.
     module_load_overwrite : str
         Overwrite the location the functionality will be set from.
-        This allows preserving functionality without polluting new
-        module with code just for the sake of it.
-        , by default ''
+        This allows preserving functionality without polluting a new
+        module with code just for the sake of it. By default ''
 
     Returns
     -------
@@ -703,9 +702,8 @@ def deprecate_submodule(
         Version the support for this usage will be removed.
     module_load_overwrite : str
         Overwrite the location for the new module the deprecated functionality is loaded from.
-        This allows preserving functionality without polluting new
-        module with code just for the sake of it.
-        , by default ''
+        This allows preserving functionality without polluting a new
+        module with code just for the sake of it. By default ''
 
     Returns
     -------

glotaran/deprecation/modules/examples/sequential.py

@@ -7,8 +7,8 @@
     "scheme": "SCHEME",
 }
 shared_deprecation_mapping = {
-    "wanted_parameter": "SIMULATION_PARAMETER",
-    "parameter": "PARAMETER",
+    "wanted_parameter": "SIMULATION_PARAMETERS",
+    "parameter": "PARAMETERS",
     "_time": "TIME_AXIS",
     "_spectral": "SPECTRAL_AXIS",
 }

glotaran/deprecation/modules/test/test_changed_imports.py

@@ -136,7 +136,7 @@ def test_io_read_data_file(recwarn: WarningsRecorder):
     "attribute_name", ("sim_model", "dataset", "model", "scheme", "wanted_parameter", "parameter")
 )
 def test_examples_sequential(recwarn: WarningsRecorder, attribute_name: str):
-    """glotaran.examples.sequential exported addributes"""
+    """glotaran.examples.sequential exported attributes"""
     from glotaran.examples import sequential  # noqa: F401
 
     recwarn.clear()

glotaran/deprecation/modules/test/test_parameter_parameter_group.py

@@ -3,14 +3,14 @@
 from textwrap import dedent
 
 from glotaran.deprecation.modules.test import deprecation_warning_on_call_test_helper
-from glotaran.testing.simulated_data.sequential_spectral_decay import PARAMETER
+from glotaran.testing.simulated_data.sequential_spectral_decay import PARAMETERS
 
 
 def test_parameter_group_to_csv_no_stderr(tmp_path: Path):
     """``ParameterGroup.to_csv`` raises deprecation warning and saves file."""
     parameter_path = tmp_path / "test_parameter.csv"
     deprecation_warning_on_call_test_helper(
-        PARAMETER.to_csv, args=[parameter_path.as_posix()], raise_exception=True
+        PARAMETERS.to_csv, args=[parameter_path.as_posix()], raise_exception=True
     )
     expected = dedent(
         """\

glotaran/deprecation/modules/test/test_project_scheme.py

@@ -10,7 +10,7 @@
 from glotaran.project.scheme import Scheme
 from glotaran.testing.simulated_data.parallel_spectral_decay import DATASET
 from glotaran.testing.simulated_data.parallel_spectral_decay import MODEL
-from glotaran.testing.simulated_data.parallel_spectral_decay import PARAMETER
+from glotaran.testing.simulated_data.parallel_spectral_decay import PARAMETERS
 
 if TYPE_CHECKING:
     from pathlib import Path
@@ -58,7 +58,7 @@ def test_scheme_from_yaml_file_method(tmp_path: Path):
 
 def test_scheme_group_tolerance():
     """Argument ``group_tolerance`` raises deprecation and maps to ``clp_link_tolerance``."""
-    model, parameters, dataset = MODEL, PARAMETER, DATASET
+    model, parameters, dataset = MODEL, PARAMETERS, DATASET
 
     warnings, result = deprecation_warning_on_call_test_helper(
         Scheme,
@@ -78,7 +78,7 @@ def test_scheme_group_tolerance():
 )
 def test_scheme_group(group: bool):
     """Argument ``group`` raises deprecation and maps to ``dataset_groups.default.link_clp``."""
-    model, parameters, dataset = MODEL, PARAMETER, DATASET
+    model, parameters, dataset = MODEL, PARAMETERS, DATASET
 
     warnings, result = deprecation_warning_on_call_test_helper(
         Scheme,
@@ -100,7 +100,7 @@ def test_scheme_non_negative_least_squares(non_negative_least_squares: bool, exp
     """Argument ``non_negative_least_squares`` raises deprecation and maps to
     ``dataset_groups.default.residual_function``.
     """
-    model, parameters, dataset = MODEL, PARAMETER, DATASET
+    model, parameters, dataset = MODEL, PARAMETERS, DATASET
 
     warnings, result = deprecation_warning_on_call_test_helper(
         Scheme,

glotaran/parameter/parameter.py

@@ -31,10 +31,10 @@ class Keys:
     VARY = "vary"
 
 
-PARAMETER_EXPRESION_REGEX = re.compile(r"\$(?P<parameter_expression>[\w\d\.]+)((?![\w\d\.]+)|$)")
-"""A regexpression to find and replace parameter names in expressions."""
+PARAMETER_EXPRESSION_REGEX = re.compile(r"\$(?P<parameter_expression>[\w\d\.]+)((?![\w\d\.]+)|$)")
+"""A regular expression to find and replace parameter names in expressions."""
 VALID_LABEL_REGEX = re.compile(r"\W", flags=re.ASCII)
-"""A regexpression to validate labels."""
+"""A regular expression to validate labels."""
 
 
 class Parameter(_SupportsArray):
@@ -394,7 +394,7 @@ def transformed_expression(self) -> str | None:
             The transformed expression.
         """
         if self.expression is not None and self._transformed_expression is None:
-            self._transformed_expression = PARAMETER_EXPRESION_REGEX.sub(
+            self._transformed_expression = PARAMETER_EXPRESSION_REGEX.sub(
                 r"group.get('\g<parameter_expression>').value", self.expression
             )
         return self._transformed_expression
@@ -500,7 +500,7 @@ def markdown(
         elif parameter.expression is not None:
             expression = parameter.expression
             if all_parameters is not None:
-                for match in PARAMETER_EXPRESION_REGEX.findall(expression):
+                for match in PARAMETER_EXPRESSION_REGEX.findall(expression):
                     label = match[0]
                     parameter = all_parameters.get(label)
                     expression = expression.replace(

glotaran/testing/simulated_data/parallel_spectral_decay.py

@@ -4,10 +4,9 @@
 from glotaran.io import load_model
 from glotaran.project import Scheme
 from glotaran.project.generators import generate_model_yml
-from glotaran.testing.simulated_data.shared_decay import PARAMETER
+from glotaran.testing.simulated_data.shared_decay import PARAMETERS
 from glotaran.testing.simulated_data.shared_decay import SIMULATION_COORDINATES
-from glotaran.testing.simulated_data.shared_decay import SIMULATION_PARAMETER
-from glotaran.testing.simulated_data.shared_decay import *  # noqa F403
+from glotaran.testing.simulated_data.shared_decay import SIMULATION_PARAMETERS
 
 SIMULATION_MODEL_YML = generate_model_yml(
     generator_name="spectral_decay_parallel",
@@ -24,10 +23,10 @@
 DATASET = simulate(
     SIMULATION_MODEL,
     "dataset_1",
-    SIMULATION_PARAMETER,
+    SIMULATION_PARAMETERS,
     SIMULATION_COORDINATES,
     noise=True,
     noise_std_dev=1e-2,
 )
 
-SCHEME = Scheme(model=MODEL, parameters=PARAMETER, data={"dataset_1": DATASET})
+SCHEME = Scheme(model=MODEL, parameters=PARAMETERS, data={"dataset_1": DATASET})

glotaran/testing/simulated_data/sequential_spectral_decay.py

@@ -4,10 +4,9 @@
 from glotaran.io import load_model
 from glotaran.project import Scheme
 from glotaran.project.generators import generate_model_yml
-from glotaran.testing.simulated_data.shared_decay import PARAMETER
+from glotaran.testing.simulated_data.shared_decay import PARAMETERS
 from glotaran.testing.simulated_data.shared_decay import SIMULATION_COORDINATES
-from glotaran.testing.simulated_data.shared_decay import SIMULATION_PARAMETER
-from glotaran.testing.simulated_data.shared_decay import *  # noqa F403
+from glotaran.testing.simulated_data.shared_decay import SIMULATION_PARAMETERS
 
 SIMULATION_MODEL_YML = generate_model_yml(
     generator_name="spectral_decay_sequential",
@@ -25,10 +24,10 @@
 DATASET = simulate(
     SIMULATION_MODEL,
     "dataset_1",
-    SIMULATION_PARAMETER,
+    SIMULATION_PARAMETERS,
     SIMULATION_COORDINATES,
     noise=True,
     noise_std_dev=1e-2,
 )
 
-SCHEME = Scheme(model=MODEL, parameters=PARAMETER, data={"dataset_1": DATASET})
+SCHEME = Scheme(model=MODEL, parameters=PARAMETERS, data={"dataset_1": DATASET})

glotaran/testing/simulated_data/shared_decay.py

@@ -3,7 +3,7 @@
 
 from glotaran.io import load_parameters
 
-SIMULATION_PARAMETER_YML = """
+SIMULATION_PARAMETERS_YML = """
 rates:
   - [species_1, 0.5]
   - [species_2, 0.3]
@@ -27,9 +27,9 @@
     - [location, 650]
     - [width, 60]
 """
-SIMULATION_PARAMETER = load_parameters(SIMULATION_PARAMETER_YML, format_name="yml_str")
+SIMULATION_PARAMETERS = load_parameters(SIMULATION_PARAMETERS_YML, format_name="yml_str")
 
-PARAMETER_YML = """
+PARAMETERS_YML = """
 rates:
   - [species_1, 0.5]
   - [species_2, 0.3]
@@ -39,7 +39,7 @@
   - [center, 0.3]
   - [width, 0.1]
 """
-PARAMETER = load_parameters(PARAMETER_YML, format_name="yml_str")
+PARAMETERS = load_parameters(PARAMETERS_YML, format_name="yml_str")
 
 TIME_AXIS = np.arange(-1, 20, 0.01)
 SPECTRAL_AXIS = np.arange(600, 700, 1.4)