ran ruff pydocstyle ruleset

Author: alexhroom

RATapi/controls.py

@@ -205,10 +205,11 @@ def initialise_IPC(self):
     def sendStopEvent(self):
         """Sends the stop event via the inter-process communication file.
 
-        Warnings
+        Warnings:
         --------
         UserWarning
             Raised if we try to delete an IPC file that was not initialised.
+
         """
         if os.path.isfile(self._IPCFilePath):
             with open(self._IPCFilePath, "wb") as f:

RATapi/examples/bayes_benchmark/bayes_benchmark.py

@@ -1,5 +1,4 @@
-"""
-This example compares three Bayesian posteriors for a low-dimensional
+"""This example compares three Bayesian posteriors for a low-dimensional
 example: a posterior generated by DREAM, one generated by NS, and
 one calculated directly.
 
@@ -191,6 +190,7 @@ def calculate_posterior(roughness_index: int, background_index: int) -> float:
         -------
         float
             The value of exp(-chi^2 / 2) for the given roughness and background values.
+
         """
         problem.parameters[0].value = roughness[roughness_index]
         problem.background_parameters[0].value = background[background_index]
@@ -265,6 +265,7 @@ def calculate_posterior(roughness_index: int, background_index: int, scalefactor
         -------
         float
             The value of exp(-chi^2 / 2) for the given roughness and background values.
+
         """
         problem.parameters[0].value = roughness[roughness_index]
         problem.background_parameters[0].value = background[background_index]
@@ -300,6 +301,7 @@ def plot_posterior_comparison(
         The BayesResults object from a DREAM calculation.
     calc_results : CalculationResults
         The results from a direct calculation.
+
     """
     num_params = calc_results.distribution.ndim
     fig, axes = plt.subplots(3, num_params, figsize=(3 * num_params, 9))

RATapi/inputs.py

@@ -46,6 +46,7 @@ class FileHandles:
     ----------
     files : ClassList[CustomFile]
         A list of custom file models.
+
     """
 
     def __init__(self, files=None):

RATapi/models.py

@@ -179,7 +179,6 @@ class Contrast(RATModel):
     @classmethod
     def domain_ratio_error(cls, data: Any):
         """If the extra input 'domain_ratio' is given, give a more descriptive error."""
-
         if isinstance(data, dict) and data.get("domain_ratio", False):
             raise ValueError(
                 "The Contrast class does not support domain ratios. Use the ContrastWithRatio class instead."
@@ -474,7 +473,6 @@ class Layer(RATModel, populate_by_name=True):
     @classmethod
     def sld_imaginary_error(cls, data: Any):
         """If the extra input 'sld_imaginary' is given, give a more descriptive error."""
-
         if isinstance(data, dict) and data.get("SLD_imaginary", False):
             raise ValueError("The Layer class does not support imaginary SLD. Use the AbsorptionLayer class instead.")
 

RATapi/outputs.py

@@ -26,6 +26,7 @@ def get_field_string(field: str, value: Any, array_limit: int):
     -------
     field_string : str
         The string representation of the field in the RAT output class.
+
     """
     array_text = "Data array: "
     if isinstance(value, list) and len(value) > 0:
@@ -182,6 +183,7 @@ class PredictionIntervals(RATResult):
         The prediction interval data for SLD of each contrast.
     sampleChi : np.ndarray
         The value of sumChi at each point of the Markov chain.
+
     """
 
     reflectivity: list
@@ -191,8 +193,7 @@ class PredictionIntervals(RATResult):
 
 @dataclass
 class ConfidenceIntervals(RATResult):
-    """
-    The 65% and 95% confidence intervals for the best fit results.
+    """The 65% and 95% confidence intervals for the best fit results.
 
     Attributes
     ----------
@@ -202,6 +203,7 @@ class ConfidenceIntervals(RATResult):
         The 65% confidence intervals for each fit parameter.
     mean : np.ndarray
         The mean values for each fit parameter.
+
     """
 
     percentile95: np.ndarray

RATapi/run.py

@@ -16,6 +16,7 @@ class ProgressBar:
     ----------
     display : bool, default: True
             Indicates if displaying is allowed
+
     """
 
     def __init__(self, display=True):
@@ -41,6 +42,7 @@ def updateProgress(self, event):
         ----------
         event: ProgressEventData
             The progress event data.
+
         """
         if self.pbar is None:
             self.pbar = tqdm(**self.tqdm_kwargs)
@@ -64,6 +66,7 @@ class TextOutput:
     ----------
     display : bool, default: True
             Indicates if displaying is allowed
+
     """
 
     def __init__(self, display=True):
@@ -82,6 +85,7 @@ def printMessage(self, msg):
         ----------
         msg: str
             The event message.
+
         """
         print(msg, end="")
 

RATapi/utils/convert.py

@@ -46,7 +46,8 @@ def r1_to_project_class(filename: Union[str, PathLike]) -> Project:
     def zip_if_several(*params) -> Union[tuple, list[tuple]]:
         """Zips parameters if necessary, but can handle single-item parameters.
 
-        Examples:
+        Examples
+        --------
         zip_if_several([1, 2], [3, 4]) = [(1, 3), (2, 4)]
         zip_if_several(1, 2, 3) = [(1, 2, 3)]
 
@@ -79,6 +80,7 @@ def read_param(names, constrs, values, fits):
         -------
         ClassList
             A list of all relevant parameters.
+
         """
 
         def fix_invalid_constraints(name: str, constrs: tuple[float, float], value: float) -> tuple[float, float]:
@@ -334,6 +336,7 @@ def project_class_to_r1(
     -------
     dict or None
         If `return_struct` is True, return the r1 struct. Else, return nothing.
+
     """
 
     def convert_parameters(
@@ -355,6 +358,7 @@ def convert_parameters(
         -------
         dict
             A dict of the relevant struct fields.
+
         """
         output = {
             name: [p.name for p in params],

RATapi/utils/plotting.py

@@ -79,6 +79,7 @@ def plot_ref_sld_helper(
             Controls whether the grid is shown
     show_legend : bool, default: True
             Controls whether the lengend is shown
+
     Returns
     -------
     fig : matplotlib.pyplot.figure
@@ -345,6 +346,7 @@ def plotEvent(self, event):
         ----------
         event: PlotEventData
             The plot event data.
+
         """
         if not self.closed and self.figure.number in plt.get_fignums():
             plot_ref_sld_helper(event, self.figure)
@@ -675,6 +677,7 @@ def panel_plot_helper(plot_func: Callable, indices: list[int]) -> matplotlib.fig
     -------
     matplotlib.figure.Figure
         A figure containing a grid of plots over the indices in `indices`.
+
     """
     nplots = len(indices)
     nrows, ncols = ceil(sqrt(nplots)), round(sqrt(nplots))
@@ -747,7 +750,6 @@ def plot_hists(
         If `return_fig` is True, return the figure - otherwise, return nothing.
 
     """
-
     # first convert names to indices if given
     fitname_to_index = partial(name_to_index, names=results.fitNames)
 

pyproject.toml

@@ -11,8 +11,18 @@ line-length = 120
 extend-exclude = ["*.ipynb"]
 
 [tool.ruff.lint]
-select = ["E", "F", "UP", "B", "SIM", "I"]
-ignore = ["SIM103", "SIM108"]
+select = ["E",   # pycodestyle errors
+          "F",   # pyflakes
+          "UP",  # pyupgrade
+          "B",   # flake8-bugbear
+          "SIM", # flake8-simplify
+          "I",   # isort
+          "D"]  # pydocstyle
+
+ignore = ["SIM103", # needless bool
+          "SIM108", # if-else block instead of ternary operator
+          "D105",   # undocumented __init__
+          "D107"]   # undocumented magic method
 
 [tool.ruff.lint.flake8-pytest-style]
 fixture-parentheses = false

tests/conftest.py

@@ -6548,7 +6548,6 @@ def dream_results():
 @pytest.fixture
 def r1_default_project():
     """The Project corresponding to the data in R1defaultProject.mat."""
-
     project = RATapi.Project(
         name="defaultProject",
         calculation="normal",