fix: add todos and docstring

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.9.7
+  rev: v0.11.2
   hooks:
     - id: ruff
     - id: ruff-format
@@ -12,21 +12,6 @@ repos:
     exclude: ^(examples/dyna_decks\/|tests/heart/assets\/)
     args: [-L solf, "--ignore-words", "doc/styles/config/vocabularies/ANSYS/accept.txt", "-w"]
 
-- repo: https://github.com/pycqa/pydocstyle
-  rev: 6.3.0
-  hooks:
-  - id: pydocstyle
-    additional_dependencies: [toml]
-    args: ["--convention=numpy"]
-    exclude: |
-      (?x)^(
-        tests/|
-        examples/|
-        src/ansys/heart/misc/|
-        src/ansys/heart/writer/custom_keywords/|
-        .*__init__.py
-      )
-
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v5.0.0
   hooks:
@@ -37,12 +22,12 @@ repos:
     exclude: ^(tests/heart/assets\/)
 
 - repo: https://github.com/python-jsonschema/check-jsonschema
-  rev: 0.31.2
+  rev: 0.32.1
   hooks:
     - id: check-github-workflows
 
 - repo: https://github.com/ansys/pre-commit-hooks
-  rev: v0.5.1
+  rev: v0.5.2
   hooks:
     - id: add-license-headers
       files: '(ansys|examples|tests)/.*\.(py)'

doc/source/changelog/972.fixed.md

@@ -0,0 +1 @@
+add todos and docstring

pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "flit_core.buildapi"
 # Check https://flit.readthedocs.io/en/latest/pyproject_toml.html for all available sections
 name = "pyansys-heart"
 version = "0.11.dev0"
-description = "Python framework for heart modeling using ANSYS tools."
+description = "Python framework for heart modeling using Ansys tools."
 readme = "README.rst"
 requires-python = ">=3.10,<4"
 license = { file = "LICENSE" }
@@ -21,6 +21,7 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
 ]
 
 dependencies = [
@@ -93,6 +94,8 @@ select = [
     "I",    # isort, see https://docs.astral.sh/ruff/rules/#isort-i
     "N",    # pep8-naming, see https://docs.astral.sh/ruff/rules/#pep8-naming-n
     "TD",   # flake8-todos, https://docs.astral.sh/ruff/rules/#flake8-todos-td
+    # TODO: convert the path to pathlib in all modules
+    #"PTH",  # flake8-use-pathlib, https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
 ]
 ignore = [
     "TD002", # Missing author in TODOs comment

src/ansys/heart/core/utils/connectivity.py

@@ -255,6 +255,7 @@ def _dfs(visited, graph, node):
         for edge_group in edge_groups:
             counts = np.unique(edge_group, return_counts=True)[1]
             if np.all(counts == 2):
+                # TODO: @mhoeijm - remove all print statements
                 # print("Closed edge loop")
                 group_types.append("closed")
             elif np.any(counts != 2):

src/ansys/heart/postprocessor/auto_process.py

@@ -45,16 +45,15 @@ def zerop_post(directory: str, model: HeartModel) -> tuple[dict, np.ndarray, np.
     Parameters
     ----------
     directory : str
-        Path to simulation folder
+        Path to simulation folder.
     model : HeartModel
-        model to post-process
+        model to post-process.
 
     Returns
     -------
     tuple[dict, np.ndarray, np.ndarray]
-        dictionary with convergence information
-        stress free configuration
-        computed end-of-diastolic configuration
+        dictionary with convergence information, stress free configuration,
+        computed end-of-diastolic configuration.
     """
     folder = "post"
     os.makedirs(os.path.join(directory, folder), exist_ok=True)
@@ -149,9 +148,9 @@ def mech_post(directory: str, model: HeartModel):
     Parameters
     ----------
     directory : str
-        d3plot folder
+        d3plot folder.
     model : HeartModel
-        heart model
+        heart model.
     """
     last_cycle_duration = 800
     folder = "post"

src/ansys/heart/postprocessor/dpf_utils.py

@@ -105,7 +105,18 @@ def get_initial_coordinates(self):
         return self.model.results.initial_coordinates.eval()[0].data
 
     def get_ep_fields(self, at_step: int = None) -> dpf.FieldsContainer:
-        """Get EP fields container."""
+        """Get EP fields container.
+
+        Parameters
+        ----------
+        at_step : int, optional
+            At this step, by default None.
+
+        Returns
+        -------
+        dpf.FieldsContainer
+            Fields container.
+        """
         fields = dpf.FieldsContainer()
 
         time_ids = (
@@ -300,7 +311,7 @@ def get_time(self) -> np.ndarray:
         Returns
         -------
         np.ndarray
-            time array
+            time array.
         """
         # see pydpf examples, lsdyna-operators
         icvout_op = dpf.Operator("lsdyna::binout::ICV_P")
@@ -318,12 +329,12 @@ def get_pressure(self, icv_id: int) -> np.ndarray:
         Parameters
         ----------
         icv_id : int
-            control volume id
+            control volume id.
 
         Returns
         -------
         np.ndarray
-            pressure array
+            pressure array.
         """
         if icv_id not in self._icv_ids:
             raise ValueError("icv_id not found.")
@@ -336,12 +347,12 @@ def get_volume(self, icv_id: int) -> np.ndarray:
         Parameters
         ----------
         icv_id : int
-            control volume id
+            control volume id.
 
         Returns
         -------
         np.ndarray
-            volume array
+            volume array.
         """
         if icv_id not in self._icv_ids:
             raise ValueError("icv_id not found.")
@@ -359,12 +370,12 @@ def get_flowrate(self, icvi_id: int) -> np.ndarray:
         Parameters
         ----------
         icvi_id : int
-            control volume interaction id
+            control volume interaction id.
 
         Returns
         -------
         np.ndarray
-            flowrate array
+            flowrate array.
         """
         if icvi_id not in self._icvi_ids:
             raise ValueError("icvi_id not found.")
@@ -588,15 +599,15 @@ def compute_12_lead_ECGs(  # noqa: N802
         ECGs : np.ndarray
             mxn array containing ECGs, where m is the number of time steps
             and n the 10 electrodes in this order:
-            "V1" "V2" "V3" "V4" "V5" "V6" "RA" "LA" "RL" "LL"
+            "V1" "V2" "V3" "V4" "V5" "V6" "RA" "LA" "RL" "LL".
         plot : bool, optional
-            plot option, by default True
+            plot option, by default True.
 
         Returns
         -------
         np.ndarray
             12-Lead ECGs in this order:
-            "I" "II" "III" "aVR" "aVL" "aVF" "V1" "V2" "V3" "V4" "V5" "V6"
+            "I" "II" "III" "aVR" "aVL" "aVF" "V1" "V2" "V3" "V4" "V5" "V6".
         """
         right_arm = ECGs[:, 6]
         left_arm = ECGs[:, 7]
@@ -713,12 +724,12 @@ def convert_to_pvgrid_at_t(self, time: float, fname: str = None) -> pv.Unstructu
         time : float
             time to convert
         fname : str
-            filename to be save save data, default is None
+            filename to be save save data, default is None.
 
         Returns
         -------
         pv.UnstructuredGrid
-            result in pyvista object
+            result in pyvista object.
         """
         mesh = self.data.meshgrid.copy()
         i_frame = np.where(self.data.time == time)[0][0]

src/ansys/heart/postprocessor/klotz_curve.py

@@ -45,9 +45,9 @@ def __init__(self, vm: float, pm: float):
         Parameters
         ----------
         vm : float
-            Volume in mL
+            Volume in mL.
         pm : float
-            Pressure in mmHg
+            Pressure in mmHg.
         """
         self.vm = vm
         self.pm = pm
@@ -78,7 +78,7 @@ def get_pressure(self, volume: float | np.ndarray) -> float | np.ndarray:
         Returns
         -------
         float| np.ndarray
-            pressure in mmHg
+            pressure in mmHg.
         """
         return self.Alpha * volume**self.Beta
 
@@ -88,12 +88,12 @@ def get_volume(self, pressure: np.ndarray) -> np.ndarray:
         Parameters
         ----------
         pressure : np.ndarray
-            pressure in mmHg
+            pressure in mmHg.
 
         Returns
         -------
         np.ndarray
-            volume in mmL
+            volume in mmL.
         """
         if not isinstance(pressure, np.ndarray):
             raise TypeError("Input must be 1-dimensioanl np.array.")
@@ -111,12 +111,12 @@ def plot_EDPVR(self, simulation_data: list = None) -> matplotlib.figure.Figure:
         Parameters
         ----------
         simulation_data : list, optional
-            [volume, pressure] from simulation, by default None
+            [volume, pressure] from simulation, by default None.
 
         Returns
         -------
         matplotlib.figure.Figure
-            figure
+            figure.
         """
         vv = np.linspace(0, 1.1 * self.vm, num=101)
         pp = self.get_pressure(vv)

src/ansys/heart/postprocessor/laplace_post.py

@@ -41,14 +41,14 @@ def read_laplace_solution(
     Parameters
     ----------
     directory : str
-        directory of d3plot files
+        directory of d3plot files.
     field_list : list[str]
-        name of each d3plot file/field
+        name of each d3plot file/field.
 
     Returns
     -------
     pv.UnstructuredGrid
-        grid with point data of each field
+        grid with point data of each field.
     """
     data = D3plotReader(os.path.join(directory, field_list[0] + ".d3plot"))
     grid: pv.UnstructuredGrid = data.model.metadata.meshed_region.grid
@@ -84,19 +84,19 @@ def update_transmural_by_normal(grid: pv.UnstructuredGrid, surface: pv.PolyData)
     Note
     ----
     Assume mesh is coarse compared to the thinkness, solid cell normal
-    is interpolated from closest surface normal
+    is interpolated from closest surface normal.
 
     Parameters
     ----------
-    grid : pv.UnstructuredGrid
+    grid : pv.UnstructuredGrid.
         atrium grid
     surface : pv.PolyData
-        atrium endocardium surface
+        atrium endocardium surface.
 
     Returns
     -------
     np.ndarray
-        cell transmural direction vector
+        cell transmural direction vector.
     """
     surface_normals = surface.clean().compute_normals()
 
@@ -120,14 +120,14 @@ def orthogonalization(
     Parameters
     ----------
     grad_trans : np.ndarray
-        transmural vector
+        transmural vector.
     k : np.ndarray
-        Bundle selection vector
+        Bundle selection vector.
 
     Returns
     -------
     tuple[np.ndarray, np.ndarray, np.ndarray]
-        local coordinate system e_l,e_n,e_t
+        local coordinate system e_l,e_n,e_t.
     """
     norm = np.linalg.norm(grad_trans, axis=1)
     bad_cells = np.argwhere(norm == 0).ravel()
@@ -241,7 +241,7 @@ def compute_ra_fiber_cs(
     settings : AtrialFiber
         Atrial fiber settings.
     endo_surface : pv.PolyData, optional
-        _description_, by default None
+        _description_, by default None.
         If given, normal direction will be updated by surface normal instead of Laplace solution.
 
     Notes
@@ -376,18 +376,18 @@ def set_rotation_bounds(
     Parameters
     ----------
     w : np.ndarray
-        intra-ventricular interpolation weight if outflow_tracts is not None
+        intra-ventricular interpolation weight if outflow_tracts is not None.
     endo : float
-        rotation angle at endocardium
+        rotation angle at endocardium.
     epi : float
-        rotation angle at epicardium
+        rotation angle at epicardium.
     outflow_tracts : list[float, float], optional
-        rotation angle of enendocardium do and epicardium on outflow tract, by default None
+        rotation angle of enendocardium do and epicardium on outflow tract, by default None.
 
     Returns
     -------
     tuple[np.ndarray, np.ndarray]
-        cell-wise rotation bounds for endocardium and epicardium
+        cell-wise rotation bounds for endocardium and epicardium.
     """
 
     def _sigmoid(z):