annotate for pyo3 0.28

jonaspleyer · jonaspleyer · commit d04327ae93ec · 2026-03-05T14:55:55.000+01:00
diff --git a/cellular_raza-building-blocks/src/cell_building_blocks/cycle.rs b/cellular_raza-building-blocks/src/cell_building_blocks/cycle.rs
@@ -8,7 +8,7 @@ use pyo3::prelude::*;
 
 /// No cycle of the cell.
 #[derive(Clone, Debug, Serialize, Deserialize)]
-#[cfg_attr(feature = "pyo3", pyclass)]
+#[cfg_attr(feature = "pyo3", pyclass(from_py_object))]
 pub struct NoCycle;
 
 impl<Cel, Float> Cycle<Cel, Float> for NoCycle {
diff --git a/cellular_raza-building-blocks/src/cell_building_blocks/interaction.rs b/cellular_raza-building-blocks/src/cell_building_blocks/interaction.rs
@@ -11,7 +11,7 @@ use approx::RelativeEq;
 
 /// No interaction of the cell with any other.
 #[derive(Clone, Debug, Serialize, Deserialize, PartialEq)]
-#[cfg_attr(feature = "pyo3", pyclass)]
+#[cfg_attr(feature = "pyo3", pyclass(from_py_object))]
 pub struct NoInteraction;
 
 impl<Pos, Vel, For> Interaction<Pos, Vel, For> for NoInteraction
@@ -82,7 +82,7 @@ impl InteractionInformation<()> for NoInteraction {
 /// [10.1098/rspa.1924.0081](https://doi.org/10.1098/rspa.1924.0081).
 ///
 #[derive(Clone, Debug, Serialize, Deserialize, PartialEq)]
-#[cfg_attr(feature = "pyo3", pyclass(get_all, set_all))]
+#[cfg_attr(feature = "pyo3", pyclass(get_all, set_all, from_py_object))]
 #[cfg_attr(feature = "approx", derive(RelativeEq))]
 pub struct BoundLennardJones {
     /// Interaction strength $\epsilon$ of the potential.
@@ -96,7 +96,7 @@ pub struct BoundLennardJones {
 }
 
 #[derive(Clone, Debug, Serialize, Deserialize, PartialEq)]
-#[cfg_attr(feature = "pyo3", pyclass(get_all, set_all))]
+#[cfg_attr(feature = "pyo3", pyclass(get_all, set_all, from_py_object))]
 #[cfg_attr(feature = "approx", derive(RelativeEq))]
 /// Identical to [BoundLennardJones] but for `f32` type.
 pub struct BoundLennardJonesF32 {
@@ -210,7 +210,7 @@ macro_rules! implement_morse_potential(
         /// pp. 57–64, Jul. 01, 1929.
         /// doi: [10.1103/physrev.34.57](https://doi.org/10.1103/PhysRev.34.57).
         #[derive(Clone, Debug, Serialize, Deserialize, PartialEq)]
-        #[cfg_attr(feature = "pyo3", pyclass(set_all, get_all))]
+        #[cfg_attr(feature = "pyo3", pyclass(set_all, get_all, from_py_object))]
         #[cfg_attr(feature = "approx", derive(RelativeEq))]
         pub struct $struct_name {
             /// Radius of the object
@@ -316,7 +316,7 @@ macro_rules! implement_mie_potential(
         /// G. Mie, “Zur kinetischen Theorie der einatomigen Körper,”
         /// Annalen der Physik, vol. 316, no. 8. Wiley, pp. 657–697, Jan. 1903.
         /// doi: [10.1002/andp.19033160802](https://doi.org/10.1002/andp.19033160802).
-        #[cfg_attr(feature = "pyo3", pyclass(get_all, set_all))]
+        #[cfg_attr(feature = "pyo3", pyclass(get_all, set_all, from_py_object))]
         #[cfg_attr(feature = "approx", derive(RelativeEq))]
         #[derive(Clone, Debug, Deserialize, Serialize, PartialEq)]
         pub struct $name {
diff --git a/cellular_raza-building-blocks/src/cell_building_blocks/mechanics.rs b/cellular_raza-building-blocks/src/cell_building_blocks/mechanics.rs
@@ -48,7 +48,7 @@ macro_rules! implement_newton_damped_mechanics(
         /// Both operations need to be implemented by other concepts such as
         /// [Cycle](cellular_raza_concepts::Cycle).
         #[derive(Clone, Debug, Serialize, Deserialize, PartialEq)]
-        #[cfg_attr(feature = "pyo3", pyclass)]
+        #[cfg_attr(feature = "pyo3", pyclass(from_py_object))]
         #[cfg_attr(feature = "approx", derive(RelativeEq))]
         #[cfg_attr(feature = "approx", approx(epsilon_type = $float_type))]
         pub struct $struct_name {
@@ -247,7 +247,7 @@ macro_rules! implement_brownian_mechanics(
         /// If we choose this value larger than one, we can
         /// resolve smaller timesteps to more accurately solve the equations.
         #[derive(Clone, Debug, Deserialize, Serialize, PartialEq)]
-        #[cfg_attr(feature = "pyo3", pyclass)]
+        #[cfg_attr(feature = "pyo3", pyclass(from_py_object))]
         #[cfg_attr(feature = "approx", derive(RelativeEq))]
         #[cfg_attr(feature = "approx", approx(epsilon_type = $float_type))]
         pub struct $struct_name {
@@ -407,7 +407,7 @@ macro_rules! define_langevin_nd(
         ///     M \ddot{\mathbf{X}} = - \mathbf{\nabla} U(\mathbf{X}) - \gamma M\dot{\mathbf{X}} + \sqrt{2 M \gamma k_{\rm B} T}\mathbf{R}(t)
         /// \\end{equation}
         #[derive(Clone, Debug, Deserialize, Serialize, PartialEq)]
-        #[cfg_attr(feature = "pyo3", pyclass)]
+        #[cfg_attr(feature = "pyo3", pyclass(from_py_object))]
         #[cfg_attr(feature = "approx", derive(RelativeEq))]
         #[cfg_attr(feature = "approx", approx(epsilon_type = $float_type))]
         pub struct $struct_name {
diff --git a/cellular_raza-building-blocks/src/cell_models/pool_bacteria.rs b/cellular_raza-building-blocks/src/cell_models/pool_bacteria.rs
@@ -20,7 +20,7 @@ pub type ReactionVector = nalgebra::SVector<f64, NUMBER_OF_REACTION_COMPONENTS>;
 
 /// Bacteria-Agent as used in the pool-model example
 #[derive(CellAgent, Clone, Debug, Deserialize, Serialize)]
-#[pyclass(get_all, set_all)]
+#[pyclass(get_all, set_all, from_py_object)]
 pub struct Bacteria {
     /// See [NewtonDamped2D](crate::cell_building_blocks::NewtonDamped2D) mechanics
     #[Mechanics]
@@ -45,7 +45,7 @@ pub struct Bacteria {
 /// It contains heap-allocated instances of the python classes for the individual aspects.
 /// This is useful when modifying said properties from python directly via dot-notation.
 #[derive(Clone, Debug, Deserialize, Serialize)]
-#[pyclass(get_all, set_all)]
+#[pyclass(get_all, set_all, from_py_object)]
 pub struct BacteriaTemplate {
     /// See [NewtonDamped2D](crate::cell_building_blocks::NewtonDamped2D) mechanics
     pub mechanics: pyo3::Py<NewtonDamped2D>,
@@ -192,7 +192,7 @@ impl Interaction<Vector2<f64>, Vector2<f64>, Vector2<f64>, f64> for BacteriaReac
 
 /// Implementation of the [cellular_raza_concepts::Cycle] trait for the [Bacteria] struct
 #[derive(Serialize, Deserialize, Debug, Clone)]
-#[pyclass(get_all, set_all)]
+#[pyclass(get_all, set_all, from_py_object)]
 pub struct BacteriaCycle {
     /// Threshold for the volume when the cell should divide
     pub volume_division_threshold: f64,
@@ -294,7 +294,7 @@ impl Cycle<Bacteria> for BacteriaCycle {
 
 /// Species of the cells (S1, S2)
 #[derive(Clone, Debug, Deserialize, Serialize, Eq, PartialEq)]
-#[pyclass(eq, eq_int)]
+#[pyclass(eq, eq_int, from_py_object)]
 pub enum Species {
     /// Species 1
     S1,
@@ -305,7 +305,7 @@ pub enum Species {
 /// Implementation of the [cellular_raza_concepts::CellularReactions] trait and
 /// [cellular_raza_concepts::Interaction] trait for [Bacteria].
 #[derive(Serialize, Deserialize, Clone, Debug)]
-#[pyclass(get_all, set_all)]
+#[pyclass(get_all, set_all, from_py_object)]
 pub struct BacteriaReactions {
     /// Overall interaction strength for physical interaction
     pub potential_strength: f64,
@@ -431,7 +431,7 @@ impl Volume for Bacteria {
 
 /// This struct does nothing
 #[derive(Clone, Debug, Serialize, Deserialize)]
-#[pyclass]
+#[pyclass(from_py_object)]
 pub struct GradientSensing;
 
 impl
diff --git a/cellular_raza-concepts/src/cell.rs b/cellular_raza-concepts/src/cell.rs
@@ -13,7 +13,7 @@ use serde::{Deserialize, Serialize};
 /// This can be due to initial setup or due to other methods such as division in a cell cycle.
 /// The second parameter is a counter which is unique for each voxel.
 /// This ensures that each cell obtains a unique identifier over the course of the simulation.
-#[cfg_attr(feature = "pyo3", pyo3::pyclass)]
+#[cfg_attr(feature = "pyo3", pyo3::pyclass(from_py_object))]
 #[derive(Clone, Copy, Debug, Deserialize, Hash, PartialEq, Eq, Ord, PartialOrd, Serialize)]
 pub enum CellIdentifier {
     /// Produced from a division process
diff --git a/cellular_raza-concepts/src/domain.rs b/cellular_raza-concepts/src/domain.rs
@@ -4,7 +4,7 @@ use std::collections::{BTreeMap, BTreeSet};
 use crate::errors::{BoundaryError, DecomposeError};
 
 /// Identifier for voxels used internally to get rid of user-defined ones.
-#[cfg_attr(feature = "pyo3", pyo3::pyclass)]
+#[cfg_attr(feature = "pyo3", pyo3::pyclass(from_py_object))]
 #[derive(Clone, Copy, Debug, Deserialize, Hash, PartialEq, Eq, Ord, PartialOrd, Serialize)]
 pub struct VoxelPlainIndex(pub usize);
 
@@ -28,7 +28,7 @@ impl VoxelPlainIndex {
 
 /// Identifier or subdomains
 #[derive(Clone, Copy, Debug, Deserialize, Hash, PartialEq, Eq, Ord, PartialOrd, Serialize)]
-#[cfg_attr(feature = "pyo3", pyo3::pyclass)]
+#[cfg_attr(feature = "pyo3", pyo3::pyclass(from_py_object))]
 pub struct SubDomainPlainIndex(pub usize);
 
 /// Provides an abstraction of the physical total simulation domain.
diff --git a/cellular_raza-core/src/storage/concepts.rs b/cellular_raza-core/src/storage/concepts.rs
@@ -124,7 +124,7 @@ impl Error for StorageError {}
 ///
 /// We currently support saving results in a [sled] database, or as a json file by using
 /// [serde_json].
-#[cfg_attr(feature = "pyo3", pyo3::pyclass(eq, eq_int))]
+#[cfg_attr(feature = "pyo3", pyo3::pyclass(eq, eq_int, from_py_object))]
 #[derive(Clone, Debug, Deserialize, PartialEq, Eq, Serialize)]
 pub enum StorageOption {
     /// Save results as [sled] database.
