Python documentation improvements.

py-rgrow/rgrow/rgrow.pyi

@@ -12,7 +12,6 @@ class TileShape(Enum):
     Horizontal = ...
 
 class EvolveOutcome(object): ...
-
 class NeededUpdate(object): ...
 
 class State(object):
@@ -27,9 +26,7 @@ class State(object):
     def time(self) -> float: ...
     @property
     def total_events(self) -> int: ...
-    def print_debug(self) -> None: 
-        "Print rust Debug string for the state object."
-        ...
+    def print_debug(self) -> None: ...
 
 class System(object):
     @overload
@@ -83,9 +80,7 @@ class System(object):
     ) -> "Axes": ...
     def get_param(self, name: str) -> Any: ...
     def set_param(self, name: str, value: Any): ...
-    def print_debug(self) -> None: 
-        "Print rust Debug string for the system object."
-        ...
+    def print_debug(self) -> None: ...
 
 class FissionHandling(object): ...
 class CanvasType(object): ...
@@ -106,30 +101,18 @@ class FFSStateRef(object):
     def tracking_copy(self) -> np.ndarray: ...
     def clone_state(self) -> State: ...
     def rate_at_point(self, point: tuple[int, int]) -> float: ...
-
 
 class FFSLevelRef(object):
     @property
-    def configs(self) -> list[np.ndarray]:
-        """List of configurations at this level, as arrays (not full states)."""
-        ...
+    def configs(self) -> list[np.ndarray]: ...
     @property
-    def states(self) -> list[FFSStateRef]:
-        """List of states at this level."""
-        ...
+    def states(self) -> list[FFSStateRef]: ...
     @property
-    def previous_indices(self) -> list[int]:
-        """For each configuration, the index of the configuration in the previous
-        level that resulted in it."""
-        ...
+    def previous_indices(self) -> list[int]: ...
 
 class FFSRunResult(object):
     @property
-    def nucleation_rate(self) -> float:
-        """
-        The calculated nucleation rate, in M/s.
-        """
-        ...
+    def nucleation_rate(self) -> float: ...
     @property
     def forward_vec(self) -> np.ndarray: ...
     @property

rgrow/src/ffs.rs

@@ -58,7 +58,7 @@ use system::{DynSystem, Orientation, System, SystemEnum};
 
 /// Configuration options for FFS.
 #[derive(Debug, Clone, Serialize, Deserialize)]
-#[cfg_attr(feature = "python", pyclass(get_all, set_all))]
+#[cfg_attr(feature = "python", pyclass(get_all, set_all, module = "rgrow"))]
 pub struct FFSRunConfig {
     /// Use constant-variance, variable-configurations-per-surface method.
     /// If false, use max_configs for each surface.
@@ -644,7 +644,7 @@ impl<St: ClonableState + StateWithCreate<Params = (usize, usize)>> FFSLevel<St>
 
 // RESULTS CODE
 
-#[cfg_attr(feature = "python", pyclass)]
+#[cfg_attr(feature = "python", pyclass(module = "rgrow"))]
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct FFSRunResult {
     #[serde(skip)]
@@ -656,7 +656,7 @@ pub struct FFSRunResult {
     pub system: Option<SystemEnum>,
 }
 
-#[cfg_attr(feature = "python", pyclass)]
+#[cfg_attr(feature = "python", pyclass(module = "rgrow"))]
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct FFSRunResultDF {
     #[serde(skip)]
@@ -758,7 +758,7 @@ where
     }
 }
 
-#[cfg_attr(feature = "python", pyclass)]
+#[cfg_attr(feature = "python", pyclass(module = "rgrow"))]
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct FFSLevelResult {
     pub state_list: Vec<Arc<StateEnum>>,
@@ -1218,6 +1218,11 @@ impl FFSRunResultDF {
     //         .collect()
     // }
 
+    /// Get the surfaces as a Polars DataFrame.
+    ///
+    /// Returns
+    /// -------
+    /// pl.DataFrame
     #[pyo3(name = "surfaces_dataframe")]
     fn py_surfaces_dataframe(&self) -> PyResult<pyo3_polars::PyDataFrame> {
         Ok(PyDataFrame(self.surfaces_df.clone()))
@@ -1248,12 +1253,25 @@ impl FFSRunResultDF {
     //         .collect()
     // }
 
+    /// Write dataframes and result data to files.
+    ///
+    /// Parameters
+    /// ----------
+    /// prefix : str
+    ///    Prefix for the filenames.  The files will be named
+    ///    `{prefix}.surfaces.parquet`, `{prefix}.configurations.parquet`, and
+    ///    `{prefix}.ffs_result.json`.
     #[pyo3(name = "write_files")]
     fn py_write_files(&mut self, prefix: &str) -> PyResult<()> {
         self.write_files(prefix)
             .map_err(|e| PyPolarsErr::from(e).into())
     }
 
+    /// Read dataframes and result data from files.
+    ///
+    /// Returns
+    /// -------
+    /// Self
     #[pyo3(name = "read_files")]
     #[staticmethod]
     fn py_read_files(prefix: &str) -> PyResult<Self> {
@@ -1268,7 +1286,7 @@ impl FFSRunResultDF {
     // }
 }
 
-#[cfg_attr(feature = "python", pyclass)]
+#[cfg_attr(feature = "python", pyclass(module = "rgrow"))]
 #[allow(dead_code)] // This is used in the python interface
 pub struct FFSLevelRef(Arc<FFSLevelResult>);
 
@@ -1323,7 +1341,7 @@ impl FFSLevelRef {
     }
 }
 
-#[cfg_attr(feature = "python", pyclass)]
+#[cfg_attr(feature = "python", pyclass(module = "rgrow"))]
 #[allow(dead_code)] // This is used in the python interface
 #[derive(Clone)]
 pub struct FFSStateRef(Arc<StateEnum>);

rgrow/src/models/ktam.rs

@@ -116,14 +116,23 @@ pub struct KTAM {
     /// at point P if tile T is in that direction.  Eg, friends_e[T]
     /// is a set of tiles that might attach at point P if T is east of
     /// point P.  The ones other than NESW are only for duples.
+    #[serde(skip)]
     friends_n: Vec<HashSetType<Tile>>,
+    #[serde(skip)]
     friends_e: Vec<HashSetType<Tile>>,
+    #[serde(skip)]
     friends_s: Vec<HashSetType<Tile>>,
+    #[serde(skip)]
     friends_w: Vec<HashSetType<Tile>>,
+    #[serde(skip)]
     friends_ne: Vec<HashSetType<Tile>>,
+    #[serde(skip)]
     friends_ee: Vec<HashSetType<Tile>>,
+    #[serde(skip)]
     friends_se: Vec<HashSetType<Tile>>,
+    #[serde(skip)]
     friends_ss: Vec<HashSetType<Tile>>,
+    #[serde(skip)]
     friends_sw: Vec<HashSetType<Tile>>,
 
     has_duples: bool,