fluxfem 0.2.0__py3-none-any.whl → 0.2.1__py3-none-any.whl

fluxfem/solver/sparse.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 from dataclasses import dataclass
+from typing import Any, Iterable, Sequence, TYPE_CHECKING, TypeAlias
 
 import numpy as np
 import jax
@@ -12,7 +13,18 @@ except Exception:  # pragma: no cover
     sp = None
 
 
-def coalesce_coo(rows, cols, data):
+if TYPE_CHECKING:
+    from jax import Array as JaxArray
+
+    ArrayLike: TypeAlias = np.ndarray | JaxArray
+else:
+    ArrayLike: TypeAlias = np.ndarray
+COOTuple: TypeAlias = tuple[jnp.ndarray, jnp.ndarray, jnp.ndarray, int]
+
+
+def coalesce_coo(
+    rows: ArrayLike, cols: ArrayLike, data: ArrayLike
+) -> tuple[np.ndarray, np.ndarray, np.ndarray]:
     """
     Sum duplicate COO entries by sorting (CPU-friendly).
     Returns (rows_u, cols_u, data_u) as NumPy arrays.
@@ -35,7 +47,7 @@ def coalesce_coo(rows, cols, data):
     return r_u, c_u, d_u
 
 
-def _normalize_flux_mats(mats):
+def _normalize_flux_mats(mats: Sequence["FluxSparseMatrix"]) -> tuple["FluxSparseMatrix", ...]:
     if len(mats) == 1 and isinstance(mats[0], (list, tuple)):
         mats = tuple(mats[0])
     if not mats:
@@ -43,7 +55,7 @@ def _normalize_flux_mats(mats):
     return mats
 
 
-def concat_flux(*mats, n_dofs: int | None = None):
+def concat_flux(*mats: "FluxSparseMatrix", n_dofs: int | None = None) -> "FluxSparseMatrix":
     """
     Concatenate COO entries from multiple FluxSparseMatrix objects.
     All matrices must share the same n_dofs unless n_dofs is provided.
@@ -63,7 +75,7 @@ def concat_flux(*mats, n_dofs: int | None = None):
     return FluxSparseMatrix(rows, cols, data, int(n_dofs))
 
 
-def block_diag_flux(*mats):
+def block_diag_flux(*mats: "FluxSparseMatrix") -> "FluxSparseMatrix":
     """Block-diagonal concatenation for FluxSparseMatrix objects."""
     mats = _normalize_flux_mats(mats)
     rows_out = []
@@ -153,7 +165,14 @@ class FluxSparseMatrix:
     - data stores the numeric values for the current nonlinear iterate
     """
 
-    def __init__(self, rows_or_pattern, cols=None, data=None, n_dofs: int | None = None, meta: dict | None = None):
+    def __init__(
+        self,
+        rows_or_pattern: SparsityPattern | ArrayLike,
+        cols: ArrayLike | None = None,
+        data: ArrayLike | None = None,
+        n_dofs: int | None = None,
+        meta: dict | None = None,
+    ):
         # New signature: FluxSparseMatrix(pattern, data)
         if isinstance(rows_or_pattern, SparsityPattern):
             pattern = rows_or_pattern
@@ -188,35 +207,35 @@ class FluxSparseMatrix:
         self.meta = dict(meta) if meta is not None else None
 
     @classmethod
-    def from_bilinear(cls, coo_tuple):
+    def from_bilinear(cls, coo_tuple: COOTuple) -> "FluxSparseMatrix":
         """Construct from assemble_bilinear_dense(..., sparse=True)."""
         rows, cols, data, n_dofs = coo_tuple
         return cls(rows, cols, data, n_dofs)
 
     @classmethod
-    def from_linear(cls, coo_tuple):
+    def from_linear(cls, coo_tuple: tuple[jnp.ndarray, jnp.ndarray, int]) -> "FluxSparseMatrix":
         """Construct from assemble_linear_form(..., sparse=True) (matrix interpretation only)."""
         rows, data, n_dofs = coo_tuple
         cols = jnp.zeros_like(rows)
         return cls(rows, cols, data, n_dofs)
 
-    def with_data(self, data):
+    def with_data(self, data: ArrayLike) -> "FluxSparseMatrix":
         """Return a new FluxSparseMatrix sharing the same pattern with updated data."""
         return FluxSparseMatrix(self.pattern, data, meta=self.meta)
 
-    def add_dense(self, dense):
+    def add_dense(self, dense: ArrayLike) -> "FluxSparseMatrix":
         """Return a new FluxSparseMatrix with dense entries added on the pattern."""
         dense_vals = jnp.asarray(dense)[self.pattern.rows, self.pattern.cols]
         return FluxSparseMatrix(self.pattern, self.data + dense_vals)
 
-    def to_coo(self):
+    def to_coo(self) -> COOTuple:
         return self.pattern.rows, self.pattern.cols, self.data, self.pattern.n_dofs
 
     @property
     def nnz(self) -> int:
         return int(self.data.shape[0])
 
-    def coalesce(self):
+    def coalesce(self) -> "FluxSparseMatrix":
         """Return a new FluxSparseMatrix with duplicate entries summed."""
         rows_u, cols_u, data_u = coalesce_coo(self.pattern.rows, self.pattern.cols, self.data)
         return FluxSparseMatrix(rows_u, cols_u, data_u, self.pattern.n_dofs)
@@ -238,7 +257,7 @@ class FluxSparseMatrix:
         d = np.array(self.data, copy=True)
         return sp.csr_matrix((d, (r, c)), shape=(self.pattern.n_dofs, self.pattern.n_dofs))
 
-    def to_dense(self):
+    def to_dense(self) -> jnp.ndarray:
         # small debug helper
         dense = jnp.zeros((self.pattern.n_dofs, self.pattern.n_dofs), dtype=self.data.dtype)
         dense = dense.at[self.pattern.rows, self.pattern.cols].add(self.data)
@@ -253,7 +272,7 @@ class FluxSparseMatrix:
         idx = jnp.stack([self.pattern.rows, self.pattern.cols], axis=-1)
         return jsparse.BCOO((self.data, idx), shape=(self.pattern.n_dofs, self.pattern.n_dofs))
 
-    def matvec(self, x):
+    def matvec(self, x: ArrayLike) -> jnp.ndarray:
         """Compute y = A x in JAX (iterative solvers)."""
         xj = jnp.asarray(x)
         contrib = self.data * xj[self.pattern.cols]

fluxfem/tools/jit.py

@@ -1,10 +1,22 @@
+from __future__ import annotations
+
 import jax
 
-from ..core.assembly import assemble_residual, assemble_jacobian
+from typing import Callable, TypeVar
+
+from ..core.assembly import JacobianReturn, LinearReturn, ResidualForm, assemble_jacobian, assemble_residual
 from ..core.space import FESpace
 
+P = TypeVar("P")
+
 
-def make_jitted_residual(space: FESpace, res_form, params, *, sparse: bool = False):
+def make_jitted_residual(
+    space: FESpace,
+    res_form: ResidualForm[P],
+    params: P,
+    *,
+    sparse: bool = False,
+) -> Callable[[jax.Array], LinearReturn]:
     """
     Create a jitted residual assembler: u -> R(u).
     params and space are closed over.
@@ -13,7 +25,7 @@ def make_jitted_residual(space: FESpace, res_form, params, *, sparse: bool = Fal
     params_jax = params
 
     @jax.jit
-    def residual(u):
+    def residual(u: jax.Array) -> LinearReturn:
         return assemble_residual(space_jax, res_form, u, params_jax, sparse=sparse)
 
     return residual
@@ -21,12 +33,12 @@ def make_jitted_residual(space: FESpace, res_form, params, *, sparse: bool = Fal
 
 def make_jitted_jacobian(
     space: FESpace,
-    res_form,
-    params,
+    res_form: ResidualForm[P],
+    params: P,
     *,
     sparse: bool = False,
     return_flux_matrix: bool = False,
-):
+) -> Callable[[jax.Array], JacobianReturn]:
     """
     Create a jitted Jacobian assembler: u -> J(u).
     params and space are closed over.
@@ -35,7 +47,7 @@ def make_jitted_jacobian(
     params_jax = params
 
     @jax.jit
-    def jacobian(u):
+    def jacobian(u: jax.Array) -> JacobianReturn:
         return assemble_jacobian(
             space_jax,
             res_form,

fluxfem/tools/timer.py

@@ -5,13 +5,15 @@ from contextlib import AbstractContextManager
 from collections import defaultdict
 from contextlib import contextmanager
 from dataclasses import dataclass
-from typing import Callable, DefaultDict, Dict, Iterator, List, Optional
+from typing import Any, Callable, DefaultDict, Dict, Iterator, List, Optional, TypeAlias
 
 import logging
 
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
+PlotResult: TypeAlias = tuple[Any, Any]
+
 
 @dataclass
 class SectionStats:
@@ -30,7 +32,7 @@ class BaseTimer(ABC):
 
 class NullTimer(BaseTimer):
     @contextmanager
-    def section(self, name: str):
+    def section(self, name: str) -> Iterator[None]:
         yield
 
 
@@ -85,7 +87,7 @@ class SectionTimer(BaseTimer):
             self._records[full_name].append(duration)
             self._stack.pop()
 
-    def wrap(self, name: str):
+    def wrap(self, name: str) -> Callable[[Callable[..., Any]], Callable[..., Any]]:
         """
         Decorator form of :meth:`section`.
 
@@ -97,8 +99,8 @@ class SectionTimer(BaseTimer):
                 ...
         """
 
-        def _decorator(func):
-            def _wrapper(*args, **kwargs):
+        def _decorator(func: Callable[..., Any]) -> Callable[..., Any]:
+            def _wrapper(*args: Any, **kwargs: Any) -> Any:
                 with self.section(name):
                     return func(*args, **kwargs)
             return _wrapper
@@ -211,7 +213,7 @@ class SectionTimer(BaseTimer):
         self,
         sort_by: str = "total",
         descending: bool = True,
-        logger_instance=None,
+        logger_instance: logging.Logger | None = None,
     ) -> str:
         stats = self.summary(sort_by=sort_by, descending=descending)
         if not stats:
@@ -231,7 +233,7 @@ class SectionTimer(BaseTimer):
 
     def plot_bar(
         self,
-        ax=None,
+        ax: Any | None = None,
         sort_by: str = "total",
         value: str = "total",
         descending: bool = True,
@@ -240,7 +242,7 @@ class SectionTimer(BaseTimer):
         stacked_nested: bool = False,
         moving_average: bool = False,
         use_self_time: bool = False,
-    ):
+    ) -> PlotResult:
         """
         Plot timing results as a horizontal bar chart without relying on pyplot state.
 
@@ -417,7 +419,7 @@ class SectionTimer(BaseTimer):
 
     def plot_pie(
         self,
-        ax=None,
+        ax: Any | None = None,
         sort_by: str = "total",
         value: str = "total",
         descending: bool = True,
@@ -430,7 +432,7 @@ class SectionTimer(BaseTimer):
         show_total: bool = True,
         moving_average: bool = False,
         use_self_time: bool = False,
-    ):
+    ) -> PlotResult:
         """
         Plot timing results as a pie chart to show relative time share.
 
@@ -552,7 +554,7 @@ class SectionTimer(BaseTimer):
 
     def plot(
         self,
-        ax=None,
+        ax: Any | None = None,
         sort_by: str = "total",
         value: str = "total",
         descending: bool = True,
@@ -563,7 +565,7 @@ class SectionTimer(BaseTimer):
         moving_average: bool = False,
         use_self_time: bool = False,
         **kwargs,
-    ):
+    ) -> PlotResult:
         """
         Plot timing results choosing between pie (default) or bar chart.
 

fluxfem/tools/visualizer.py

@@ -3,14 +3,14 @@ from typing import Mapping
 
 import numpy as np
 
-from ..mesh import HexMesh, TetMesh
+from ..mesh import BaseMesh, HexMesh, TetMesh
 
 
 VTK_HEXAHEDRON = 12
 VTK_TETRA = 10
 
 
-def _cell_type_for_mesh(mesh):
+def _cell_type_for_mesh(mesh: BaseMesh) -> int:
     if isinstance(mesh, HexMesh):
         return VTK_HEXAHEDRON
     if isinstance(mesh, TetMesh):
@@ -25,7 +25,13 @@ def _write_dataarray(name: str, data: np.ndarray, ncomp: int = 1) -> str:
     return f'<DataArray type="Float32" Name="{name}" format="ascii"{comp_attr}>{values}</DataArray>'
 
 
-def write_vtu(mesh, filepath: str, *, point_data: Mapping[str, np.ndarray] | None = None, cell_data: Mapping[str, np.ndarray] | None = None):
+def write_vtu(
+    mesh: BaseMesh,
+    filepath: str,
+    *,
+    point_data: Mapping[str, np.ndarray] | None = None,
+    cell_data: Mapping[str, np.ndarray] | None = None,
+) -> None:
     """
     Write an UnstructuredGrid VTU for HexMesh or TetMesh.
     point_data/cell_data: dict name -> ndarray. Point data length must match n_points;
@@ -87,7 +93,13 @@ def write_vtu(mesh, filepath: str, *, point_data: Mapping[str, np.ndarray] | Non
         f.write("\n".join(lines))
 
 
-def write_displacement_vtu(mesh, u, filepath: str, *, name: str = "displacement"):
+def write_displacement_vtu(
+    mesh: BaseMesh,
+    u: np.ndarray,
+    filepath: str,
+    *,
+    name: str = "displacement",
+) -> None:
     """
     Convenience wrapper: reshape displacement vector to point data and write VTU.
     Assumes 3 dof/node ordering [u0,v0,w0, u1,v1,w1, ...].

{fluxfem-0.2.0.dist-info → fluxfem-0.2.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fluxfem
-Version: 0.2.0
+Version: 0.2.1
 Summary: FluxFEM: A weak-form-centric differentiable finite element framework in JAX
 License: Apache-2.0
 Author: Kohei Watanabe
@@ -94,9 +94,9 @@ import jax.numpy as jnp
 
 space = ff.make_hex_space(mesh, dim=1, intorder=2)
 
-   # bilinear: kernel(ctx) -> (n_ldofs, n_ldofs)
-   ker_K = ff.make_element_bilinear_kernel(ff.diffusion_form, 1.0, jit=True)
-   K = space.assemble(ff.diffusion_form, 1.0, kernel=ker_K)
+# bilinear: kernel(ctx) -> (n_ldofs, n_ldofs)
+ker_K = ff.make_element_bilinear_kernel(ff.diffusion_form, 1.0, jit=True)
+K = space.assemble(ff.diffusion_form, 1.0, kernel=ker_K)
 
 # linear: kernel(ctx) -> (n_ldofs,)
 def linear_kernel(ctx):
@@ -104,8 +104,8 @@ def linear_kernel(ctx):
     wJ = ctx.w * ctx.test.detJ
     return (integrand * wJ[:, None]).sum(axis=0)
 
-   ker_F = jax.jit(linear_kernel)
-   F = space.assemble(ff.scalar_body_force_form, 2.0, kernel=ker_F)
+ker_F = jax.jit(linear_kernel)
+F = space.assemble(ff.scalar_body_force_form, 2.0, kernel=ker_F)
 ```
 
 ### tensor-based vs weak-form-based (diffusion example)
@@ -182,7 +182,7 @@ def neo_hookean_residual_wf(v, u, params):
     dE = 0.5 * (h_wf.matmul(h_wf.grad(v), F) + h_wf.transpose(h_wf.matmul(h_wf.grad(v), F)))
     return h_wf.ddot(S, dE) * h_wf.dOmega()
 
-  res_form = ff.ResidualForm.volume(neo_hookean_residual_wf).get_compiled()
+res_form = ff.ResidualForm.volume(neo_hookean_residual_wf).get_compiled()
 ```
 
 
@@ -203,6 +203,14 @@ loss_theta_jit = jax.jit(loss_theta)
 grad_fn = jax.jit(jax.grad(loss_theta))
 ```
 
+### FESpace vs FESpacePytree
+
+Use `FESpace` for standard workflows with a fixed mesh. When you need to carry
+the space through JAX transformations (e.g., shape optimization where mesh
+coordinates are part of the computation), use `FESpacePytree` via
+`make_*_space_pytree(...)`. This keeps the mesh/basis in the pytree so
+`jax.jit`/`jax.grad` can see geometry changes.
+
 ### Mixed systems
 
 Mixed problems can be assembled from residual blocks and solved as a coupled system.
@@ -243,6 +251,9 @@ blocks = ff_solver.make_block_matrix(
     symmetric=True,
     transpose_rule="T",
 )
+
+# Lazy container; assemble when you need the global matrix.
+K = blocks.assemble()
 ```
 
 FluxFEM also provides contact utilities like `ContactSurfaceSpace` to build constraint contributions.

fluxfem-0.2.1.dist-info/RECORD

@@ -0,0 +1,59 @@
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+fluxfem/core/__init__.py,sha256=av60HQ0K8oaLko0vKc_GNsNs35TayR8BPGp463GKFN4,10898
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