cardiac-geometriesx 0.0.4__tar.gz → 0.1.1__tar.gz

{cardiac_geometriesx-0.0.4 → cardiac_geometriesx-0.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cardiac-geometriesx
-Version: 0.0.4
+Version: 0.1.1
 Summary: A python library for cardiac geometries
 Author-email: Henrik Finsberg <henriknf@simula.no>
 License: MIT
@@ -29,13 +29,14 @@ Requires-Dist: pre-commit; extra == "test"
 Requires-Dist: pytest; extra == "test"
 Requires-Dist: pytest-cov; extra == "test"
 
+
 # Cardiac geometries
 
 Cardiac geometries for `dolfinx` (targeting v0.8).
 
 Install
 ```
-python3 -m pip install git+https://github.com/ComputationalPhysiology/cardiac-geometriesx
+python3 -m pip install cardiac-geometriesx
 ```
 
 Example usage

{cardiac_geometriesx-0.0.4 → cardiac_geometriesx-0.1.1}/README.md

@@ -1,10 +1,11 @@
+
 # Cardiac geometries
 
 Cardiac geometries for `dolfinx` (targeting v0.8).
 
 Install
 ```
-python3 -m pip install git+https://github.com/ComputationalPhysiology/cardiac-geometriesx
+python3 -m pip install cardiac-geometriesx
 ```
 
 Example usage

{cardiac_geometriesx-0.0.4 → cardiac_geometriesx-0.1.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "cardiac-geometriesx"
-version = "0.0.4"
+version = "0.1.1"
 description = "A python library for cardiac geometries"
 authors = [{name = "Henrik Finsberg", email = "henriknf@simula.no"}]
 license = {text = "MIT"}
@@ -156,7 +156,7 @@ tag = true
 sign_tags = false
 tag_name = "v{new_version}"
 tag_message = "Bump version: {current_version} → {new_version}"
-current_version = "0.0.4"
+current_version = "0.1.1"
 
 
 [[tool.bumpversion.files]]

{cardiac_geometriesx-0.0.4 → cardiac_geometriesx-0.1.1}/src/cardiac_geometries/fibers/utils.py

@@ -1,5 +1,5 @@
 from pathlib import Path
-from typing import NamedTuple
+from typing import NamedTuple, Sequence
 
 import adios4dolfinx
 import dolfinx
@@ -15,28 +15,25 @@ class Microstructure(NamedTuple):
 
 
 def save_microstructure(
-    mesh: dolfinx.mesh.Mesh, system: Microstructure, outdir: str | Path
+    mesh: dolfinx.mesh.Mesh, functions: Sequence[dolfinx.fem.Function], outdir: str | Path
 ) -> None:
     from ..utils import element2array
 
     # Save for paraview visualization
-    with dolfinx.io.XDMFFile(mesh.comm, Path(outdir) / "microstructure.xdmf", "w") as file:
-        file.write_mesh(mesh)
-        file.write_function(system.f0)
-        file.write_function(system.s0)
-        file.write_function(system.n0)
-
+    with dolfinx.io.VTXWriter(mesh.comm, Path(outdir) / "microstructure-viz.bp", functions, engine="BP4") as file:
+        file.write(0.0)
+        
     # Save with proper function space
     filename = Path(outdir) / "microstructure.bp"
-    adios4dolfinx.write_function(u=system.f0, filename=filename)
-    adios4dolfinx.write_function(u=system.s0, filename=filename)
-    adios4dolfinx.write_function(u=system.n0, filename=filename)
-    arr = element2array(system.f0.ufl_element().basix_element)
+    for function in functions:
+        adios4dolfinx.write_function(u=function, filename=filename)
+
+    attributes = {f.name: element2array(f.ufl_element().basix_element) for f in functions}
     adios4dolfinx.write_attributes(
         comm=mesh.comm,
         filename=filename,
         name="function_space",
-        attributes={k: arr for k in ("f0", "s0", "n0")},
+        attributes=attributes,
     )
 
 

{cardiac_geometriesx-0.0.4 → cardiac_geometriesx-0.1.1}/src/cardiac_geometries/geometry.py

@@ -12,7 +12,7 @@ import numpy as np
 from . import utils
 
 
-@dataclass(frozen=True, slots=True)
+@dataclass#(frozen=True, slots=True)
 class Geometry:
     mesh: dolfinx.mesh.Mesh
     markers: dict[str, tuple[str, str]] = field(default_factory=dict)

{cardiac_geometriesx-0.0.4 → cardiac_geometriesx-0.1.1}/src/cardiac_geometriesx.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cardiac-geometriesx
-Version: 0.0.4
+Version: 0.1.1
 Summary: A python library for cardiac geometries
 Author-email: Henrik Finsberg <henriknf@simula.no>
 License: MIT
@@ -29,13 +29,14 @@ Requires-Dist: pre-commit; extra == "test"
 Requires-Dist: pytest; extra == "test"
 Requires-Dist: pytest-cov; extra == "test"
 
+
 # Cardiac geometries
 
 Cardiac geometries for `dolfinx` (targeting v0.8).
 
 Install
 ```
-python3 -m pip install git+https://github.com/ComputationalPhysiology/cardiac-geometriesx
+python3 -m pip install cardiac-geometriesx
 ```
 
 Example usage