Merge remote-tracking branch 'origin/main' into active-dev

Author: finsberg

.github/workflows/test_package_coverage.yml

@@ -32,8 +32,9 @@ jobs:
       - name: Install development versions of dependencies
         if: ${{ matrix.container == 'ghcr.io/fenics/dolfinx/dolfinx:nightly' }}
         run: |
-          python3 -m pip install git+https://github.com/jorgensd/adios4dolfinx.git
-          python3 -m pip install git+https://github.com/scientificcomputing/scifem.git
+          python3 -m pip install git+https://github.com/scientificcomputing/io4dolfinx.git
+          python3 -m pip install git+https://github.com/scientificcomputing/scifem.git --no-build-isolation
+          python3 -m pip install git+https://github.com/ComputationalPhysiology/cardiac-geometriesx.git
 
       - name: Install package
         run: |

.pre-commit-config.yaml

@@ -14,7 +14,7 @@ repos:
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: 'v0.14.14'
+    rev: 'v0.15.2'
     hooks:
        # Run the linter.
       - id: ruff
@@ -35,7 +35,7 @@ repos:
       - id: mypy
 
   - repo: https://github.com/streetsidesoftware/cspell-cli
-    rev: v9.6.0
+    rev: v9.7.0
     hooks:
       - id: cspell
         files: src/|docs|tests|README.md

demo/benchmark/problem1.py

@@ -27,7 +27,6 @@
 from mpi4py import MPI
 import numpy as np
 import dolfinx
-from dolfinx import log
 import pulse
 
 # ## 1. Geometry and Mesh
@@ -119,8 +118,6 @@ def dirichlet_bc(V: dolfinx.fem.FunctionSpace):
 
 problem = pulse.StaticProblem(model=model, geometry=geo, bcs=bcs)
 
-log.set_log_level(log.LogLevel.INFO)
-
 target_pressure = 0.004
 steps = [0.0005, 0.001, 0.002, 0.003, 0.004]
 
@@ -129,8 +126,6 @@ def dirichlet_bc(V: dolfinx.fem.FunctionSpace):
     pressure.assign(p)
     problem.solve()
 
-log.set_log_level(log.LogLevel.WARNING)
-
 # ## 5. Post-processing
 #
 # We save the final displacement and evaluate the deflection at the specific target point $(10, 0.5, 1)$.

demo/benchmark/problem2.py

@@ -24,7 +24,6 @@
 
 from pathlib import Path
 from mpi4py import MPI
-from dolfinx import log
 import logging
 import dolfinx
 import numpy as np
@@ -114,8 +113,6 @@
     model=model, geometry=geometry, bcs=bcs, parameters={"base_bc": pulse.BaseBC.fixed},
 )
 
-log.set_log_level(log.LogLevel.INFO)
-
 # ### Continuation Solver
 # We ramp the pressure up to 10 kPa. We use a custom continuation loop to handle the nonlinearity.
 

demo/benchmark/problem3.py

@@ -30,15 +30,12 @@
 
 from pathlib import Path
 from mpi4py import MPI
-from dolfinx import log
 import dolfinx
 import numpy as np
 import math
 import cardiac_geometries
 import pulse
 
-# log.set_log_level(log.LogLevel.INFO)
-
 # ## 1. Geometry and Fibers
 # We regenerate the mesh with the specific fiber angles required for Problem 3 ($+90^\circ$ to $-90^\circ$).
 

demo/bleeding_biv.py

@@ -20,7 +20,7 @@
 import matplotlib.pyplot as plt
 import numpy as np
 import gotranx
-import adios4dolfinx
+import io4dolfinx
 import cardiac_geometries
 import cardiac_geometries.geometry
 import pulse
@@ -30,6 +30,7 @@
 def mmHg_to_kPa(x):
     return x * 0.133322
 
+
 def custom_json(obj):
     if isinstance(obj, np.float64):
         return float(obj)
@@ -141,8 +142,6 @@ def run_zenker(outdir: Path):
         history["before_index"] = before_index
         history["after_index"] = after_index
 
-
-
         Path(zenker_file).write_text(json.dumps(history, indent=4, default=custom_json))
 
     return json.loads(zenker_file.read_text())
@@ -202,7 +201,6 @@ def solve_beat(times, states, dt, p, V_index, Ca_index, Vs, Cais, Tas):
                 monitor = mon(ti, states, p)
                 Tas[i] = monitor[Ta_index]
 
-
         nbeats = 10 if os.environ.get("CI") else 200
         times = np.arange(0, T, dt_cell)
         all_times = np.arange(0, T * nbeats, dt_cell)
@@ -261,7 +259,6 @@ def run_3D_model(
     mesh_unit: str = "m",
     volume2ml: float = 1000.0,
 ):
-
     geometry = pulse.HeartGeometry.from_cardiac_geometries(
         geo,
         metadata={"quadrature_degree": 6},
@@ -274,7 +271,8 @@ def run_3D_model(
     # We use an active stress approach with 30% transverse active stress (see {py:meth}`pulse.active_stress.transversely_active_stress`)
 
     Ta = pulse.Variable(
-        dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(0.0)), "kPa",
+        dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(0.0)),
+        "kPa",
     )
     active_model = pulse.ActiveStress(geo.f0, activation=Ta)
 
@@ -312,11 +310,15 @@ def run_3D_model(
     robin = [robin_epi, robin_epi_perp, robin_base]
 
     lvv_initial = comm.allreduce(geometry.volume("LV"), op=MPI.SUM)
-    lv_volume = dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(lvv_initial))
+    lv_volume = dolfinx.fem.Constant(
+        geometry.mesh, dolfinx.default_scalar_type(lvv_initial),
+    )
     lv_cavity = pulse.problem.Cavity(marker="LV", volume=lv_volume)
 
     rvv_initial = comm.allreduce(geometry.volume("RV"), op=MPI.SUM)
-    rv_volume = dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(rvv_initial))
+    rv_volume = dolfinx.fem.Constant(
+        geometry.mesh, dolfinx.default_scalar_type(rvv_initial),
+    )
     rv_cavity = pulse.problem.Cavity(marker="RV", volume=rv_volume)
 
     print("Initial volumes", lvv_initial * volume2ml, rvv_initial * volume2ml)
@@ -325,7 +327,11 @@ def run_3D_model(
     parameters = {"base_bc": pulse.problem.BaseBC.free, "mesh_unit": mesh_unit}
     bcs = pulse.BoundaryConditions(robin=robin)
     problem = pulse.problem.StaticProblem(
-        model=model, geometry=geometry, bcs=bcs, cavities=cavities, parameters=parameters,
+        model=model,
+        geometry=geometry,
+        bcs=bcs,
+        cavities=cavities,
+        parameters=parameters,
     )
 
     problem.solve()
@@ -339,7 +345,7 @@ def run_3D_model(
     vtx.write(0.0)
 
     filename = outdir / Path(f"function_checkpoint_{label}.bp")
-    adios4dolfinx.write_mesh(filename, geometry.mesh)
+    io4dolfinx.write_mesh(filename, geometry.mesh)
     output_file = outdir / f"output_{label}.json"
 
     Ta_history = []
@@ -348,9 +354,9 @@ def callback(model, i: int, t: float, save=True):
         Ta_history.append(get_activation(t))
 
         if save:
-            adios4dolfinx.write_function(filename, problem.u, time=t, name="displacement")
+            io4dolfinx.write_function(filename, problem.u, time=t, name="displacement")
             vtx.write(t)
-            out = {k: v[:i+1] for k, v in model.history.items()}
+            out = {k: v[: i + 1] for k, v in model.history.items()}
             out["Ta"] = Ta_history
             if comm.rank == 0:
                 output_file.write_text(json.dumps(out, indent=4, default=custom_json))
@@ -396,7 +402,9 @@ def callback(model, i: int, t: float, save=True):
     def p_BiV_func(V_LV, V_RV, t):
         print("Calculating pressure at time", t)
         value = get_activation(t)
-        print(f"Time{t} with activation: {value} and volumes: {V_LV} mL (LV) {V_RV} mL (RV)")
+        print(
+            f"Time{t} with activation: {value} and volumes: {V_LV} mL (LV) {V_RV} mL (RV)",
+        )
         old_Ta = Ta.value.value
         dTa = value - old_Ta
 
@@ -422,8 +430,12 @@ def p_BiV_func(V_LV, V_RV, t):
                 Ta.assign(value)
                 problem.solve()
 
-        lv_pendo_mmHg = circulation.units.kPa_to_mmHg(problem.cavity_pressures[0].x.array[0] * 1e-3)
-        rv_pendo_mmHg = circulation.units.kPa_to_mmHg(problem.cavity_pressures[1].x.array[0] * 1e-3)
+        lv_pendo_mmHg = circulation.units.kPa_to_mmHg(
+            problem.cavity_pressures[0].x.array[0] * 1e-3,
+        )
+        rv_pendo_mmHg = circulation.units.kPa_to_mmHg(
+            problem.cavity_pressures[1].x.array[0] * 1e-3,
+        )
         print(f"Compute pressures: {lv_pendo_mmHg} mmHg (LV) {rv_pendo_mmHg} mmHg (RV)")
         return lv_pendo_mmHg, rv_pendo_mmHg
 
@@ -432,19 +444,23 @@ def p_BiV_func(V_LV, V_RV, t):
     s = circulation.units.ureg("s")
     add_units = False
     lvv_init = (
-        geo.mesh.comm.allreduce(geometry.volume("LV", u=problem.u), op=MPI.SUM) * 1e6 * 1.0
+        geo.mesh.comm.allreduce(geometry.volume("LV", u=problem.u), op=MPI.SUM)
+        * 1e6
+        * 1.0
     )
     rvv_init = (
-        geo.mesh.comm.allreduce(geometry.volume("RV", u=problem.u), op=MPI.SUM) * 1e6 * 1.0
+        geo.mesh.comm.allreduce(geometry.volume("RV", u=problem.u), op=MPI.SUM)
+        * 1e6
+        * 1.0
     )
     print(f"Initial volume (LV): {lvv_init} mL and (RV): {rvv_init} mL")
     init_state = {
         "V_LV": lvv_initial * 1e6 * mL,
         "V_RV": rvv_initial * 1e6 * mL,
-        'p_AR_PUL': p_AR_PUL * mmHg,
-        'p_AR_SYS': p_AR_SYS * mmHg,
-        'p_VEN_PUL': p_VEN_PUL * mmHg,
-        'p_VEN_SYS': p_VEN_SYS * mmHg,
+        "p_AR_PUL": p_AR_PUL * mmHg,
+        "p_AR_SYS": p_AR_SYS * mmHg,
+        "p_VEN_PUL": p_VEN_PUL * mmHg,
+        "p_VEN_SYS": p_VEN_SYS * mmHg,
     }
 
     regazzoni_parmeters = circulation.regazzoni2020.Regazzoni2020.default_parameters()
@@ -475,7 +491,9 @@ def p_BiV_func(V_LV, V_RV, t):
     )
     # Set end time for early stopping if running in CI
     end_time = 2 * dt if os.getenv("CI") else None
-    regazzoni.solve(num_beats=num_beats, initial_state=init_state, dt=dt, T=end_time) #, checkpoint=RR)
+    regazzoni.solve(
+        num_beats=num_beats, initial_state=init_state, dt=dt, T=end_time,
+    )  # , checkpoint=RR)
     regazzoni.print_info()
 
 
@@ -534,10 +552,20 @@ def p_BiV_func(V_LV, V_RV, t):
 print(f"HR before: {HR_before}, HR after: {HR_after}")
 
 get_activation_before = run_TorOrdLand(
-    comm, outdir, HR_before, Ta_factor=1, label="before", dt=dt,
+    comm,
+    outdir,
+    HR_before,
+    Ta_factor=1,
+    label="before",
+    dt=dt,
 )
 get_activation_after = run_TorOrdLand(
-    comm, outdir, HR_after, Ta_factor=C_PRSW_factor, label="after", dt=dt,
+    comm,
+    outdir,
+    HR_after,
+    Ta_factor=C_PRSW_factor,
+    label="after",
+    dt=dt,
 )
 
 run_3D_model(

demo/boundary_conditions/lv_ellipsoid_fixed_x.py

@@ -131,8 +131,6 @@ def dirichlet_bc(V: dolfinx.fem.FunctionSpace):
     bcs=bcs,
 )
 
-log.set_log_level(log.LogLevel.INFO)
-
 # ### Phase 1: Passive Inflation
 
 vtx = dolfinx.io.VTXWriter(geometry.mesh.comm, outdir / "lv_displacement.bp", [problem.u], engine="BP4")

demo/boundary_conditions/ukb_bcs.py

@@ -23,7 +23,6 @@
 from pathlib import Path
 from mpi4py import MPI
 import dolfinx
-from dolfinx import log
 import cardiac_geometries
 import cardiac_geometries.geometry
 import pulse
@@ -192,8 +191,6 @@ def dirichlet_bc(V: dolfinx.fem.FunctionSpace):
     bcs=bcs,
 )
 
-log.set_log_level(log.LogLevel.INFO)
-
 # ### Phase 1: Passive Inflation
 # We ramp up the pressure in both ventricles.
 

demo/geometries/biv_ellipsoid.py

@@ -35,16 +35,11 @@
 from mpi4py import MPI
 import numpy as np
 import dolfinx
-from dolfinx import log
 import ldrb
 import cardiac_geometries
 import cardiac_geometries.geometry
 import pulse
 
-# We enable info logging to track solver progress.
-
-# log.set_log_level(log.LogLevel.INFO)
-
 # ## Geometry and Microstructure
 #
 # We generate the mesh and fibers if they don't already exist.