Add support for both ufl and ufl-legacy

.github/workflows/conda.yml

@@ -0,0 +1,33 @@
+name: Test package in conda environment
+
+on: [workflow_dispatch]
+
+jobs:
+    test-conda:
+      name: Test with conda environment
+      runs-on: "ubuntu-latest"
+      strategy:
+        fail-fast: false
+        matrix:
+          python-version: ["3.8", "3.11"]
+      steps:
+        - uses: actions/checkout@v4
+        - uses: conda-incubator/setup-miniconda@v3
+          with:
+            auto-update-conda: true
+            python-version: ${{ matrix.python-version }}
+        - name: Conda install fenics
+          shell: bash -el {0}
+          run: conda install -c conda-forge fenics
+
+        - name: Upgrade pip
+          shell: bash -l {0}
+          run: python3 -m pip install --upgrade pip
+
+        - name: Install package
+          shell: bash -l {0}
+          run: python3 -m pip install -e .[test]
+
+        - name: Run tests
+          shell: bash -l {0}
+          run: python3 -m pytest --cov=beat --cov-report=html --cov-report=term-missing -v

demos/endocardial_stimulation.py

@@ -17,7 +17,11 @@
 import matplotlib.pyplot as plt
 
 import dolfin
-import ufl_legacy as ufl
+
+try:
+    import ufl_legacy as ufl
+except ImportError:
+    import ufl
 
 try:
     from tqdm import tqdm

demos/endocardial_stimulation_odefile.py

@@ -17,7 +17,11 @@
 import matplotlib.pyplot as plt
 
 import dolfin
-import ufl_legacy as ufl
+
+try:
+    import ufl_legacy as ufl
+except ImportError:
+    import ufl
 
 try:
     from tqdm import tqdm

pyproject.toml

@@ -12,7 +12,6 @@ requires-python = ">=3.8"
 keywords = ["cardiac", "electrophysiology"]
 dependencies = [
     "numpy",
-    "scipy",
 ]
 
 [project.urls]

src/beat/base_model.py

@@ -5,8 +5,13 @@
 from enum import Enum, auto
 
 import dolfin
-import ufl_legacy as ufl
-from ufl_legacy.core.expr import Expr
+
+try:
+    import ufl_legacy as ufl
+    from ufl_legacy.core.expr import Expr
+except ImportError:
+    import ufl
+    from ufl.core.expr import Expr
 
 
 logger = logging.getLogger(__name__)

src/beat/bidomain_model.py

@@ -1,9 +1,14 @@
 from __future__ import annotations
 import logging
-import ufl_legacy as ufl
-from ufl_legacy.core.expr import Expr
 import dolfin
 
+try:
+    import ufl_legacy as ufl
+    from ufl_legacy.core.expr import Expr
+except ImportError:
+    import ufl
+    from ufl.core.expr import Expr
+
 from .base_model import BaseModel, Stimulus
 
 

src/beat/ecg.py

@@ -1,8 +1,13 @@
+from __future__ import annotations
 import dolfin
 from typing import NamedTuple
-import ufl_legacy as ufl
 import numpy as np
 
+try:
+    import ufl_legacy as ufl
+except ImportError:
+    import ufl
+
 
 def ecg_recovery(
     *,

src/beat/monodomain_model.py

@@ -2,8 +2,13 @@
 import logging
 
 import dolfin
-import ufl_legacy as ufl
-from ufl_legacy.core.expr import Expr
+
+try:
+    import ufl_legacy as ufl
+    from ufl_legacy.core.expr import Expr
+except ImportError:
+    import ufl
+    from ufl.core.expr import Expr
 
 from .base_model import BaseModel, Stimulus
 

src/beat/utils.py

@@ -1,13 +1,17 @@
 from __future__ import annotations
 from typing import Any
 import logging
+from contextlib import contextmanager
 import dolfin
 import numpy.typing as npt
 import numpy as np
-import ufl_legacy as ufl
-from contextlib import contextmanager
 from mpi4py import MPI as pyMPI
 
+try:
+    import ufl_legacy as ufl
+except ImportError:
+    import ufl
+
 
 logger = logging.getLogger(__name__)