Add ukb-atlas

.github/workflows/spack-matrix.yml

@@ -370,3 +370,52 @@ jobs:
         run: |
           spack env activate ./env
           python -c "import pulse"
+
+  py-ukb-atlas:
+    needs: style-check
+    runs-on: ubuntu-latest
+    container: ubuntu:24.04
+    strategy:
+      fail-fast: false
+      matrix:
+        version: ["main", "1.2.3"]
+        spec: [""]
+
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          path: spack_repos
+      - uses: ./spack_repos/.github/actions/test-package
+        with:
+          spec: py-ukb-atlas@${{ matrix.version }} ${{ matrix.spec }}
+
+      - name: Import test
+        shell: spack-bash {0}
+        run: |
+          spack env activate ./env
+          python -c "import ukb"
+
+
+  py-fenicsx-ldrb:
+    needs: style-check
+    runs-on: ubuntu-latest
+    container: ubuntu:24.04
+    strategy:
+      fail-fast: false
+      matrix:
+        version: ["main", "0.1.17"]
+        spec: ["^py-fenics-dolfinx%c,cxx=gcc@13.3.0"]
+
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          path: spack_repos
+      - uses: ./spack_repos/.github/actions/test-package
+        with:
+          spec: py-fenicsx-ldrb@${{ matrix.version }} ${{ matrix.spec }}
+
+      - name: Import test
+        shell: spack-bash {0}
+        run: |
+          spack env activate ./env
+          python -c "import ldrb"

spack_repo/scientificcomputing/packages/py_cardiac_geometries_core/package.py

@@ -25,7 +25,7 @@
 
 
 class PyCardiacGeometriesCore(PythonPackage):
-    """General ODE translator"""
+    """Core utilities for cardiac geometries, including mesh generation and IO."""
 
     homepage = "https://computationalphysiology.github.io/cardiac-geometries-core"
     git = "https://github.com/ComputationalPhysiology/cardiac-geometries-core.git"

spack_repo/scientificcomputing/packages/py_cardiac_geometriesx/package.py

@@ -10,11 +10,11 @@
 # next to all the things you'll want to change. Once you've handled
 # them, you can save this file and test your package like this:
 #
-#     spack install py-cardiac-geometries-core
+#     spack install py-cardiac-geometriesx
 #
 # You can edit this file again by typing:
 #
-#     spack edit py-cardiac-geometries-core
+#     spack edit py-cardiac-geometriesx
 #
 # See the Spack documentation for more information on packaging.
 # ----------------------------------------------------------------------------
@@ -25,7 +25,7 @@
 
 
 class PyCardiacGeometriesx(PythonPackage):
-    """General ODE translator"""
+    """Cardiac geometries for FEniCS."""
 
     homepage = "https://computationalphysiology.github.io/cardiac-geometriesx"
     git = "https://github.com/ComputationalPhysiology/cardiac-geometriesx.git"
@@ -46,6 +46,9 @@ class PyCardiacGeometriesx(PythonPackage):
     depends_on("python@3.10:", type=("build", "run"))
     depends_on("py-setuptools@61.2:", type="build")
 
+    variant("ukb", default=True, description="Add ukb-atla")
+    variant("ldrb", default=True, description="Add fenicsx-ldrb")
+
     # Core dependencies
     depends_on("py-fenics-dolfinx+petsc4py", type=("build", "run"))
     depends_on("py-rich-click", type=("build", "run"))
@@ -55,3 +58,9 @@ class PyCardiacGeometriesx(PythonPackage):
     depends_on("py-io4dolfinx+adios2+xdmf", type=("build", "run"), when="@main:")
     depends_on("py-adios4dolfinx", type=("build", "run"), when="@:0.12")
     depends_on("py-scifem", type=("build", "run"))
+
+    with when("+ukb"):
+        depends_on("py-ukb-atlas", type=("build", "run"))
+
+    with when("+ldrb"):
+        depends_on("py-fenicsx-ldrb", type=("build", "run"))

spack_repo/scientificcomputing/packages/py_fenicsx_beat/package.py

@@ -21,12 +21,15 @@ class PyFenicsxBeat(PythonPackage):
     version("main", branch="main")
     version("0.2.4", sha256="ddba1ee2a4ded52a846b1ee11b1bd6e7d97522608dd6206436ae0fd58b12b17b")
 
+    variant(
+        "cardiac-geometries", default=True, description="Add cardiac geometries as a dependency"
+    )
+
     depends_on("python@3.10:", type=("build", "run"))
 
     depends_on("py-setuptools@42:", type="build")
 
-    depends_on("py-fenics-dolfinx@0.10:+petsc4py", when="@0.2:", type=("build", "run"))
-    depends_on("py-fenics-dolfinx@main+petsc4py", when="@main", type=("build", "run"))
+    depends_on("py-fenics-dolfinx+petsc4py", type=("build", "run"))
     depends_on("py-fenics-basix", type=("build", "run"))
     depends_on("py-fenics-ufl", type=("build", "run"))
     depends_on("py-mpi4py", type=("build", "run"))
@@ -37,3 +40,6 @@ class PyFenicsxBeat(PythonPackage):
     depends_on("py-rich", type=("build", "run"))
     depends_on("py-pint", type=("build", "run"))
     depends_on("py-scipy", type=("build", "run"))
+
+    with when("+cardiac-geometries"):
+        depends_on("py-cardiac-geometriesx", type=("build", "run"))

spack_repo/scientificcomputing/packages/py_fenicsx_ldrb/package.py

@@ -0,0 +1,38 @@
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack_repo.builtin.build_systems.python import PythonPackage
+
+from spack.package import *
+
+
+class PyFenicsxLdrb(PythonPackage):
+    """Library to run cardiac EP simulations in FEniCSx"""
+
+    homepage = "https://finsberg.github.io/fenicsx-ldrb/"
+    url = "https://github.com/finsberg/fenicsx-ldrb/archive/refs/tags/v0.1.17.tar.gz"
+    git = "https://github.com/finsberg/fenicsx-ldrb.git"
+
+    maintainers("finsberg")
+
+    license("MIT", checked_by="finsberg")
+
+    version("main", branch="main")
+    version("0.1.17", sha256="19ce4660b9711d2efb2f9109d0bc6380eb9f2359a43f8f85f4207ee63f79f30c")
+
+    depends_on("python@3.10:", type=("build", "run"))
+
+    depends_on("py-setuptools@42:", type="build")
+
+    depends_on("py-io4dolfinx+adios2+xdmf", type=("build", "run"), when="@0.2:,main")
+    depends_on("py-adios4dolfinx", type=("build", "run"), when="@:0.1")
+
+    depends_on("py-fenics-dolfinx+petsc4py", type=("build", "run"))
+    depends_on("py-fenics-basix", type=("build", "run"))
+    depends_on("py-fenics-ufl", type=("build", "run"))
+    depends_on("py-mpi4py", type=("build", "run"))
+    depends_on("petsc+mumps", type=("build", "run"))
+    depends_on("py-numpy", type=("build", "run"))
+    depends_on("py-numba", type=("build", "run"))
+    depends_on("py-scipy", type=("build", "run"))

spack_repo/scientificcomputing/packages/py_fenicsx_pulse/package.py

@@ -21,6 +21,11 @@ class PyFenicsxPulse(PythonPackage):
     version("main", branch="main")
     version("0.6.0", sha256="fddfb2fa554e6537b8205a1a7806549fbbd5b55cb913338387f54f27bef87818")
 
+    variant(
+        "cardiac-geometries", default=True, description="Add cardiac geometries as a dependency"
+    )
+    variant("circulation", default=True, description="Add circulation models as a dependency")
+
     depends_on("python@3.10:", type=("build", "run"))
 
     depends_on("py-setuptools@42:", type="build")
@@ -37,3 +42,9 @@ class PyFenicsxPulse(PythonPackage):
     depends_on("py-pint", type=("build", "run"))
     depends_on("py-scipy", type=("build", "run"))
     depends_on("py-rich-argparse", type=("build", "run"))
+
+    with when("+cardiac-geometries"):
+        depends_on("py-cardiac-geometriesx", type=("build", "run"))
+
+    with when("+circulation"):
+        depends_on("py-circulation", type=("build", "run"))

spack_repo/scientificcomputing/packages/py_ukb_atlas/package.py

@@ -0,0 +1,63 @@
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+# ----------------------------------------------------------------------------
+# If you submit this package back to Spack as a pull request,
+# please first remove this boilerplate and all FIXME comments.
+#
+# This is a template package file for Spack.  We've put "FIXME"
+# next to all the things you'll want to change. Once you've handled
+# them, you can save this file and test your package like this:
+#
+#     spack install py-ukb-atlas
+#
+# You can edit this file again by typing:
+#
+#     spack edit py-ukb-atlas
+#
+# See the Spack documentation for more information on packaging.
+# ----------------------------------------------------------------------------
+
+from spack_repo.builtin.build_systems.python import PythonPackage
+
+from spack.package import *
+
+
+class PyUkbAtlas(PythonPackage):
+    """Biventricular atlas of the heart based on the UK Biobank dataset."""
+
+    homepage = "https://computationalphysiology.github.io/ukb-atlas"
+    git = "https://github.com/ComputationalPhysiology/ukb-atlas.git"
+    url = "https://github.com/ComputationalPhysiology/ukb-atlas/archive/refs/tags/v0.12.0.tar.gz"
+
+    # notify when the package is updated.
+    maintainers("finsberg")
+
+    # FIXME: Add the SPDX identifier of the project's license below.
+    # See https://spdx.org/licenses/ for a list. Upon manually verifying
+    # the license, set checked_by to your Github username.
+    license("MIT", checked_by="finsberg")
+
+    version("main", branch="main")
+    version("1.2.3", sha256="65bed1747a9e47f59300d39336af2282bb6fe5a6dc6dd7a7038dd6ba06af7333")
+
+    # Python version and Build backend
+    depends_on("python@3.10:", type=("build", "run"))
+    depends_on("py-setuptools@61.2:", type="build")
+
+    # Core dependencies
+    depends_on("py-scipy", type=("build", "run"))
+    depends_on("py-meshio@2.3.5:", type=("build", "run"))
+    depends_on("py-numpy", type=("build", "run"))
+    depends_on("py-h5py+mpi", type=("build", "run"))
+    depends_on("py-pyvista", type=("build", "run"))
+    depends_on("py-gmsh@:4.13.1", type=("build", "run"))
+    depends_on("gmsh@:4.13.1", type=("build", "run"))
+    # OpenGL dependency for gmsh
+    depends_on("mesa-glu", type=("build", "run"))
+    # X11 library
+    depends_on("libxcursor", type=("build", "run"))
+    depends_on("libxft", type=("build", "run"))
+    depends_on("libxrender", type=("build", "run"))
+    depends_on("libxinerama", type=("build", "run"))