Add cardiac-geometriesx

.github/workflows/spack-matrix.yml

@@ -322,3 +322,27 @@ jobs:
         run: |
           spack env activate ./env
           python -c "import circulation"
+
+  py-cardiac-geometriesx:
+    needs: style-check
+    runs-on: ubuntu-latest
+    container: ubuntu:24.04
+    strategy:
+      fail-fast: false
+      matrix:
+        version: ["main", "0.12.0"]
+        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-cardiac-geometriesx@${{ matrix.version }} ${{ matrix.spec }}
+
+      - name: Import test
+        shell: spack-bash {0}
+        run: |
+          spack env activate ./env
+          python -c "import cardiac_geometries"

spack_repo/scientificcomputing/packages/py_cardiac_geometries_core/package.py

@@ -0,0 +1,60 @@
+# 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-cardiac-geometries-core
+#
+# You can edit this file again by typing:
+#
+#     spack edit py-cardiac-geometries-core
+#
+# See the Spack documentation for more information on packaging.
+# ----------------------------------------------------------------------------
+
+from spack_repo.builtin.build_systems.python import PythonPackage
+
+from spack.package import *
+
+
+class PyCardiacGeometriesCore(PythonPackage):
+    """General ODE translator"""
+
+    homepage = "https://computationalphysiology.github.io/cardiac-geometries-core"
+    git = "https://github.com/ComputationalPhysiology/cardiac-geometries-core.git"
+    url = "https://github.com/ComputationalPhysiology/cardiac-geometries-core/archive/refs/tags/v1.2.2.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("1.2.2", sha256="bb7a003474d2f2013dcb2190ca1d30527f1e7aee3626114083f0656dc3830b9d")
+
+    # Python version and Build backend
+    depends_on("python@3.8:", type=("build", "run"))
+    depends_on("py-setuptools@61.2:", type="build")
+
+    # Core dependencies
+    depends_on("py-rich-click", type=("build", "run"))
+    depends_on("py-numpy", 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"))

spack_repo/scientificcomputing/packages/py_cardiac_geometriesx/package.py

@@ -0,0 +1,57 @@
+# 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-cardiac-geometries-core
+#
+# You can edit this file again by typing:
+#
+#     spack edit py-cardiac-geometries-core
+#
+# See the Spack documentation for more information on packaging.
+# ----------------------------------------------------------------------------
+
+from spack_repo.builtin.build_systems.python import PythonPackage
+
+from spack.package import *
+
+
+class PyCardiacGeometriesx(PythonPackage):
+    """General ODE translator"""
+
+    homepage = "https://computationalphysiology.github.io/cardiac-geometriesx"
+    git = "https://github.com/ComputationalPhysiology/cardiac-geometriesx.git"
+    url = "https://github.com/ComputationalPhysiology/cardiac-geometriesx/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("0.12.0", sha256="93698a5d0d8ac7751c458dde963116a9c050c6d534b45cd034aa13dd668cc904")
+
+    # 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-fenics-dolfinx+petsc4py", type=("build", "run"))
+    depends_on("py-rich-click", type=("build", "run"))
+    depends_on("py-cardiac-geometries-core", type=("build", "run"))
+    depends_on("py-structlog", type=("build", "run"))
+
+    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"))

spack_repo/scientificcomputing/packages/py_io4dolfinx/package.py

@@ -37,25 +37,25 @@ class PyIo4dolfinx(PythonPackage):
 
     depends_on("cxx", type="build")
 
-    depends_on("py-fenics-dolfinx@0.9:", when="@1.1:", type="run")
-    depends_on("py-fenics-dolfinx@main", when="@main", type="run")
-    depends_on("py-numpy", type="run")
-    depends_on("py-packaging", type="run")
+    depends_on("py-fenics-dolfinx@0.10:", when="@1.1:", type=("build", "run"))
+    depends_on("py-fenics-dolfinx@main", when="@main", type=("build", "run"))
+    depends_on("py-numpy", type=("build", "run"))
+    depends_on("py-packaging", type=("build", "run"))
     depends_on("py-setuptools@42:", type="build")
 
     with when("+adios2"):
         depends_on("adios2@2.9:+python+hdf5+mpi", type=("build", "run"))
         depends_on(
-            "hdf5@1.12:", type="build"
+            "hdf5@1.12:", type=("build", "run")
         )  # NOTE: Remove when https://github.com/spack/spack-packages/issues/3566 is resolved
     with when("+h5py"):
-        depends_on("py-h5py+mpi", type="run")
+        depends_on("py-h5py+mpi", type=("build", "run"))
 
     with when("+vtkhdf"):
-        depends_on("py-h5py+mpi", type="run")
+        depends_on("py-h5py+mpi", type=("build", "run"))
 
     with when("+xdmf"):
-        depends_on("py-h5py+mpi", type="run")
+        depends_on("py-h5py+mpi", type=("build", "run"))
 
     with when("+pyvista"):
-        depends_on("py-pyvista", type="run")
+        depends_on("py-pyvista", type=("build", "run"))