su2 fixes and improvements: AD, scipy/numpy, and Mutationpp setup, environment variable (#46774)

* su2 fixes and improvements: AD, scipy/numpy, and Mutationpp setup, environment variable

* su2: Conflict %gcc@13: when @:7, mpp was added with @7.1.0

* py-scipy: SciPy 1.14: requires GCC >= 9.1

---------

Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>

3 files changed, 56 insertions, 24 deletions

diff --git a/var/spack/repos/builtin/packages/medipack/package.py b/var/spack/repos/builtin/packages/medipack/package.py
index 02c046215b..ec07e792fb 100644
--- a/var/spack/repos/builtin/packages/medipack/package.py
+++ b/var/spack/repos/builtin/packages/medipack/package.py
@@ -13,12 +13,14 @@ class Medipack(CMakePackage):
     homepage = "https://github.com/SciCompKL/MeDiPack"
     url = "https://github.com/SciCompKL/MeDiPack/archive/refs/tags/v1.2.2.tar.gz"
 
+    version("1.3.0", sha256="81daf8391ca00286a1276408badc7f1c9f76af889eb16940601c0ffb5f229e1d")
     version("1.2.2", sha256="8937fa1025c6fb12f516cacf38a7f776221e7e818b30f17ce334c63f78513aa7")
     version("1.2.1", sha256="c746196b98cfe24a212584cdb88bd12ebb14f4a54728070d605e0c6d0e75db8a")
 
     depends_on("cxx", type="build")  # generated
 
     depends_on("cmake@3.12:", type="build", when="@1.2.2:")
+    depends_on("mpi")
 
     build_system(
         conditional("cmake", when="@1.2.2:"),
@@ -27,7 +29,7 @@ class Medipack(CMakePackage):
     )
 
     def install(self, spec, prefix):
-        mkdirp(join_path(prefix, "include"))
-        install_tree(join_path(self.stage.source_path, "include"), join_path(prefix, "include"))
-        mkdirp(join_path(prefix, "src"))
-        install_tree(join_path(self.stage.source_path, "src"), join_path(prefix, "src"))
+        mkdirp(self.prefix.include)
+        install_tree(join_path(self.stage.source_path, "include"), self.prefix.include)
+        mkdirp(self.prefix.src)
+        install_tree(join_path(self.stage.source_path, "src"), self.prefix.src)
diff --git a/var/spack/repos/builtin/packages/py-scipy/package.py b/var/spack/repos/builtin/packages/py-scipy/package.py
index 2d81ea8a63..11161d997f 100644
--- a/var/spack/repos/builtin/packages/py-scipy/package.py
+++ b/var/spack/repos/builtin/packages/py-scipy/package.py
@@ -136,7 +136,8 @@ class PyScipy(PythonPackage):
 
     # meson.build
     # https://docs.scipy.org/doc/scipy/dev/toolchain.html#compilers
-    conflicts("%gcc@:7", when="@1.10:", msg="SciPy requires GCC >= 8.0")
+    conflicts("%gcc@:7", when="@1.10:", msg="SciPy 1.10-1.13 requires GCC >= 8.0")
+    conflicts("%gcc@:9.0", when="@1.14:", msg="SciPy 1.14: requires GCC >= 9.1")
     conflicts("%gcc@:4.7", when="@:1.9", msg="SciPy requires GCC >= 4.8")
     conflicts("%apple-clang@:9", when="@1.10:", msg="SciPy requires Apple Clang >= 10")
     conflicts(
diff --git a/var/spack/repos/builtin/packages/su2/package.py b/var/spack/repos/builtin/packages/su2/package.py
index 5ec32895a4..4b0d056ae7 100644
--- a/var/spack/repos/builtin/packages/su2/package.py
+++ b/var/spack/repos/builtin/packages/su2/package.py
@@ -38,6 +38,9 @@ class Su2(MesonPackage):
     version("7.0.0", sha256="6207dcca15eaebc11ce12b2866c937b4ad9b93274edf6f23d0487948ac3963b8")
     version("6.2.0", sha256="ffc953326e8432a1a6534556a5f6cf086046d3149cfcec6b4e7390eebe30ce2e")
 
+    # @:7 is missing few <cstdint> includes, causing a few files to fail with %gcc@13:
+    conflicts("%gcc@13:", when="@:7")
+
     depends_on("c", type="build")  # generated
     depends_on("cxx", type="build")  # generated
     depends_on("fortran", type="build")  # generated
@@ -60,6 +63,8 @@ class Su2(MesonPackage):
 
     depends_on("meson@0.61.1:", type=("build"))
     depends_on("python@3:", type=("build", "run"))
+    depends_on("py-numpy", type="run")
+    depends_on("py-scipy", type="run")
     depends_on("zlib-api")
     depends_on("pkgconfig")
     depends_on("mpi", when="+mpi")
@@ -69,14 +74,12 @@ class Su2(MesonPackage):
     depends_on("openblas", when="+openblas ~mkl")
     depends_on("cmake", type="build", when="+mpp")
 
-    depends_on("codipack@:1.9.3", when="+autodiff")
-    depends_on("codipack@:1.9.3", when="+directdiff")
-    depends_on("medipack", when="+autodiff +mpi")
-    depends_on("medipack", when="+directdiff +mpi")
+    for diff_type in ("+autodiff", "+directdiff"):
+        with when(diff_type):
+            depends_on("codipack@1.9.3", when="@:7.5.1")
+            depends_on("codipack@2.2.0:", when="@8.0.0:")
+            depends_on("medipack", when="+mpi")
     depends_on("opdilib", when="+autodiff +openmp")
-    depends_on("opdilib", when="+directdiff +openmp")
-    depends_on("codipack@openmp", when="+autodiff +openmp")
-    depends_on("codipack@openmp", when="+directdiff +openmp")
 
     # Remove the part that fixes the meson version to 0.61.1.
     # This fix is considered meaningless and will be removed in the next version(@7.6:) of SU2.
@@ -93,17 +96,13 @@ class Su2(MesonPackage):
                 "meson.build",
             )
 
-        if (
-            self.spec.satisfies("+autodiff") or self.spec.satisfies("+directdiff")
-        ) and self.spec.satisfiles("+mpi"):
-            filter_file(
-                "externals/medi/include", self.spec["medipack"].prefix.include, "meson.build"
-            )
-            filter_file("externals/medi/src", self.spec["medipack"].prefix.src, "meson.build")
+            if self.spec.satisfies("+mpi"):
+                filter_file(
+                    "externals/medi/include", self.spec["medipack"].prefix.include, "meson.build"
+                )
+                filter_file("externals/medi/src", self.spec["medipack"].prefix.src, "meson.build")
 
-        if (
-            self.spec.satisfies("+autodiff") or self.spec.satisfies("+directdiff")
-        ) and self.spec.satisfies("+openmp"):
+        if self.spec.satisfies("+autodiff") and self.spec.satisfies("+openmp"):
             filter_file(
                 "externals/opdi/include", self.spec["opdilib"].prefix.include, "meson.build"
             )
@@ -113,6 +112,13 @@ class Su2(MesonPackage):
                 "meson.build",
             )
 
+        if self.spec.satisfies("+mpp") and self.spec.satisfies("@8.0:"):
+            filter_file(
+                r"join_paths\(meson\.project_source_root\(\), 'ninja'\)",
+                f"join_paths('{self.spec['ninja'].prefix.bin}', 'ninja')",
+                "meson.build",
+            )
+
     def meson_args(self):
         args = [
             "-Dwith-omp={}".format("+openmp" in self.spec),
@@ -123,16 +129,39 @@ class Su2(MesonPackage):
             "-Denable-pywrapper={}".format("+pywrapper" in self.spec),
             "-Denable-mkl={}".format("+mkl" in self.spec),
             "-Denable-openblas={}".format("+openblas" in self.spec),
-            "-Denable-mpp={}".format("+mpp" in self.spec),
             "-Denable-mixedprec={}".format("+midexprec" in self.spec),
         ]
+        if self.spec.version >= Version("7.1.0"):
+            args.append("-Denable-mpp={}".format("+mpp" in self.spec))
 
         if "+mkl" in self.spec:
             args.append("-Dmkl_root=" + self.spec["intel-oneapi-mkl"].prefix)
 
         if "+mpi" in self.spec:
-            args.append("-Dwith-mpi=enabled")
+            args.append("-Dwith-mpi=auto")
         else:
             args.append("-Dwith-mpi=disabled")
 
         return args
+
+    @run_after("install")
+    def install_mpp(self):
+        if "+mpp" in self.spec:
+            mkdirp(join_path(self.prefix, "mpp-data"))
+            mkdirp(join_path(self.prefix, "lib"))
+            install_tree(
+                join_path(self.stage.source_path, "subprojects", "Mutationpp", "data"),
+                join_path(self.prefix, "mpp-data"),
+            )
+            install_tree(
+                join_path(self.build_directory, "subprojects", "Mutationpp"), self.prefix.lib
+            )
+
+    def setup_run_environment(self, env):
+        env.set("su2_run", self.prefix.bin)
+        env.set("su2_home", self.prefix)
+        env.prepend_path("path", self.prefix.bin)
+        env.prepend_path("pythonpath", self.prefix.bin)
+        if "+mpp" in self.spec:
+            env.set("mpp_data_directory", join_path(self.prefix, "mpp-data"))
+            env.prepend_path("ld_library_path", self.prefix.lib)