Update exodusii package (#43379)

* SEACAS: Update package.py to handle new SEACAS project name
  The base project name for the SEACAS project has changed from
  "SEACASProj" to "SEACAS" as of @2022-10-14, so the package
  needed to be updated to use the new project name when needed.
  The refactor also changes several:
      "-DSome_CMAKE_Option:BOOL=ON"
  to
     define("Some_CMAKE_Option", True)
* exodusii -- refactor and bring up-to-date
* Add missed patch file
* [@spackbot] updating style on behalf of gsjaardema
* Apply seacas windows patch here also.
* Update url so old checksums valid; redo new checksums

---------

Co-authored-by: gsjaardema <gsjaardema@users.noreply.github.com>

var/spack/repos/builtin/packages/exodusii/Fix-ioss-tpl.patch

@@ -0,0 +1,25 @@
+From 4d3884f65a6a4df08ee8dd68ddaee5449f1dd378 Mon Sep 17 00:00:00 2001
+From: Greg Sjaardema <gsjaardema@gmail.com>
+Date: Tue, 26 Mar 2024 12:42:08 -0600
+Subject: [PATCH] Remove ioss as required library
+
+---
+ packages/seacas/cmake/Dependencies.cmake | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/packages/seacas/cmake/Dependencies.cmake b/packages/seacas/cmake/Dependencies.cmake
+index 3b1b3d6598..e75f5073f2 100644
+--- a/packages/seacas/cmake/Dependencies.cmake
++++ b/packages/seacas/cmake/Dependencies.cmake
+@@ -4,7 +4,7 @@ TRIBITS_PACKAGE_DEFINE_DEPENDENCIES(
+   Exodus_for  libraries/exodus_for    PT  OPTIONAL
+   ExoIIv2for32 libraries/exoIIv2for32 PT  OPTIONAL
+   Nemesis     libraries/nemesis       PT  OPTIONAL
+-  Ioss        libraries/ioss          PT  REQUIRED
++  Ioss        libraries/ioss          PT  OPTIONAL
+   Chaco       libraries/chaco         PT  OPTIONAL
+   Aprepro_lib libraries/aprepro_lib   PT  OPTIONAL
+   Supes       libraries/supes         PT  OPTIONAL
+-- 
+2.39.3 (Apple Git-145)
+

var/spack/repos/builtin/packages/exodusii/package.py

@@ -3,10 +3,12 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import sys
+
+from spack.operating_systems.mac_os import macos_version
 from spack.package import *
 
-# TODO: Add support for a C++11 enabled installation that filters out the
+is_windows = sys.platform == "win32"
-# TODO: "C++11-Disabled" flag (but only if the spec compiler supports C++11).
 
 
 class Exodusii(CMakePackage):
@@ -15,15 +17,50 @@ class Exodusii(CMakePackage):
     (problem definition), postprocessing (results visualization), and
     data transfer between codes.  An Exodus II data file is a random
     access, machine independent, binary file that is written and read
-    via C, C++, or Fortran API routines.
+    via C, C++, or Fortran API routines.  This package *only* installs
+    the C and optionally Fortran library for exodus.  If you want the full
+    suite of exodus-releated tools including the IOSS library, install
+    the seacas package instead of this package.
     """
 
-    homepage = "https://github.com/gsjaardema/seacas"
+    homepage = "https://sandialabs.github.io/seacas/"
-    git = "https://github.com/gsjaardema/seacas.git"
+    git = "https://github.com/sandialabs/seacas.git"
-    url = "https://github.com/gsjaardema/seacas/archive/refs/tags/v2021-04-05.zip"
+    url = "https://github.com/sandialabs/seacas/archive/refs/tags/v2019-08-20.zip"
+    maintainers("gsjaardema")
 
-    license("X11")
+    license("BSD-3-Clause")
 
+    version("master", branch="master")
+    version(
+        "2024-03-11", sha256="5d417aa652e4ec8d66e27714c63b8cb5a7f878fb7b2ec55f629636fcff7c0f00"
+    )
+    version(
+        "2023-11-27", sha256="00c444b2def2c9cf5694bee5bb0284ce289e83f7c84ac28c6701c746cfde9a4c"
+    )
+    version(
+        "2023-05-30", sha256="d2cbd43596ed3ad77186f865fe8aa81a2efe389ff345b24622ac76c16614b532"
+    )
+    version(
+        "2022-10-14", sha256="a96f29de3b69e7e3f5f344396c8cf791fe277dab0217fc0b90b02e38e75bbdc1"
+    )
+    version(
+        "2022-08-01", sha256="c12a677ba2178cf5161d63fef3b1da4d3888622199cea3e611f59649085681dc"
+    )
+    version(
+        "2022-05-16", sha256="80f6b0dee91766ab207a366b8eea546cc1afa33cea24deebaa6583f283d80fab"
+    )
+    version(
+        "2022-03-04", sha256="b2e09f0f64d75634b7d3f9844c2cea7acbc877c4ceebb6b91e8e494bb3653166"
+    )
+    version(
+        "2022-02-16", sha256="e1907f6831d9a0dd2c65879ca5746b9a0ef57d7ccce0036d55c0c6c5628ac981"
+    )
+    version(
+        "2022-01-27", sha256="d21c14b9b30f773cef8e2029773f3cc35da021eebe9060298231f95021eb814f"
+    )
+    version(
+        "2021-10-11", sha256="5c04d252e1c4a10b037aa352b89487e581ec6b52bdb46e9e85f101bbdcd9c388"
+    )
     version(
         "2021-04-05", sha256="f40d318674753287b8b28d2b4e5cca872cd772d4c7383af4a8f3eeb48fcc7ec0"
     )
@@ -55,61 +92,85 @@ class Exodusii(CMakePackage):
         "2019-10-14", sha256="f143d90e8a7516d25979d1416e580dea638332db723f26ae94a712dfe4052e8f"
     )
     version("2016-08-09", commit="2ffeb1bd39454ad5aa230e12969ce976f3d1c92b")
-    version("master", branch="master")
 
+    patch("Fix-ioss-tpl.patch", when="@2021-10-11:")
+
+    # Build options
+    variant("fortran", default=False, description="Compile with Fortran support")
+    variant("shared", default=True, description="Enables the build of shared libraries")
     variant("mpi", default=True, description="Enables MPI parallelism.")
-    variant("fortran", default=False, description="Build Fortran wrapper libraries.")
+    variant("thread_safe", default=False, description="Enable thread-safe exodus library")
 
-    depends_on("cmake@2.8.11:", type="build")
+    depends_on("cmake@3.22:", when="@2023-10-24:", type="build")
+    depends_on("cmake@3.17:", when="@:2023-05-30", type="build")
     depends_on("mpi", when="+mpi")
 
-    # https://github.com/gsjaardema/seacas/blob/master/NetCDF-Mapping.md
+    # Always depends on netcdf-c
-    depends_on("netcdf-c@4.6.1:+mpi", when="+mpi")
+    depends_on("netcdf-c@4.8.0:+mpi+parallel-netcdf", when="+mpi")
-    depends_on("netcdf-c@4.6.1:~mpi", when="~mpi")
+    depends_on("netcdf-c@4.8.0:~mpi", when="~mpi")
+    depends_on("hdf5+hl~mpi", when="~mpi")
+    depends_on("hdf5+hl+mpi", when="+mpi")
 
-    depends_on("python@2.7:")
+    depends_on("python@3.0:")
+    conflicts("+shared", when="platform=windows")
+
+    def setup_run_environment(self, env):
+        env.prepend_path("PYTHONPATH", self.prefix.lib)
 
     def cmake_args(self):
         spec = self.spec
+        from_variant = self.define_from_variant
+        define = self.define
 
-        cc_path = spec["mpi"].mpicc if "+mpi" in spec else self.compiler.cc
+        if self.spec.satisfies("@2022-10-14:"):
-        cxx_path = spec["mpi"].mpicxx if "+mpi" in spec else self.compiler.cxx
+            project_name_base = "Seacas"
+        else:
+            project_name_base = "SEACASProj"
 
-        options = [
+        options = []
-            # General Flags #
+
-            "-DSEACASProj_ENABLE_SEACASExodus=ON",
+        # #################### Base Settings #######################
-            "-DSEACASProj_ENABLE_TESTS=ON",
+        # Only want to enable the Exodus library.  If want anything else, use the seacas package.
-            "-DBUILD_SHARED_LIBS:BOOL=ON",
-            "-DTPL_ENABLE_Netcdf:BOOL=ON",
-            "-DHDF5_NO_SYSTEM_PATHS=ON",
-            "-DSEACASProj_SKIP_FORTRANCINTERFACE_VERIFY_TEST:BOOL=ON",
-            "-DSEACASProj_ENABLE_CXX11:BOOL=OFF",
-            "-DSEACASProj_ENABLE_Zoltan:BOOL=OFF",
-            "-DNetCDF_DIR:PATH={0}".format(spec["netcdf-c"].prefix),
-            # MPI Flags #
-            "-DTPL_ENABLE_MPI={0}".format("ON" if "+mpi" in spec else "OFF"),
-            "-DCMAKE_C_COMPILER={0}".format(cc_path),
-            "-DCMAKE_CXX_COMPILER={0}".format(cxx_path),
-        ]
-        if "+fortran" in spec:
-            fc_path = spec["mpi"].mpifc if "+mpi" in spec else self.compiler.f90
         options.extend(
             [
-                    "-DSEACASProj_ENABLE_Fortran:BOOL=ON",
+                define(project_name_base + "_ENABLE_ALL_PACKAGES", False),
-                    "-DCMAKE_Fortran_COMPILER={0}".format(fc_path),
+                define(project_name_base + "_ENABLE_ALL_OPTIONAL_PACKAGES", False),
-                    "-DSEACASProj_ENABLE_SEACASExodus_for:BOOL=ON",
+                define(project_name_base + "_ENABLE_SECONDARY_TESTED_CODE", False),
-                    "-DSEACASProj_ENABLE_SEACASExoIIv2for32:BOOL=ON",
+                define(project_name_base + "_ENABLE_SEACASExodus", True),
+                from_variant(project_name_base + "_ENABLE_SEACASExodus_for", "fortran"),
+                from_variant(project_name_base + "_ENABLE_SEACASExoIIv2for32", "fortran"),
+                define(project_name_base + "_HIDE_DEPRECATED_CODE", False),
+                from_variant("CMAKE_INSTALL_RPATH_USE_LINK_PATH", "shared"),
+                from_variant("BUILD_SHARED_LIBS", "shared"),
+                from_variant("SEACASExodus_ENABLE_THREADSAFE", "thread_safe"),
+                from_variant("TPL_ENABLE_Pthread", "thread_safe"),
+                from_variant(project_name_base + "_ENABLE_Fortran", "fortran"),
             ]
         )
-        # Python #
+        if "~shared" in self.spec and not is_windows:
-        # Handle v2016 separately because of older tribits
+            options.append(self.define(project_name_base + "_EXTRA_LINK_FLAGS", "z;dl"))
-        if spec.satisfies("@:2016-08-09"):
+        options.append(from_variant("TPL_ENABLE_MPI", "mpi"))
-            options.append(
+        if "+mpi" in spec and not is_windows:
-                "-DPYTHON_EXECUTABLE={0}".format(
+            options.extend(
-                    join_path(self.spec["python"].prefix.bin, "python")
+                [
+                    define("CMAKE_C_COMPILER", spec["mpi"].mpicc),
+                    define("CMAKE_CXX_COMPILER", spec["mpi"].mpicxx),
+                    define("CMAKE_Fortran_COMPILER", spec["mpi"].mpifc),
+                    define("MPI_BASE_DIR", spec["mpi"].prefix),
+                ]
             )
+
+        # ##################### Dependencies ##########################
+        # Always need NetCDF-C
+        options.extend(
+            [define("TPL_ENABLE_Netcdf", True), define("NetCDF_ROOT", spec["netcdf-c"].prefix)]
         )
+
+        # ################# RPath Handling ######################
+        if sys.platform == "darwin" and macos_version() >= Version("10.12"):
+            # use @rpath on Sierra due to limit of dynamic loader
+            options.append(define("CMAKE_MACOSX_RPATH", True))
         else:
-            options.append("-DPython_ROOT={0}".format(spec["python"].prefix))
+            options.append(define("CMAKE_INSTALL_NAME_DIR", self.prefix.lib))
 
         return options