[root] New variants, checksum changes, sundry improvements (#41463)

* New variants:
  - `tmvz-cpu`
  - `tmvz-gpu`
  - `tmvz-pymva`
  - `tmvz-sofie`

* Improve X-related dependencies.

* Improve TMVA-related dependencies with more specificity.

* Patch possible missing standard header include in Eve7.

* Patch Protobuf handling to support new Protobuf-provided CMake config
  files required to handle transitive `abseil-cpp` dependence.

* Add missing terminal newline to `webgui` patch to remove patch
  warning.

* Handle deprecated/removed build options.

* Handle unwanted system paths in various `PATH`-like environment
  variables.

3 files changed, 174 insertions, 8 deletions

diff --git a/var/spack/repos/builtin/packages/root/package.py b/var/spack/repos/builtin/packages/root/package.py
index 9d5e8dc2bb..5fba621082 100644
--- a/var/spack/repos/builtin/packages/root/package.py
+++ b/var/spack/repos/builtin/packages/root/package.py
@@ -32,6 +32,7 @@ class Root(CMakePackage):
     version("master", branch="master")
 
     # Development version (when more recent than production).
+    version("develop", branch="master")
 
     # Production version
     version("6.30.02", sha256="7965a456d1ad1ee0d5fe4769bf5a8fec291af684ed93db0f3080a9c362435183")
@@ -48,6 +49,7 @@ class Root(CMakePackage):
     version("6.26.04", sha256="a271cf82782d6ed2c87ea5eef6681803f2e69e17b3036df9d863636e9358421e")
     version("6.26.02", sha256="7ba96772271a726079506c5bf629c3ceb21bf0682567ed6145be30606d7cd9bb")
     version("6.26.00", sha256="5fb9be71fdf0c0b5e5951f89c2f03fcb5e74291d043f6240fb86f5ca977d4b31")
+    version("6.24.08", sha256="882c41fe36e94456fb10443d08ef9152375a90d1f910a10add1793d6e838bc44")
     version("6.24.06", sha256="907f69f4baca1e4f30eeb4979598ca7599b6aa803ca046e80e25b6bbaa0ef522")
     version("6.24.02", sha256="0507e1095e279ccc7240f651d25966024325179fa85a1259b694b56723ad7c1c")
     version("6.24.00", sha256="9da30548a289211c3122d47dacb07e85d35e61067fac2be6c5a5ff7bda979989")
@@ -108,6 +110,10 @@ class Root(CMakePackage):
         sha256="397f2de7db95a445afdb311fc91c40725fcfad485d58b4d72e6c3cdd0d0c5de7",
         when="@6.26:6.26.06 +root7 ^nlohmann-json@3.11:",
     )
+    # Support recent versions of protobuf with their own CMake config
+    # (provided the CMake being used supports targets), _cf_
+    # https://github.com/root-project/root/commit/f6cfe3bdab544e5f7fd49514562147ebd5d67d7c
+    patch("protobuf-config.patch", level=0, when="@:6.30.02 ^protobuf ^cmake@3.9:")
 
     patch("webgui.patch", level=0, when="@6.26.00:6.26.10,6.28.00:6.28.08,6.30.00 +webgui")
 
@@ -125,6 +131,8 @@ class Root(CMakePackage):
 
     variant("aqua", default=False, description="Enable Aqua interface")
     variant("arrow", default=False, description="Enable Arrow interface")
+    variant("cuda", when="@6.08.00:", default=False, description="Enable CUDA support")
+    variant("cudnn", when="@6.20.02:", default=False, description="Enable cuDNN support")
     variant("davix", default=True, description="Compile with external Davix")
     variant("dcache", default=False, description="Enable support for dCache")
     variant("emacs", default=False, description="Enable Emacs support")
@@ -186,6 +194,31 @@ class Root(CMakePackage):
     variant("tbb", default=True, description="TBB multi-threading support")
     variant("threads", default=True, description="Enable using thread library")
     variant("tmva", default=False, description="Build TMVA multi variate analysis library")
+    variant(
+        "tmva-cpu",
+        when="@6.15.02:",
+        default=True,
+        description="Build TMVA with CPU support for deep learning (requires BLAS)",
+    )
+    variant(
+        "tmva-gpu",
+        when="@6.15.02:",
+        default=False,
+        description="Build TMVA with GPU support for deep learning (requries CUDA)",
+    )
+    variant(
+        "tmva-pymva",
+        when="@6.17.02:",
+        default=False,
+        description="Enable support for Python in TMVA (requires numpy)",
+    )
+    variant(
+        "tmva-sofie",
+        when="@6.25.02:",
+        default=False,
+        description="Build TMVA with support for sofie - "
+        "fast inference code generation (requires protobuf 3)",
+    )
     variant("unuran", default=True, description="Use UNURAN for random number generation")
     variant("vc", default=False, description="Enable Vc for adding new types for SIMD programming")
     variant("vdt", default=True, description="Enable set of fast and vectorisable math functions")
@@ -220,7 +253,6 @@ class Root(CMakePackage):
     depends_on("cmake@3.19:", type="build", when="@6.28.00: platform=darwin")
     depends_on("pkgconfig", type="build")
 
-    depends_on("blas")
     depends_on("freetype")
     depends_on("jpeg")
     depends_on("libice")
@@ -241,6 +273,9 @@ class Root(CMakePackage):
     depends_on("libxft", when="+x")
     depends_on("libxpm", when="+x")
     depends_on("libsm", when="+x")
+    depends_on("fontconfig", when="+x", type="build")
+    depends_on("xproto", when="+x", type="build")
+    depends_on("xextproto", when="+x", type="build")
 
     # OpenGL
     depends_on("ftgl@2.4.0:", when="+opengl")
@@ -255,14 +290,20 @@ class Root(CMakePackage):
     # Python
     depends_on("python@2.7:", when="+python", type=("build", "run"))
     depends_on("python@2.7:3.10", when="@:6.26.09 +python", type=("build", "run"))
-    depends_on("py-numpy", type=("build", "run"), when="+tmva")
-    # This numpy dependency was not intended and will hopefully
-    # be fixed in 6.20.06.
+    depends_on("py-numpy", type=("build", "run"), when="+tmva-pymva")
     # See: https://sft.its.cern.ch/jira/browse/ROOT-10626
     depends_on("py-numpy", type=("build", "run"), when="@6.20.00:6.20.05 +python")
 
+    # TMVA
+    depends_on("blas", when="+tmva-cpu")
+    depends_on("cuda", when="+tmva-gpu")
+    depends_on("protobuf@3:", when="+tmva-sofie")
+
     # Optional dependencies
     depends_on("arrow", when="+arrow")
+    depends_on("cuda", when="+cuda")
+    depends_on("cuda", when="+cudnn")
+    depends_on("cudnn", when="+cudnn")
     depends_on("davix @0.7.1:", when="+davix")
     depends_on("dcap", when="+dcache")
     depends_on("cfitsio", when="+fits")
@@ -327,6 +368,12 @@ class Root(CMakePackage):
     conflicts("+math", when="~gsl", msg="root+math requires GSL")
     conflicts("+tmva", when="~gsl", msg="root+tmva requires GSL")
     conflicts("+tmva", when="~mlp", msg="root+tmva requires MLP")
+    conflicts("+tmva-cpu", when="~tmva", msg="root+tmva-cpu requires TMVA")
+    conflicts("+tmva-gpu", when="~tmva", msg="root+tmva-gpu requires TMVA")
+    conflicts("+tmva-gpu", when="~cuda", msg="root+tmva-gpu requires CUDA")
+    conflicts("+tmva-pymva", when="~tmva", msg="root+tmva-pymva requires TMVA")
+    conflicts("+tmva-sofie", when="~tmva", msg="root+tmva-sofie requires TMVA")
+    conflicts("~http", when="@6.29.00: +webgui", msg="root+webgui requires HTTP")
     conflicts("cxxstd=11", when="+root7", msg="root7 requires at least C++14")
     conflicts("cxxstd=11", when="@6.25.02:", msg="This version of root requires at least C++14")
     conflicts("cxxstd=14", when="@6.30.00:", msg="This version of root requires at least C++17")
@@ -348,6 +395,13 @@ class Root(CMakePackage):
     # See https://github.com/root-project/root/issues/11135
     conflicts("+ipo", msg="LTO is not a supported configuration for building ROOT")
 
+    def patch(self):
+        filter_file(
+            r"#include <sstream>",
+            "#include <sstream>\n#include <cstdint>",
+            "graf3d/eve7/inc/ROOT/REveTypes.hxx",
+        )
+
     @classmethod
     def filter_detected_exes(cls, prefix, exes_in_prefix):
         result = []
@@ -436,6 +490,10 @@ class Root(CMakePackage):
         _add_variant(v, f, "table", "+table")
         _add_variant(v, f, "thread", "+threads")
         _add_variant(v, f, "tmva", "+tmva")
+        _add_variant(v, f, "tmva-cpu", "+tmva-cpu")
+        _add_variant(v, f, "tmva-gpu", "+tmva-gpu")
+        _add_variant(v, f, "tmva-pymva", "+tmva-pymva")
+        _add_variant(v, f, "tmva-sofie", "+tmva-sofie")
         _add_variant(v, f, "unuran", "+unuran")
         _add_variant(v, f, "vc", "+vc")
         _add_variant(v, f, "vdt", "+vdt")
@@ -457,7 +515,6 @@ class Root(CMakePackage):
 
         # Options controlling gross build / config behavior.
         options += [
-            define("cxxmodules", False),
             define("exceptions", True),
             define("explicitlink", True),
             define("fail-on-missing", True),
@@ -478,6 +535,9 @@ class Root(CMakePackage):
             define("CLING_CXX_PATH", self.compiler.cxx),
         ]
 
+        if self.spec.satisfies("@:6.28.99"):
+            options.append(define("cxxmodules", False))
+
         # Options related to ROOT's ability to download and build its own
         # dependencies. Per Spack convention, this should generally be avoided.
 
@@ -585,6 +645,9 @@ class Root(CMakePackage):
             define_from_variant("xrootd"),
         ]
 
+        if self.spec.satisfies("@6.08.00:"):
+            options.append(define_from_variant("cuda"))
+
         # Necessary due to name change of variant (webui->webgui)
         # https://github.com/root-project/root/commit/d631c542909f2f793ca7b06abc622e292dfc4934
         if self.spec.satisfies("@:6.17.02"):
@@ -593,11 +656,22 @@ class Root(CMakePackage):
             options.append(define_from_variant("webgui", "webgui"))
 
         # Some special features
+        if self.spec.satisfies("@6.15.02:"):
+            options.append(define_from_variant("tmva-cpu"))
+            options.append(define_from_variant("tmva-gpu"))
+
+        if self.spec.satisfies("@6.17.02:"):
+            options.append(define_from_variant("tmva-pymva"))
+
         if self.spec.satisfies("@6.20.02:"):
+            options.append(define_from_variant("cudnn"))
             options.append(define_from_variant("pyroot", "python"))
         else:
             options.append(define_from_variant("python"))
 
+        if self.spec.satisfies("@6.25.02:"):
+            options.append(define_from_variant("tmva-sofie"))
+
         # #################### Compiler options ####################
 
         if sys.platform == "darwin" and self.compiler.cc == "gcc":
@@ -659,6 +733,8 @@ class Root(CMakePackage):
             # override with an empty value even though it may lead to link
             # warnings when building against ROOT
             env.unset("MACOSX_DEPLOYMENT_TARGET")
+        # Cleanup.
+        self.sanitize_environments(env)
 
     def setup_run_environment(self, env):
         env.set("ROOTSYS", self.prefix)
@@ -667,8 +743,12 @@ class Root(CMakePackage):
         # the following vars are copied from thisroot.sh; silence a cppyy warning
         env.set("CLING_STANDARD_PCH", "none")
         env.set("CPPYY_API_PATH", "none")
+        # Cleanup.
+        self.sanitize_environments(env)
 
-    def setup_dependent_build_environment(self, env, dependent_spec):
+    def setup_dependent_build_environment(
+        self, env: spack.util.environment.EnvironmentModifications, dependent_spec
+    ):
         env.set("ROOTSYS", self.prefix)
         env.set("ROOT_VERSION", "v{0}".format(self.version.up_to(1)))
         env.prepend_path("PYTHONPATH", self.prefix.lib.root)
@@ -680,8 +760,12 @@ class Root(CMakePackage):
         if "platform=darwin" in self.spec:
             # Newer deployment targets cause fatal errors in rootcling
             env.unset("MACOSX_DEPLOYMENT_TARGET")
+        # Cleanup.
+        self.sanitize_environments(env)
 
-    def setup_dependent_run_environment(self, env, dependent_spec):
+    def setup_dependent_run_environment(
+        self, env: spack.util.environment.EnvironmentModifications, dependent_spec
+    ):
         env.set("ROOTSYS", self.prefix)
         env.set("ROOT_VERSION", "v{0}".format(self.version.up_to(1)))
         env.prepend_path("PYTHONPATH", self.prefix.lib.root)
@@ -689,3 +773,28 @@ class Root(CMakePackage):
         env.prepend_path("ROOT_INCLUDE_PATH", dependent_spec.prefix.include)
         if "+rpath" not in self.spec:
             env.prepend_path("LD_LIBRARY_PATH", self.prefix.lib.root)
+        # Cleanup.
+        self.sanitize_environments(env)
+
+    def sanitize_environments(self, env: spack.util.environment.EnvironmentModifications, *vars):
+        target = self.spec.target
+        special_separators = {"LDSHARED": " -L"}
+        if not vars:
+            vars = (
+                "PATH",
+                "LDSHARED",
+                "LD_LIBRARY_PATH",
+                "DYLD_LIBRARY_PATH",
+                "LIBRARY_PATH",
+                "CMAKE_PREFIX_PATH",
+                "ROOT_INCLUDE_PATH",
+            )
+        for var in vars:
+            kwargs = {}
+            if var in special_separators:
+                kwargs["separator"] = special_separators[var]
+            env.prune_duplicate_paths(var, **kwargs)
+            if var == "PATH":
+                env.deprioritize_system_paths(var, target=target, **kwargs)
+            else:
+                env.remove_system_paths(var, **kwargs)
diff --git a/var/spack/repos/builtin/packages/root/protobuf-config.patch b/var/spack/repos/builtin/packages/root/protobuf-config.patch
new file mode 100644
index 0000000000..da02b775f6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/root/protobuf-config.patch
@@ -0,0 +1,57 @@
+--- cmake/modules/SearchInstalledSoftware.cmake	2023-08-28 06:26:43.000000000 -0500
++++ cmake/modules/SearchInstalledSoftware.cmake	2023-11-03 10:26:13.383171830 -0500
+@@ -1711,8 +1711,12 @@
+ 
+ if(tmva-sofie)
+   message(STATUS "Looking for Protobuf")
+-  find_package(Protobuf)
++  set(protobuf_MODULE_COMPATIBLE TRUE)
++  find_package(Protobuf CONFIG)
+   if(NOT Protobuf_FOUND)
++    find_package(Protobuf MODULE)
++  endif()
++  if(NOT Protobuf_FOUND)
+     if(fail-on-missing)
+       message(FATAL_ERROR "Protobuf libraries not found and they are required (tmva-sofie option enabled)")
+     else()
+--- tmva/sofie/test/CMakeLists.txt	2023-08-28 06:26:43.000000000 -0500
++++ tmva/sofie/test/CMakeLists.txt	2023-11-03 10:41:04.048362415 -0500
+@@ -46,7 +46,7 @@
+    ${CMAKE_BINARY_DIR}/ginclude   # this is for RConfigure.h
+ )
+ 
+-target_link_libraries(emitFromONNX ${Protobuf_LIBRARIES} ROOTTMVASofie ROOTTMVASofieParser)
++target_link_libraries(emitFromONNX protobuf::libprotobuf ROOTTMVASofie ROOTTMVASofieParser)
+ set_target_properties(emitFromONNX PROPERTIES POSITION_INDEPENDENT_CODE TRUE)
+ ## silence protobuf warnings seen in version 3.0 and 3.6. Not needed from protobuf version 3.17
+ target_compile_options(emitFromONNX PRIVATE -Wno-unused-parameter -Wno-array-bounds)
+@@ -88,7 +88,7 @@
+    ${CMAKE_SOURCE_DIR}/core/foundation/inc
+    ${CMAKE_BINARY_DIR}/ginclude   # this is for RConfigure.h
+ )
+-target_link_libraries(emitFromROOT ${Protobuf_LIBRARIES} ROOTTMVASofie ROOTTMVASofieParser)
++target_link_libraries(emitFromROOT protobuf::libprotobuf ROOTTMVASofie ROOTTMVASofieParser)
+ set_target_properties(emitFromROOT PROPERTIES POSITION_INDEPENDENT_CODE TRUE)
+ ## silence protobuf warnings seen in version 3.0 and 3.6. Not needed from protobuf version 3.17
+ target_compile_options(emitFromROOT PRIVATE -Wno-unused-parameter -Wno-array-bounds)
+--- tmva/sofie_parsers/CMakeLists.txt	2023-08-28 06:26:43.000000000 -0500
++++ tmva/sofie_parsers/CMakeLists.txt	2023-11-03 10:46:44.101759248 -0500
+@@ -55,8 +55,8 @@
+     src/ParseFuseConvTransposeAdd.cxx
+     src/ParseFuseMatMulAdd.cxx
+     ${PROTO_SRCS}
+-  LIBRARIES
+-    ${Protobuf_LIBRARIES}
++  LIBRARIES PUBLIC
++    protobuf::libprotobuf
+   DEPENDENCIES
+     TMVA
+     ROOTTMVASofie
+@@ -64,7 +64,5 @@
+ 
+ target_include_directories(ROOTTMVASofieParser PUBLIC
+   $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}>)
+-target_include_directories(ROOTTMVASofieParser PUBLIC
+-  ${Protobuf_INCLUDE_DIRS})
+ set_target_properties(ROOTTMVASofieParser PROPERTIES
+   POSITION_INDEPENDENT_CODE TRUE)
diff --git a/var/spack/repos/builtin/packages/root/webgui.patch b/var/spack/repos/builtin/packages/root/webgui.patch
index 932bb1023f..54233d514f 100644
--- a/var/spack/repos/builtin/packages/root/webgui.patch
+++ b/var/spack/repos/builtin/packages/root/webgui.patch
@@ -22,4 +22,4 @@
 +WebGui.HttpLoopback:        yes
  # Use https protocol for the http server (default - no)
  WebGui.UseHttps:            no
- WebGui.ServerCert:          rootserver.pem
\ No newline at end of file
+ WebGui.ServerCert:          rootserver.pem