feat: align packages with Spack v0.23.0 upstream

packages/ambertools/package.py

-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack import *
-
-class Ambertools (CMakePackage):
-    """AmberTools is a free, useful standalone package and a prerequisite for installing Amber itself.
-    The AmberTools suite is free of charge, and its components are mostly released under the GNU General Public License (GPL).
-    A few components are included that are in the public domain or which have other, open-source, licenses.
-    The libsander and libpbsa libraries use the LGPL license."""
-
-    # Set the homepage and download url
-    homepage = "http://ambermd.org/AmberTools.php"
-    url      = "http://ambermd.org/downloads/AmberTools22jlmrcc.tar.bz2"
-
-    # Set the gitlab accounts of this package maintainers
-    maintainers = ['dbeltran', 'elmath']
-
-    version('22jlmrcc', sha256='1571d4e0f7d45b2a71dce5999fa875aea8c90ee219eb218d7916bf30ea229121')
-
-    # Dependencies
-    depends_on("flex",                      type="build") # This is necessary for sure (experimentally tested)
-    depends_on("bison",                     type="build") # This is necessary for sure (experimentally tested)
-    depends_on("tcsh",                      type="build")
-    depends_on("zlib",                      type=("build", "link", "run"))
-    depends_on("bzip2",                     type=("build", "run"))
-    depends_on("blas",                      type=("build", "run"))
-    depends_on("lapack",                    type=("build", "run"))
-    depends_on("arpack-ng",                 type=("build", "run"))
-    depends_on("netcdf-c",                  type=("build", "run"))
-    depends_on("netcdf-fortran",            type=("build", "run"))
-    depends_on("fftw",                      type=("build", "run"))
-    depends_on("readline",                  type=("build", "run"))
-    depends_on("netlib-xblas~plain_blas",   type=("build", "run"))
-    # specific variants needed for boost - from the build log "Could NOT find Boost (missing: thread system program_options iostreams regex timer chrono filesystem graph)"
-    depends_on("boost+thread+system+program_options+iostreams+regex+timer+chrono+filesystem+graph", type=("build", "run"))
-
-    # Python dependencies
-    # WARNING: If a python 3.8 version is already installed in spack then the '+tkinter' variant makes spack ignore the version
-    # WARNING: Spack may try to install the preferred python version (i.e. python 3.10.8)
-    # WARNING: The soultion is uninstall python and reinstall with this variant
-    depends_on('python@3.8: +tkinter',      type=('build', 'run'))
-    depends_on("py-numpy",                  type=("build", "run"))
-    depends_on("py-matplotlib",             type=("build", "run"))
-    depends_on("py-scipy",                  type=("build", "run"))
-
-    def cmake_args(self):
-        # Translated from ambertools build/run_cmake script
-        # We also add the TRUST_SYSTEM_LIBS argument that is mentioned in the ambertools CMake guide
-        #   https://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Guide-to-Options
-        args = [
-            self.define("COMPILER", "GNU"),
-            self.define("MPI", False),
-            self.define("CUDA", False),
-            self.define("INSTALL_TESTS", True),
-            self.define("DOWNLOAD_MINICONDA", False),
-            self.define("TRUST_SYSTEM_LIBS", True),
-            # This is to avoid the x11 (X11_Xext_LIB) error
-            # It is equivalent to the '-noX11' flag accoridng to the docs:
-            # https://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Common-Options
-            self.define("BUILD_GUI", False)
-        ]
-        return args
-
-    def setup_run_environment(self, env):
-        env.set("AMBER_PREFIX", self.prefix)
-        env.set("AMBERHOME", self.prefix)
-
-    def setup_build_environment(self, env):
-        env.set("AMBER_PREFIX", self.prefix)
-        env.set("AMBERHOME", self.prefix)
-
-    @run_after('install')
-    @on_package_attributes(run_tests=True)
-    def check_install(self):
-        make("test.serial")

packages/bazel/bazelconfiguration-0.3.patch

---- a/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java
-+++ b/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java
-@@ -150,6 +150,13 @@
-       builder.put("PATH", null);
-       builder.put("LD_LIBRARY_PATH", null);
-     }
-+
-+    Map<String, String> spackEnv = System.getenv();
-+    for (String envName : spackEnv.keySet()) {
-+      if (envName.startsWith("SPACK_")) {
-+        builder.put(envName, spackEnv.get(envName));
-+      }
-+    }
-   }
- 
-   private static PathFragment determineShellExecutable(OS os, PathFragment fromOption) {

packages/bazel/bazelruleclassprovider-0.14.patch

---- a/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelRuleClassProvider.java
-+++ b/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelRuleClassProvider.java
-@@ -168,6 +168,13 @@ public class BazelRuleClassProvider {
-       env.put("PATH", null);
-     }
- 
-+    Map<String, String> spackEnv = System.getenv();
-+    for (String envName : spackEnv.keySet()) {
-+      if (envName.startsWith("SPACK_")) {
-+        env.put(envName, spackEnv.get(envName));
-+      }
-+    }
-+
-     // Shell environment variables specified via options take precedence over the
-     // ones inherited from the fragments. In the long run, these fragments will
-     // be replaced by appropriate default rc files anyway.

packages/bazel/build-0.29.1.patch

-From 9c9d27561780bc56d9f0867e325c7421a94ee1cb Mon Sep 17 00:00:00 2001
-From: Harsh Bhatia <bhatia4@llnl.gov>
-Date: Tue, 15 Dec 2020 15:56:10 -0800
-Subject: [PATCH] https://github.com/bazelbuild/bazel/commit/ab62a6e097590dac5ec946ad7a796ea0e8593ae0 
-
----
- src/conditions/BUILD | 6 ++++++
- third_party/BUILD    | 8 ++++++--
- 2 files changed, 12 insertions(+), 2 deletions(-)
-
-diff --git a/src/conditions/BUILD b/src/conditions/BUILD
-index 2b28e28057..faa41a439d 100644
---- a/src/conditions/BUILD
-+++ b/src/conditions/BUILD
-@@ -10,6 +10,12 @@ filegroup(
-     visibility = ["//src:__pkg__"],
- )
- 
-+config_setting(
-+    name = "linux_ppc",
-+    values = {"cpu": "ppc"},
-+    visibility = ["//visibility:public"],
-+)
-+
- config_setting(
-     name = "linux_x86_64",
-     values = {"cpu": "k8"},
-diff --git a/third_party/BUILD b/third_party/BUILD
-index 159006d741..4fcae54c00 100644
---- a/third_party/BUILD
-+++ b/third_party/BUILD
-@@ -523,12 +523,13 @@ UNNECESSARY_DYNAMIC_LIBRARIES = select({
-     "//src/conditions:darwin": "*.so *.dll",
-     "//src/conditions:darwin_x86_64": "*.so *.dll",
-     "//src/conditions:linux_x86_64": "*.jnilib *.dll",
-+    "//src/conditions:linux_ppc": "*.so *.jnilib *.dll",
-     # The .so file is an x86 one, so we can just remove it if the CPU is not x86
-     "//src/conditions:arm": "*.so *.jnilib *.dll",
-     "//src/conditions:linux_aarch64": "*.so *.jnilib *.dll",
-     # Play it safe -- better have a big binary than a slow binary
-     # zip -d does require an argument. Supply something bogus.
--    "//conditions:default": "*.bogusextension",
-+    "//conditions:default": "",
- })
- 
- # Remove native libraries that are for a platform different from the one we are
-@@ -537,7 +538,10 @@ genrule(
-     name = "filter_netty_dynamic_libs",
-     srcs = ["netty_tcnative/netty-tcnative-boringssl-static-2.0.24.Final.jar"],
-     outs = ["netty_tcnative/netty-tcnative-filtered.jar"],
--    cmd = "cp $< $@ && zip -qd $@ " + UNNECESSARY_DYNAMIC_LIBRARIES,
-+    cmd = "cp $< $@ && " +
-+      # End successfully if there is nothing to be deleted from the archive
-+      "if [ -n '" + UNNECESSARY_DYNAMIC_LIBRARIES + "' ]; then " +
-+      "zip -qd $@ " + UNNECESSARY_DYNAMIC_LIBRARIES + "; fi",
- )
- 
- java_import(
--- 
-2.21.0 (Apple Git-122.2)
-

packages/bazel/cc_configure-0.3.0.patch

---- a/tools/cpp/cc_configure.bzl
-+++ b/tools/cpp/cc_configure.bzl
-@@ -173,8 +173,19 @@
-   else:
-     inc_dirs = result.stderr[index1 + 1:index2].strip()
- 
--  return [repository_ctx.path(_cxx_inc_convert(p))
--          for p in inc_dirs.split("\n")]
-+  default_inc_directories = [
-+    repository_ctx.path(_cxx_inc_convert(p))
-+    for p in inc_dirs.split("\n")
-+  ]
-+
-+  env = repository_ctx.os.environ
-+  if "SPACK_INCLUDE_DIRS" in env:
-+    for path in env["SPACK_INCLUDE_DIRS"].split(":"):
-+      default_inc_directories.append(
-+        repository_ctx.path(_cxx_inc_convert(path))
-+      )
-+
-+  return default_inc_directories
- 
- def _add_option_if_supported(repository_ctx, cc, option):
-   """Checks that `option` is supported by the C compiler."""

packages/bazel/cc_configure-0.5.0.patch

---- a/tools/cpp/cc_configure.bzl
-+++ b/tools/cpp/cc_configure.bzl
-@@ -200,8 +200,19 @@
-   else:
-     inc_dirs = result.stderr[index1 + 1:index2].strip()
- 
--  return [_escape_string(repository_ctx.path(_cxx_inc_convert(p)))
--          for p in inc_dirs.split("\n")]
-+  default_inc_directories = [
-+    _escape_string(repository_ctx.path(_cxx_inc_convert(p)))
-+    for p in inc_dirs.split("\n")
-+  ]
-+
-+  env = repository_ctx.os.environ
-+  if "SPACK_INCLUDE_DIRS" in env:
-+    for path in env["SPACK_INCLUDE_DIRS"].split(":"):
-+      default_inc_directories.append(
-+        repository_ctx.path(_cxx_inc_convert(path))
-+      )
-+
-+  return default_inc_directories
- 
- 
- def _add_option_if_supported(repository_ctx, cc, option):

packages/bazel/compile-0.13.patch

---- a/compile.sh
-+++ b/compile.sh
-@@ -92,7 +92,7 @@
- log "Building output/bazel"
- # We set host and target platform directly since the defaults in @bazel_tools
- # have not yet been generated.
--bazel_build "src:bazel${EXE_EXT}" \
-+CC=$SPACK_CC CXX=$SPACK_CXX bazel_build "src:bazel${EXE_EXT}" \
-   --host_platform=@bazel_tools//platforms:host_platform \
-   --platforms=@bazel_tools//platforms:target_platform \
-   || fail "Could not build Bazel"

packages/bazel/compile-0.16.patch

---- a/compile.sh
-+++ b/compile.sh
-@@ -92,7 +92,7 @@ display "."
- log "Building output/bazel"
- # We set host and target platform directly since the defaults in @bazel_tools
- # have not yet been generated.
--bazel_build "src:bazel_nojdk${EXE_EXT}" \
-+CC=$SPACK_CC CXX=$SPACK_CXX bazel_build "src:bazel_nojdk${EXE_EXT}" \
-   --host_platform=@bazel_tools//platforms:host_platform \
-   --platforms=@bazel_tools//platforms:target_platform \
-   || fail "Could not build Bazel"

packages/bazel/compile-0.21.patch

---- a/compile.sh
-+++ b/compile.sh
-@@ -92,7 +92,7 @@ display "."
- log "Building output/bazel"
- # We set host and target platform directly since the defaults in @bazel_tools
- # have not yet been generated.
--bazel_build "src:bazel_nojdk${EXE_EXT}" \
-+CC=$SPACK_CC CXX=$SPACK_CXX bazel_build "src:bazel_nojdk${EXE_EXT}" \
-   --action_env=PATH \
-   --host_platform=@bazel_tools//platforms:host_platform \
-   --platforms=@bazel_tools//platforms:target_platform \

packages/bazel/compile-0.3.patch

---- a/compile.sh
-+++ b/compile.sh
-@@ -99,7 +99,7 @@
-   new_step 'Building Bazel with Bazel'
-   display "."
-   log "Building output/bazel"
--  bazel_build "src:bazel${EXE_EXT}"
-+  CC=$SPACK_CC CXX=$SPACK_CXX bazel_build "src:bazel${EXE_EXT}"
-   cp -f "bazel-bin/src/bazel${EXE_EXT}" "output/bazel${EXE_EXT}"
-   chmod 0755 "output/bazel${EXE_EXT}"
-   BAZEL="$(pwd)/output/bazel${EXE_EXT}"

packages/bazel/compile-0.9.patch

---- a/compile.sh
-+++ b/compile.sh
-@@ -92,7 +92,7 @@
- log "Building output/bazel"
- # We set host and target platform directly since the defaults in @bazel_tools
- # have not yet been generated.
--bazel_build "src:bazel${EXE_EXT}" \
-+CC=$SPACK_CC CXX=$SPACK_CXX bazel_build "src:bazel${EXE_EXT}" \
-   --host_platform=//tools/platforms:host_platform \
-   --platforms=//tools/platforms:target_platform \
-   || fail "Could not build Bazel"

packages/bazel/cppcompileaction-0.3.0.patch

---- a/src/main/java/com/google/devtools/build/lib/rules/cpp/CppCompileAction.java.orig    2020-06-08 13:42:14.035342560 -0400
-+++ b/src/main/java/com/google/devtools/build/lib/rules/cpp/CppCompileAction.java 2020-06-08 13:42:25.149375458 -0400
-@@ -963,7 +963,7 @@
-           // are, it's probably due to a non-hermetic #include, & we should stop
-           // the build with an error.
-           if (execPath.startsWith(execRoot)) {
--            execPathFragment = execPath.relativeTo(execRoot); // funky but tolerable path
-+             //  execPathFragment = execPath.relativeTo(execRoot); // funky but tolerable path
-           } else {
-             problems.add(execPathFragment.getPathString());
-             continue;

packages/bazel/cppcompileaction-7.0.0.patch

+diff --color=auto --color=auto -Naur a/src/main/java/com/google/devtools/build/lib/rules/cpp/HeaderDiscovery.java b/src/main/java/com/google/devtools/build/lib/rules/cpp/HeaderDiscovery.java
+--- a/src/main/java/com/google/devtools/build/lib/rules/cpp/HeaderDiscovery.java	1980-01-01 00:00:00
++++ b/src/main/java/com/google/devtools/build/lib/rules/cpp/HeaderDiscovery.java	2024-02-15 13:36:37
+@@ -143,7 +143,7 @@
+               LabelConstants.EXPERIMENTAL_EXTERNAL_PATH_PREFIX.getRelative(
+                   execPath.relativeTo(execRoot.getParentDirectory()));
+         } else {
+-          absolutePathProblems.add(execPathFragment.getPathString());
++          // absolutePathProblems.add(execPathFragment.getPathString());
+           continue;
+         }
+       }

packages/bazel/unix_cc_configure-0.10.patch

---- a/tools/cpp/unix_cc_configure.bzl
-+++ b/tools/cpp/unix_cc_configure.bzl
-@@ -147,9 +147,18 @@ def get_escaped_cxx_inc_directories(repository_ctx, cc, additional_flags = []):
-   else:
-     inc_dirs = result.stderr[index1 + 1:index2].strip()
- 
--  return [_prepare_include_path(repository_ctx, _cxx_inc_convert(p))
--          for p in inc_dirs.split("\n")]
-+  default_inc_directories = [
-+    _prepare_include_path(repository_ctx, _cxx_inc_convert(p))
-+      for p in inc_dirs.split("\n")
-+  ]
-+ 
-+  env = repository_ctx.os.environ
-+  if "SPACK_INCLUDE_DIRS" in env:
-+    for path in env["SPACK_INCLUDE_DIRS"].split(":"):
-+      default_inc_directories.append(path)
-+
-+  return default_inc_directories
- 
-
- def _is_option_supported(repository_ctx, cc, option):

packages/bazel/unix_cc_configure-0.5.3.patch

---- a/tools/cpp/unix_cc_configure.bzl
-+++ b/tools/cpp/unix_cc_configure.bzl
-@@ -117,9 +117,19 @@ def get_escaped_cxx_inc_directories(repository_ctx, cc):
-   else:
-     inc_dirs = result.stderr[index1 + 1:index2].strip()
- 
--  return [escape_string(repository_ctx.path(_cxx_inc_convert(p)))
--          for p in inc_dirs.split("\n")]
-+  default_inc_directories = [
-+    escape_string(repository_ctx.path(_cxx_inc_convert(p)))
-+          for p in inc_dirs.split("\n")
-+  ]
- 
-+  env = repository_ctx.os.environ
-+  if "SPACK_INCLUDE_DIRS" in env:
-+    for path in env["SPACK_INCLUDE_DIRS"].split(":"):
-+      default_inc_directories.append(
-+        repository_ctx.path(_cxx_inc_convert(path))
-+      )
-+
-+  return default_inc_directories
- 
- def _add_option_if_supported(repository_ctx, cc, option):
-   """Checks that `option` is supported by the C compiler. Doesn't %-escape the option."""

packages/gcc/darwin/apfs.patch

-diff -uNr gcc-7.2.0.orig/libstdc++-v3/include/Makefile.in gcc-7.2.0/libstdc++-v3/include/Makefile.in
---- gcc-7.2.0.orig/libstdc++-v3/include/Makefile.in     2017-07-25 14:05:07.000000000 -0400
-+++ gcc-7.2.0/libstdc++-v3/include/Makefile.in  2017-09-02 12:22:08.000000000 -0400
-@@ -1764,6 +1764,8 @@
- @GLIBCXX_HOSTED_TRUE@install-data-local: install-headers
- @GLIBCXX_HOSTED_FALSE@install-data-local: install-freestanding-headers
- 
-+.NOTPARALLEL: install-headers
-+
- # This is a subset of the full install-headers rule.  We only need <ciso646>,
- # <cstddef>, <cfloat>, <limits>, <climits>, <cstdint>, <cstdlib>, <new>,
- # <typeinfo>, <exception>, <initializer_list>, <cstdalign>, <cstdarg>,

packages/gcc/darwin/clang13.patch

---- a/gcc/genconditions.c	2019-01-01 12:37:19.064943662 +0100
-+++ b/gcc/genconditions.c	2019-10-11 10:57:11.464595789 +0200
-@@ -57,8 +57,9 @@ write_header (void)
- \n\
- /* It is necessary, but not entirely safe, to include the headers below\n\
-    in a generator program.  As a defensive measure, don't do so when the\n\
--   table isn't going to have anything in it.  */\n\
--#if GCC_VERSION >= 3001\n\
-+   table isn't going to have anything in it.\n\
-+   Clang 9 is buggy and doesn't handle __builtin_constant_p correctly.  */\n\
-+#if GCC_VERSION >= 3001 && __clang_major__ < 9\n\
- \n\
- /* Do not allow checking to confuse the issue.  */\n\
- #undef CHECKING_P\n\
-@@ -170,7 +171,7 @@ struct c_test\n\
-    vary at run time.  It works in 3.0.1 and later; 3.0 only when not\n\
-    optimizing.  */\n\
- \n\
--#if GCC_VERSION >= 3001\n\
-+#if GCC_VERSION >= 3001 && __clang_major__ < 9\n\
- static const struct c_test insn_conditions[] = {\n");
- 
-   traverse_c_tests (write_one_condition, 0);
-@@ -191,7 +192,7 @@ write_writer (void)
- 	"  unsigned int i;\n"
-         "  const char *p;\n"
-         "  puts (\"(define_conditions [\");\n"
--	"#if GCC_VERSION >= 3001\n"
-+	"#if GCC_VERSION >= 3001 && __clang_major__ < 9\n"
- 	"  for (i = 0; i < ARRAY_SIZE (insn_conditions); i++)\n"
- 	"    {\n"
- 	"      printf (\"  (%d \\\"\", insn_conditions[i].value);\n"

packages/gcc/darwin/gcc-4.9.patch1

-diff --git a/gcc/configure b/gcc/configure
-index 9523773..52b0bf7 100755
---- a/gcc/configure
-+++ b/gcc/configure
-@@ -24884,7 +24884,7 @@ if test "${gcc_cv_as_ix86_filds+set}" = set; then :
- else
-   gcc_cv_as_ix86_filds=no
-   if test x$gcc_cv_as != x; then
--    $as_echo 'filds mem; fists mem' > conftest.s
-+    $as_echo 'filds (%ebp); fists (%ebp)' > conftest.s
-     if { ac_try='$gcc_cv_as $gcc_cv_as_flags  -o conftest.o conftest.s >&5'
-   { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_try\""; } >&5
-   (eval $ac_try) 2>&5
-@@ -24915,7 +24915,7 @@ if test "${gcc_cv_as_ix86_fildq+set}" = set; then :
- else
-   gcc_cv_as_ix86_fildq=no
-   if test x$gcc_cv_as != x; then
--    $as_echo 'fildq mem; fistpq mem' > conftest.s
-+    $as_echo 'fildq (%ebp); fistpq (%ebp)' > conftest.s
-     if { ac_try='$gcc_cv_as $gcc_cv_as_flags  -o conftest.o conftest.s >&5'
-   { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_try\""; } >&5
-   (eval $ac_try) 2>&5
-diff --git a/gcc/configure.ac b/gcc/configure.ac
-index 68b0ee8..bd53978 100644
---- a/gcc/configure.ac
-+++ b/gcc/configure.ac
-@@ -3869,13 +3869,13 @@ foo:	nop
- 
-     gcc_GAS_CHECK_FEATURE([filds and fists mnemonics],
-        gcc_cv_as_ix86_filds,,,
--       [filds mem; fists mem],,
-+       [filds (%ebp); fists (%ebp)],,
-        [AC_DEFINE(HAVE_AS_IX86_FILDS, 1,
-          [Define if your assembler uses filds and fists mnemonics.])])
- 
-     gcc_GAS_CHECK_FEATURE([fildq and fistpq mnemonics],
-        gcc_cv_as_ix86_fildq,,,
--       [fildq mem; fistpq mem],,
-+       [fildq (%ebp); fistpq (%ebp)],,
-        [AC_DEFINE(HAVE_AS_IX86_FILDQ, 1,
-          [Define if your assembler uses fildq and fistq mnemonics.])])
- 

packages/gcc/darwin/gcc-4.9.patch2

-From 82f81877458ea372176eabb5de36329431dce99b Mon Sep 17 00:00:00 2001
-From: Iain Sandoe <iain@codesourcery.com>
-Date: Sat, 21 Dec 2013 00:30:18 +0000
-Subject: [PATCH] don't try to mark local symbols as no-dead-strip
-
----
- gcc/config/darwin.c | 5 +++++
- 1 file changed, 5 insertions(+)
-
-diff --git a/gcc/config/darwin.c b/gcc/config/darwin.c
-index 40804b8..0080299 100644
---- a/gcc/config/darwin.c
-+++ b/gcc/config/darwin.c
-@@ -1259,6 +1259,11 @@ darwin_encode_section_info (tree decl, rtx rtl, int first ATTRIBUTE_UNUSED)
- void
- darwin_mark_decl_preserved (const char *name)
- {
-+  /* Actually we shouldn't mark any local symbol this way, but for now
-+     this only happens with ObjC meta-data.  */
-+  if (darwin_label_is_anonymous_local_objc_name (name))
-+    return;
-+
-   fprintf (asm_out_file, "\t.no_dead_strip ");
-   assemble_name (asm_out_file, name);
-   fputc ('\n', asm_out_file);
--- 
-2.2.1
-