Accumulated tweaks from Marc M.

* Be less specific about gettext with ~libxml2

* can use libc+iconv or gettext with or without libxml2

* initial round of ups compatability from prev release

* readonly bootstrap (cvmfs) workaround

* package updates from fnal-develop

* added ups compat files

* more missing files

* moderncmakedomain package

* per_os_scope

* Redo of FNALssi/spack #94

* redo of FNALssi #162

* Revert "redo of FNALssi #162"

* This reverts commit f92ed6e.

  Someone fixed the geant4 recipe with a for loop in the recipe instead,
  so not doing this after all.

* redo of FNALssi #161

* more cleanups from fnal-develop

* More lib64 fun

* speling of startswith

* version

* Style fixes

lib/spack/llnl/util/filesystem.py

@@ -2351,7 +2351,7 @@ def find_libraries(libraries, root, shared=True, recursive=False, runtime=True):
     # perform first non-recursive search in root/lib then in root/lib64 and
     # finally search all of root recursively. The search stops when the first
     # match is found.
-    common_lib_dirs = ["lib", "lib64"]
+    common_lib_dirs = ["lib64", "lib"]
     if sys.platform == "win32":
         common_lib_dirs.extend(["bin", "Lib"])
 

lib/spack/spack/build_systems/cmake.py

@@ -11,11 +11,14 @@
 import sys
 from typing import List, Optional, Tuple
 
+import archspec.cpu
+
 import llnl.util.filesystem as fs
 
 import spack.build_environment
 import spack.builder
 import spack.package_base
+import spack.util.path
 from spack.directives import build_system, conflicts, depends_on, variant
 from spack.multimethod import when
 
@@ -274,8 +277,13 @@ def std_args(pkg, generator=None):
             generator,
             define("CMAKE_INSTALL_PREFIX", pathlib.Path(pkg.prefix).as_posix()),
             define("CMAKE_BUILD_TYPE", build_type),
+            define("BUILD_TESTING", pkg.run_tests),
         ]
 
+        # if we're building for a 64 bit system, prefer lib64 paths
+        if str(archspec.cpu.host().generic).find("_64_") > 0:
+            args.append(define("FIND_LIBRARY_USE_LIB64_PATHS", True))
+
         # CMAKE_INTERPROCEDURAL_OPTIMIZATION only exists for CMake >= 3.9
         if pkg.spec.satisfies("^cmake@3.9:"):
             args.append(define("CMAKE_INTERPROCEDURAL_OPTIMIZATION", ipo))
@@ -450,6 +458,7 @@ def cmake_args(self):
 
             * CMAKE_INSTALL_PREFIX
             * CMAKE_BUILD_TYPE
+            * BUILD_TESTING
 
         which will be set automatically.
         """

lib/spack/spack/config.py

@@ -154,7 +154,10 @@ def _write_section(self, section):
             with open(filename, "w") as f:
                 syaml.dump_config(data, stream=f, default_flow_style=False)
         except (syaml.SpackYAMLError, IOError) as e:
-            raise ConfigFileError(f"cannot write to '{filename}'") from e
+            if hasattr(e, "errno") and e.errno in [13, 30]:
+                tty.warn("Ignoring write error on readonly %s" % filename)
+            else:
+                raise ConfigFileError(f"cannot write to '{filename}'") from e
 
     def clear(self):
         """Empty cached config information."""
@@ -753,9 +756,9 @@ def _add_platform_scope(cfg, scope_type, name, path):
 def _add_os_scope(cfg, scope_type, name, path):
     """Add an os-specific subdirectory for the current platform."""
     host_platform = spack.platforms.host()
-    oss = host_platform.operating_system("frontend")
-    os_name = "%s/%s" % (name, oss)
-    os_path = "%s/%s" % (path, oss)
+    oss = str(host_platform.operating_system("frontend"))
+    os_name = os.path.join(name, oss)
+    os_path = os.path.join(path, oss)
     cfg.push_scope(scope_type(os_name, os_path))
 
 

lib/spack/spack/modules/ups_table.py

@@ -37,7 +37,9 @@ def make_configuration(spec, module_set_name, explicit):
     try:
         return configuration_registry[key]
     except KeyError:
-        return configuration_registry.setdefault(key, UpsTableConfiguration(spec, module_set_name))
+        return configuration_registry.setdefault(
+            key, UpsTableConfiguration(spec, module_set_name, explicit)
+        )
 
 
 def make_layout(spec, module_set_name, explicit):

lib/spack/spack/modules/ups_version.py

@@ -38,7 +38,7 @@ def make_configuration(spec, module_set_name, explicit):
         return configuration_registry[key]
     except KeyError:
         return configuration_registry.setdefault(
-            key, UpsVersionConfiguration(spec, module_set_name)
+            key, UpsVersionConfiguration(spec, module_set_name, explicit)
         )
 
 

lib/spack/spack/package_base.py

@@ -1236,10 +1236,10 @@ def extendee_spec(self):
                 deps.append(dep)
 
         if deps:
-            # assert len(deps) == 1
+            # we may not still need this, but just in case... mengel
             if len(deps) == 2:
                 assert repr(deps[0]) == repr(deps[1])
-                tty.debug("duplicated extendee deps?! {0}".format(repr(deps[0])))
+                tty.debug("Duplicated extendee deps?! {0}".format(repr(deps[0])))
             else:
                 assert len(deps) == 1
             return deps[0]

lib/spack/spack/relocate.py

@@ -496,7 +496,7 @@ def new_relocate_elf_binaries(binaries, prefix_to_prefix):
 
     # Transform to binary string
     prefix_to_prefix = OrderedDict(
-        (k.encode("utf-8"), v.encode("utf-8")) for (k, v) in prefix_to_prefix.items()
+        (k.encode("utf-8"), v.encode("utf-8")) for (k, v) in prefix_to_prefix.items() if k and v
     )
 
     for path in binaries:

lib/spack/spack/relocate_text.py

@@ -20,7 +20,9 @@ def encode_path(p: Prefix) -> bytes:
 
 
 def _prefix_to_prefix_as_bytes(prefix_to_prefix) -> Dict[bytes, bytes]:
-    return OrderedDict((encode_path(k), encode_path(v)) for (k, v) in prefix_to_prefix.items())
+    return OrderedDict(
+        (encode_path(k), encode_path(v)) for (k, v) in prefix_to_prefix.items() if k and v
+    )
 
 
 def utf8_path_to_binary_regex(prefix: str):

lib/spack/spack/spec.py

@@ -2848,6 +2848,7 @@ def inject_patches_variant(root):
                 # don't blow up if there is a package in the buildcache we do not have
                 # a recipe for -- mengel
                 continue
+
             if dspec.spec.name not in pkg_deps:
                 continue
 

share/spack/templates/modules/modulefile.ups_table

@@ -25,7 +25,7 @@ QUALIFIERS=""
 
 
 {%set spack_root = os.environ['SPACK_ROOT'] %}
-{%set install_root =  spack_root[0:spack_root.find('/spack/')] %}
+{%set install_root = spack_root[0:spack_root.find('/spack/')] %}
 {%if spec.prefix.startswith(install_root) %}
 
 Action = setup

var/spack/repos/builtin/packages/gobject-introspection/package.py

@@ -94,7 +94,7 @@ def setup_run_environment(self, env):
     def setup_dependent_build_environment(self, env, dependent_spec):
         env.prepend_path("XDG_DATA_DIRS", self.prefix.share)
         env.prepend_path("GI_TYPELIB_PATH", join_path(self.prefix.lib, "girepository-1.0"))
-        env.prepend_path("LD_LIBRARY_PATH", self.spec['glib'].prefix.lib)
+        env.prepend_path("LD_LIBRARY_PATH", self.spec["glib"].prefix.lib)
 
     def setup_dependent_run_environment(self, env, dependent_spec):
         env.prepend_path("XDG_DATA_DIRS", self.prefix.share)

var/spack/repos/builtin/packages/hdf5/package.py

@@ -197,11 +197,11 @@ class Hdf5(CMakePackage):
     variant("hl", default=False, description="Enable the high-level library")
     variant("cxx", default=False, description="Enable C++ support")
     variant(
-        "cxxstd", 
-        default="11", 
-        values=("11","14","17","20","23"), 
-        multi=False, 
-        sticky=True, 
+        "cxxstd",
+        default="11",
+        values=("11", "14", "17", "20", "23"),
+        multi=False,
+        sticky=True,
         description="C++ standard",
     )
     variant("map", when="@1.14:", default=False, description="Enable MAP API support")
@@ -606,7 +606,9 @@ def cmake_args(self):
                 spec.satisfies("@1.8.22+shared+tools"),
             ),
             self.define("CXX_STANDARD_REQUIRED", True),
-            self.define("CMAKE_CXX_FLAGS", "-std=c++{0}".format(self.spec.variants["cxxstd"].value)),
+            self.define(
+                "CMAKE_CXX_FLAGS", "-std=c++{0}".format(self.spec.variants["cxxstd"].value)
+            ),
             self.define_from_variant("CMAKE_CXX_STANDARD", "cxxstd"),
             self.define_from_variant("HDF5_ENABLE_MAP_API", "map"),
             self.define("HDF5_ENABLE_Z_LIB_SUPPORT", True),

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

@@ -47,3 +47,6 @@ def patch(self):
             "configure",
             string=True,
         )
+        filter_file(
+            "#include *<string.h>", "#include <string.h>\n#include <limits.h>", "src/gd_gd2.c"
+        )

var/spack/repos/builtin/packages/perl-http-message/package.py

@@ -48,9 +48,7 @@ class PerlHttpMessage(PerlPackage):
     depends_on("perl-encode-locale@1:", type="run")
     depends_on("perl-extutils-makemaker", type=("build", "test"))
     depends_on("perl-http-date@6:", type="run")
-    depends_on(
-        "perl-io-uncompress-brotli@0.4.1:", type=("build", "run", "test")
-    )
+    depends_on("perl-io-uncompress-brotli@0.4.1:", type=("build", "run", "test"))
     depends_on("perl-io-compress-bzip2@2.21:", type="run")
     depends_on("perl-io-compress-deflate", type="run")
     depends_on("perl-io-compress-gzip", type="run")