flake

* Add gsl-lite from JCSDA/NOAA-EMC spack fork
* Black-format var/spack/repos/builtin/packages/gsl-lite/package.py
* Update maintainers and remove redundant dependency in var/spack/repos/builtin/packages/gsl-lite/package.py

lib/spack/docs/environments.rst

@@ -346,7 +346,7 @@ the Environment and then install the concretized specs.
    (see :ref:`build-jobs`). To speed up environment builds further, independent
    packages can be installed in parallel by launching more Spack instances. For
    example, the following will build at most four packages in parallel using
-   three background jobs: 
+   three background jobs:
 
    .. code-block:: console
 
@@ -394,7 +394,7 @@ version (and other constraints) passed as the spec argument to the
 
 For packages with ``git`` attributes, git branches, tags, and commits can
 also be used as valid concrete versions (see :ref:`version-specifier`).
-This means that for a package ``foo``, ``spack develop foo@git.main`` will clone 
+This means that for a package ``foo``, ``spack develop foo@git.main`` will clone
 the ``main`` branch of the package, and ``spack install`` will install from
 that git clone if ``foo`` is in the environment.
 Further development on ``foo`` can be tested by reinstalling the environment,
@@ -630,6 +630,35 @@ The following two Environment manifests are identical:
 Spec matrices can be used to install swaths of software across various
 toolchains.
 
+Note that ordering of matrices is important. For example, the
+following environments are identical:
+
+.. code-block:: yaml
+
+   spack:
+     specs:
+       - matrix:
+           - [hdf5@1.10.2+mpi]
+           - [^mpich, ^openmpi]
+           - ['%gcc']
+       - matrix:
+           - [hdf5@1.12.1+mpi]
+           - ['%gcc']
+           - [^mpich, ^openmpi]
+
+   spack:
+     specs:
+       - hdf5@1.10.2+mpi ^mpich%gcc
+       - hdf5@1.10.2+mpi ^openmpi%gcc
+       - hdf5@1.12.1+mpi %gcc ^mpich
+       - hdf5@1.12.1+mpi %gcc ^openmpi
+
+Notice how the first matrix applies the compiler constraints to the
+mpi dependencies, whereas the second matrix applies the compiler
+constraints directly to the root hdf5 node. This gives users the full
+breadth of expressiveness of the spec syntax through the matrix
+interface.
+
 ^^^^^^^^^^^^^^^^^^^^
 Spec List References
 ^^^^^^^^^^^^^^^^^^^^
@@ -1120,19 +1149,19 @@ index once every package is pushed. Note how this target uses the generated
 
    SPACK ?= spack
    BUILDCACHE_DIR = $(CURDIR)/tarballs
-   
+
    .PHONY: all
-   
+
    all: push
-   
+
    include env.mk
-   
+
    example/push/%: example/install/%
    	@mkdir -p $(dir $@)
    	$(info About to push $(SPEC) to a buildcache)
    	$(SPACK) -e . buildcache create --allow-root --only=package --directory $(BUILDCACHE_DIR) /$(HASH)
    	@touch $@
-   
+
    push: $(addprefix example/push/,$(example/SPACK_PACKAGE_IDS))
    	$(info Updating the buildcache index)
    	$(SPACK) -e . buildcache update-index --directory $(BUILDCACHE_DIR)

lib/spack/spack/compilers/cce.py

@@ -89,6 +89,11 @@ def cxx14_flag(self):
             return "-std=c++14"
         return "-h std=c++14"
 
+    @property
+    def cxx17_flag(self):
+        if self.is_clang_based:
+            return "-std=c++17"
+
     @property
     def c99_flag(self):
         if self.is_clang_based:

lib/spack/spack/environment/environment.py

@@ -2265,15 +2265,12 @@ def _concretize_from_constraints(spec_constraints, tests=False):
         m += "concretization target. all specs must have a single name "
         m += "constraint for concretization."
         raise InvalidSpecConstraintError(m)
-    spec_constraints.remove(root_spec[0])
 
     invalid_constraints = []
     while True:
-        # Attach all anonymous constraints to one named spec
-        s = root_spec[0].copy()
-        for c in spec_constraints:
-            if c not in invalid_constraints:
-                s.constrain(c)
+        # Combine constraints into a single spec
+        s = Spec(" ".join([str(c) for c in spec_constraints if c not in invalid_constraints]))
+
         try:
             return s.concretized(tests=tests)
         except spack.spec.InvalidDependencyError as e:

lib/spack/spack/spec_list.py

@@ -51,7 +51,9 @@ def specs_as_constraints(self):
             constraints = []
             for item in self.specs_as_yaml_list:
                 if isinstance(item, dict):  # matrix of specs
-                    constraints.extend(_expand_matrix_constraints(item))
+                    expanded = _expand_matrix_constraints(item)
+                    for e in expanded:
+                        constraints.append([Spec(x) for x in e])
                 else:  # individual spec
                     constraints.append([Spec(item)])
             self._constraints = constraints
@@ -62,13 +64,11 @@ def specs_as_constraints(self):
     def specs(self):
         if self._specs is None:
             specs = []
-            # This could be slightly faster done directly from yaml_list,
-            # but this way is easier to maintain.
-            for constraint_list in self.specs_as_constraints:
-                spec = constraint_list[0].copy()
-                for const in constraint_list[1:]:
-                    spec.constrain(const)
-                specs.append(spec)
+            for item in self.specs_as_yaml_list:
+                if isinstance(item, dict):  # matrix of specs
+                    specs.extend([Spec(" ".join(x)) for x in _expand_matrix_constraints(item)])
+                else:  # individual spec
+                    specs.append(Spec(item))
             self._specs = specs
 
         return self._specs
@@ -193,11 +193,7 @@ def _expand_matrix_constraints(matrix_config):
     for combo in itertools.product(*expanded_rows):
         # Construct a combined spec to test against excludes
         flat_combo = [constraint for constraint_list in combo for constraint in constraint_list]
-        flat_combo = [Spec(x) for x in flat_combo]
-
-        test_spec = flat_combo[0].copy()
-        for constraint in flat_combo[1:]:
-            test_spec.constrain(constraint)
+        test_spec = Spec(" ".join(flat_combo))
 
         # Abstract variants don't have normal satisfaction semantics
         # Convert all variants to concrete types.
@@ -213,7 +209,7 @@ def _expand_matrix_constraints(matrix_config):
             continue
 
         if sigil:
-            flat_combo[0] = Spec(sigil + str(flat_combo[0]))
+            flat_combo[0] = sigil + flat_combo[0]
 
         # Add to list of constraints
         results.append(flat_combo)

lib/spack/spack/test/env.py

@@ -75,8 +75,8 @@ def test_env_change_spec(tmpdir, mock_packages, config):
   - desired_specs: ["mpileaks@2.1"]
   specs:
   - matrix:
-    - [$compilers]
     - [$desired_specs]
+    - [$compilers]
 """
 
 

lib/spack/spack/test/spec_list.py

@@ -61,25 +61,25 @@ def test_spec_list_expansions(self):
     @pytest.mark.parametrize(
         "specs,expected",
         [
-            # Constraints are ordered randomly
+            # Constraints are ordered carefully to apply to appropriate node
             (
                 [
                     {
                         "matrix": [
-                            ["^zmpi"],
-                            ["%gcc@4.5.0"],
                             ["hypre", "libelf"],
                             ["~shared"],
-                            ["cflags=-O3", 'cflags="-g -O0"'],
                             ["^foo"],
+                            ["^zmpi"],
+                            ["%gcc@4.5.0"],
+                            ["cflags=-O3", 'cflags="-g -O0"'],
                         ]
                     }
                 ],
                 [
-                    "hypre cflags=-O3 ~shared %gcc@4.5.0 ^foo ^zmpi",
-                    'hypre cflags="-g -O0" ~shared %gcc@4.5.0 ^foo ^zmpi',
-                    "libelf cflags=-O3 ~shared %gcc@4.5.0 ^foo ^zmpi",
-                    'libelf cflags="-g -O0" ~shared %gcc@4.5.0 ^foo ^zmpi',
+                    "hypre ~shared ^foo ^zmpi cflags=-O3 %gcc@4.5.0",
+                    'hypre ~shared ^foo ^zmpi cflags="-g -O0" %gcc@4.5.0',
+                    "libelf ~shared ^foo ^zmpi cflags=-O3 %gcc@4.5.0",
+                    'libelf ~shared ^foo ^zmpi cflags="-g -O0" %gcc@4.5.0',
                 ],
             ),
             # A constraint affects both the root and a dependency

share/spack/gitlab/cloud_pipelines/stacks/gpu-tests/spack.yaml

@@ -59,8 +59,6 @@ spack:
 
   specs:
   - kokkos +rocm amdgpu_target=gfx90a
-  - kokkos +wrapper +cuda cuda_arch=80 ^cuda@11.7.1
-  - raja +cuda cuda_arch=80 ^cuda@11.7.1
   - raja +cuda cuda_arch=80 ^cuda@12.0.0
 
   # FAILURES
@@ -109,14 +107,6 @@ spack:
           variables:
             CI_JOB_SIZE: large
 
-      - match:
-        - kokkos +cuda cuda_arch=80 ^cuda@11.7.1
-        - raja +cuda cuda_arch=80 ^cuda@11.7.1
-        runner-attributes:
-          tags: [ "nvidia-515.65.01", "cuda-11.7", "a100" ]
-          variables:
-            CI_JOB_SIZE: large
-
       - match:
         - kokkos +cuda cuda_arch=80 ^cuda@12.0.0
         - raja +cuda cuda_arch=80 ^cuda@12.0.0

var/spack/repos/builtin/packages/gsl-lite/package.py

@@ -0,0 +1,50 @@
+# Copyright 2013-2023 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.package import *
+
+
+class GslLite(CMakePackage):
+    """A single-file header-only version of ISO C++ Guidelines Support Library
+    (GSL) for C++98, C++11, and later"""
+
+    homepage = "https://github.com/gsl-lite/gsl-lite"
+    git = "https://github.com/gsl-lite/gsl-lite.git"
+    url = "https://github.com/gsl-lite/gsl-lite/archive/refs/tags/v0.38.1.tar.gz"
+
+    maintainers("AlexanderRichert-NOAA", "climbfuji", "edwardhartnett", "Hang-Lei-NOAA")
+
+    version("0.40.0", commit="d6c8af99a1d95b3db36f26b4f22dc3bad89952de")
+    version("0.39.0", commit="d0903fa87ff579c30f608bc363582e6563570342")
+    version("0.38.1", sha256="c2fa2315fff312f3897958903ed4d4e027f73fa44235459ecb467ad7b7d62b18")
+    version("0.38.0", sha256="5d25fcd31ea66dac9e14da1cad501d95450ccfcb2768fffcd1a4170258fcbc81")
+    version("0.37.0", sha256="a31d51b73742bb234acab8d2411223cf299e760ed713f0840ffed0dabe57ca38")
+    version("0.36.0", sha256="c052cc4547b33cedee6f000393a7005915c45c6c06b35518d203db117f75c71c")
+    version("0.34.0", sha256="a7d5b2672b78704ca03df9ef65bc274d8f8cacad3ca950365eef9e25b50324c5")
+
+    variant("tests", default=False)
+    variant("cuda_tests", default=False)
+    variant("examples", default=False)
+    variant("static_analysis_demos", default=False)
+    variant("cmake_export_package_registry", default=False)
+    variant("compat_header", default=False)
+    variant("legacy_headers", default=False)
+
+    def cmake_args(self):
+        args = [
+            self.define_from_variant("GSL_LITE_OPT_BUILD_TESTS", "tests"),
+            self.define_from_variant("GSL_LITE_OPT_BUILD_CUDA_TESTS", "cuda_tests"),
+            self.define_from_variant("GSL_LITE_OPT_BUILD_EXAMPLES", "examples"),
+            self.define_from_variant(
+                "GSL_LITE_LOPT_BUILD_STATIC_ANALYSIS_DEMOS", "static_analysis_demos"
+            ),
+            self.define_from_variant(
+                "CMAKE_EXPORT_PACKAGE_REGISTRY", "cmake_export_package_registry"
+            ),
+            self.define_from_variant("GSL_LITE_OPT_INSTALL_COMPAT_HEADER", "compat_header"),
+            self.define_from_variant("GSL_LITE_OPT_INSTALL_LEGACY_HEADERS", "legacy_headers"),
+        ]
+        return args

var/spack/repos/builtin/packages/intel-tbb/package.py

@@ -255,7 +255,7 @@ def build(self, pkg, spec, prefix):
         #
         self.coerce_to_spack("build")
 
-        if spec.satisfies("%clang") or spec.satisfies("%apple-clang"):
+        if spec.satisfies("%clang") or spec.satisfies("%apple-clang") or spec.satisfies("%rocmcc"):
             tbb_compiler = "clang"
         elif spec.satisfies("%intel"):
             tbb_compiler = "icc"

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

@@ -16,6 +16,7 @@ class Libmonitor(AutotoolsPackage):
     maintainers("mwkrentel")
 
     version("master", branch="master")
+    version("2023.02.13", commit="6db182b25202552f75a087116ab57193652d150f")
     version("2022.09.02", commit="4ae16dab0ba5fbda0ffe28df523613ea22cb85ae")
     version("2021.11.08", commit="22aa52c621534f12d401fa37f6963bfca7441e20")
     version("2021.04.27", commit="a2d1b6be23410ef1ad2c9d0006672453803243c2")

var/spack/repos/builtin/packages/netcdf-fortran/nag_libtool_2.4.2.patch

@@ -1,124 +0,0 @@
---- a/configure
-+++ b/configure
-@@ -9584,6 +9584,10 @@ for cc_temp in $compiler""; do
-   esac
- done
- cc_basename=`$ECHO "$cc_temp" | $SED "s%.*/%%; s%^$host_alias-%%"`
-+case $cc_basename in
-+  nagfor*) ;;
-+  *) $cc_temp -V 2>&1 | $GREP '^NAG Fortran Compiler Release' >/dev/null 2>&1 && cc_basename='nagfor-wrapper' ;;
-+esac
- 
- 
- # Only perform the check for file, if the check method requires it
-@@ -10657,6 +10661,10 @@ _LT_EOF
- 	lf95*)				# Lahey Fortran 8.1
- 	  whole_archive_flag_spec=
- 	  tmp_sharedflag='--shared' ;;
-+	nagfor*)
-+	  whole_archive_flag_spec='${wl}--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` ${wl}--no-whole-archive'
-+	  compiler_needs_object=yes
-+	  tmp_sharedflag='-Wl,-shared' ;;
- 	xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
- 	  tmp_sharedflag='-qmkshrobj'
- 	  tmp_addflag= ;;
-@@ -13415,6 +13423,10 @@ $RM -r conftest*
-   esac
- done
- cc_basename=`$ECHO "$cc_temp" | $SED "s%.*/%%; s%^$host_alias-%%"`
-+case $cc_basename in
-+  nagfor*) ;;
-+  *) $cc_temp -V 2>&1 | $GREP '^NAG Fortran Compiler Release' >/dev/null 2>&1 && cc_basename='nagfor-wrapper' ;;
-+esac
- 
-   GCC=$G77
-   if test -n "$compiler"; then
-@@ -14252,6 +14264,10 @@ _LT_EOF
- 	lf95*)				# Lahey Fortran 8.1
- 	  whole_archive_flag_spec_F77=
- 	  tmp_sharedflag='--shared' ;;
-+	nagfor*)
-+	  whole_archive_flag_spec_F77='${wl}--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` ${wl}--no-whole-archive'
-+	  compiler_needs_object_F77=yes
-+	  tmp_sharedflag='-Wl,-shared' ;;
- 	xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
- 	  tmp_sharedflag='-qmkshrobj'
- 	  tmp_addflag= ;;
-@@ -16142,6 +16158,10 @@ $RM -r conftest*
-   esac
- done
- cc_basename=`$ECHO "$cc_temp" | $SED "s%.*/%%; s%^$host_alias-%%"`
-+case $cc_basename in
-+  nagfor*) ;;
-+  *) $cc_temp -V 2>&1 | $GREP '^NAG Fortran Compiler Release' >/dev/null 2>&1 && cc_basename='nagfor-wrapper' ;;
-+esac
- 
- 
-   if test -n "$compiler"; then
-@@ -17142,6 +17162,10 @@ _LT_EOF
- 	lf95*)				# Lahey Fortran 8.1
- 	  whole_archive_flag_spec_FC=
- 	  tmp_sharedflag='--shared' ;;
-+	nagfor*)
-+	  whole_archive_flag_spec_FC='${wl}--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` ${wl}--no-whole-archive'
-+	  compiler_needs_object_FC=yes
-+	  tmp_sharedflag='-Wl,-shared' ;;
- 	xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
- 	  tmp_sharedflag='-qmkshrobj'
- 	  tmp_addflag= ;;
---- a/ltmain.sh
-+++ b/ltmain.sh
-@@ -180,6 +180,24 @@ func_basename ()
-     func_basename_result=`$ECHO "${1}" | $SED "$basename"`
- } # func_basename may be replaced by extended shell implementation
- 
-+# Calculate cc_basename.  Skip known compiler wrappers and cross-prefix.
-+func_cc_basename ()
-+{
-+    for cc_temp in $*""; do
-+      case $cc_temp in
-+        compile | *[\\/]compile | ccache | *[\\/]ccache ) ;;
-+        distcc | *[\\/]distcc | purify | *[\\/]purify ) ;;
-+        \-*) ;;
-+        *) break;;
-+      esac
-+    done
-+    func_cc_basename_result=`$ECHO "$cc_temp" | $SED "s%.*/%%; s%^$host_alias-%%"`
-+    case $func_cc_basename_result in
-+      nagfor*) ;;
-+      *) $cc_temp -V 2>&1 | $GREP '^NAG Fortran Compiler Release' >/dev/null 2>&1 && func_cc_basename_result='nagfor-wrapper' ;;
-+    esac
-+}
-+
- 
- # func_dirname_and_basename file append nondir_replacement
- # perform func_basename and func_dirname in a single function
-@@ -6422,6 +6440,13 @@ func_mode_link ()
- 	# Convert "-framework foo" to "foo.ltframework"
- 	if test -n "$inherited_linker_flags"; then
- 	  tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g'`
-+
-+	  # Additionally convert " -pthread" to " -Wl,-pthread" for nagfor
-+	  func_cc_basename $CC
-+	  case $func_cc_basename_result in
-+	    nagfor*) tmp_inherited_linker_flags=`$ECHO "$tmp_inherited_linker_flags" | $SED 's/ -pthread/ -Wl,-pthread/g'` ;;
-+	  esac
-+
- 	  for tmp_inherited_linker_flag in $tmp_inherited_linker_flags; do
- 	    case " $new_inherited_linker_flags " in
- 	      *" $tmp_inherited_linker_flag "*) ;;
-@@ -8007,6 +8032,14 @@ EOF
- 	  ;;
-       esac
- 
-+      # Time to revert the changes made for nagfor.
-+
-+      func_cc_basename $CC
-+      case $func_cc_basename_result in
-+        nagfor*)
-+          new_inherited_linker_flags=`$ECHO " $new_inherited_linker_flags" | $SED 's% -Wl,-pthread% -pthread%g'` ;;
-+      esac
-+
-       # move library search paths that coincide with paths to not yet
-       # installed libraries to the beginning of the library search list
-       new_libs=

var/spack/repos/builtin/packages/netcdf-fortran/nag_libtool_2.4.6.patch

@@ -1,96 +0,0 @@
---- a/configure
-+++ b/configure
-@@ -9034,6 +9034,12 @@ func_cc_basename ()
-       esac
-     done
-     func_cc_basename_result=`$ECHO "$cc_temp" | $SED "s%.*/%%; s%^$host_alias-%%"`
-+
-+    # Set result to 'nagfor-wrapper' when NAG compiler is called via a wrapper (e.g. mpif90).
-+    case $func_cc_basename_result in
-+      nagfor*) ;;
-+      *) $cc_temp -V 2>&1 | $GREP '^NAG Fortran Compiler Release' >/dev/null 2>&1 && func_cc_basename_result='nagfor-wrapper' ;;
-+    esac
- }
- 
- # Check whether --enable-libtool-lock was given.
-@@ -11811,6 +11817,8 @@ _LT_EOF
- 	  whole_archive_flag_spec=
- 	  tmp_sharedflag='--shared' ;;
-         nagfor*)                        # NAGFOR 5.3
-+          whole_archive_flag_spec='$wl--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive'
-+          compiler_needs_object=yes
-           tmp_sharedflag='-Wl,-shared' ;;
- 	xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
- 	  tmp_sharedflag='-qmkshrobj'
-@@ -15663,6 +15671,8 @@ _LT_EOF
- 	  whole_archive_flag_spec_F77=
- 	  tmp_sharedflag='--shared' ;;
-         nagfor*)                        # NAGFOR 5.3
-+          whole_archive_flag_spec_F77='$wl--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive'
-+          compiler_needs_object_F77=yes
-           tmp_sharedflag='-Wl,-shared' ;;
- 	xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
- 	  tmp_sharedflag='-qmkshrobj'
-@@ -18788,6 +18798,8 @@ _LT_EOF
- 	  whole_archive_flag_spec_FC=
- 	  tmp_sharedflag='--shared' ;;
-         nagfor*)                        # NAGFOR 5.3
-+          whole_archive_flag_spec_FC='$wl--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive'
-+          compiler_needs_object_FC=yes
-           tmp_sharedflag='-Wl,-shared' ;;
- 	xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
- 	  tmp_sharedflag='-qmkshrobj'
-@@ -26086,6 +26098,12 @@ func_cc_basename ()
-       esac
-     done
-     func_cc_basename_result=`$ECHO "$cc_temp" | $SED "s%.*/%%; s%^$host_alias-%%"`
-+
-+    # Set result to 'nagfor-wrapper' when NAG compiler is called via a wrapper (e.g. mpif90).
-+    case $func_cc_basename_result in
-+      nagfor*) ;;
-+      *) $cc_temp -V 2>&1 | $GREP '^NAG Fortran Compiler Release' >/dev/null 2>&1 && func_cc_basename_result='nagfor-wrapper' ;;
-+    esac
- }
- 
- 
---- a/ltmain.sh
-+++ b/ltmain.sh
-@@ -7868,6 +7868,13 @@ func_mode_link ()
- 	# Convert "-framework foo" to "foo.ltframework"
- 	if test -n "$inherited_linker_flags"; then
- 	  tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g'`
-+
-+	  # Additionally convert " -pthread" to " -Wl,-pthread" for nagfor
-+	  func_cc_basename $CC
-+	  case $func_cc_basename_result in
-+	    nagfor*) tmp_inherited_linker_flags=`$ECHO "$tmp_inherited_linker_flags" | $SED 's/ -pthread/ -Wl,-pthread/g'` ;;
-+	  esac
-+
- 	  for tmp_inherited_linker_flag in $tmp_inherited_linker_flags; do
- 	    case " $new_inherited_linker_flags " in
- 	      *" $tmp_inherited_linker_flag "*) ;;
-@@ -8890,7 +8897,8 @@ func_mode_link ()
- 	  xlcverstring="$wl-compatibility_version $wl$minor_current $wl-current_version $wl$minor_current.$revision"
- 	  verstring="-compatibility_version $minor_current -current_version $minor_current.$revision"
-           # On Darwin other compilers
--          case $CC in
-+          func_cc_basename $CC
-+          case $func_cc_basename_result in
-               nagfor*)
-                   verstring="$wl-compatibility_version $wl$minor_current $wl-current_version $wl$minor_current.$revision"
-                   ;;
-@@ -9502,6 +9510,14 @@ EOF
- 	  ;;
-       esac
- 
-+      # Time to revert the changes made for nagfor.
-+
-+      func_cc_basename $CC
-+      case $func_cc_basename_result in
-+        nagfor*)
-+          new_inherited_linker_flags=`$ECHO " $new_inherited_linker_flags" | $SED 's% -Wl,-pthread% -pthread%g'` ;;
-+      esac
-+
-       # move library search paths that coincide with paths to not yet
-       # installed libraries to the beginning of the library search list
-       new_libs=

var/spack/repos/builtin/packages/netcdf-fortran/package.py

@@ -37,14 +37,6 @@ class NetcdfFortran(AutotoolsPackage):
     depends_on("netcdf-c@4.7.4:", when="@4.5.3:")  # nc_def_var_szip required
     depends_on("doxygen", when="+doc", type="build")
 
-    # The default libtool.m4 is too old to handle NAG compiler properly:
-    # https://github.com/Unidata/netcdf-fortran/issues/94
-    # Moreover, Libtool can't handle '-pthread' flag coming from libcurl,
-    # doesn't inject convenience libraries into the shared ones, and is unable
-    # to detect NAG when it is called with an MPI wrapper.
-    patch("nag_libtool_2.4.2.patch", when="@:4.4.4%nag")
-    patch("nag_libtool_2.4.6.patch", when="@4.4.5:%nag")
-
     # Enable 'make check' for NAG, which is too strict.
     patch("nag_testing.patch", when="@4.4.5%nag")
 
@@ -136,54 +128,6 @@ def configure_args(self):
 
         return config_args
 
-    @run_after("configure")
-    def patch_libtool(self):
-        """AOCC support for NETCDF-F"""
-        if "%aocc" in self.spec:
-            # Libtool does not fully support the compiler toolchain, therefore
-            # we have to patch the script. The C compiler normally gets
-            # configured correctly, the variables of interest in the
-            # 'BEGIN LIBTOOL CONFIG' section are set to non-empty values and,
-            # therefore, are not affected by the replacements below. A more
-            # robust solution would be to extend the filter_file function with
-            # an additional argument start_at and perform the replacements
-            # between the '# ### BEGIN LIBTOOL TAG CONFIG: FC' and
-            # '# ### END LIBTOOL TAG CONFIG: FC' markers for the Fortran
-            # compiler, and between the '# ### BEGIN LIBTOOL TAG CONFIG: F77'
-            # and '# ### END LIBTOOL TAG CONFIG: F77' markers for the Fortran 77
-            # compiler.
-
-            # How to pass a linker flag through the compiler:
-            filter_file(r'^wl=""$', 'wl="{0}"'.format(self.compiler.linker_arg), "libtool")
-
-            # Additional compiler flags for building library objects (we need
-            # this to enable shared libraries when building with ~pic). Note
-            # that the following will set fc_pic_flag for both FC and F77, which
-            # in the case of AOCC, should not be a problem. If it is, the
-            # aforementioned modification of the filter_file function could be
-            # a solution.
-            filter_file(
-                r'^pic_flag=""$', 'pic_flag=" {0}"'.format(self.compiler.fc_pic_flag), "libtool"
-            )
-
-            # The following is supposed to tell the compiler to use the GNU
-            # linker. However, the replacement does not happen (at least for
-            # NetCDF-Fortran 4.5.3) because the replaced substring (i.e. the
-            # first argument passed to the filter_file function) is not present
-            # in the file. The flag should probably be added to 'ldflags' in the
-            # flag_handler method above (another option is to add the flag to
-            # 'ldflags' in compilers.yaml automatically as it was done for other
-            # flags in https://github.com/spack/spack/pull/22219).
-            filter_file(
-                r"\${wl}-soname \$wl\$soname",
-                r"-fuse-ld=ld -Wl,-soname,\$soname",
-                "libtool",
-                string=True,
-            )
-
-        # TODO: resolve the NAG-related issues in a similar way: remove the
-        #  respective patch files and tune the generated libtool script instead.
-
     @when("@:4.4.5")
     def check(self):
         with working_dir(self.build_directory):

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

@@ -89,7 +89,7 @@ class Octave(AutotoolsPackage, GNUMirrorPackage):
     # Optional dependencies
     depends_on("arpack-ng", when="+arpack")
     depends_on("curl", when="+curl")
-    depends_on("fftw", when="+fftw")
+    depends_on("fftw-api@3", when="+fftw")
     depends_on("fltk", when="+fltk")
     depends_on("fontconfig", when="+fontconfig")
     depends_on("freetype", when="+freetype")
@@ -222,12 +222,13 @@ def configure_args(self):
             config_args.append("--without-curl")
 
         if "+fftw" in spec:
+            fftw_string = "fftw-api"
             config_args.extend(
                 [
-                    "--with-fftw3-includedir=%s" % spec["fftw"].prefix.include,
-                    "--with-fftw3-libdir=%s" % spec["fftw"].prefix.lib,
-                    "--with-fftw3f-includedir=%s" % spec["fftw"].prefix.include,
-                    "--with-fftw3f-libdir=%s" % spec["fftw"].prefix.lib,
+                    "--with-fftw3-includedir=%s" % spec[fftw_string].prefix.include,
+                    "--with-fftw3-libdir=%s" % spec[fftw_string].prefix.lib,
+                    "--with-fftw3f-includedir=%s" % spec[fftw_string].prefix.include,
+                    "--with-fftw3f-libdir=%s" % spec[fftw_string].prefix.lib,
                 ]
             )
         else:

var/spack/repos/builtin/packages/openmpi/nag_pthread/1.10.4_1.10.999.patch

@@ -1,49 +0,0 @@
---- a/config/ltmain.sh
-+++ b/config/ltmain.sh
-@@ -7860,14 +7860,15 @@ func_mode_link ()
- 	func_source "$lib"
- 
- 	# Convert "-framework foo" to "foo.ltframework"
--        # and "-pthread" to "-Wl,-pthread" if NAG compiler
- 	if test -n "$inherited_linker_flags"; then
--          case "$CC" in
--            nagfor*)
--	      tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g' | $SED 's/-pthread/-Wl,-pthread'`;;
--            *)
--	      tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g'`;;
--          esac
-+	  tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g'`
-+
-+	  # Additionally convert " -pthread" to " -Wl,-pthread" for nagfor
-+	  func_cc_basename $CC
-+	  case $func_cc_basename_result in
-+	    nagfor*) tmp_inherited_linker_flags=`$ECHO "$tmp_inherited_linker_flags" | $SED 's/ -pthread/ -Wl,-pthread/g'` ;;
-+	  esac
-+
- 	  for tmp_inherited_linker_flag in $tmp_inherited_linker_flags; do
- 	    case " $new_inherited_linker_flags " in
- 	      *" $tmp_inherited_linker_flag "*) ;;
-@@ -8887,7 +8888,8 @@ func_mode_link ()
- 	  xlcverstring="$wl-compatibility_version $wl$minor_current $wl-current_version $wl$minor_current.$revision"
- 	  verstring="-compatibility_version $minor_current -current_version $minor_current.$revision"
-           # On Darwin other compilers
--          case $CC in
-+          func_cc_basename $CC
-+          case $func_cc_basename_result in
-               nagfor*)
-                   verstring="$wl-compatibility_version $wl$minor_current $wl-current_version $wl$minor_current.$revision"
-                   ;;
-@@ -9499,6 +9501,13 @@ EOF
- 	  ;;
-       esac
- 
-+      # Time to revert the changes made for nagfor.
-+      func_cc_basename $CC
-+      case $func_cc_basename_result in
-+        nagfor*)
-+          new_inherited_linker_flags=`$ECHO " $new_inherited_linker_flags" | $SED 's% -Wl,-pthread% -pthread%g'` ;;
-+      esac
-+
-       # move library search paths that coincide with paths to not yet
-       # installed libraries to the beginning of the library search list
-       new_libs=

var/spack/repos/builtin/packages/openmpi/nag_pthread/2.0.0_2.1.1.patch

@@ -1,40 +0,0 @@
---- a/config/ltmain.sh
-+++ b/config/ltmain.sh
-@@ -7862,6 +7862,13 @@ func_mode_link ()
- 	# Convert "-framework foo" to "foo.ltframework"
- 	if test -n "$inherited_linker_flags"; then
- 	  tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g'`
-+
-+	  # Additionally convert " -pthread" to " -Wl,-pthread" for nagfor
-+	  func_cc_basename $CC
-+	  case $func_cc_basename_result in
-+	    nagfor*) tmp_inherited_linker_flags=`$ECHO "$tmp_inherited_linker_flags" | $SED 's/ -pthread/ -Wl,-pthread/g'` ;;
-+	  esac
-+
- 	  for tmp_inherited_linker_flag in $tmp_inherited_linker_flags; do
- 	    case " $new_inherited_linker_flags " in
- 	      *" $tmp_inherited_linker_flag "*) ;;
-@@ -8881,7 +8888,8 @@ func_mode_link ()
- 	  xlcverstring="$wl-compatibility_version $wl$minor_current $wl-current_version $wl$minor_current.$revision"
- 	  verstring="-compatibility_version $minor_current -current_version $minor_current.$revision"
-           # On Darwin other compilers
--          case $CC in
-+          func_cc_basename $CC
-+          case $func_cc_basename_result in
-               nagfor*)
-                   verstring="$wl-compatibility_version $wl$minor_current $wl-current_version $wl$minor_current.$revision"
-                   ;;
-@@ -9493,6 +9501,13 @@ EOF
- 	  ;;
-       esac
- 
-+      # Time to revert the changes made for nagfor.
-+      func_cc_basename $CC
-+      case $func_cc_basename_result in
-+        nagfor*)
-+          new_inherited_linker_flags=`$ECHO " $new_inherited_linker_flags" | $SED 's% -Wl,-pthread% -pthread%g'` ;;
-+      esac
-+
-       # move library search paths that coincide with paths to not yet
-       # installed libraries to the beginning of the library search list
-       new_libs=

var/spack/repos/builtin/packages/openmpi/nag_pthread/2.1.2_2.1.3_3.0.0.patch

@@ -1,49 +0,0 @@
---- a/config/ltmain.sh
-+++ b/config/ltmain.sh
-@@ -7860,14 +7860,15 @@ func_mode_link ()
- 	func_source "$lib"
- 
- 	# Convert "-framework foo" to "foo.ltframework"
--        # and "-pthread" to "-Wl,-pthread" if NAG compiler
- 	if test -n "$inherited_linker_flags"; then
--          case "$CC" in
--            nagfor*)
--	      tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g' | $SED 's/-pthread/-Wl,-pthread/g'`;;
--            *)
--	      tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g'`;;
--          esac
-+	  tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g'`
-+
-+	  # Additionally convert " -pthread" to " -Wl,-pthread" for nagfor
-+	  func_cc_basename $CC
-+	  case $func_cc_basename_result in
-+	    nagfor*) tmp_inherited_linker_flags=`$ECHO "$tmp_inherited_linker_flags" | $SED 's/ -pthread/ -Wl,-pthread/g'` ;;
-+	  esac
-+
- 	  for tmp_inherited_linker_flag in $tmp_inherited_linker_flags; do
- 	    case " $new_inherited_linker_flags " in
- 	      *" $tmp_inherited_linker_flag "*) ;;
-@@ -8887,7 +8888,8 @@ func_mode_link ()
- 	  xlcverstring="$wl-compatibility_version $wl$minor_current $wl-current_version $wl$minor_current.$revision"
- 	  verstring="-compatibility_version $minor_current -current_version $minor_current.$revision"
-           # On Darwin other compilers
--          case $CC in
-+          func_cc_basename $CC
-+          case $func_cc_basename_result in
-               nagfor*)
-                   verstring="$wl-compatibility_version $wl$minor_current $wl-current_version $wl$minor_current.$revision"
-                   ;;
-@@ -9499,6 +9501,13 @@ EOF
- 	  ;;
-       esac
- 
-+      # Time to revert the changes made for nagfor.
-+      func_cc_basename $CC
-+      case $func_cc_basename_result in
-+        nagfor*)
-+          new_inherited_linker_flags=`$ECHO " $new_inherited_linker_flags" | $SED 's% -Wl,-pthread% -pthread%g'` ;;
-+      esac
-+
-       # move library search paths that coincide with paths to not yet
-       # installed libraries to the beginning of the library search list
-       new_libs=

var/spack/repos/builtin/packages/openmpi/nag_pthread/2.1.4_2.1.999_3.0.1_4.patch

@@ -1,49 +0,0 @@
---- a/config/ltmain.sh
-+++ b/config/ltmain.sh
-@@ -7860,14 +7860,15 @@ func_mode_link ()
- 	func_source "$lib"
- 
- 	# Convert "-framework foo" to "foo.ltframework"
--        # and "-pthread" to "-Wl,-pthread" if NAG compiler
- 	if test -n "$inherited_linker_flags"; then
--          case "$CC" in
--            *nagfor*)
--	      tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g' | $SED 's/-pthread/-Wl,-pthread/g'`;;
--            *)
--	      tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g'`;;
--          esac
-+	  tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g'`
-+
-+	  # Additionally convert " -pthread" to " -Wl,-pthread" for nagfor
-+	  func_cc_basename $CC
-+	  case $func_cc_basename_result in
-+	    nagfor*) tmp_inherited_linker_flags=`$ECHO "$tmp_inherited_linker_flags" | $SED 's/ -pthread/ -Wl,-pthread/g'` ;;
-+	  esac
-+
- 	  for tmp_inherited_linker_flag in $tmp_inherited_linker_flags; do
- 	    case " $new_inherited_linker_flags " in
- 	      *" $tmp_inherited_linker_flag "*) ;;
-@@ -8887,7 +8888,8 @@ func_mode_link ()
- 	  xlcverstring="$wl-compatibility_version $wl$minor_current $wl-current_version $wl$minor_current.$revision"
- 	  verstring="-compatibility_version $minor_current -current_version $minor_current.$revision"
-           # On Darwin other compilers
--          case $CC in
-+          func_cc_basename $CC
-+          case $func_cc_basename_result in
-               nagfor*)
-                   verstring="$wl-compatibility_version $wl$minor_current $wl-current_version $wl$minor_current.$revision"
-                   ;;
-@@ -9499,6 +9501,13 @@ EOF
- 	  ;;
-       esac
- 
-+      # Time to revert the changes made for nagfor.
-+      func_cc_basename $CC
-+      case $func_cc_basename_result in
-+        nagfor*)
-+          new_inherited_linker_flags=`$ECHO " $new_inherited_linker_flags" | $SED 's% -Wl,-pthread% -pthread%g'` ;;
-+      esac
-+
-       # move library search paths that coincide with paths to not yet
-       # installed libraries to the beginning of the library search list
-       new_libs=

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

@@ -382,14 +382,6 @@ class Openmpi(AutotoolsPackage, CudaPackage):
     patch("btl_vader.patch", when="@3.0.1:3.0.2")
     patch("btl_vader.patch", when="@3.1.0:3.1.2")
 
-    # Make NAG compiler pass the -pthread option to the linker:
-    # https://github.com/open-mpi/ompi/pull/6378
-    # We support only versions based on Libtool 2.4.6.
-    patch("nag_pthread/2.1.4_2.1.999_3.0.1_4.patch", when="@2.1.4:2.1,3.0.1:4%nag")
-    patch("nag_pthread/2.1.2_2.1.3_3.0.0.patch", when="@2.1.2:2.1.3,3.0.0%nag")
-    patch("nag_pthread/2.0.0_2.1.1.patch", when="@2.0.0:2.1.1%nag")
-    patch("nag_pthread/1.10.4_1.10.999.patch", when="@1.10.4:1.10%nag")
-
     # Fix MPI_Sizeof() in the "mpi" Fortran module for compilers that do not
     # support "IGNORE TKR" functionality (e.g. NAG).
     # The issue has been resolved upstream in two steps:

var/spack/repos/builtin/packages/parallel-netcdf/cray_pgi_libtool_master.patch

@@ -1,10 +0,0 @@
---- a/m4/libtool.m4
-+++ b/m4/libtool.m4
-@@ -5282,7 +5282,6 @@ _LT_EOF
- 	tmp_sharedflag='-shared'
- 	case $cc_basename,$host_cpu in
-         pgcc*)				# Portland Group C compiler
--	  _LT_TAGVAR(whole_archive_flag_spec, $1)='$wl--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive'
- 	  tmp_addflag=' $pic_flag'
- 	  ;;
- 	pgf77* | pgf90* | pgf95* | pgfortran*)

var/spack/repos/builtin/packages/parallel-netcdf/cray_pgi_libtool_release.patch

@@ -1,26 +0,0 @@
---- a/configure
-+++ b/configure
-@@ -11858,7 +11858,6 @@ _LT_EOF
- 	tmp_sharedflag='-shared'
- 	case $cc_basename,$host_cpu in
-         pgcc*)				# Portland Group C compiler
--	  whole_archive_flag_spec='$wl--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive'
- 	  tmp_addflag=' $pic_flag'
- 	  ;;
- 	pgf77* | pgf90* | pgf95* | pgfortran*)
-@@ -21326,7 +21325,6 @@ _LT_EOF
- 	tmp_sharedflag='-shared'
- 	case $cc_basename,$host_cpu in
-         pgcc*)				# Portland Group C compiler
--	  whole_archive_flag_spec_F77='$wl--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive'
- 	  tmp_addflag=' $pic_flag'
- 	  ;;
- 	pgf77* | pgf90* | pgf95* | pgfortran*)
-@@ -25066,7 +25064,6 @@ _LT_EOF
- 	tmp_sharedflag='-shared'
- 	case $cc_basename,$host_cpu in
-         pgcc*)				# Portland Group C compiler
--	  whole_archive_flag_spec_FC='$wl--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive'
- 	  tmp_addflag=' $pic_flag'
- 	  ;;
- 	pgf77* | pgf90* | pgf95* | pgfortran*)

var/spack/repos/builtin/packages/parallel-netcdf/nag_libtool.patch

@@ -1,69 +0,0 @@
---- a/configure
-+++ b/configure
-@@ -11745,6 +11745,8 @@ _LT_EOF
- 	  whole_archive_flag_spec=
- 	  tmp_sharedflag='--shared' ;;
-         nagfor*)                        # NAGFOR 5.3
-+          whole_archive_flag_spec='$wl--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive'
-+          compiler_needs_object=yes
-           tmp_sharedflag='-Wl,-shared' ;;
- 	xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
- 	  tmp_sharedflag='-qmkshrobj'
-@@ -21030,6 +21032,8 @@ _LT_EOF
- 	  whole_archive_flag_spec_F77=
- 	  tmp_sharedflag='--shared' ;;
-         nagfor*)                        # NAGFOR 5.3
-+          whole_archive_flag_spec_F77='$wl--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive'
-+          compiler_needs_object_F77=yes
-           tmp_sharedflag='-Wl,-shared' ;;
- 	xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
- 	  tmp_sharedflag='-qmkshrobj'
-@@ -24765,6 +24769,8 @@ _LT_EOF
- 	  whole_archive_flag_spec_FC=
- 	  tmp_sharedflag='--shared' ;;
-         nagfor*)                        # NAGFOR 5.3
-+          whole_archive_flag_spec_FC='$wl--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive'
-+          compiler_needs_object_FC=yes
-           tmp_sharedflag='-Wl,-shared' ;;
- 	xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
- 	  tmp_sharedflag='-qmkshrobj'
---- a/scripts/ltmain.sh
-+++ b/scripts/ltmain.sh
-@@ -7862,6 +7862,13 @@ func_mode_link ()
- 	# Convert "-framework foo" to "foo.ltframework"
- 	if test -n "$inherited_linker_flags"; then
- 	  tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g'`
-+
-+	  # Additionally convert " -pthread" to " -Wl,-pthread" for nagfor
-+	  func_cc_basename $CC
-+	  case $func_cc_basename_result in
-+	    nagfor*) tmp_inherited_linker_flags=`$ECHO "$tmp_inherited_linker_flags" | $SED 's/ -pthread/ -Wl,-pthread/g'` ;;
-+	  esac
-+
- 	  for tmp_inherited_linker_flag in $tmp_inherited_linker_flags; do
- 	    case " $new_inherited_linker_flags " in
- 	      *" $tmp_inherited_linker_flag "*) ;;
-@@ -8881,7 +8888,8 @@ func_mode_link ()
- 	  xlcverstring="$wl-compatibility_version $wl$minor_current $wl-current_version $wl$minor_current.$revision"
- 	  verstring="-compatibility_version $minor_current -current_version $minor_current.$revision"
-           # On Darwin other compilers
--          case $CC in
-+          func_cc_basename $CC
-+          case $func_cc_basename_result in
-               nagfor*)
-                   verstring="$wl-compatibility_version $wl$minor_current $wl-current_version $wl$minor_current.$revision"
-                   ;;
-@@ -9493,6 +9501,13 @@ EOF
- 	  ;;
-       esac
- 
-+      # Time to revert the changes made for nagfor.
-+      func_cc_basename $CC
-+      case $func_cc_basename_result in
-+        nagfor*)
-+          new_inherited_linker_flags=`$ECHO " $new_inherited_linker_flags" | $SED 's% -Wl,-pthread% -pthread%g'` ;;
-+      esac
-+
-       # move library search paths that coincide with paths to not yet
-       # installed libraries to the beginning of the library search list
-       new_libs=

var/spack/repos/builtin/packages/parallel-netcdf/package.py

@@ -79,23 +79,6 @@ def url_for_version(self, version):
     # (see below).
     conflicts("+shared", when="@:1.9%nag+fortran")
 
-    # https://github.com/Parallel-NetCDF/PnetCDF/pull/59
-    patch("nag_libtool.patch", when="@1.9:1.12.1%nag")
-
-    # We could apply the patch unconditionally. However, it fixes a problem
-    # that manifests itself only when we build shared libraries with Spack on
-    # a Cray system with PGI compiler. Based on the name of the $CC executable,
-    # Libtool "thinks" that it works with PGI compiler directly but on a Cray
-    # system it actually works with the Cray's wrapper. PGI compiler (at least
-    # since the version 15.7) "understands" two formats of the
-    # '--whole-archive' argument. Unluckily, Cray's wrapper "understands" only
-    # one of them but Libtool switches to another one. The following patch
-    # discards the switching.
-    patch("cray_pgi_libtool_release.patch", when="@1.8:999%pgi+shared platform=cray")
-    # Given that the bug manifests itself in rather specific conditions, it is
-    # not reported upstream.
-    patch("cray_pgi_libtool_master.patch", when="@master%pgi+shared platform=cray")
-
     @property
     def libs(self):
         libraries = ["libpnetcdf"]

var/spack/repos/builtin/packages/py-fortls/package.py

@@ -0,0 +1,26 @@
+# Copyright 2013-2023 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.package import *
+
+
+class PyFortls(PythonPackage):
+    """A Language Server for Fortran providing code completion, diagnostics, hovering and more."""
+
+    homepage = "https://fortls.fortran-lang.org"
+    pypi = "fortls/fortls-2.13.0.tar.gz"
+
+    maintainers("RMeli")
+
+    version("2.13.0", sha256="23c5013e8dd8e1d65bf07be610d0827bc48aa7331a7a7ce13612d4c646d0db31")
+
+    depends_on("py-setuptools@45:", type="build")
+    depends_on("py-packaging", type=("build", "run"))
+    depends_on("py-setuptools-scm@6.2:+toml", type="build")
+    depends_on("py-setuptools-scm-git-archive", type="build")
+
+    depends_on("py-json5", type=("build", "run"))
+    depends_on("py-importlib-metadata", type=("build", "run"), when="^python@:3.7")
+    depends_on("py-typing-extensions", type=("build", "run"), when="^python@:3.7")

var/spack/repos/builtin/packages/py-matplotlib/package.py

@@ -37,6 +37,7 @@ class PyMatplotlib(PythonPackage):
         "pylab",
     ]
 
+    version("3.7.0", sha256="8f6efd313430d7ef70a38a3276281cb2e8646b3a22b3b21eb227da20e15e6813")
     version("3.6.3", sha256="1f4d69707b1677560cd952544ee4962f68ff07952fb9069ff8c12b56353cb8c9")
     version("3.6.2", sha256="b03fd10a1709d0101c054883b550f7c4c5e974f751e2680318759af005964990")
     version("3.6.1", sha256="e2d1b7225666f7e1bcc94c0bc9c587a82e3e8691da4757e357e5c2515222ee37")
@@ -138,16 +139,12 @@ class PyMatplotlib(PythonPackage):
     # https://matplotlib.org/stable/devel/dependencies.html
     # Runtime dependencies
     # Mandatory dependencies
-    extends("python", ignore=r"bin/nosetests.*$|bin/pbr$")
     depends_on("python@3.8:", when="@3.6:", type=("build", "link", "run"))
-    depends_on("python@3.7:", when="@3.4:", type=("build", "link", "run"))
-    depends_on("python@3.6:", when="@3.1:", type=("build", "link", "run"))
-    depends_on("python@3.5:", when="@3:", type=("build", "link", "run"))
-    depends_on("python@2.7:2.8,3.4:", when="@:2", type=("build", "link", "run"))
     depends_on("py-contourpy@1.0.1:", when="@3.6:", type=("build", "run"))
     depends_on("py-cycler@0.10:", type=("build", "run"))
     depends_on("py-fonttools@4.22:", when="@3.5:", type=("build", "run"))
     depends_on("py-kiwisolver@1.0.1:", type=("build", "run"), when="@2.2.0:")
+    depends_on("py-numpy@1.20:", when="@3.7:", type=("build", "run"))
     depends_on("py-numpy@1.19:", when="@3.6:", type=("build", "run"))
     depends_on("py-numpy@1.17:", when="@3.5:", type=("build", "run"))
     depends_on("py-numpy@1.16:", when="@3.4:", type=("build", "run"))
@@ -156,11 +153,13 @@ class PyMatplotlib(PythonPackage):
     depends_on("py-packaging@20:", when="@3.6:", type=("build", "run"))
     depends_on("py-packaging", when="@3.5:", type=("build", "run"))
     depends_on("pil@6.2:", when="@3.3:", type=("build", "run"))
+    depends_on("py-pyparsing@2.3.1:", when="@3.7:", type=("build", "run"))
     depends_on("py-pyparsing@2.2.1:", when="@3.4:", type=("build", "run"))
     depends_on("py-pyparsing@2.0.3,2.0.5:2.1.1,2.1.3:2.1.5,2.1.7:", type=("build", "run"))
     depends_on("py-python-dateutil@2.7:", when="@3.4:", type=("build", "run"))
     depends_on("py-python-dateutil@2.1:", type=("build", "run"))
     depends_on("py-setuptools", type=("build", "run"))
+    depends_on("py-importlib-resources@3.2:", when="@3.7: ^python@:3.9", type=("build", "run"))
 
     # Historical dependencies
     depends_on("py-pytz", type=("build", "run"), when="@:2")
@@ -225,6 +224,7 @@ class PyMatplotlib(PythonPackage):
     # Dependencies for building matplotlib
     # Setup dependencies
     depends_on("py-certifi@2020.6.20:", when="@3.3.1:", type="build")
+    depends_on("py-pybind11@2.6:", when="@3.7:", type="build")
     depends_on("py-setuptools-scm@7:", when="@3.6:", type="build")
     depends_on("py-setuptools-scm@4:6", when="@3.5", type="build")
     depends_on("py-setuptools-scm-git-archive", when="@3.5", type="build")

var/spack/repos/builtin/packages/py-radiant-mlhub/package.py

@@ -14,6 +14,8 @@ class PyRadiantMlhub(PythonPackage):
 
     maintainers("adamjstewart")
 
+    version("0.5.5", sha256="93cabc3c8e9ba343cdb3b0bfaec01bf7a36aae75704fabfe96c8bf5cab9fa899")
+    version("0.5.3", sha256="f111983910e41f2ce40bf401ccf9e33b393e52cc1989f8f8b74c6b4e2bdd0127")
     version("0.5.2", sha256="d310afce962508a44c60f5738fef164c50e78f76c3e85813653824b39a189ca3")
     version("0.5.1", sha256="b7daff4a127e96e27c64eda66e393d9727e61a87c887f86738753486cc44fa46")
     version("0.5.0", sha256="fff788aaa5f8afcb0f6eabff4147eaaf7de375f0a43ecaf2238033fc3a62e2c2")
@@ -23,10 +25,9 @@ class PyRadiantMlhub(PythonPackage):
     version("0.3.0", sha256="dd66479f12317e7bf366abe8d692841485e9497918c30ab14cd6db9e69ce3dbb")
     version("0.2.2", sha256="0d9f634b7e29c7f7294b81a10cf712ac63251949a9c5a07aa6c64c0d5b77e1ba")
     version("0.2.1", sha256="75a2f096b09a87191238fe557dc64dda8c44156351b4026c784c848c7d84b6fb")
+    version("0.2.0", sha256="4a3e4c301c5e74f282bbf77b7d65db5a1d6c2a4dc6d18637eff6e1228ca2eb9d")
 
     depends_on("python@3.8:", when="@0.5:", type=("build", "run"))
-    depends_on("python@3.7:", when="@0.3:", type=("build", "run"))
-    depends_on("python@3.6:", type=("build", "run"))
     depends_on("py-setuptools", type="build")
     depends_on("py-click@7.1.2:8", when="@0.3:", type=("build", "run"))
     depends_on("py-click@7.1.2:7.1", when="@:0.2", type=("build", "run"))
@@ -48,4 +49,7 @@ class PyRadiantMlhub(PythonPackage):
     depends_on("py-tqdm@4.64:4", when="@0.5.0:0.5.1", type=("build", "run"))
     depends_on("py-tqdm@4.56:4", when="@0.3:0.4", type=("build", "run"))
     depends_on("py-tqdm@4.56", when="@:0.2", type=("build", "run"))
+    depends_on("py-urllib3@1.26.11:1.26", when="@0.5.5:", type=("build", "run"))
+
+    # Historical dependencies
     depends_on("py-typing-extensions@3.7:", when="@0.4.1:0.4 ^python@:3.7", type=("build", "run"))

var/spack/repos/builtin/packages/py-rasterio/package.py

@@ -20,6 +20,7 @@ class PyRasterio(PythonPackage):
     maintainers("adamjstewart")
 
     version("master", branch="master")
+    version("1.3.6", sha256="c8b90eb10e16102d1ab0334a7436185f295de1c07f0d197e206d1c005fc33905")
     version("1.3.5", sha256="92358c3d4d5d6f3c7cd2812c8832d5175abce02b11bc101ac9548ff07163e8e2")
     version("1.3.4", sha256="5a8771405276ecf00b8ee927bd0a81ec21778dcfc97e4a37d0b388f10c9a41a8")
     version("1.3.3", sha256="b6fb1f12489f3a678c05ddcb78a74f0b6f63836219f51c0541e505f5e5208e7d")
@@ -33,32 +34,32 @@ class PyRasterio(PythonPackage):
     version("1.0.24", sha256="4839479621045211f66868ec49625979693450bc2e476f23e7e8ac4804eaf452")
     version("1.0a12", sha256="47d460326e04c64590ff56952271a184a6307f814efc34fb319c12e690585f3c")
 
-    # From README.rst
-    depends_on("python@3.8:", when="@1.3:", type=("build", "link", "run"))
-    depends_on("python@3.6:3.9", when="@1.2", type=("build", "link", "run"))
-    depends_on("python@2.7:2.8,3.5:3.8", when="@1.1", type=("build", "link", "run"))
-    depends_on("python@2.7:2.8,3.5:3.7", when="@:1.0", type=("build", "link", "run"))
-    depends_on("py-numpy@1.18:", when="@1.3:", type=("build", "link", "run"))
-    depends_on("py-numpy@1.15:", when="@1.2:", type=("build", "link", "run"))
-    depends_on("py-numpy", type=("build", "link", "run"))
-    depends_on("gdal@3.1:", when="@1.3:")
-    depends_on("gdal@2.4:3.3", when="@1.2.7:1.2")
-    depends_on("gdal@2.3:3.2", when="@1.2.0:1.2.6")
-    depends_on("gdal@1.11:3.2", when="@1.1.0:1.1")
-    depends_on("gdal@1.11:3.0", when="@1.0.25:1.0")
-    depends_on("gdal@1.11:2", when="@:1.0.24")
-
     # From pyproject.toml
     depends_on("py-cython@0.29.29:", when="@1.3.3:", type="build")
     depends_on("py-cython@0.29.24:0.29", when="@1.3.0:1.3.2", type="build")
 
     # From setup.py
+    depends_on("python@3.8:", when="@1.3:", type=("build", "link", "run"))
+    depends_on("python@3.6:3.9", when="@1.2", type=("build", "link", "run"))
+    depends_on("python@2.7:2.8,3.5:3.8", when="@1.1", type=("build", "link", "run"))
+    depends_on("python@2.7:2.8,3.5:3.7", when="@:1.0", type=("build", "link", "run"))
     depends_on("py-affine", type=("build", "run"))
     depends_on("py-attrs", type=("build", "run"))
     depends_on("py-certifi", when="@1.2:", type=("build", "run"))
     depends_on("py-click@4:", when="@1.2.4:", type=("build", "run"))
     depends_on("py-click@4:7", when="@:1.2.3", type=("build", "run"))
     depends_on("py-cligj@0.5:", type=("build", "run"))
+    depends_on("py-numpy@1.18:", when="@1.3:", type=("build", "link", "run"))
+    depends_on("py-numpy@1.15:", when="@1.2:", type=("build", "link", "run"))
+    depends_on("py-numpy", type=("build", "link", "run"))
     depends_on("py-snuggs@1.4.1:", type=("build", "run"))
     depends_on("py-click-plugins", type=("build", "run"))
     depends_on("py-setuptools", type=("build", "run"))
+
+    # From README.rst and setup.py
+    depends_on("gdal@3.1:", when="@1.3:")
+    depends_on("gdal@2.4:3.3", when="@1.2.7:1.2")
+    depends_on("gdal@2.3:3.2", when="@1.2.0:1.2.6")
+    depends_on("gdal@1.11:3.2", when="@1.1.0:1.1")
+    depends_on("gdal@1.11:3.0", when="@1.0.25:1.0")
+    depends_on("gdal@1.11:2", when="@:1.0.24")

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

@@ -14,6 +14,7 @@ class Shtools(MakefilePackage):
 
     maintainers("eschnett")
 
+    version("4.10.1", sha256="f4fb5c86841fe80136b520d2040149eafd4bc2d49da6b914d8a843b812f20b61")
     version("4.9.1", sha256="5c22064f9daf6e9aa08cace182146993aa6b25a6ea593d92572c59f4013d53c2")
     version("4.8", sha256="c36fc86810017e544abbfb12f8ddf6f101a1ac8b89856a76d7d9801ffc8dac44")
     version("4.5", sha256="1975a2a2bcef8c527d321be08c13c2bc479e0d6b81c468a3203f95df59be4f89")
@@ -24,12 +25,12 @@ class Shtools(MakefilePackage):
 
     # The Makefile expects the "other" libtool, not the GNU libtool we have in
     # Spack
-    patch("nolibtool.patch")
+    patch("nolibtool.patch", when="@:4.9")
 
     variant("openmp", default=True, description="Enable OpenMP support")
 
     depends_on("blas")
-    depends_on("fftw")
+    depends_on("fftw precision=double")
     depends_on("lapack")
     depends_on("py-flake8", type="test")