Update spack-packages submodule from upstream spack-packages/develop (includes #2025)

.github/workflows/ubuntu-ci-x86_64-oneapi-ifx.cfg

@@ -17,3 +17,6 @@
     externals:
     - spec: intel-oneapi-mpi@2021.13
       prefix: /opt/intel/oneapi
+  qt:
+    require:
+    - '%c,cxx=gcc'

.github/workflows/ubuntu-ci-x86_64-oneapi.cfg

@@ -17,3 +17,6 @@
     externals:
     - spec: intel-oneapi-mpi@2021.13
       prefix: /opt/intel/oneapi
+  qt:
+    require:
+    - '%c,cxx=gcc'

configs/common/config.yaml

@@ -1,5 +1,9 @@
 # Set package and module installation directories
 config:
+  # Old installer - needed for py-pynacl amongst others
+  # https://github.com/spack/spack-packages/issues/5106
+  installer: old
+
   install_hash_length: 7
   install_tree:
     root: $env/install

configs/common/packages.yaml

@@ -58,9 +58,6 @@ packages:
       require:
       - '@0.0.5'
       - +python
-    cairo:
-      require:
-      - +pic
     cdo:
       require:
       - ~openmp
@@ -212,11 +209,12 @@ packages:
       require:
       - '@1.1.3'
     harfbuzz:
+      # cmake-based harfbuzz fails during build; autotools is only available
+      # for the deprecated @2.9.1 which doesn't compile against ICU >= 76
+      # (-Werror=redundant-decls on u_strlen). Force meson.
       # cmake-based harfbuzz fails during build
       require:
-      - one_of:
-        - 'build_system=meson'
-        - 'build_system=autotools'
+      - 'build_system=meson'
     hdf:
       require:
       - '@4.2.15'
@@ -387,6 +385,10 @@ packages:
     py-cartopy:
       require:
       - +plotting
+    # See py-pycparser
+    py-click:
+      require:
+      - '@8.1.8'
     # Pin py-colorama to avoid duplicate packages, hopefully can be removed soon
     py-colorama:
       require:
@@ -395,10 +397,6 @@ packages:
     py-cryptography:
       require:
       - '@42'
-    # To avoid duplicate packages
-    py-flit-core:
-      require:
-      - '@3.8.0'
     py-h5py:
       require:
       - ~mpi
@@ -429,6 +427,15 @@ packages:
     py-poetry-core:
       require:
       - '@1.7'
+    # See py-pycparser
+    py-pooch:
+      require:
+      - '@1.7.0'
+    # Need older version of py-pycparser until we can update setuputils to >= 77 ?
+    # https://github.com/pydata/xarray/issues/10588
+    py-pycparser:
+      require:
+      - '@2.21'
     # Need at least py-pygithub@2.7 for self-hosted runner management
     py-pygithub:
       require:
@@ -437,6 +444,10 @@ packages:
     py-pyogrio:
       require:
       - '@0.9.0'
+    # See py-pycparser
+    py-pyparsing:
+      require:
+      - '@3.1.2'
     # To avoid duplicate packages
     py-python-dateutil:
       require:
@@ -454,6 +465,10 @@ packages:
     py-setuptools:
       require:
       - '@73.0.1'
+    # See py-pycparser
+    py-sphinxcontrib-bibtex:
+      require:
+      - '@2.5.0'
     py-torch:
       require:
       - +custom-protobuf
@@ -466,7 +481,7 @@ packages:
     # To avoid duplicate packages
     py-versioneer:
       require:
-      - '@0.29'
+      - '@=0.28'
     # On a per-site basis, either set qt to buildable: false
     # or add requirement to build with gcc for Intel oneAPI
     qt:

configs/sites/tier1/atlantis/packages_clang-22.1.0.yaml

@@ -31,4 +31,5 @@ packages:
     - spec: openmpi@4.1.8 ~internal-hwloc +two_level_namespace
       prefix: /gpfs/neptune/spack-stack/openmpi-4.1.8/llvm-22.1.0
       modules:
+      - llvm/22.1.0
       - openmpi/4.1.8

configs/sites/tier1/atlantis/packages_gcc-13.4.0.yaml

@@ -25,4 +25,5 @@ packages:
     - spec: openmpi@4.1.8 ~internal-hwloc +two_level_namespace
       prefix: /gpfs/neptune/spack-stack/openmpi-4.1.8/gcc-13.4.0
       modules:
+      - gcc/13.4.0
       - openmpi/4.1.8

configs/sites/tier1/atlantis/packages_oneapi-2024.2.1.yaml

@@ -47,6 +47,9 @@ packages:
     - spec: intel-oneapi-mpi@2021.13
       prefix: /cm/shared/apps/intel/oneapi-2024.2.1
       modules:
+      - intel-oneapi-2024.2.1
+      - tbb/2021.13
+      - compiler-rt/2024.2.1
       - mpi/2021.13
       - slurm
   intel-oneapi-mkl:

configs/sites/tier1/atlantis/packages_oneapi-2025.3.0.yaml

@@ -47,12 +47,13 @@ packages:
     - spec: intel-oneapi-mpi@2021.17
       prefix: /gpfs/neptune/spack-stack/oneapi-2025.3.0
       modules:
+      - umf/1.0.2
+      - tbb/2022.3
+      - compiler-rt/2025.3.0
       - mpi/2021.17
       - slurm
   intel-oneapi-mkl:
     buildable: false
     externals:
     - spec: intel-oneapi-mkl@2025.3
       prefix: /gpfs/neptune/spack-stack/oneapi-2025.3.0
-      modules:
-      - mkl/2025.3

configs/templates/cylc-dev/spack.yaml

@@ -21,7 +21,7 @@ spack:
   include: []
 
   specs:
-  - py-cylc-flow@8.4.2
-  - py-cylc-rose@1.5.1
-  - py-cylc-uiserver@1.6.1
+  # These versions work with Python 3.11
+  - py-cylc-flow@8.5.4
+  - py-cylc-uiserver@1.7.1
   - bats

repos/spack_stack/spack_repo/spack_stack/packages/dev_utils_env/package.py

@@ -31,7 +31,7 @@ class DevUtilsEnv(BundlePackage):
 
     # Scalasca/ScoreP
     depends_on("scalasca", when="+scalasca", type="run")
-    depends_on("cube +gui", when="+scalasca", type="run")
+    depends_on("cube", when="+scalasca", type="run")
 
     # Miscellaneous
     depends_on("bats", type="run")