Support python 3.13 and oneAPI 2026.1 (#2086)

Dependencies
 py-xarray: improve version constraints for pandas spack/spack-packages#5537
 bufr: Add meson dependency for newer python spack/spack-packages#5627
 ecflow: add v5.18.0 spack/spack-packages#5628
 hdf-eos2: fix "incompatible-pointer-types" error on modern compilers spack/spack-packages#6096
 ecflow: Add version bound to pybind for ecflow >= 5.18 spack/spack-packages#6084
 uwtools: add 2.9.1, 2.10.0, 2.11.0, 2.17.0 spack/spack-packages#5631
 py-xarray: apply py-pandas version constraints to intermediate releases spack-packages#72
 Add meson dependency for newer python spack-packages#73
 Cherry pick "ecflow add v5.18.0 (#5628)" from spack/spack-packages spack-packages#74
 hdf-eos2: oneapi fix. Sync with spack-packages upstream and cherry patch from #6096. spack-packages#76
 Cherry-pick #6084: ecflow add version bound to pybind for ecflow >= 5.18 spack-packages#77
 Cherry-pick #5631: uwtools add 2.17.0 spack-packages#78
 Fix meta-modules preferred compiler bug #2084
 Bump the repos/builtin submodule in this PR once all cherry-picks are merged

Author: eap

.github/workflows/ubuntu-ci-x86_64-gnu.yaml

@@ -110,7 +110,7 @@ jobs:
 
             # Concretize, check for duplicates and for correct compilers being used
             spack concretize --force --fresh 2>&1 | tee log.concretize.${ENVNAME}
-            ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env -i fms -i ip
+            ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env -i fms -i ip -i py-versioneer
             spack stack check-preferred-compiler 2>&1 | tee log.check-preferred-compiler.${ENVNAME}
 
             # Add and update source cache
@@ -182,7 +182,7 @@ jobs:
 
           # Concretize, check for duplicates and for correct compilers being used
           spack concretize --force --fresh 2>&1 | tee log.concretize.${ENVNAME}
-          ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env -i fms -i ip
+          ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env -i fms -i ip -i py-versioneer
           spack stack check-preferred-compiler 2>&1 | tee log.check-preferred-compiler.${ENVNAME}
 
           # Install from cache

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

@@ -126,7 +126,7 @@ jobs:
 
             # Concretize, check for duplicates and for correct compilers being used
             spack concretize --force --fresh 2>&1 | tee log.concretize.${ENVNAME}
-            ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env -i fms -i ip
+            ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env -i fms -i ip -i py-versioneer
             spack stack check-preferred-compiler 2>&1 | tee log.check-preferred-compiler.${ENVNAME}
 
             # Add and update source cache
@@ -201,7 +201,7 @@ jobs:
 
           # Concretize, check for duplicates and for correct compilers being used
           spack concretize --force --fresh 2>&1 | tee log.concretize.${ENVNAME}
-          ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env -i fms -i ip
+          ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env -i fms -i ip -i py-versioneer
           spack stack check-preferred-compiler 2>&1 | tee log.check-preferred-compiler.${ENVNAME}
 
           # Install from cache

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

@@ -126,7 +126,7 @@ jobs:
 
             # Concretize, check for duplicates and for correct compilers being used
             spack concretize --force --fresh 2>&1 | tee log.concretize.${ENVNAME}
-            ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env -i fms -i ip
+            ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env -i fms -i ip -i py-versioneer
             spack stack check-preferred-compiler 2>&1 | tee log.check-preferred-compiler.${ENVNAME}
 
             # Add and update source cache
@@ -201,7 +201,7 @@ jobs:
 
           # Concretize, check for duplicates and for correct compilers being used
           spack concretize --force --fresh 2>&1 | tee log.concretize.${ENVNAME}
-          ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env -i fms -i ip
+          ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env -i fms -i ip -i py-versioneer
           spack stack check-preferred-compiler 2>&1 | tee log.check-preferred-compiler.${ENVNAME}
 
           # Install from cache

configs/common/packages.yaml

@@ -64,6 +64,15 @@ packages:
       require:
       - '@0.0.5'
       - +python
+    # cairo@1.18.0: is uses the meson recipe. The meson build enforces variants
+    # that are all-enabled or all-disabled. The "all-enabled" variants are set to help
+    # the concretizer resolve the correct version without disabling all variants.
+    # pango/harfbuzz/gobject-introspection need cairo+gobject; without pinning it
+    # the concretizer builds cairo both ways and the two collide on one modulefile.
+    cairo:
+      require:
+      - '@1.18:'
+      - +zlib+ft+fc+png+pdf+gobject
     cdo:
       require:
       - ~openmp
@@ -109,10 +118,11 @@ packages:
       - +netcdf
       - +png
       - +tools
+    # uwtools@2.17: needs ecflow@5.16:; leave the version to the concretizer
     ecflow:
       require:
-      - '@5.11.4'
       - +ui
+      - '@5.18:'
     eckit:
       require:
       - '@2.0.7'
@@ -404,30 +414,37 @@ packages:
     # are removed, which itself is problematic.
     python:
       require:
-      - '@3.11'
-      - ~crypt
+      - '@3.13'
+      # The crypt variant only exists for python<=3.12 since the module was dropped.
+      # An unconditional ~crypt caps python at 3.12
+      - spec: ~crypt
+        when: '@:3.12'
     # Not sure about the exact version requirements, but earlier
     # versions (definitely 4.5.3 and earlier) don't work with newer
     # py-setuptools (version 68 and later) because of a breaking
     # change: error in beautifulsoup4 setup command: use_2to3 is invalid
     py-beautifulsoup4:
       require:
       - '@4.12.3:'
+    # Pin to avoid duplicates
+    py-pybind11:
+      require:
+      - '@:2'
     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:
       - '@0.4.6'
-    # Pin to version 42 to avoid maturin dependency that breaks Intel oneAPI builds
-    py-cryptography:
+    # No tutorials extras; prevent py-pandas-datareader dep with broken configparser call
+    py-arch:
+      require:
+      - ~tutorial
+    # Exclude @:2021.3.0 (broken configparser call), which its default +bag/+delayed variants select
+    py-dask:
       require:
-      - '@42'
+      - '@2023.4.1:'
     py-h5py:
       require:
       - ~mpi
@@ -453,65 +470,45 @@ packages:
     # To avoid duplicate packages
     py-numpy:
       require:
-      - '@1'
+      - '@=2.4.6'
     # Restrict py-pandas to older versions compatible with py-numpy and py-xarray
     py-pandas:
       require:
       - '@:2'
-    # See py-pycparser
-    py-pandas-datareader:
-      require:
-      - '@:0.10'
+      # py-versioneer is unavoidably duplicated by pins in py-pyogrio (@0.28) and
+      # py-partd (@0.29). py-pandas is unconstrained and can further cascade splits
+      # into py-xarray/met/metplus/jedi-base-env. This constraints py-versioneer to @0.28
+      # (shared with py-pyogrio) so only py-versioneer itself is duplicated.
+      - ^py-versioneer@0.28
     # To avoid duplicate 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:
       - '@2.7:'
-    # See py-pycparser
-    py-imageio:
-      require:
-      - '@2.37.0'
     # This version builds with Intel oneAPI compilers, newer versions don't
     py-pyogrio:
       require:
       - '@0.9.0'
-    # See py-pycparser
-    py-pyparsing:
-      require:
-      - '@3.1.2'
     # To avoid duplicate packages
     py-python-dateutil:
       require:
       - '@2'
-    # To avoid duplicate packages
+    # To avoid duplicate packages, pin to recent version.
     py-requests:
       require:
-      - '@2.32.3'
+      - '@2.32:'
     # To avoid duplicate packages
     py-ruamel-yaml:
       require:
       - '@0.17.16'
     # https://github.com/JCSDA/spack-stack/issues/1942
     # https://github.com/spack/spack-packages/issues/3695
-    py-setuptools:
-      require:
-      - '@73.0.1'
-    # See py-pycparser
-    py-sphinxcontrib-bibtex:
-      require:
-      - '@2.5.0'
+    # NOTE: py-setuptools was pinned @73.0.1 for the py3.11 stack; removed for the
+    # py3.12/numpy2 migration since modern packages (e.g. py-xarray@2025.7) require
+    # py-setuptools@77.0.3:. Re-evaluate issue #3695 if setuptools duplicates recur.
     py-torch:
       require:
       - +custom-protobuf
@@ -521,10 +518,10 @@ packages:
       require:
       - '@1.26.20'
       # OR - '@1.26.12' ?
-    # To avoid duplicate packages
+    # Not '@=0.28'; py-pyogrio needs 0.28 and py-partd/py-dask 0.29, build-only so a split is fine
     py-versioneer:
       require:
-      - '@=0.28'
+      - '@0.28:'
     # On a per-site basis, either set qt to buildable: false
     # or add requirement to build with gcc for Intel oneAPI
     qt:
@@ -565,9 +562,10 @@ packages:
     upp:
       require:
       - '@10.0.10'
+    # Upper bound keeps the branch version 'main' out; spack sorts it above 2.x
     uwtools:
       require:
-      - '@2.7.2'
+      - '@2.17:2'
     w3emc:
       require:
       - '@2.13.0'

configs/common/packages_oneapi.yaml

@@ -56,6 +56,10 @@ packages:
     nco:
       require:
       - '%c,cxx=gcc'
+    # The py-numpy cannot be built with oneAPI.
+    py-numpy:
+      require:
+      - '%c,cxx=gcc'
     oops:
       require:
       - +mkl
@@ -65,6 +69,11 @@ packages:
     patchelf:
       require:
       - '%c=gcc'
+    # Require a recent py-sphinx; unpinned the concretizer prefers 6.X. The old sphinx creates version
+    # splits in py-attrs, py-docutils, and py-eccodes affecting jedi-base-env and jedi-fv3-env.
+    py-sphinx:
+      require:
+      - '@9:'
     py-maturin:
       require:
       - '%c=gcc'

configs/sites/tier1/acorn/packages.yaml

@@ -41,7 +41,7 @@ packages:
     require:: ['%oneapi']
   py-colorama:: {}
   py-pandas:
-    require:: ['~excel']
+    require: ['~excel']
   subversion:
     require: ['~serf', '+pic']
   zlib-ng:

configs/sites/tier1/acorn/packages_intel-19.1.3.304.yaml

@@ -107,7 +107,7 @@ packages:
   py-maturin:
     require: ['%gcc']
   py-numpy:
-    require:: ['@1.26', '%gcc']
+    require: ['%gcc']
   py-scipy:
     require: ['@1.10.1']
   qt:

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

@@ -85,8 +85,6 @@ packages:
     require: ['build_system=meson']
   proj:
     require: ['@9.4.1']
-  py-numpy::
-    require:: ['@1.26']
   subversion:
     require: ['%gcc']
   zlib-ng:

configs/sites/tier1/aws-pcluster/packages_intel.yaml

@@ -31,5 +31,6 @@ packages:
     - '@1.4.2 ~mkl'
   py-numpy:
     require::
+    - '@2'
     - '^openblas'
   # *DH

configs/sites/tier1/container/packages.yaml

@@ -1,9 +1,6 @@
 packages:
   all:
     target: [x86_64_v3]
-  awscli-v2:
-    require:
-    - "@2.22.4"
   cairo:
     variants: +pic
   ewok-env: