Unpin or update many packages (mostly Python) in configs/common/packages.yaml, fix S4 site config

configs/common/packages.yaml

@@ -26,7 +26,18 @@ packages:
   cairo:
     require: '+pic'
   cdo:
-    require: '@2.3.0 ~openmp'
+    prefer:
+    - '@2.4.4 ~openmp'
+    require:
+    - any_of: ['@2.3.0 ~openmp']
+      when: '%intel@2021:'
+      message: '2.3.0 is the last version to use C++17, use with Intel Classic'
+    - any_of: ['@2.3.0 ~openmp']
+      when: '%apple-clang@:14'
+      message: '2.3.0 is the last version to use C++17, use with Apple Clang 14 and earlier'
+    - any_of: ['@2.0.5 ~openmp']
+      when: '%intel@:2020'
+      message: '2.0.5 is the last version to use C++14, use with Intel Classic 2020 and earlier'
   cmake:
     version: ['3.27.9']
     require: '+ownlibs'
@@ -143,9 +154,9 @@ packages:
     require: '@2.46.3 ~shared ~f2py'
     variants: '+pflogger'
   # To avoid duplicate packages being built
-  meson:
-    require:
-    - '@1.5.1:'
+  #meson:
+  #  require:
+  #  - '@1.5.1:'
   # If making changes here, also check the Discover site configs and the CI workflows
   met:
     require: '@11.1.1 +python +grib2'
@@ -156,7 +167,7 @@ packages:
   mpich:
     require: '~hwloc'
   nco:
-    require: '@5.1.6 ~doc'
+    require: '@5.2.4 ~doc'
   # ncview - when adding information here, also check Orion
   # and Discover site configs
   nemsio:
@@ -199,9 +210,9 @@ packages:
     require: '~tiff'
   python:
     require: '@3.11.7'
-  py-attrs:
-    # https://github.com/JCSDA/spack-stack/issues/740
-    require: '@21.4.0'
+  #py-attrs:
+  #  # https://github.com/JCSDA/spack-stack/issues/740
+  #  require: '@21.4.0'
   py-cartopy:
     require: '+plotting'
   # Avoid full rust dependency: version 43+ requires py-maturin
@@ -229,36 +240,38 @@ packages:
   # https://github.com/JCSDA/spack-stack/issues/1276
   py-matplotlib:
      require: '@3.7.4'
-  py-meson-python:
-     require: '@0.15.0'
+  #py-meson-python:
+  #   require: '@0.15.0'
   # Comment out for now until build problems are solved
   # https://github.com/jcsda/spack-stack/issues/522
   # see also ewok-env virtual package and container
   # README.md
   #py-mysql-connector-python:
   #  require: '@8.0.32'
+  # Variant ~mpi not working for latest py-netcdf4
+  # https://github.com/spack/spack/issues/47652
   py-netcdf4:
-    require: '@1.5.8 ~mpi'
+    require: '@1.7.1 +mpi'
   # [email protected] causes many build problems with older Python packages
   # also check Nautilus site config when making changes here
   # https://github.com/JCSDA/spack-stack/issues/1276
-  py-numpy:
-    require:
-    - '@:1.23.5'
+  #py-numpy:
+  #  require:
+  #  - '@:1.23.5'
   py-pandas:
     require: '+excel'
-  py-pybind11:
-    require: '@2.11.0'
+  #py-pybind11:
+  #  require: '@2.11.0'
   # To avoid duplicate packages
   py-ruamel-yaml:
     require: '@0.17.16'
   # Pin the py-setuptools version to avoid duplicate Python packages
   py-setuptools:
-    require: '@63.4.3'
+    require: '@69'
   py-setuptools-rust:
     require: '+rust_bootstrap'
-  py-shapely:
-    require: '@1.8.0'
+  #py-shapely:
+  #  require: '@1.8.0'
   py-torch:
     require: '+custom-protobuf ~mkldnn'
   # To avoid duplicate packages
@@ -294,4 +307,5 @@ packages:
   wrf-io:
     require: '@1.2.0'
   zstd:
-    require: '@1.5.2 +programs'
+    #require: '@1.5.2 +programs'
+    require: '+programs'