Merge upstream branch

Author: climbfuji

configs/common/packages.yaml

@@ -211,10 +211,9 @@ packages:
   # Avoid full rust dependency: version 43+ requires py-maturin
   py-cryptography:
     require: '@:42 +rust_bootstrap'
-  # Introduced in https://github.com/JCSDA/spack-stack/pull/894, pin py-cython
-  # to avoid duplicate packages being built (cylc dependencies soft-want @3:)
+  # Pin py-cython to avoid duplicate packages
   py-cython:
-    require: '@0.29.36'
+    require: '@3'
   # As long as we need the "delayed" variant for py-dask,
   # we are restricted to version 2021.03.0 (last one that has it)
   # and newer than 2021.01.0 because of these issues:
@@ -230,12 +229,34 @@ packages:
   # https://github.com/JCSDA/spack-stack/issues/1276
   py-matplotlib:
      require: '@3.7.4'
+<<<<<<< Updated upstream
+=======
+  #py-meson-python:
+  #   require: '@0.15.0'
+>>>>>>> Stashed changes
   # Variant ~mpi not working for latest py-netcdf4
   # https://github.com/spack/spack/issues/47652
   py-netcdf4:
     require: '@1.7.1 +mpi'
+<<<<<<< Updated upstream
   py-pandas:
     require: '+excel'
+=======
+  # [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'
+  # Sigh, it's complicated. With py-cython@3 (needed to avoid duplicate packages),
+  # pandas must be 2.2 or later. For those versions, the +excel variant adds dependencies
+  # on py-python-calamina, py-maturin, and rust (full rust, not just rust-bootstrap).
+  # @climbfuji thinks we can live without the excel variant ...
+  #py-pandas:
+  #  require: '+excel'
+  #py-pybind11:
+  #  require: '@2.11.0'
+>>>>>>> Stashed changes
   # To avoid duplicate packages
   py-ruamel-yaml:
     require: '@0.17.16'

configs/sites/tier1/atlantis/packages.yaml

@@ -89,10 +89,11 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
-  libtool:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
+  # Don't use, incomplete installation
+  #libtool:
+  #  externals:
+  #  - spec: [email protected]
+  #    prefix: /usr
   findutils:
     externals:
     - spec: [email protected]