Reorganize JEDI meta-module enviornments to separate advanced python dependencies.

configs/common/packages.yaml

@@ -479,13 +479,13 @@ packages:
     py-pandas:
       require:
       - '@:2'
-      prefer:
-      - '~performance'
       # 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
+      prefer:
+      - '~performance'
     # To avoid duplicate packages
     py-poetry-core:
       require:

configs/sites/tier1/container/packages_oneapi.yaml

@@ -10,7 +10,7 @@ packages:
   intel-oneapi-compilers:
     buildable: false
     externals:
-    - spec: intel-oneapi-compilers@2025.3.0
+    - spec: intel-oneapi-compilers@2025.3.0 +fix_rt_linkage
       prefix: /opt/intel/oneapi
       modules:
       - umf/1.0.2

configs/sites/tier2/aws-ubuntu2404/README.md

@@ -314,7 +314,7 @@ pico ${PWD}/site/packages.yaml
 #   intel-oneapi-compilers:
 #     buildable: false
 #     externals:
-#     - spec: intel-oneapi-compilers@2026.1.1
+#     - spec: intel-oneapi-compilers@2026.1.1 +fix_rt_linkage
 #       prefix: /opt/intel/oneapi
 #       modules:
 #       - umf/1.1.0
@@ -362,9 +362,11 @@ cat << 'EOF' >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml
       - 'cxxflags="-O1"'
     jedi-base-env:
       require:
-      - ~bufrquery
       - +fftw
       - +hdf4
+    jedi-python-env:
+      require:
+      - ~bufrquery
     py-pyyaml:
       require:
       - +libyaml

configs/sites/tier2/aws-ubuntu2404/packages.yaml

@@ -18,7 +18,9 @@ packages:
     require:
     - "@1.7.2"
   jedi-base-env:
-    require: [+fftw, +hdf4, +bufrquery]
+    require: [+fftw, +hdf4]
+  jedi-python-env:
+    require: [+bufrquery]
 
   # System packages.
   autoconf:

configs/sites/tier2/aws-ubuntu2404/packages_oneapi.yaml

@@ -19,7 +19,7 @@ packages:
   intel-oneapi-compilers:
     buildable: false
     externals:
-    - spec: intel-oneapi-compilers@2026.1.1
+    - spec: intel-oneapi-compilers@2026.1.1 +fix_rt_linkage
       prefix: /opt/intel/oneapi
       modules:
        - umf/1.1.0
@@ -84,7 +84,9 @@ packages:
 
   # Package constraints.
   jedi-base-env:
-    require: [+fftw, +hdf4, +bufrquery]
+    require: [+fftw, +hdf4]
+  jedi-python-env:
+    require: [+bufrquery]
   eccodes:
     require:
     - "jp2k=jasper"

configs/templates/skylab-dev/spack.yaml

@@ -15,6 +15,7 @@ spack:
   - jedi-geos-env         ^esmf@=8.9.1
   - jedi-mpas-env
   - jedi-neptune-env      ^esmf@=9.0.0b18
+  - jedi-python-env
   - jedi-tools-env
   - jedi-ufs-env          ^esmf@=8.8.0
   - neptune-env           ^esmf@=9.0.0b18

configs/templates/unified-dev/spack.yaml

@@ -20,6 +20,7 @@ spack:
   - jedi-geos-env         ^esmf@=9.0.0b18
   - jedi-mpas-env
   - jedi-neptune-env      ^esmf@=9.0.0b18
+  - jedi-python-env
   - jedi-ufs-env          ^esmf@=8.8.0
   - neptune-env           ^esmf@=9.0.0b18
   - neptune-python-env    ^esmf@=9.0.0b18

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

@@ -19,6 +19,7 @@ class AiEnv(BundlePackage):
     version("1.0.0")
 
     depends_on("jedi-base-env", type="run")
+    depends_on("jedi-python-env", type="run")
     depends_on("py-torch", type="run")
 
     # There is no need for install() since there is no code.

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

@@ -39,6 +39,7 @@ class EwokEnv(BundlePackage):
     )
 
     depends_on("jedi-base-env", type="run")
+    depends_on("jedi-python-env", type="run")
     depends_on("awscli-v2", type="run")
     depends_on("py-boto3", type="run")
     depends_on("py-cartopy", type="run")

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

@@ -20,6 +20,7 @@ class GmaoSwellEnv(BundlePackage):
 
     # Main JEDI modules
     depends_on("jedi-base-env", type="run")
+    depends_on("jedi-python-env", type="run")
 
     # Add CRTM 2.4.0
     depends_on("crtm", type="run")

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

@@ -21,15 +21,12 @@ class JediBaseEnv(BundlePackage):
     # Need to find a free fftw provider for fftw-api ...
     variant("fftw", default=True, description="Build fftw")
     variant("hdf4", default=True, description="Build hdf4 library and python hdf module")
-    variant("bufrquery", default=True, description="Build bufr-query library")
 
     depends_on("libbacktrace", type="run")
     depends_on("base-env", type="run")
     depends_on("bison", type="run")
     depends_on("blas", type="run")
     depends_on("boost", type="run")
-    depends_on("bufr", type="run")
-    depends_on("bufr-query", when="+bufrquery", type="run")
     # Force users to load manually
     # depends_on("crtm@v2.4.1-jedi", type="run")
     depends_on("ecbuild", type="run")
@@ -54,19 +51,9 @@ class JediBaseEnv(BundlePackage):
     #depends_on("sp", type="run", when="^ip@:4")
     depends_on("udunits", type="run")
 
-    # Python packages
-    depends_on("py-eccodes", type="run")
-    depends_on("py-f90nml", type="run")
-    depends_on("py-h5py", type="run")
-    depends_on("py-netcdf4", type="run")
-    depends_on("py-pandas", type="run")
-    depends_on("py-pycodestyle", type="run")
+    # Python packages. Everything else moved to jedi-python-env; py-pybind11
+    # stays because core JEDI packages link its headers.
     depends_on("py-pybind11", type="run")
-    depends_on("py-pyhdf", when="+hdf4", type="run")
-    depends_on("py-python-dateutil", type="run")
-    depends_on("py-pyyaml", type="run")
-    depends_on("py-scipy", type="run")
-    depends_on("py-xarray", type="run")
 
     conflicts(
         "platform=darwin %gcc",

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

@@ -18,6 +18,7 @@ class JediGeosEnv(BundlePackage):
     version("1.0.0")
 
     depends_on("jedi-base-env", type="run")
+    depends_on("jedi-python-env", type="run")
     #depends_on("blas", type="run")
     depends_on("mepo", type="run")
     depends_on("esmf", type="run")

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

@@ -27,6 +27,7 @@ class JediNeptuneEnv(BundlePackage):
     variant("jedi", default=False, description="Build JEDI components required for JEDI-NEPTUNE")
 
     depends_on("jedi-base-env", type="run")
+    depends_on("jedi-python-env", type="run")
     depends_on("neptune-env", type="run")
     depends_on("neptune-python-env", type="run")
 

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

@@ -0,0 +1,46 @@
+# Copyright 2013-2022 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_repo.builtin.build_systems.bundle import BundlePackage
+from spack.package import *
+
+
+class JediPythonEnv(BundlePackage):
+    """Python dependencies for JEDI applications, on top of jedi-base-env"""
+
+    homepage = "https://github.com/jcsda/spack-stack"
+    git = "https://github.com/jcsda/spack-stack.git"
+
+    maintainers("eap", "srherbener")
+
+    version("1.0.0")
+
+    # Mirrors the jedi-base-env variant so py-pyhdf tracks the hdf4 library
+    variant("hdf4", default=True, description="Build hdf4 library and python hdf module")
+    variant("bufrquery", default=True, description="Build bufr-query library")
+
+    depends_on("jedi-base-env", type="run")
+    depends_on("jedi-base-env +hdf4", when="+hdf4", type="run")
+    depends_on("jedi-base-env ~hdf4", when="~hdf4", type="run")
+
+    # bufr is built +python in configs/common/packages.yaml, so it carries a
+    # py-numpy run dependency; bufr-query is its python-bindings companion.
+    depends_on("bufr", type="run")
+    depends_on("bufr-query", when="+bufrquery", type="run")
+
+    # Python packages
+    depends_on("py-eccodes", type="run")
+    depends_on("py-f90nml", type="run")
+    depends_on("py-h5py", type="run")
+    depends_on("py-netcdf4", type="run")
+    depends_on("py-pandas", type="run")
+    depends_on("py-pycodestyle", type="run")
+    depends_on("py-pyhdf", when="+hdf4", type="run")
+    depends_on("py-python-dateutil", type="run")
+    depends_on("py-pyyaml", type="run")
+    depends_on("py-scipy", type="run")
+    depends_on("py-xarray", type="run")
+
+    # There is no need for install() since there is no code.

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

@@ -18,6 +18,7 @@ class JediUfsEnv(BundlePackage):
     version("1.0.0")
 
     depends_on("jedi-base-env", type="run")
+    depends_on("jedi-python-env", type="run")
     depends_on("fms +gfs_phys constants=GFS", type="run")
 
     depends_on("bacio", type="run")

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

@@ -20,6 +20,7 @@ class JediUmEnv(BundlePackage):
     version("1.0.0")
 
     depends_on("jedi-base-env", type="run")
+    depends_on("jedi-python-env", type="run")
     depends_on("ectrans", type="run")
     depends_on("fiat", type="run")
     depends_on("shumlib", type="run")

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

@@ -18,6 +18,7 @@ class SocaEnv(BundlePackage):
     version("1.0.0")
 
     depends_on("jedi-base-env", type="run")
+    depends_on("jedi-python-env", type="run")
     depends_on("nco", type="run")
 
     # There is no need for install() since there is no code.