Update to spack-stack 2.2

.github/workflows/build_with_pinned_versions.yml

@@ -28,7 +28,7 @@ jobs:
         lfs: true
 
     - name: Install JEDI bundle and dependencies
-      run: python -m pip install --use-deprecated=legacy-resolver -r requirements.txt --user .
+      run: python -m pip install --use-deprecated=legacy-resolver --user .
     - name: Put executables in the path
       run: echo "$HOME/.local/bin" >> $GITHUB_PATH
 

docs/_platforms/building_jedi_code_on_discover_sles15.md

@@ -4,14 +4,14 @@
 
 ``` bash
 module purge
-source /discover/nobackup/projects/gmao/advda/swell/jedi_modules/spackstack_1.9_intel_bundle
+source /discover/nobackup/projects/gmao/advda/swell/jedi_modules/spackstack_2.0_intel
 ```
 
 2) Load the SLES15 `jedi_bundle` module:
 
 ``` bash
 module use -a /discover/nobackup/projects/gmao/advda/JediOpt/modulefiles/core/
-module load jedi_bundle/sles15_skylab9
+module load jedi_bundle/sles15_spack_2.0
 ```
 
 3) Create a directory where the source code and build directory will be stored e.g.:

pyproject.toml

@@ -0,0 +1,58 @@
+# (C) Copyright 2021-2022 United States Government as represented by the Administrator of the
+# National Aeronautics and Space Administration. All Rights Reserved.
+#
+# This software is licensed under the terms of the Apache Licence Version 2.0
+# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+
+# --------------------------------------------------------------------------------------------------
+
+# Setup and installation script
+#
+# Usage: "pip install --prefix=/path/to/install ."
+
+# --------------------------------------------------------------------------------------------------
+
+[build-system]
+requires = ["setuptools>=68.0.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "jedi_bundle"
+version = "1.0.40"
+authors = [{name = "NASA Global Modeling and Assimilation Office"}]
+description = "Tools for installing JEDI code"
+readme = "README.md"
+requires-python = ">=3.10"
+classifiers=[
+    'Development Status :: 1 - Planning',
+    'Environment :: Console',
+    'Intended Audience :: Science/Research',
+    'Programming Language :: Python :: 3 :: Only',
+    'License :: OSI Approved :: Apache Software License',
+    'Natural Language :: English',
+    'Operating System :: OS Independent'
+]
+
+dependencies = [
+    'pyyaml>=5.4',
+    'pycodestyle>=2.8.0',
+    'requests>=2.23.0'
+]
+
+[project.urls]
+Repository = "https://github.com/geos-esm/jedi_bundle"
+Documentation = "https://geos-esm.github.io/jedi_bundle/#/"
+
+[tool.setuptools.package-dir]
+"" = "src"
+
+[tool.setuptools.package-data]
+jedi_bundle = [
+    'config/*',
+    'config/bundles/*',
+    'config/platforms/*',
+]
+
+[project.scripts]
+jedi_bundle = "jedi_bundle.bin.jedi_bundle:jedi_bundle"
+jedi_bundle_update_hash = "jedi_bundle.bin.jedi_bundle_update_hash:jedi_bundle_update_hash"

src/jedi_bundle/config/pinned_versions.yaml

@@ -1,43 +1,40 @@
-# Pinned versions for 2026-08-14
+# Pinned versions for 2026-09-28
 - jedicmake:
     branch: 40d521f9a2d796fcbc6234d77abceeffefb8eb7f
     commit: true
-- oops:
-    branch: 57b45967ee775e602bb23f773202650fa2fb4261
-    commit: true
 - saber:
-    branch: 5f0c875f8fc19e6a9abc4c20cd04c38e7234436c
+    branch: 0480bda4f1bdc0a67e2ab486bb73b1d9fb888872
     commit: true
 - ioda:
-    branch: 2014b79b77d2edaddeb4914eb096ff86df4165e3
+    branch: 1a15b7233f9f67019acd53239fffe524bac5b118
     commit: true
 - ufo:
-    branch: 9b4ee5c2af2b07fbdc631bc8360c71d5ee978bd3
+    branch: fd94c3b24a31e1110c6dd3ad919ad457da2edc4d
     commit: true
 - vader:
-    branch: b0275351b33fcb67b6880ca85660c443aa1f2647
+    branch: 5b212bc6804b22ce97350a45413d2252278c4760
     commit: true
 - fv3-jedi-lm:
     branch: b7ce387d6049d41034b55fbf50bfa1d2dd919d06
     commit: true
 - fv3-jedi:
-    branch: b1409a31ef08d1ddf5d0ae4591c87f0248f58a5e
+    branch: 5e626668f2aca6aee1f7681ca57bf45dfa7089d2
     commit: true
 - ioda-data:
-    branch: 86b9275ef21a52e9990f48895477bf3951c54d5c
+    branch: c5ae3c398532b2afdd9779c8319cb515e974d31a
     commit: true
 - fv3-jedi-data:
     branch: 778db21e835351b3340b0af13dbcea5df4982c85
     commit: true
 - soca:
-    branch: c455883f3f7a5ed53708cf82e9a9e9bce6b7c45f
+    branch: ffbf0b0681bd037c3e81badfc38b132a2be7e1e3
     commit: true
 - iodaconv:
-    branch: 60ae176e26aeaca381c9a41c71068ca449be1e01
+    branch: ca3e8f0336f3352a00437e12ffb46e054adf020f
     commit: true
 - gsw:
     branch: 697cbeb7605d70ed3857664c5f54a5c05346e31f
     commit: true
 - ufo-data:
-    branch: 636e43e4f528ff53da2736b85f24723f006d92f8
+    branch: 4039a869b197b229f3fd9d8264c44f2e8b958061
     commit: true

src/jedi_bundle/config/platforms/nccs_discover_sles15.yaml

@@ -15,54 +15,54 @@ modules:
       - module purge
       - module use /discover/swdev/gmao_SIteam/modulefiles-SLES15
       - module use /discover/swdev/jcsda/spack-stack/scu17/modulefiles
-      - module use /gpfsm/dswdev/jcsda/spack-stack/scu17/spack-stack-1.9.0/envs/ue-intel-2021.10.0/install/modulefiles/Core
-      - module load stack-intel/2021.10.0
-      - module load stack-intel-oneapi-mpi/2021.10.0
-      - module load stack-python/3.11.7
+      - module use -a /discover/nobackup/projects/gmao/SIteam/spack-stack/spack-stack-siteam/envs/ue-oneapi-2024.2.0/modules/Core
+      - module load stack-intel-oneapi-compilers/2024.2.0
+      - module load stack-intel-oneapi-mpi/2021.13
       - module load jedi-fv3-env
       - module load soca-env
       - module load gmao-swell-env/1.0.0
       - module unload gsibec bufr-query crtm fms
-      - module load fms/2024.02
-      - module load ip/5.1.0
-      - module load py-wxflow
-    configure: -DMPIEXEC_EXECUTABLE="/usr/local/intel/oneapi/2021/mpi/2021.10.0/bin/mpirun" -DMPIEXEC_NUMPROC_FLAG="-np"
+      - module load fms/2024.03-geos-constants
+      - module load ip/5.4.0
+      - module load libyaml/0.2.5
+    configure: -DMPIEXEC_EXECUTABLE="/usr/local/intel/oneapi/2024/mpi/2021.13/bin/mpirun" -DMPIEXEC_NUMPROC_FLAG="-np"
   intel-geos:
     init:
       - source /usr/share/lmod/lmod/init/bash
     load:
       - module purge
       - module use /discover/swdev/gmao_SIteam/modulefiles-SLES15
       - module use /discover/swdev/jcsda/spack-stack/scu17/modulefiles
-      - module use /gpfsm/dswdev/jcsda/spack-stack/scu17/spack-stack-1.9.0/envs/ue-intel-2021.10.0/install/modulefiles/Core
-      - module load stack-intel/2021.10.0
-      - module load stack-intel-oneapi-mpi/2021.10.0
-      - module load stack-python/3.11.7
+      - module use -a /discover/nobackup/projects/gmao/SIteam/spack-stack/spack-stack-siteam/envs/ue-oneapi-2024.2.0/modules/Core
+      - module load stack-intel-oneapi-compilers/2024.2.0
+      - module load stack-intel-oneapi-mpi/2021.13
       - module load jedi-fv3-env
       - module load soca-env
       - module load gmao-swell-env/1.0.0
       - module unload gsibec bufr-query crtm fms
-      - module load fms/2024.02
-      - module load ip/5.1.0
+      - module load fms/2024.03-geos-constants
+      - module load crtm/v2.4.1-jedi.2
+      - module load ip/5.4.0
+      - module load libyaml/0.2.5
       - module load esmf python py-pyyaml py-numpy pflogger fargparse zlib-ng cmake
-    configure: -DMPIEXEC_EXECUTABLE="/usr/local/intel/oneapi/2021/mpi/2021.10.0/bin/mpirun" -DMPIEXEC_NUMPROC_FLAG="-np"
+    configure: -DMPIEXEC_EXECUTABLE="/usr/local/intel/oneapi/2024/mpi/2021.13/bin/mpirun" -DMPIEXEC_NUMPROC_FLAG="-np"
   intel-oneapi:
     init:
       - source /usr/share/lmod/lmod/init/bash
     load:
       - module purge
       - module use /discover/swdev/gmao_SIteam/modulefiles-SLES15
       - module use /discover/swdev/jcsda/spack-stack/scu17/modulefiles
-      - module use /gpfsm/dswdev/jcsda/spack-stack/scu17/spack-stack-1.9.0/envs/ue-oneapi-2024.2.0/install/modulefiles/Core
-      - module load stack-oneapi/2024.2.0
+      - module use -a /discover/nobackup/projects/gmao/SIteam/spack-stack/spack-stack-siteam/envs/ue-oneapi-2024.2.0/modules/Core
+      - module load stack-intel-oneapi-compilers/2024.2.0
       - module load stack-intel-oneapi-mpi/2021.13
-      - module load stack-python/3.11.7
       - module load jedi-fv3-env
       - module load soca-env
       - module load gmao-swell-env/1.0.0
       - module unload gsibec bufr-query crtm fms
-      - module load fms/2024.02
-      - module load ip/5.1.0
+      - module load fms/2024.03-geos-constants
+      - module load ip/5.4.0
+      - module load libyaml/0.2.5
     configure: -DMPIEXEC_EXECUTABLE="/usr/local/intel/oneapi/2024/mpi/2021.13/bin/mpirun" -DMPIEXEC_NUMPROC_FLAG="-np"
   intel-oneapi-geos:
     init:
@@ -71,16 +71,16 @@ modules:
       - module purge
       - module use /discover/swdev/gmao_SIteam/modulefiles-SLES15
       - module use /discover/swdev/jcsda/spack-stack/scu17/modulefiles
-      - module use /gpfsm/dswdev/jcsda/spack-stack/scu17/spack-stack-1.9.0/envs/ue-oneapi-2024.2.0/install/modulefiles/Core
-      - module load stack-oneapi/2024.2.0
+      - module use -a /discover/nobackup/projects/gmao/SIteam/spack-stack/spack-stack-siteam/envs/ue-oneapi-2024.2.0/modules/Core
+      - module load stack-intel-oneapi-compilers/2024.2.0
       - module load stack-intel-oneapi-mpi/2021.13
-      - module load stack-python/3.11.7
       - module load jedi-fv3-env
       - module load soca-env
       - module load gmao-swell-env/1.0.0
       - module unload gsibec bufr-query crtm fms
-      - module load fms/2024.02
-      - module load ip/5.1.0
+      - module load fms/2024.03-geos-constants
+      - module load ip/5.4.0
+      - module load libyaml/0.2.5
       - module load cmake esmf/8.8.0 gftl gftl-shared pflogger fargparse udunits
     configure: -DMPIEXEC_EXECUTABLE="/usr/local/intel/oneapi/2024/mpi/2021.13/bin/mpirun" -DMPIEXEC_NUMPROC_FLAG="-np"
   gnu:
@@ -90,16 +90,16 @@ modules:
       - module purge
       - module use /discover/swdev/gmao_SIteam/modulefiles-SLES15
       - module use /discover/swdev/jcsda/spack-stack/scu17/modulefiles
-      - module use /gpfsm/dswdev/jcsda/spack-stack/scu17/spack-stack-1.9.0/envs/ue-gcc-12.3.0/install/modulefiles/Core
-      - module load stack-gcc/12.3.0
-      - module load stack-openmpi/4.1.6
-      - module load stack-python/3.11.7
+      - module use -a /discover/nobackup/projects/gmao/SIteam/spack-stack/spack-stack-siteam/envs/ue-oneapi-2024.2.0/modules/Core
+      - module load stack-gcc/13.4.0
       - module load jedi-fv3-env
       - module load soca-env
       - module load gmao-swell-env/1.0.0
       - module unload gsibec bufr-query crtm fms
-      - module load fms/2024.02
-      - module load ip/5.1.0
+      - module load fms/2024.03-geos-constants
+      - module load ip/5.4.0
+      - module load libyaml/0.2.5
+      - module unload py-netcdf4/1.7.2
     configure: -DMPIEXEC_EXECUTABLE="/usr/bin/srun" -DMPIEXEC_NUMPROC_FLAG="-n"
   gnu-geos:
     init:
@@ -108,15 +108,14 @@ modules:
       - module purge
       - module use /discover/swdev/gmao_SIteam/modulefiles-SLES15
       - module use /discover/swdev/jcsda/spack-stack/scu17/modulefiles
-      - module use /gpfsm/dswdev/jcsda/spack-stack/scu17/spack-stack-1.9.0/envs/ue-gcc-12.3.0/install/modulefiles/Core
-      - module load stack-gcc/12.3.0
-      - module load stack-openmpi/4.1.6
-      - module load stack-python/3.11.7
+      - module use -a /discover/nobackup/projects/gmao/SIteam/spack-stack/spack-stack-siteam/envs/ue-oneapi-2024.2.0/modules/Core
+      - module load stack-gcc/13.4.0
       - module load jedi-fv3-env
       - module load soca-env
       - module load gmao-swell-env/1.0.0
       - module unload gsibec bufr-query crtm fms
-      - module load fms/2024.02
-      - module load ip/5.1.0
+      - module load fms/2024.03-geos-constants
+      - module load ip/5.4.0
       - module load esmf python py-pyyaml py-numpy pflogger fargparse zlib-ng cmake
+      - module load libyaml/0.2.5
     configure: -DMPIEXEC_EXECUTABLE="/usr/bin/srun" -DMPIEXEC_NUMPROC_FLAG="-n"