Merge branch 'develop' into feature/python-updates

Author: eap

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

@@ -73,6 +73,7 @@ jobs:
             # Turn off certain variants for neptune-dev (NRL internal only)
             if [[ "${TEMPLATE}" == *"neptune-dev"* ]]; then
               sed -i 's/+adp/~adp/g' ${ENVDIR}/spack.yaml
+              sed -i 's/+sdp/~sdp/g' ${ENVDIR}/spack.yaml
               sed -i 's/+jedi/~jedi/g' ${ENVDIR}/spack.yaml
               sed -i 's/+lis-ncoda-utils/~lis-ncoda-utils/g' ${ENVDIR}/spack.yaml
             fi

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

@@ -73,6 +73,7 @@ jobs:
             # Turn off certain variants for neptune-dev (NRL internal only)
             if [[ "${TEMPLATE}" == *"neptune-dev"* ]]; then
               sed -i 's/+adp/~adp/g' ${ENVDIR}/spack.yaml
+              sed -i 's/+sdp/~sdp/g' ${ENVDIR}/spack.yaml
               sed -i 's/+jedi/~jedi/g' ${ENVDIR}/spack.yaml
               sed -i 's/+lis-ncoda-utils/~lis-ncoda-utils/g' ${ENVDIR}/spack.yaml
             fi

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

@@ -73,6 +73,7 @@ jobs:
             # Turn off certain variants for neptune-dev (NRL internal only)
             if [[ "${TEMPLATE}" == *"neptune-dev"* ]]; then
               sed -i 's/+adp/~adp/g' ${ENVDIR}/spack.yaml
+              sed -i 's/+sdp/~sdp/g' ${ENVDIR}/spack.yaml
               sed -i 's/+jedi/~jedi/g' ${ENVDIR}/spack.yaml
               sed -i 's/+lis-ncoda-utils/~lis-ncoda-utils/g' ${ENVDIR}/spack.yaml
             fi

configs/templates/neptune-dev-llvm/spack.yaml

@@ -13,12 +13,7 @@ spack:
   - neptune-env +debug +openmp +espc +ncview ^esmf@=9.0.0b11
   - neptune-env ~debug ~openmp +espc +ncview ^esmf@=9.0.0b11
   - neptune-env +debug ~openmp +espc +ncview ^esmf@=9.0.0b11
-  # Until we can build the entire set of dependencies for
-  # neptune-python-env and jedi-neptune-env, we need to
-  # add the required packages for the NEPTUNE standalone
-  # model manually
-  #- neptune-python-env    ^neptune-env ~debug +openmp +espc +ncview ^esmf@=9.0.0b11
-  #- jedi-neptune-env +adp ^neptune-env ~debug +openmp +espc +ncview ^esmf@=9.0.0b11
+
   - py-numpy
   - crtm@3.1.3
 

configs/templates/neptune-dev/spack.yaml

@@ -27,7 +27,7 @@ spack:
   - neptune-env ~debug ~openmp +espc +ncview ^esmf@=9.0.0b11
   - neptune-env +debug ~openmp +espc +ncview ^esmf@=9.0.0b11
   - neptune-python-env +gittools +lis-ncoda-utils ^neptune-env ~debug +openmp +espc +ncview ^esmf@=9.0.0b11
-  - jedi-neptune-env +adp +jedi                   ^neptune-env ~debug +openmp +espc +ncview ^esmf@=9.0.0b11
+  - jedi-neptune-env +adp +sdp +jedi              ^neptune-env ~debug +openmp +espc +ncview ^esmf@=9.0.0b11
   - crtm@3.1.3
 
   packages:

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

@@ -14,16 +14,19 @@ class AdpPreprocessors(MakefilePackage):
     """Unified, model-agnostic software system that processes atmospheric observations for the Navy's numerical weather prediction data assimilation systems"""
 
     homepage = "https://github.nrlmry.navy.mil/ADP/adp-preprocessors/wiki"
-    #git = "https://github.nrlmry.navy.mil/ADP/adp-preprocessors.git"
-    git = "https://github.nrlmry.navy.mil/climbfuji/adp-preprocessors.git"
+    git = "https://github.nrlmry.navy.mil/ADP/adp-preprocessors.git"
 
     maintainers("climbfuji")
 
-    #license("UNKNOWN", checked_by="github_user1")
+    license("custom", checked_by="climbfuji")
 
-    # Update commit once 1.2.0 is released
-    version("1.2.0", commit="c6f15e46496309c3893416ba4ccec7f003b93550")
-    version("1.1.0", commit="b2d9d4ffb472eff9ab973ef2a12f574d92c9754b")
+    # These are not official versions; 1.1.1 lives in @climbfuji's fork.
+    version("1.1.2", commit="729b0e7572a497b1103d0b8b1e6ff3972efd0d29")
+    version(
+        "1.1.1",
+        git="https://github.nrlmry.navy.mil/climbfuji/adp-preprocessors.git",
+        commit="c6f15e46496309c3893416ba4ccec7f003b93550"
+    )
 
     # MakefilePackage dependencies
     depends_on("c", type="build")
@@ -58,7 +61,7 @@ def build(self, spec, prefix):
                 raise InstallError(f"Compiler {self.compiler.name} not configured")
 
     def install(self, spec, prefix):
-        for subdir in ['bin', 'lib', 'mod']:
+        for subdir in ['bin', 'etc', 'lib', 'mod']:
             copy_tree(join_path(self.stage.source_path, subdir), join_path(prefix, subdir))
 
     def check(self):

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

@@ -17,10 +17,11 @@ class Ioda(CMakePackage):
     maintainers("climbfuji")
 
     version("develop", branch="develop", no_cache=True)
+    version("2.9.0.20260326", commit="9e0eb39fb87ae66667ef966cf27b62d5a804cc54")
     version("2.9.0.20250826", commit="6e76616001067384f7d0ca4341ad78e81527af8b")
 
     patch("ioda_cmake_import.patch", when="@2.9.0.20250826")
-    patch("ioda_yaml_root.patch", when="@2.9.0.20250826")
+    patch("ioda_yaml_root.patch", when="@2.9.0.20250826:")
 
     variant("doc", default=False, description="Build IODA documentation")
     # Let's always assume IODA_BUILD_LANGUAGE_FORTRAN=on.
@@ -43,7 +44,8 @@ class Ioda(CMakePackage):
     depends_on("bufr@12.0.1:", when="@2.9:")
     depends_on("bufr-query@0.0.4:", when="@2.9:")
     depends_on("cmake", type=("build"))
-    depends_on("cmake@3.14:", type=("build"), when="@2.9:")
+    depends_on("cmake@3.15:", type=("build"), when="@2.9.0.20260326")
+    depends_on("cmake@3.14:", type=("build"), when="@2.9.0.20250826")
     depends_on("ecbuild", type=("build"))
     depends_on("ecbuild@3.3.2:", type=("build"), when="@2.9:")
     depends_on("eckit")
@@ -55,7 +57,8 @@ class Ioda(CMakePackage):
     depends_on("hdf5@1.12.0: +mpi")
     depends_on("hdf5@1.14.0: +mpi", when="@2.9:")
     depends_on("ioda-data", type=("build", "test"))
-    depends_on("ioda-data@2.9.0.20250805", type=("build", "test"), when="@2.9:")
+    depends_on("ioda-data@2.9.0.20260319", type=("build", "test"), when="@2.9.0.20260326")
+    depends_on("ioda-data@2.9.0.20250805", type=("build", "test"), when="@2.9.0.20250826")
     depends_on("jedi-cmake", type=("build"))
     depends_on("llvm-openmp", when="+openmp %apple-clang", type=("build", "link", "run"))
     depends_on("mpi")
@@ -65,7 +68,8 @@ class Ioda(CMakePackage):
     depends_on("odc@1.4.6:", when="@2.9: +odc")
     depends_on("oops+openmp", when="+openmp")
     depends_on("oops~openmp", when="~openmp")
-    depends_on("oops@1.10", when="@2.9:")
+    depends_on("oops@1.10.0.20260331", when="@2.9.0.20260326")
+    depends_on("oops@1.10.0.20250827", when="@2.9.0.20250826")
     depends_on("python")
     depends_on("python@3.9:3.11", when="@2.9:")
     depends_on("py-pybind11")
@@ -94,19 +98,16 @@ def check(self):
                 "test_ioda_bufr_python_encoder",
                 "test_ioda_bufr_python_parallel",
             ]
+        with when("@2.9.0.20260326"):
+            # No time to deal with the bufr Python dependency
+            skipped_tests = [
+                "ioda_bufr_python_encoder",
+                "ioda_bufr_python_parallel",
+            ]
 
         ctest = Executable(self.spec["cmake"].prefix.bin.ctest)
         with working_dir(self.build_directory):
             if skipped_tests:
                 ctest("--timeout", "120", "-E", "|".join(skipped_tests))
             else:
                 ctest("--timeout", "120")
-
-    #@run_after("install")
-    #def fix_ioda_yaml_root_path(self):
-    #    with when("@2.9.0.20250826"):
-    #        filter_file(
-    #            join_path(self.build_directory, "share/test/testinput/"),
-    #            join_path(self.prefix, "share/ioda/yaml"),
-    #            join_path(self.prefix, "lib64/cmake/ioda/ioda-import.cmake"),
-    #        )

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

@@ -80,6 +80,14 @@ def check(self):
                 #  >> 2169    The following tests FAILED:
                 # 52 - test_iodaconv_mrms (Timeout)                      iodaconv
                 "test_iodaconv_mrms",
+                #2: ./gsi_ncdiag.py:80:77: E502 the backslash is redundant between brackets
+                #2: ./gsi_ncdiag.py:81:53: E502 the backslash is redundant between brackets
+                #2: checking ./ncdiag_to_feedback.py
+                #2: checking ./proc_gsi_ncdiag.py
+                #2: checking ./test_gsidiag.py
+                #2: 2       E502 the backslash is redundant between brackets
+                #1/1 Test #2: iodaconv_gsi_ncdiag_coding_norms ...***Failed    0.30 sec
+                "iodaconv_gsi_ncdiag_coding_norms",
             ]
 
         ctest = Executable(self.spec["cmake"].prefix.bin.ctest)

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

@@ -17,19 +17,9 @@ class IodaData(CMakePackage):
     maintainers("climbfuji")
 
     version("develop", branch="develop", no_cache=True)
+    version("2.9.0.20260319", commit="2886c75398b4b3bdd3a4235298af188370727c2e")
     version("2.9.0.20250805", commit="c6f8842648ea473eebc9f66d7c27e2204e5220d6")
 
-#    patch("ioda_cmake_import.patch", when="@2.9.0.20250826")
-#
-#    variant("doc", default=False, description="Build IODA documentation")
-#    # Let's always assume IODA_BUILD_LANGUAGE_FORTRAN=on.
-#    # variant('fortran', default=True, description='Build the ioda Fortran interface')
-#    variant("odc", default=True, description="Build ODC bindings")
-#    # ioda has no explicit OpenMP calls, but header files from Eigen and oops do use openmp.
-#    variant("openmp", default=True, description="Build with OpenMP support")
-#    # Let's always BUILD_PYTHON_BINDINGS.
-#    # variant('python', default=True, description='Build the ioda Python interface')
-
     generator("make")
 
     depends_on("c", type=("build"))

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

@@ -17,9 +17,11 @@ class JediNeptuneEnv(BundlePackage):
 
     maintainers("climbfuji", "areineke")
 
+    version("1.1.0")
     version("1.0.0")
 
     variant("adp", default=False, description="Build ADP preprocessors")
+    variant("sdp", default=False, description="Build SDP preprocessors")
 
     variant("jedi", default=False, description="Build JEDI components required for JEDI-NEPTUNE")
 
@@ -30,7 +32,10 @@ class JediNeptuneEnv(BundlePackage):
     with when("+adp"):
         depends_on("adp-preprocessors", type="run")
 
-    with when("+jedi"):
+    with when("+sdp"):
+        depends_on("sdp-preprocessors", type="run")
+
+    with when("@1.0.0 +jedi"):
         # https://github.com/JCSDA/spack-stack/issues/2015
         # Changed type from "run" to "build" so that
         # the modules don't get loaded automatically
@@ -40,3 +45,12 @@ class JediNeptuneEnv(BundlePackage):
         depends_on("ioda-converters@0.0.1.20250830", type="build")
         depends_on("ropp-ufo@11.0.20251022", type="build")
         depends_on("ufo@1.10.0.20250821 +ropp", type="build")
+
+    with when("@1.1.0 +jedi"):
+        depends_on("oops@1.10.0.20260331", type="build")
+        depends_on("crtm@3.1.3", type="build")
+        depends_on("ioda@2.9.0.20260326", type="build")
+        # Same ioda-converters and ropp-ufo as for 1.0.0
+        depends_on("ioda-converters@0.0.1.20250830", type="build")
+        depends_on("ropp-ufo@11.0.20251022", type="build")
+        depends_on("ufo@1.10.0.20260331 +ropp", type="build")