Adjustments to UM and CABLE spack packages for CABLE library

.github/build-ci/actions/generate-manifest-matrix/README.md

@@ -34,6 +34,7 @@ Each matrix entry contains:
 | Name | Type | Description |
 | ---- | ---- | ----------- |
 | `matrix` | JSON array | A GitHub Actions matrix of `{template_value, repository, ref, filepath}` tuples |
+| `exclude-matrix` | JSON array | A GitHub Actions matrix of packages to exlude from matrix generation |
 
 ## Example
 
@@ -58,7 +59,8 @@ jobs:
     needs: setup
     strategy:
       matrix:
-        config: ${{ fromJson(needs.setup.outputs.matrix) }}
+        packages: ${{ fromJson(needs.setup.outputs.matrix) }}
+        exclude: ${{ fromJson(needs.setup.outputs.exclude-matrix) }}
     uses: access-nri/build-ci/.github/workflows/ci.yml@v3
     with:
       spack-manifest-repository: ${{ matrix.config.repository }}
@@ -70,6 +72,8 @@ jobs:
 
 ## Example Output
 
+### Matrix
+
 ```json
 [
   {
@@ -93,6 +97,25 @@ jobs:
 ]
 ```
 
+### Exclude Matrix
+
+In this example, the packages below are excluded because they are all Spack Bundle Recipes (SBRs), which are tested and deployed separately in Model Deployment Repositories (MDRs).
+
+```json
+[
+  "access-om2",
+  "access-om2-bgc",
+  "access-om3",
+  "access-esm1p5",
+  "access-esm1p6",
+  "access-am3",
+  "access-ram3",
+  "access-issm",
+  "access-test",
+  "coastri-roms"
+]
+```
+
 ## Notes
 
 - `repository` is extracted from HTTPS git URLs in `owner/repo` format.

.github/build-ci/actions/generate-manifest-matrix/action.yaml

@@ -21,6 +21,10 @@ outputs:
     description: |
       A GitHub Actions matrix of repository, ref, manifest path, and package name tuples.
     value: ${{ steps.gen.outputs.matrix }}
+  exclude-matrix:
+    description: |
+      A GitHub Actions matrix of excluded matrix entries
+    value: ${{ steps.exclude.outputs.matrix }}
 runs:
   using: composite
   steps:
@@ -159,4 +163,17 @@ runs:
         echo "$json_entries"
 
         # Remove the trailing comma and wrap in square brackets
-        echo "matrix=[${json_entries%,}]" >> $GITHUB_OUTPUT
+        echo "matrix=[${json_entries%,}]" >> $GITHUB_OUTPUT
+
+    - name: Generate exclude matrix
+      shell: bash
+      id: exclude
+      env:
+        EXCLUSION_MATRIX_FILE_PATH: .github/build-ci/data/exclude.json
+      run: |
+        matrix="$(jq -cr '[.[] | {package: {template_value: .}}]' ${{ env.EXCLUSION_MATRIX_FILE_PATH }})"
+
+        echo "Exclusion matrix from ${{ env.EXCLUSION_MATRIX_FILE_PATH }}:"
+        echo "$matrix"
+
+        echo "matrix=$matrix" >> $GITHUB_OUTPUT

.github/build-ci/data/exclude.json

@@ -0,0 +1,12 @@
+[
+	"access-om2",
+	"access-om2-bgc",
+	"access-om3",
+	"access-esm1p5",
+	"access-esm1p6",
+	"access-am3",
+	"access-ram3",
+	"access-issm",
+	"access-test",
+	"coastri-roms"
+]

.github/workflows/ci.yml

@@ -42,7 +42,9 @@ jobs:
       BUILD_CI_WORKFLOW_VERSION: v3
       PACKAGES_ROOT_DIR: spack_repo/access/nri/packages
     outputs:
+      # Output both a matrix of {repo, ref, path, package}s, and a matrix of packages for exclusion
       matrix: ${{ steps.set-matrix.outputs.matrix }}
+      exclude-matrix: ${{ steps.set-matrix.outputs.exclude-matrix }}
       builtin-spack-packages-ref: ${{ inputs.builtin-spack-packages-ref }}
       access-spack-packages-ref: ${{ inputs.access-spack-packages-ref || github.event.pull_request.head.sha }}
       spack-config-ref: ${{ inputs.spack-config-ref || steps.defaults.outputs.spack-config-ref }}
@@ -139,21 +141,10 @@ jobs:
       - setup-ci
     strategy:
       fail-fast: false
-      max-parallel: 5
+      max-parallel: 10
       matrix:
         package: ${{ fromJson(needs.setup-ci.outputs.matrix) }}
-        exclude:
-          - package: {template_value: "access-om2"}
-          - package: {template_value: "access-om2-bgc"}
-          - package: {template_value: "access-om3"}
-          - package: {template_value: "access-esm1p5"}
-          - package: {template_value: "access-esm1p6"}
-          - package: {template_value: "access-am3"}
-          - package: {template_value: "access-ram3"}
-          - package: {template_value: "access-issm"}
-          - package: {template_value: "access-test"}
-          - package: {template_value: "coastri-roms"}
-          - package: {template_value: "gcom4"}
+        exclude: ${{ fromJson(needs.setup-ci.outputs.exclude-matrix) }}
     uses: access-nri/build-ci/.github/workflows/ci.yml@v3
     with:
       spack-manifest-repository: ${{ matrix.package.repository }}

spack_repo/access/nri/build_systems/um_base.py

@@ -58,17 +58,18 @@ class UmBasePackage(Package):
     _bool_variants = (
         "DR_HOOK",
         "eccodes",
-        "netcdf")
+        "netcdf",
+        "cable")
     for var in _bool_variants:
-        variant(var, default=True, description=var)
+        variant(var, default=True, sticky=True, description=var)
 
     # Off/on variants have 3-value "none" "off", "on" logic.
     _off_on_variants = (
         "openmp",
         "platagnostic",
         "thread_utils")
     for var in _off_on_variants:
-        variant(var, default="none", description=var,
+        variant(var, default="none", sticky=True, description=var,
             values=("none", "off", "on"), multi=False)
 
     # String variants have their default values set to "none" here.
@@ -89,19 +90,31 @@ class UmBasePackage(Package):
         if _project != "um":
             _rev_var = f"{_project}_rev"
             _rev_variants.append(_rev_var)
-            variant(_rev_var, default="none", values="*", multi=False,
+            variant(
+                _rev_var,
+                default="none",
+                sticky=True,
+                values="*",
+                multi=False,
                 description=f"Subversion revision for {_project}. "
-                            f"Defaults to automatic versioning if 'none'.")
+                            f"Defaults to automatic versioning if 'none'."
+            )
 
         # Sources variants
         _sources_var = f"{_project}_sources"
         _sources_variants.append(_sources_var)
-        variant(_sources_var, default="none", values="*", multi=False,
-            description=f"FCM diff extract location of {_project}.")
+        variant(
+            _sources_var,
+            default="none",
+            sticky=True,
+            values="*",
+            multi=False,
+            description=f"FCM diff extract location of {_project}."
+        )
 
         # Git reference variants.
         _ref_var = f"{_project}_ref"
-        variant(_ref_var, default="none", values="*", multi=False,
+        variant(_ref_var, default="none", sticky=True, values="*", multi=False,
             description=f"Git branch/tag/commit for {_project}. "
                         f"Overrides Subversion. "
                         f"Defaults to automatic tagging if 'none'.")
@@ -147,7 +160,14 @@ class UmBasePackage(Package):
     ]
 
     for _var in _other_variants:
-        variant(_var, default="none", values="*", multi=False, description=_var)
+        variant(
+            _var,
+            default="none",
+            sticky=True,
+            values="*",
+            multi=False,
+            description=_var
+        )
 
     depends_on("c", type="build")
     depends_on("fortran", type="build")
@@ -161,6 +181,7 @@ class UmBasePackage(Package):
         when="+eccodes")
     depends_on("netcdf-fortran@4.5.2:", type=("build", "link", "run"),
         when="+netcdf")
+    depends_on("cable library='access3'", type=("build", "link", "run"))
 
     phases = ["build", "install"]
 
@@ -184,7 +205,12 @@ class UmBasePackage(Package):
             "includes": ["include"],
             "dep_name": "netcdf-fortran",
             "fcm_name": "netcdf",
-            "fcm_ld_flags": "-lnetcdff -lnetcdf"}}
+            "fcm_ld_flags": "-lnetcdff -lnetcdf"},
+        "cable": {
+            "includes": ["include"],
+            "dep_name": "cable",
+            "fcm_name": "cable",
+            "fcm_ld_flags": ""}}
 
     # List of model variants that have Github sources.
     # Should be overridden by child classes.
@@ -507,6 +533,7 @@ def check_model_vs_root_path_vs_um_ref(
         # Set environment variables based on config_env.
         for key in config_env:
             tty.info(f"{key}={config_env[key]}")
+            print(f"Debugging: {key}={config_env[key]}")
             env.set(key, config_env[key])
 
         # Add the location of the FCM executable to PATH.

spack_repo/access/nri/packages/access3_share/package.py

@@ -24,7 +24,7 @@ class Access3Share(CMakePackage):
     for tag, commit in ACCESS3_VERSIONS.items():
         version(tag, tag=tag, commit=commit)
 
-    variant("openmp", default=False, description="Enable OpenMP")
+    variant("openmp", default=False, sticky=True, description="Enable OpenMP")
 
     depends_on("c", type="build")
     depends_on("fortran", type="build")

spack_repo/access/nri/packages/access_cice/package.py

@@ -26,21 +26,24 @@ class AccessCice(CMakePackage):
     version("CICE6.6.0-3", tag="CICE6.6.0-3", commit="2c444bd9d2fad1f1df4d855debc2801d4b23487d")
     version("CICE6.6.0-1", tag="CICE6.6.0-1", commit="964a4455db3127d0c4681e6533f6d9733a5e8255")
 
-    variant("openmp", default=False, description="Enable OpenMP")
+    variant("openmp", default=False, sticky=True, description="Enable OpenMP")
     variant(
         "access3",
         default=True,
+        sticky=True,
         description="Install CICE as library for Access3 models"
     )
 
     variant("io_type", 
         default="NetCDF",
+        sticky=True,
         values=("NetCDF", "PIO", "Binary"),
         description="CICE IO Method"
     )
 
     variant("driver",
             default="none",
+            sticky=True,
             values=("none", "nuopc/cmeps", "access/cmeps", "standalone/cice"),
             description="CICE driver path"
     )

spack_repo/access/nri/packages/access_esm1p6/package.py

@@ -31,13 +31,15 @@ class AccessEsm1p6(BundlePackage):
     variant(
         "cice",
         default="5",
+        sticky=True,
         description="(Deprecated) choose the version of the CICE sea-ice model.",
         values=("5"),
         multi=False,
     )
     variant(
         "um",
         default="access-esm1.6",
+        sticky=True,
         description="Choose the branch of um7.",
         values=("access-esm1.5", "access-esm1.6"),
         multi=False,

spack_repo/access/nri/packages/access_fms/package.py

@@ -26,15 +26,16 @@ class AccessFms(CMakePackage):
     version("main", branch="main")
     version("mom5", branch="mom5", preferred=True)
 
-    variant("gfs_phys", default=False, description="Use GFS Physics")
-    variant("large_file", default=False, description="Enable compiler definition -Duse_LARGEFILE.")
+    variant("gfs_phys", default=False, sticky=True, description="Use GFS Physics")
+    variant("large_file", default=False, sticky=True, description="Enable compiler definition -Duse_LARGEFILE.")
     variant(
         "internal_file_nml",
         default=True,
+        sticky=True,
         description="Enable compiler definition -DINTERNAL_FILE_NML.",
     )
-    variant("pic", default=False, description="Build with position independent code")
-    variant("shared", default=False, description="Build shared/dynamic libraries")
+    variant("pic", default=False, sticky=True, description="Build with position independent code")
+    variant("shared", default=False, sticky=True, description="Build shared/dynamic libraries")
     # To build a shared/dynamic library, both `pic` and `shared` are required:
     requires("+pic", when="+shared", msg="The +shared variant requires +pic")
 

spack_repo/access/nri/packages/access_generic_tracers/package.py

@@ -38,13 +38,15 @@ class AccessGenericTracers(CMakePackage):
     variant(
         "shared",
         default=False,
+        sticky=True,
         description="Build shared/dynamic libraries"
     )
     # NOTE: access-fms@mom5 should be used in OM2, ESM1.5 and ESM1.6 to preserve
     # answers with previous releases
     variant(
         "use_access_fms",
         default=True,
+        sticky=True,
         description="If True, depend on access-fms, otherwise depend on fms"
     )
 

spack_repo/access/nri/packages/access_mocsy/package.py

@@ -34,18 +34,21 @@ class AccessMocsy(CMakePackage):
     variant(
         "shared",
         default=False,
+        sticky=True,
         description="Build shared/dynamic libraries",
         when="@2025.07.002:",
     )
     variant(
         "build_type",
         default="RelWithDebInfo",
+        sticky=True,
         description="CMake build type",
         values=("Debug", "Release", "RelWithDebInfo", "MinSizeRel"),
     )
     variant(
         "precision",
         default="2",
+        sticky=True,
         description="Precision to use (1 or 2)",
         values=("1", "2"),
     )

spack_repo/access/nri/packages/access_mom6/package.py

@@ -35,16 +35,18 @@ class AccessMom6(CMakePackage):
     version("2025.02.001", tag="2025.02.001", commit="a5f4397b953f749acecf06f21129c2a20aa578fe")
     version("2025.02.000", tag="2025.02.000", commit="e088c8b7f6c2b18b72edd568aa009e13396ec0c3")
 
-    variant("openmp", default=False, description="Enable OpenMP")
-    variant("asymmetric_mem", default=False, description="Use asymmetric memory in MOM6")
+    variant("openmp", default=False, sticky=True, description="Enable OpenMP")
+    variant("asymmetric_mem", default=False, sticky=True, description="Use asymmetric memory in MOM6")
     variant(
         "access3",
         default=True,
+        sticky=True,
         description="Install MOM6 as library for Access3 models"
     )
     variant(
         "mom6_solo",
         default=False,
+        sticky=True,
         description="Install MOM6 solo executable",
         when="@2025.07.001:"
     )

spack_repo/access/nri/packages/access_om2/package.py

@@ -19,7 +19,7 @@ class AccessOm2(BundlePackage):
 
     version("latest")
 
-    variant("deterministic", default=False, description="Deterministic build.")
+    variant("deterministic", default=False, sticky=True, description="Deterministic build.")
 
     depends_on("libaccessom2+deterministic", when="+deterministic", type="run")
     depends_on("libaccessom2~deterministic", when="~deterministic", type="run")

spack_repo/access/nri/packages/access_om2_bgc/package.py

@@ -19,7 +19,7 @@ class AccessOm2Bgc(BundlePackage):
 
     version("latest")
 
-    variant("deterministic", default=False, description="Deterministic build.")
+    variant("deterministic", default=False, sticky=True, description="Deterministic build.")
 
     depends_on("libaccessom2+deterministic", when="+deterministic", type="run")
     depends_on("libaccessom2~deterministic", when="~deterministic", type="run")

spack_repo/access/nri/packages/access_triangle/package.py

@@ -23,7 +23,7 @@ class AccessTriangle(MakefilePackage):
     version("1.6.1", branch="main")
 
     # variant for building the showme utility (requires X11).
-    variant("showme", default=False,
+    variant("showme", default=False, sticky=True,
             description="Build the showme utility (requires libX11).")
 
     depends_on("c", type="build")