Merge remote-tracking branch 'origin/main' into 163-om3-components

README.md

@@ -2,7 +2,7 @@
 
 This is a spack package repository maintained by ACCESS-NRI for packages that are not available by default in spack. Where possible packages developed will be contributed to the builtin spack supported packages. In some cases it is not possible to do this, for example software packages that we are not the copyright holders where it isn't appropriate to distribute a package that only supports ACCESS-NRI build use-cases.
 
-The namespace of the pacakge repository is access.nri
+The namespace of the package repository is access.nri
 
 ## How to utilise this package repository
 
@@ -22,17 +22,17 @@ $ spack list oasis3_mct
 
 To use the packages in this repository first clone the repo to a path of your choosing (represented here as `$PACKAGE_PATH`)
 ```
-git clone git@github.com:ACCESS-NRI/spack_packages.git $PACKAGE_PATH/spack_packages
+git clone git@github.com:ACCESS-NRI/spack-packages.git $PACKAGE_PATH/spack-packages
 ```
 and then add the location of the repository to your spack instance
 ```
-git repo add $PACKAGE_PATH/spack_packages
+spack repo add $PACKAGE_PATH/spack-packages
 ```
 and then confirm it is has been added correctly:
 ```
 $ spack repo list
 ==> 2 package repositories.
-access.nri    $PACKAGE_PATH/spack_packages
+access.nri    $PACKAGE_PATH/spack-packages
 builtin       $SPACK_ROOT/var/spack/repos/builtin
 ```
 Now the `oasis3-mct` package should be available to install

packages/access-om2/package.py

@@ -16,7 +16,7 @@ class AccessOm2(BundlePackage):
 
     maintainers("harshula")
 
-    version("latest")
+    version("access-om2")
 
     variant("deterministic", default=False, description="Deterministic build.")
 

packages/cice4/package.py

@@ -37,7 +37,7 @@ class Cice4(MakefilePackage):
     __targets[12]["blocks"] = "12x1"
 
     # The reason for the explicit -rpath is:
-    # https://github.com/ACCESS-NRI/spack_packages/issues/14#issuecomment-1653651447
+    # https://github.com/ACCESS-NRI/spack-packages/issues/14#issuecomment-1653651447
     def get_linker_args(self, spec, name):
         return " ".join(
                     [(spec[name].libs).ld_flags,

packages/cice5/package.py

@@ -14,9 +14,9 @@ class Cice5(MakefilePackage):
     homepage = "https://www.access-nri.org.au"
     git = "https://github.com/ACCESS-NRI/cice5.git"
 
-    maintainers = ["harshula", "anton-seaice"]
+    maintainers("harshula", "anton-seaice")
 
-    version("master", branch="master", preferred=True)
+    version("access-om2", branch="master", preferred=True)
     version("access-esm1.6", branch="access-esm1.6")
 
     variant("deterministic", default=False, description="Deterministic build.")
@@ -52,15 +52,15 @@ def url_for_version(self, version):
         return "https://github.com/ACCESS-NRI/cice5/tarball/{0}".format(version)
 
     # The reason for the explicit -rpath is:
-    # https://github.com/ACCESS-NRI/spack_packages/issues/14#issuecomment-1653651447
+    # https://github.com/ACCESS-NRI/spack-packages/issues/14#issuecomment-1653651447
     def get_linker_args(self, spec, name):
         return " ".join(
                     [(spec[name].libs).ld_flags,
                     "-Wl,-rpath=" + join_path(spec[name].prefix, "lib")]
                    )
 
     # The reason for the explicit -rpath is:
-    # https://github.com/ACCESS-NRI/spack_packages/issues/14#issuecomment-1653651447
+    # https://github.com/ACCESS-NRI/spack-packages/issues/14#issuecomment-1653651447
     def make_linker_args(self, spec, name, namespecs):
         path = join_path(spec[name].prefix, "lib")
         return " ".join(

packages/fre-nctools/package.py

@@ -0,0 +1,63 @@
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
+#
+# Copyright 2025 ACCESS-NRI
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class FreNctools(AutotoolsPackage):
+    """FRE-NCtools is a collection of tools for creating grids and mosaics
+    commonly used in climate and weather models, the remapping of data among
+    grids, and the creation and manipulation of netCDF files. These tools were
+    largely written by members of the GFDL Modeling Systems Group primarily for
+    use in the Flexible Modeling System (FMS) Runtime Environment (FRE)
+    supporting the work of the Geophysical Fluid Dynamics Laboratory (GFDL)."""
+
+    homepage = "https://github.com/NOAA-GFDL/FRE-NCtools"
+    git = "https://github.com/NOAA-GFDL/FRE-NCtools.git"
+
+    maintainers("dougiesquire")
+
+    license("LGPL-3.0-only")
+
+    # A number of versions are excluded from this spack package due to bugs:
+    # - 2024.05.01: see https://github.com/NOAA-GFDL/FRE-NCtools/issues/344
+    # - 2024.03: implicit funcion delcaration in mppncscatter.c; fixed in edcdf78
+    # - 2024.01: implicit function declaration in make_topog.c; fixed in 6b4d2fb
+    # - 2023.01.02: implicit function declaration in make_topog.c; fixed in 6b4d2fb
+    # - 2023.01.01: implicit function declaration in make_topog.c; fixed in 6b4d2fb
+    # - 2023.01: implicit function declaration in make_topog.c; fixed in 6b4d2fb
+
+    version("main", branch="main")
+    version("2024.05", sha256="61cec52aa03e066b64bed794ef9dc3eb28654c3d1b872aef1b69ce99ef7a9c65")
+    version("2024.04", sha256="e27346d7ade1b67af163bb7f327a47a288d5e475fe797323bd7cee3a46385de0")
+    version("2024.02", sha256="90d52abc1b467d635dd648185b0046efcc6d58a232143b0ccaf9a0bff23d2f5d")
+    version("2022.02", sha256="bd90c9c3becdb19ff408c0915e61141376e81c12651a5c1b054c75ced9a73ad2")
+
+    variant("mpi", default=False, description="Builds with MPI support")
+
+    depends_on("autoconf", type="build")
+    depends_on("automake", type="build")
+    depends_on("libtool", type="build")
+    depends_on("netcdf-c")
+    depends_on("netcdf-fortran")
+    depends_on("mpi", when="+mpi")
+    depends_on("nco", when="@2024.05:")
+
+    def url_for_version(self, version):
+        return "https://github.com/NOAA-GFDL/FRE-NCtools/archive/{0}.tar.gz".format(version)
+
+    def configure_args(self):
+        spec = self.spec
+        args = []
+
+        # ocean_model_grid_generator subproject removed in 2023.01
+        if spec.version <= Version("2022.02"):
+            args.append("--disable-ocean-model-grid-generator")
+
+        if "+mpi" in spec:
+            args.append("--with-mpi")
+
+        return args

packages/libaccessom2/package.py

@@ -13,9 +13,9 @@ class Libaccessom2(CMakePackage):
     homepage = "https://www.access-nri.org.au"
     git = "https://github.com/ACCESS-NRI/libaccessom2.git"
 
-    maintainers = ["harshula"]
+    maintainers("harshula")
 
-    version("master", branch="master")
+    version("access-om2", branch="master", preferred=True)
 
     variant("deterministic", default=False, description="Deterministic build.")
     variant("optimisation_report", default=False, description="Generate optimisation reports.")

packages/mom5/package.py

@@ -17,7 +17,7 @@ class Mom5(MakefilePackage):
 
     maintainers("harshula", "penguian")
 
-    version("master", branch="master", preferred=True)
+    version("access-om2", branch="master", preferred=True)
     version("access-esm1.5", branch="access-esm1.5")
     version("access-esm1.6", branch="master")
 

packages/oasis3-mct/package.py

@@ -17,7 +17,7 @@ class Oasis3Mct(MakefilePackage):
 
     maintainers("harshula", "penguian")
 
-    version("master", branch="master", preferred=True)
+    version("access-om2", branch="master", preferred=True)
     version("access-esm1.5", branch="access-esm1.5")
 
     variant("deterministic", default=False, description="Deterministic build.")

packages/um/package.py

@@ -170,7 +170,7 @@ def _get_linker_args(self, spec, fcm_libname):
             spec[dep_name].libs.ld_flags,
             self._lib_cfg[fcm_libname]["fcm_ld_flags"]]
         # The reason for the explicit -rpath is:
-        # https://github.com/ACCESS-NRI/spack_packages/issues/14#issuecomment-1653651447
+        # https://github.com/ACCESS-NRI/spack-packages/issues/14#issuecomment-1653651447
         rpaths = ["-Wl,-rpath=" + d for d in spec[dep_name].libs.directories]
 
         # Both ld_flags and rpaths are lists of strings.

packages/um7/package.py

@@ -75,7 +75,7 @@ def _exe_name(self, optim_value):
     def _get_linker_args(self, spec, name):
         """
         The reason for the explicit -rpath is:
-        https://github.com/ACCESS-NRI/spack_packages/issues/14#issuecomment-1653651447
+        https://github.com/ACCESS-NRI/spack-packages/issues/14#issuecomment-1653651447
         """
         return " ".join(
                     [(spec[name].libs).ld_flags,