Move NEPTUNE Python dependencies into its their own package neptune-p…

…ython-env, remove legacy environment variables for NEPTUNE (#1343) This PR moves the full NEPTUNE Python dependencies into their own package neptune-python-dev. Only the basic dependencies on f90nml and python-dateutil remain in neptune-env (needed by NUOPC). The espc variant is turned off by default in neptune-env, but the neptune-dev template enables it. Likewise, the xnrl variant is turned off by default in neptune-python-env, but the neptune-dev template enables it. Several legacy environment variables for hdf5, libyaml, p4est are removed from configs/common/modules_*.yaml.
JCSDA · Oct 16, 2024 · 2b363ea · 2b363ea
1 parent 7db4517
commit 2b363ea
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diff --git a/configs/common/modules_lmod.yaml b/configs/common/modules_lmod.yaml
@@ -112,20 +112,10 @@ modules:
         environment:
           set:
             'ESMFMKFILE': '{prefix}/lib/esmf.mk'
-      hdf5:
-        environment:
-          set:
-            'HDF5_DIR': '{prefix}'
       libpng:
         environment:
           set:
             'PNG_ROOT': '{prefix}'
-      libyaml:
-        environment:
-          set:
-            'YAML_DIR': '{prefix}'
-            'YAML_LIB': '{prefix}/lib'
-            'YAML_INC': '{prefix}/include'
       madis:
         environment:
           set:
@@ -151,12 +141,6 @@ modules:
           set:
             'OMPI_MCA_rmaps_base_oversubscribe': '1'
             'PRTE_MCA_rmaps_default_mapping_policy': ':oversubscribe'
-      p4est:
-        environment:
-          set:
-            'P4EST_API_DIR': '{prefix}'
-            'P4EST_API_LIB': '{prefix}/lib'
-            'P4EST_API_INC': '{prefix}/include'
       bacio:
         environment:
           set:

diff --git a/configs/common/modules_tcl.yaml b/configs/common/modules_tcl.yaml
@@ -114,20 +114,10 @@ modules:
         environment:
           set:
             'ESMFMKFILE': '{prefix}/lib/esmf.mk'
-      hdf5:
-        environment:
-          set:
-            'HDF5_DIR': '{prefix}'
       libpng:
         environment:
           set:
             'PNG_ROOT': '{prefix}'
-      libyaml:
-        environment:
-          set:
-            'YAML_DIR': '{prefix}'
-            'YAML_LIB': '{prefix}/lib'
-            'YAML_INC': '{prefix}/include'
       madis:
         environment:
           set:
@@ -153,12 +143,6 @@ modules:
           set:
             'OMPI_MCA_rmaps_base_oversubscribe': '1'
             'PRTE_MCA_rmaps_default_mapping_policy': ':oversubscribe'
-      p4est:
-        environment:
-          set:
-            'P4EST_API_DIR': '{prefix}'
-            'P4EST_API_LIB': '{prefix}/lib'
-            'P4EST_API_INC': '{prefix}/include'
       bacio:
         environment:
           set:

diff --git a/configs/templates/neptune-dev/spack.yaml b/configs/templates/neptune-dev/spack.yaml
@@ -8,7 +8,8 @@ spack:
   definitions:
   - compilers: ['%aocc', '%apple-clang', '%gcc', '%intel', '%oneapi']
   - packages:
-      - neptune-env +espc +python +xnrl ^[email protected] snapshot=b11
+      - neptune-env +espc        ^[email protected] snapshot=b11
+      - neptune-python-env +xnrl ^[email protected] snapshot=b11
 
   specs:
     - matrix:

diff --git a/configs/templates/skylab-dev/spack.yaml b/configs/templates/skylab-dev/spack.yaml
@@ -17,7 +17,8 @@ spack:
     - jedi-neptune-env      ^esmf@=8.7.0b11 snapshot=b11
     - jedi-ufs-env          ^esmf@=8.6.1
     - jedi-um-env
-    - neptune-env ~espc +python ~xnrl ^esmf@=8.7.0b11 snapshot=b11
+    - neptune-env           ^esmf@=8.7.0b11 snapshot=b11
+    - neptune-python-env    ^esmf@=8.7.0b11 snapshot=b11
     - soca-env
 
     # Various crtm tags (list all to avoid duplicate packages)

diff --git a/configs/templates/unified-dev/spack.yaml b/configs/templates/unified-dev/spack.yaml
@@ -21,7 +21,8 @@ spack:
     - jedi-tools-env
     - jedi-ufs-env          ^esmf@=8.6.1
     - jedi-um-env
-    - neptune-env ~espc +python ~xnrl ^esmf@=8.7.0b11 snapshot=b11
+    - neptune-env           ^esmf@=8.7.0b11 snapshot=b11
+    - neptune-python-env    ^esmf@=8.7.0b11 snapshot=b11
     - soca-env
     - ufs-srw-app-env       ^esmf@=8.6.1
     - ufs-weather-model-env ^esmf@=8.6.1

diff --git a/spack-ext/repos/spack-stack/packages/neptune-env/package.py b/spack-ext/repos/spack-stack/packages/neptune-env/package.py
@@ -1,4 +1,4 @@
-# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Copyright 2013-2024 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)
@@ -9,19 +9,17 @@
 
 
 class NeptuneEnv(BundlePackage):
-    """Development environment for neptune standalone"""
+    """Development environment for NEPTUNE standalone"""
 
     # Fake URL
     homepage = "https://github.com/notavalidaccount/neptune"
     git = "https://github.com/notavalidaccount/neptune.git"
 
     maintainers("climbfuji", "areinecke")
 
-    version("1.4.0")
+    version("1.5.0")
 
-    variant("python", default=True, description="Build Python dependencies")
-    variant("espc", default=True, description="Build ESPC dependencies")
-    variant("xnrl", default=True, description="Build XNRL and its extra Python dependencies")
+    variant("espc", default=False, description="Build ESPC dependencies")
 
     depends_on("base-env", type="run")
 
@@ -33,7 +31,6 @@ class NeptuneEnv(BundlePackage):
     depends_on("libyaml", type="run")
     depends_on("p4est", type="run")
     depends_on("w3emc", type="run")
-    depends_on("w3nco", type="run")
     depends_on("sp", type="run", when="%aocc")
     depends_on("ip@5:", type="run", when="%apple-clang")
     depends_on("ip@5:", type="run", when="%gcc")
@@ -43,28 +40,12 @@ class NeptuneEnv(BundlePackage):
     depends_on("nco", type="run")
     depends_on("mct", type="run")
 
-    conflicts("+xnrl", when="~python", msg="Variant xnrl requires variant python")
-
     with when("+espc"):
         depends_on("fftw", type="build")
         depends_on("netlib-lapack", type="build")
 
-    with when("+python"):
-        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-pybind11", type="run")
-        depends_on("py-pyhdf", 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")
-        depends_on("py-pytest", type="run")
-        depends_on("py-fortranformat", type="run")
-
-    with when("+xnrl"):
-        depends_on("py-xnrl", type="run")
+    # Basic Python dependencies that are always needed
+    depends_on("py-f90nml", type="run")
+    depends_on("py-python-dateutil", type="run")
 
     # There is no need for install() since there is no code.
diff --git a/spack-ext/repos/spack-stack/packages/neptune-python-env/package.py b/spack-ext/repos/spack-stack/packages/neptune-python-env/package.py
@@ -0,0 +1,41 @@
+# Copyright 2013-2024 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)
+
+import sys
+
+from spack.package import *
+
+
+class NeptunePythonEnv(BundlePackage):
+    """Development environment for NEPTUNE standalone with all Python dependencies"""
+
+    # Fake URL
+    homepage = "https://github.com/notavalidaccount/neptune"
+    git = "https://github.com/notavalidaccount/neptune.git"
+
+    maintainers("climbfuji", "areinecke")
+
+    version("1.5.0")
+
+    variant("xnrl", default=False, description="Build non-pulic XNRL")
+
+    depends_on("neptune-env", 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-pybind11", type="run")
+    depends_on("py-pyhdf", type="run")
+    depends_on("py-pyyaml", type="run")
+    depends_on("py-scipy", type="run")
+    depends_on("py-xarray", type="run")
+    depends_on("py-pytest", type="run")
+    depends_on("py-fortranformat", type="run")
+
+    with when("+xnrl"):
+        depends_on("py-xnrl", type="run")
+
+    # There is no need for install() since there is no code.