Remove dependency on py-xnrl (#1753)

Author: climbfuji

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

@@ -99,11 +99,6 @@ jobs:
             # Add additional variants for MET packages, different from config/common/packages.yaml
             spack config add "packages:met:variants:+python +grib2 +graphics +lidar2nc +modis"
 
-            # Turn off variant xnrl for neptune-python-env because xnrl is not publicly available
-            if [[ "${TEMPLATE}" == *"neptune-dev"* ]]; then
-              sed -i 's/+xnrl/~xnrl/g' ${ENVDIR}/spack.yaml
-            fi
-
             # Concretize and check for duplicates
             spack concretize 2>&1 | tee log.concretize.gnu-11.4.0-buildcache
             ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i neptune-env

configs/sites/tier1/atlantis/packages.yaml

@@ -87,11 +87,6 @@ packages:
   #  externals:
   #  - spec: openssl@1.1.1k
   #    prefix: /usr
-  # Can't use with py-xnrl
-  #perl:
-  #  externals:
-  #  - spec: perl@5.26.3~cpanm+shared+threads
-  #    prefix: /usr
   pkgconf:
     externals:
     - spec: pkgconf@1.4.2

configs/sites/tier1/nautilus/packages.yaml

@@ -17,7 +17,7 @@ packages:
     require:
         - '@2.5.1'
 
-# All other packages listed alphabetically
+  # All other packages listed alphabetically
   autoconf:
     externals:
     - spec: autoconf@2.69
@@ -30,13 +30,6 @@ packages:
     externals:
     - spec: binutils@2.30.117
       prefix: /usr
-  # Need to comment out for scotch (wants 3.4:),
-  # but how do we deal with oneapi installations?
-  # bison doesn't build with oneAPI.
-  #bison:
-  #  externals:
-  #  - spec: bison@3.0.4
-  #    prefix: /usr
   coreutils:
     externals:
     - spec: coreutils@8.30
@@ -91,11 +84,6 @@ packages:
       prefix: /p/app/projects/NEPTUNE/spack-stack/mysql-8.0.31
       modules:
       - mysql/8.0.31
-  # Needed to remove for xnrl w/intel, hopefully ok with oneapi
-  #perl:
-  #  externals:
-  #  - spec: perl@5.26.3~cpanm+open+shared+threads
-  #    prefix: /usr
   pkgconf:
     externals:
     - spec: pkgconf@1.4.2

configs/templates/neptune-dev/spack.yaml

@@ -10,7 +10,7 @@ spack:
   - packages:
       - neptune-env ~debug +espc ^esmf@=8.9.0b12 snapshot=b12
       - neptune-env +debug +espc ^esmf@=8.9.0b12 snapshot=b12
-      - neptune-python-env +xnrl ^neptune-env ~debug +espc ^esmf@=8.9.0b12 snapshot=b12
+      - neptune-python-env ^neptune-env ~debug +espc ^esmf@=8.9.0b12 snapshot=b12
 
   specs:
     - matrix:

doc/source/PreConfiguredSites.rst

@@ -24,7 +24,7 @@ The following naming conventions are used on all fully-supported (tier 1) sites.
 +----------------------------------+---------------------------------------------------------+-------------------+------------------------------+
 | ``skylab-dev``                   | JEDI/Skylab environment for JEDI, models, EWOK          | ``se``            | ``se-apple-clang-14.0.6``    |
 +----------------------------------+---------------------------------------------------------+-------------------+------------------------------+
-| ``neptune-dev``                  | NEPTUNE standalone environment (with xNRL Python)       | ``ne``            | ``ne-oneapi-2024.2.1``       |
+| ``neptune-dev``                  | NEPTUNE-JEDI standalone environment                     | ``ne``            | ``ne-oneapi-2024.2.1``       |
 +----------------------------------+---------------------------------------------------------+-------------------+------------------------------+
 | ``cylc-dev``                     | Environment for running cylc (separate from other envs) | ``ce``            | ``ce-gcc-10.3.0``            |
 +----------------------------------+---------------------------------------------------------+-------------------+------------------------------+

spack-ext/repos/spack-stack/packages/gmao-swell-env/package.py

@@ -49,11 +49,7 @@ class GmaoSwellEnv(BundlePackage):
     depends_on("py-pyyaml", type="run")
     depends_on("py-ruamel-yaml", type="run")
     depends_on("py-ruamel-yaml-clib", type="run")
-    # Note that the +delayed option is for compatibility
-    # with the py-xnrl package (this restricts py-dask
-    # to certain versions, since the newest versions
-    # don't have that option anymore.
-    depends_on("py-dask +delayed", type="run")
+    depends_on("py-dask", type="run")
 
     # Future dependencies needed
     # depends_on("py-bokeh", type="run")

spack-ext/repos/spack-stack/packages/neptune-python-env/package.py

@@ -19,8 +19,6 @@ class NeptunePythonEnv(BundlePackage):
 
     version("1.5.0")
 
-    variant("xnrl", default=False, description="Build non-pulic XNRL")
-
     depends_on("neptune-env", type="run")
     # Enable the Python variant for ESMF
     depends_on("esmf +python", type="run")
@@ -42,7 +40,4 @@ class NeptunePythonEnv(BundlePackage):
     depends_on("met", type="run")
     depends_on("metplus", type="run")
 
-    with when("+xnrl"):
-        depends_on("py-xnrl", type="run")
-
     # There is no need for install() since there is no code.