Add the marine task

.github/workflows/pytest.yaml

@@ -39,3 +39,4 @@ jobs:
         run: |
           source obsdb/bin/activate
           pytest ush/python/pyobsforge/tests/ --disable-warnings -v
+          pytest scripts/tests/ --disable-warnings -v

jobs/JOBSFORGE_GLOBAL_MARINE_DUMP

@@ -0,0 +1,45 @@
+#! /usr/bin/env bash
+
+source "${HOMEobsforge}/ush/preamble.sh"
+source "${HOMEobsforge}/ush/jjob_header.sh"
+
+##############################################
+# Set variables used in the script
+##############################################
+
+
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
+
+###############################################################
+# Run relevant script
+
+EXSCRIPT=${DUMPMARINEPY:-${HOMEobsforge}/scripts/exobsforge_global_marine_dump.py}
+${EXSCRIPT}
+status=$?
+if [[ ${status} -ne 0 ]]; then
+    exit "${status}"
+fi
+
+
+##############################################
+# End JOB SPECIFIC work
+##############################################
+
+##############################################
+# Final processing
+##############################################
+if [[ -e "${pgmout}" ]] ; then
+  cat "${pgmout}"
+fi
+
+##########################################
+# Remove the Temporary working directory
+##########################################
+cd "${DATAROOT}" || exit
+if [[ "${KEEPDATA}" == "NO" ]]; then
+    rm -rf "${DATA}"
+fi
+
+exit 0

jobs/rocoto/marinedump.sh

@@ -0,0 +1,20 @@
+#! /usr/bin/env bash
+
+source "${HOMEobsforge}/ush/preamble.sh"
+
+###############################################################
+# Source UFSDA workflow modules
+. "${HOMEobsforge}/ush/load_obsforge_modules.sh"
+status=$?
+if [[ ${status} -ne 0 ]]; then
+    exit "${status}"
+fi
+
+export job="marinedump"
+export jobid="${job}.$$"
+
+###############################################################
+# Execute the JJOB
+"${HOMEobsforge}/jobs/JOBSFORGE_GLOBAL_MARINE_DUMP"
+status=$?
+exit "${status}"

parm/config.yaml

@@ -17,3 +17,8 @@ aoddump:
   WALLTIME_AOD_DUMP: '00:30:00'
   TASK_GEOM_AOD_DUMP: '1:ppn=1:tpp=1'
   MEMORY_AOD_DUMP: 96GB
+marinedump:
+  platforms: ['npp', 'n20', 'n21']
+  WALLTIME_AOD_DUMP: '00:30:00'
+  TASK_GEOM_AOD_DUMP: '1:ppn=1:tpp=1'
+  MEMORY_AOD_DUMP: 96GB

scripts/exobsforge_global_marine_dump.py

@@ -0,0 +1,36 @@
+#!/usr/bin/env python3
+# exobsforge_global_marine_dump.py
+# This script will collect and preprocess
+# the ocean and seaice observations for
+# global marine assimilation
+import os
+
+from wxflow import AttrDict, Logger, cast_strdict_as_dtypedict, parse_j2yaml
+from pyobsforge.task.marine_prepobs import MarineObsPrep
+
+# Initialize root logger
+logger = Logger(level='DEBUG', colored_log=True)
+
+
+if __name__ == '__main__':
+
+    # Take configuration from environment and cast it as python dictionary
+    config_env = cast_strdict_as_dtypedict(os.environ)
+
+    # Take configuration from YAML file to augment/append config dict
+    config_yaml = parse_j2yaml(os.getenv('CONFIGYAML'), config_env)
+
+    # Extract obsforge specific configuration
+    obsforge_dict = {}
+    for key, value in config_yaml['obsforge'].items():
+        if key not in config_env.keys():
+            obsforge_dict[key] = value
+
+    # Combine configs together
+    config = AttrDict(**config_env, **obsforge_dict)
+    config = AttrDict(**config, **config_yaml['marinedump'])
+
+    marineObs = MarineObsPrep(config)
+    marineObs.initialize()
+    marineObs.execute()
+    marineObs.finalize()

scripts/tests/config.yaml

@@ -0,0 +1,34 @@
+obsforge:
+  PSLOT: obsforge
+  HOMEobsforge: ""
+  SDATE: 202503160000
+  EDATE: 202503170000
+  COMROOT: ./COMROOT/
+  DCOMROOT: ./dcom
+  DATAROOT: ./RUNDIRS
+  SCHEDULER: slurm
+  ACCOUNT: da-cpu
+  QUEUE: batch
+  PARTITION: hera
+  KEEPDATA: NO
+  assim_freq: 6
+aoddump:
+  platforms: ['npp', 'n20', 'n21']
+  WALLTIME_AOD_DUMP: '00:30:00'
+  TASK_GEOM_AOD_DUMP: '1:ppn=1:tpp=1'
+  MEMORY_AOD_DUMP: 96GB
+marinedump:
+  providers:
+    ghrsst:
+    - sst_viirs_n21_l3u
+    - sst_viirs_n20_l3u
+    - sst_viirs_npp_l3u
+    - sst_avhrrf_ma_l3u
+    - sst_avhrrf_mb_l3u
+    - sst_avhrrf_mc_l3u
+    - sst_ahi_h08_l3c
+    - sst_abi_g17_l3c
+    - sst_abi_g16_l3c
+  WALLTIME_DUMP: '00:30:00'
+  TASK_GEOM_DUMP: '1:ppn=1:tpp=1'
+  MEMORY_DUMP: 96GB

scripts/tests/conftest.py

@@ -0,0 +1,24 @@
+# tests/conftest.py
+import os
+import pytest
+
+
+@pytest.fixture(scope="session", autouse=True)
+def set_env_vars():
+    os.environ["HOMEobsforge"] = os.path.abspath(os.path.join(os.path.dirname(__file__), "../.."))
+    pythonpath = os.environ.get("PYTHONPATH", "")
+    sorc_path = os.path.abspath(os.path.join(os.path.dirname(__file__), "../../sorc/wxflow/src"))
+    os.environ["PYTHONPATH"] = f"{pythonpath}:{sorc_path}"
+    os.environ["PYTHONPATH"] += f":{os.path.abspath(os.path.join(os.path.dirname(__file__), '../../ush/python'))}"
+    os.environ["CONFIGYAML"] = os.path.abspath(os.path.join(os.path.dirname(__file__), "config.yaml"))
+
+
+@pytest.fixture(autouse=True, scope="session")
+def isolate_test_output():
+    home_obsforge = os.path.abspath(os.path.join(os.path.dirname(__file__), "../.."))
+    test_dir = os.path.join(home_obsforge, 'scripts', 'tests', 'tests_output')
+    run_dir = os.path.join(test_dir, 'RUNDIRS', 'obsforge')
+    os.makedirs(test_dir, exist_ok=True)
+    os.makedirs(os.path.join(run_dir), exist_ok=True)
+
+    os.chdir(os.path.join(run_dir))