Add initial changes to pythonize and yamlize staging

- Add initial new yaml files for staging information
- Add new stage.py to python tasks.
- Add first draft pythonization of stage ex-script.

Much more work is still to be done.

Refs NOAA-EMC#2475

parm/stage/da.yaml.j2

@@ -0,0 +1,6 @@
+#for ftype in ['abias', 'abias_pc', 'abias_air', 'radstat']:
+da:
+    name: "DA"
+    source: "{{ BASE_CPLIC }}/{{ CPL_ICEIC }}/{{ cycle_YMD }}{{ cycle_HH }}/{{ MEMDIR }}/ice"
+    required:
+        - "{{ COM_ICE_RESTART_PREV | relpath(ROTDIR) }}/{{ cycle_YMD }}.{{ cycle_HH }}0000.cice_model.res.nc"

parm/stage/fv3.yaml.j2

@@ -0,0 +1,36 @@
+# # First 1/2 cycle also needs a atmos increment if doing warm start
+#   if inputs.start in ['warm']:
+#       for ftype in ['atmi003.nc', 'atminc.nc', 'atmi009.nc']:
+# if inputs.nens > 0:
+#for ftype in ['ratmi003.nc', 'ratminc.nc', 'ratmi009.nc']
+fv3:
+    name: "FV3"
+    source: "{{ BASE_CPLIC }}/{{ CPL_ATMIC }}/{{ cycle_YMD }}{{ cycle_HH }}/{{ MEMDIR }}/atmos"
+    required:
+        #---------------
+        # WARM START
+        #---------------
+        {% if EXP_WARM_START %}
+        {% set head = "{{ COM_ATMOS_RESTART_PREV | relpath(ROTDIR) }}/{{ cycle_YMD }}.{{ cycle_HH }}0000." %}
+        {% for ftype in coupler.res fv_core.res.nc %}
+        - "{{ head }}{{ ftype }}"
+        {% endfor %}
+        {% for ftype in ca_data fv_core.res fv_srf_wnd.res fv_tracer.res phy_data sfc_data %}
+        {% for ntile in $(seq 1 ntiles) %}
+        - "{{ head }}{{ ftype }}.tile{{ ntile }}.nc"
+        {% endfor %} # ntile
+        {% endfor %} # ftype
+        #--------------- # end warm start
+        {% else %}
+        #---------------
+        # COLD START
+        #---------------
+        {% set head = "{{ COM_ATMOS_INPUT | relpath(ROTDIR) }}" %}
+        - "{{ head }}/gfs_ctrl.nc"
+        {% for ftype in gfs_data sfc_data %}
+        {% for ntile in $(seq 1 ntiles) %}
+        - "{{ head }}/{{ ftype }}.tile{{ ntile }}.nc"
+        {% endfor %} # ntile
+        {% endfor %} # ftype
+        #--------------- # end cold start
+        {% endif %}

parm/stage/fv3_nest.yaml.j2

@@ -0,0 +1,41 @@
+#WARM
+# for ftype in ca_data fv_core.res fv_srf_wnd.res fv_tracer.res phy_data sfc_data; do
+#       src="${BASE_CPLIC}/${CPL_ATMIC:-}/${PDY}${cyc}/${MEMDIR}/atmos/${PDY}.${cyc}0000.${ftype}.tile${tt}.nc"
+#       if (( tt > 6 )) ; then
+#           tgt="${COM_ATMOS_RESTART_PREV}/${PDY}.${cyc}0000.${ftype}.nest0$((tt-5)).tile${tt}.nc"
+#       fi
+#COLD
+# for ftype in gfs_data sfc_data; do
+#     for ((tt = 1; tt <= ntiles; tt++)); do
+#       src="${BASE_CPLIC}/${CPL_ATMIC:-}/${PDY}${cyc}/${MEMDIR}/atmos/${ftype}.tile${tt}.nc"
+#       tgt="${COM_ATMOS_INPUT}/${ftype}.tile${tt}.nc"
+# if (( ntiles > 6 )); then
+#       ${NLN} "${COM_ATMOS_INPUT}/${ftype}.tile7.nc" "${COM_ATMOS_INPUT}/${ftype}.nest02.tile7.nc"
+fv3:
+    name: "FV3"
+    source: "{{ BASE_CPLIC }}/{{ CPL_ATMIC }}/{{ cycle_YMD }}{{ cycle_HH }}/{{ MEMDIR }}/atmos"
+    {% set ntile = 7 %}
+    required:
+        #---------------
+        # WARM START
+        #---------------
+        {% if EXP_WARM_START %}
+        {% set head = "{{ COM_ATMOS_RESTART_PREV | relpath(ROTDIR) }}/{{ cycle_YMD }}.{{ cycle_HH }}0000." %}
+        {% set ntile = 7 %}
+        {% for ftype in ca_data fv_core.res fv_srf_wnd.res fv_tracer.res phy_data sfc_data %}
+        #TODO: figure out how to copy one name to the other in here
+        - "{{ head }}{{ ftype }}.nest0{{ ntile-5 }}.tile{{ ntile }}.nc"
+        {% endfor %} # ftype
+        #--------------- # end warm start
+        {% else %}
+        #---------------
+        # COLD START
+        #---------------
+        {% set head = "{{ COM_ATMOS_INPUT | relpath(ROTDIR) }}" %}
+        - "{{ head }}/gfs_ctrl.nc"
+        {% for ftype in gfs_data sfc_data %}
+        #TODO: figure out how to copy one name to the other in here
+        - "{{ head }}/{{ ftype }}.tile{{ ntile }}.nc"
+        {% endfor %} # ftype
+        #--------------- # end cold start
+        {% endif %}

parm/stage/ice.yaml.j2

@@ -0,0 +1,5 @@
+ice:
+    name: "ICE"
+    source: "{{ BASE_CPLIC }}/{{ CPL_ICEIC }}/{{ cycle_YMD }}{{ cycle_HH }}/{{ MEMDIR }}/ice"
+    required:
+        - "{{ COM_ICE_RESTART_PREV | relpath(ROTDIR) }}/{{ cycle_YMD }}.{{ cycle_HH }}0000.cice_model.res.nc"

parm/stage/master_forecast_only.yaml.j2

@@ -0,0 +1,39 @@
+{% set cycle_HH = current_cycle | strftime("%H") %}
+{% set cycle_YMD = current_cycle | to_YMD %}
+{% set cycle_YMDH = current_cycle | to_YMDH %}
+datasets:
+{% if EXP_WARM_START %}
+{% filter indent(width=4) %}
+{% include "fv3.yaml.j2" %}
+{% endfilter %}
+{% if DO_NEST %}
+{% filter indent(width=4) %}
+{% include "fv3_nest.yaml.j2" %}
+{% endfilter %}
+{% endif %}
+{% endif %}
+
+{% if DO_WAVE %}
+{% if EXP_WARM_START %}
+{% filter indent(width=4) %}
+{% include "wave.yaml.j2" %}
+{% endfilter %}
+{% endif %}
+{% endif %}
+
+{% if DO_OCEAN %}
+{% if EXP_WARM_START %}
+{% filter indent(width=4) %}
+{% include "ocean.yaml.j2" %}
+{% include "mediator.yaml.j2" %}
+{% endfilter %}
+{% endif %}
+{% endif %}
+
+{% if DO_ICE %}
+{% if EXP_WARM_START %}
+{% filter indent(width=4) %}
+{% include "ice.yaml.j2" %}
+{% endfilter %}
+{% endif %}
+{% endif %}

parm/stage/mediator.yaml.j2

@@ -0,0 +1,7 @@
+#src="${BASE_CPLIC}/${CPL_MEDIC:-}/${PDY}${cyc}/${MEMDIR}/med/${PDY}.${cyc}0000.ufs.cpld.cpl.r.nc"
+#      tgt="${COM_MED_RESTART_PREV}/${PDY}.${cyc}0000.ufs.cpld.cpl.r.nc"
+mediator:
+    name: "MEDIATOR"
+    source: "{{ BASE_CPLIC }}/{{ CPL_MEDIC }}/{{ cycle_YMD }}{{ cycle_HH }}/{{ MEMDIR }}/med"
+    required:
+        - "{{ COM_MED_RESTART_PREV | relpath(ROTDIR) }}/{{ cycle_YMD }}.{{ cycle_HH }}0000.ufs.cpld.cpl.r.nc"

parm/stage/ocean.yaml.j2

@@ -0,0 +1,20 @@
+ocean:
+    name: "OCEAN"
+    source: "{{ BASE_CPLIC }}/{{ CPL_OCNIC }}/{{ cycle_YMD }}{{ cycle_HH }}/{{ MEMDIR }}/ocean"
+    required:
+        # Ocean initial conditions
+        #-------------------------
+        - "{{ COM_OCEAN_RESTART_PREV | relpath(ROTDIR) }}/{{ cycle_YMD }}.{{ cycle_HH }}0000.MOM.res.nc"
+        # Resolution based initial conditions
+        #------------------------------------
+        #NOTE: {% if OCNRES == 500 or OCNRES == 100 %} # Nothing more to do for these resolutions
+        {% if OCNRES == 025 %}
+        {% for nn in $(seq 1 3) %}
+        - "{{ COM_OCEAN_RESTART_PREV | relpath(ROTDIR) }}/{{ cycle_YMD }}.{{ cycle_HH }}0000.MOM.res_{{ nn }}.nc"
+        {% endfor %}
+        {% endif %}
+    optional:
+        # Ocean Perturbation Files
+        #-------------------------
+        {% if MEMDIR > 0 and USE_OCN_PERTURB_FILES %}
+        - "{{ COM_OCEAN_RESTART_PREV | relpath(ROTDIR) }}/{{ cycle_YMD }}.{{ cycle_HH }}0000.mom6_increment.nc"

parm/stage/wave.yaml.j2

@@ -0,0 +1,9 @@
+#TODO: these should be placed in $RUN.$gPDY/$gcyc)
+wave:
+    #TODO: check if BASE_CPLIC/CPL_WAVIC exists?
+    name: "WAVE"
+    source: "{{ BASE_CPLIC }}/{{ CPL_WAVIC }}/{{ cycle_YMD }}{{ cycle_HH }}/{{ MEMDIR }}/wave"
+    required:
+        {% for grdID in waveGRD %}
+        - "{{ COM_WAVE_RESTART | relpath(ROTDIR) }}/{{ cycle_YMD }}.{{ cycle_HH }}0000.restart.{{ grdID }}"
+        {% endfor %}