From 0d0bc7b0e9d752c98fe431ad1056a8edf3d86747 Mon Sep 17 00:00:00 2001
From: lkugler <lukas.kugler@gmail.com>
Date: Tue, 23 May 2023 19:04:34 +0200
Subject: [PATCH] sphinx compatible config imports
---
dartwrf/__init__.py | 1 +
dartwrf/assim_synth_obs.py | 6 +-
dartwrf/create_obs_upfront.py | 5 +-
dartwrf/create_obsseq.py | 4 +-
dartwrf/create_wbubble_wrfinput.py | 4 +-
dartwrf/dart_nml.py | 4 +-
dartwrf/evaluate_obs_space.py | 4 +-
dartwrf/evaluate_posterior.py | 4 +-
dartwrf/evaluate_prior.py | 4 +-
dartwrf/exp_config.py | 6 +-
dartwrf/obs/calculate_obs_locations.py | 4 +-
dartwrf/obskind.py | 335 +++++++++++++++++++++++++
dartwrf/obsseq.py | 2 +-
dartwrf/obsseq_2dim.py | 2 +-
dartwrf/obsseq_to_netcdf.py | 4 +-
dartwrf/prep_IC_prior.py | 4 +-
dartwrf/prepare_namelist.py | 4 +-
dartwrf/prepare_wrfrundir.py | 8 +-
dartwrf/run_obs_diag.py | 4 +-
dartwrf/server_config.py | 45 +---
dartwrf/update_IC.py | 4 +-
dartwrf/utils.py | 1 -
dartwrf/workflows.py | 94 +++----
dartwrf/wrfinput_add_geo.py | 4 +-
dartwrf/wrfout_add_geo.py | 4 +-
docs/source/conf.py | 3 +-
docs/source/dartwrf.rst | 55 +++-
tests/test_assim.py | 2 +-
tests/test_dart-rttov.py | 1 -
tests/test_obsseq.py | 2 +-
30 files changed, 466 insertions(+), 158 deletions(-)
create mode 100644 dartwrf/obskind.py
mode change 100644 => 100755 dartwrf/server_config.py
diff --git a/dartwrf/__init__.py b/dartwrf/__init__.py
index e69de29..b680692 100644
--- a/dartwrf/__init__.py
+++ b/dartwrf/__init__.py
@@ -0,0 +1 @@
+__all__ = []
\ No newline at end of file
diff --git a/dartwrf/assim_synth_obs.py b/dartwrf/assim_synth_obs.py
index 7cbdfe9..48b74ac 100755
--- a/dartwrf/assim_synth_obs.py
+++ b/dartwrf/assim_synth_obs.py
@@ -10,8 +10,10 @@ from dartwrf import wrfout_add_geo
from dartwrf import obsseq
from dartwrf import dart_nml
-from exp_config import exp
-from server_config import cluster
+from dartwrf import exp_config
+exp = exp_config.exp
+from dartwrf import server_config
+cluster = server_config.cluster
wrfout_format = 'wrfout_d01_%Y-%m-%d_%H:%M:%S'
diff --git a/dartwrf/create_obs_upfront.py b/dartwrf/create_obs_upfront.py
index d89b910..4cf876b 100755
--- a/dartwrf/create_obs_upfront.py
+++ b/dartwrf/create_obs_upfront.py
@@ -4,12 +4,11 @@ import time as time_module
import datetime as dt
import numpy as np
-from exp_config import exp
-from server_config import cluster
+from dartwrf.exp_config import exp
+from dartwrf.server_config import cluster
from dartwrf.utils import copy, print
import dartwrf.create_obsseq as osq
from dartwrf import obsseq
-
from dartwrf import assim_synth_obs as aso
tformat = '%Y-%m-%d_%H:%M'
diff --git a/dartwrf/create_obsseq.py b/dartwrf/create_obsseq.py
index bf3b049..b7792f1 100755
--- a/dartwrf/create_obsseq.py
+++ b/dartwrf/create_obsseq.py
@@ -7,10 +7,10 @@ import numpy as np
import datetime as dt
from pysolar.solar import get_altitude, get_azimuth
-from server_config import cluster
+from dartwrf.server_config import cluster
from dartwrf.obs import calculate_obs_locations as col
from dartwrf import utils
-from obskind import obs_kind_nrs # dictionary string => DART internal indices
+from dartwrf.obskind import obs_kind_nrs # dictionary string => DART internal indices
# position on earth for RTTOV ray geometry
lat0 = 45.
diff --git a/dartwrf/create_wbubble_wrfinput.py b/dartwrf/create_wbubble_wrfinput.py
index 5f354ad..bc79875 100644
--- a/dartwrf/create_wbubble_wrfinput.py
+++ b/dartwrf/create_wbubble_wrfinput.py
@@ -3,8 +3,8 @@ from re import U
import datetime as dt
import numpy as np
-from exp_config import exp
-from server_config import cluster
+from dartwrf.exp_config import exp
+from dartwrf.server_config import cluster
import netCDF4 as nc
dx_km = 2
diff --git a/dartwrf/dart_nml.py b/dartwrf/dart_nml.py
index 15113e4..0792353 100644
--- a/dartwrf/dart_nml.py
+++ b/dartwrf/dart_nml.py
@@ -1,7 +1,7 @@
from dartwrf.utils import append_file
-from exp_config import exp
-from server_config import cluster
+from dartwrf.exp_config import exp
+from dartwrf.server_config import cluster
earth_radius_km = 6370
diff --git a/dartwrf/evaluate_obs_space.py b/dartwrf/evaluate_obs_space.py
index 5b113dd..0436d92 100755
--- a/dartwrf/evaluate_obs_space.py
+++ b/dartwrf/evaluate_obs_space.py
@@ -3,8 +3,8 @@ import time as time_module
import datetime as dt
import numpy as np
-from exp_config import exp
-from server_config import cluster
+from dartwrf.exp_config import exp
+from dartwrf.server_config import cluster
from dartwrf import assim_synth_obs as aso
def get_previous_obsseq_file(time):
diff --git a/dartwrf/evaluate_posterior.py b/dartwrf/evaluate_posterior.py
index 6b3c9a6..bb8465b 100755
--- a/dartwrf/evaluate_posterior.py
+++ b/dartwrf/evaluate_posterior.py
@@ -3,8 +3,8 @@ import time as time_module
import datetime as dt
import numpy as np
-from exp_config import exp
-from server_config import cluster
+from dartwrf.exp_config import exp
+from dartwrf.server_config import cluster
from dartwrf import assim_synth_obs as aso
diff --git a/dartwrf/evaluate_prior.py b/dartwrf/evaluate_prior.py
index fec5f87..b13e48f 100755
--- a/dartwrf/evaluate_prior.py
+++ b/dartwrf/evaluate_prior.py
@@ -3,8 +3,8 @@ import time as time_module
import datetime as dt
import numpy as np
-from exp_config import exp
-from server_config import cluster
+from dartwrf.exp_config import exp
+from dartwrf.server_config import cluster
from dartwrf.utils import symlink, copy, sed_inplace, append_file, mkdir, try_remove, print, shell
from dartwrf import assim_synth_obs as aso
diff --git a/dartwrf/exp_config.py b/dartwrf/exp_config.py
index c7fa14e..71650ab 100644
--- a/dartwrf/exp_config.py
+++ b/dartwrf/exp_config.py
@@ -1,16 +1,16 @@
from dartwrf import utils
exp = utils.Experiment()
-exp.expname = "exp_v1.22_P2_rr_VIS_obs20_loc10_oe3"
+exp.expname = "template_experiment"
exp.model_dx = 2000
exp.n_ens = 40
-exp.superob_km = False # False or int (spatial averaging of observations)
+exp.superob_km = False # False or int (spatial averaging of observations, unit: km)
exp.use_existing_obsseq = False # False or pathname (use precomputed obs_seq.out files)
#exp.use_existing_obsseq = '/users/students/lehre/advDA_s2023/dartwrf_tutorial/very_cold_observation.out'
# path to the nature run, where we take observations from
-exp.nature_wrfout = '/jetfs/scratch/lkugler/data/sim_archive/exp_v1.18_P1_nature/2008-07-30_06:00/1/wrfout_d01_%Y-%m-%d_%H:%M:%S'
+exp.nature_wrfout = '/mnt/jetfs/scratch/lkugler/data/sim_archive/exp_v1.18_P1_nature/2008-07-30_06:00/1/wrfout_d01_%Y-%m-%d_%H:%M:%S'
exp.input_profile = '/mnt/jetfs/home/lkugler/data/initial_profiles/wrf/ens/2022-03-31/raso.fc.<iens>.wrfprof'
diff --git a/dartwrf/obs/calculate_obs_locations.py b/dartwrf/obs/calculate_obs_locations.py
index 422808f..59647b9 100755
--- a/dartwrf/obs/calculate_obs_locations.py
+++ b/dartwrf/obs/calculate_obs_locations.py
@@ -7,8 +7,8 @@ import numpy as np
import datetime as dt
import xarray as xr
-from exp_config import exp
-from server_config import cluster
+from dartwrf.exp_config import exp
+from dartwrf.server_config import cluster
#####################
# Global variables
diff --git a/dartwrf/obskind.py b/dartwrf/obskind.py
new file mode 100644
index 0000000..73e38d0
--- /dev/null
+++ b/dartwrf/obskind.py
@@ -0,0 +1,335 @@
+# this file is autogenerated
+obs_kind_nrs = {"RADIOSONDE_U_WIND_COMPONENT": 1,
+"RADIOSONDE_V_WIND_COMPONENT": 2,
+"RADIOSONDE_GEOPOTENTIAL_HGT": 3,
+"RADIOSONDE_SURFACE_PRESSURE": 4,
+"RADIOSONDE_TEMPERATURE": 5,
+"RADIOSONDE_SPECIFIC_HUMIDITY": 6,
+"DROPSONDE_U_WIND_COMPONENT": 7,
+"DROPSONDE_V_WIND_COMPONENT": 8,
+"DROPSONDE_SURFACE_PRESSURE": 9,
+"DROPSONDE_TEMPERATURE": 10,
+"DROPSONDE_SPECIFIC_HUMIDITY": 11,
+"AIRCRAFT_U_WIND_COMPONENT": 12,
+"AIRCRAFT_V_WIND_COMPONENT": 13,
+"AIRCRAFT_TEMPERATURE": 14,
+"AIRCRAFT_SPECIFIC_HUMIDITY": 15,
+"ACARS_U_WIND_COMPONENT": 16,
+"ACARS_V_WIND_COMPONENT": 17,
+"ACARS_TEMPERATURE": 18,
+"ACARS_SPECIFIC_HUMIDITY": 19,
+"MARINE_SFC_U_WIND_COMPONENT": 20,
+"MARINE_SFC_V_WIND_COMPONENT": 21,
+"MARINE_SFC_TEMPERATURE": 22,
+"MARINE_SFC_SPECIFIC_HUMIDITY": 23,
+"MARINE_SFC_PRESSURE": 24,
+"LAND_SFC_U_WIND_COMPONENT": 25,
+"LAND_SFC_V_WIND_COMPONENT": 26,
+"LAND_SFC_TEMPERATURE": 27,
+"LAND_SFC_SPECIFIC_HUMIDITY": 28,
+"LAND_SFC_PRESSURE": 29,
+"SAT_U_WIND_COMPONENT": 30,
+"SAT_V_WIND_COMPONENT": 31,
+"ATOV_TEMPERATURE": 32,
+"AIRS_TEMPERATURE": 33,
+"AIRS_SPECIFIC_HUMIDITY": 34,
+"GPS_PRECIPITABLE_WATER": 35,
+"VADWND_U_WIND_COMPONENT": 36,
+"VADWND_V_WIND_COMPONENT": 37,
+"CIMMS_AMV_U_WIND_COMPONENT": 38,
+"CIMMS_AMV_V_WIND_COMPONENT": 39,
+"DOPPLER_RADIAL_VELOCITY": 40,
+"RADAR_REFLECTIVITY": 41,
+"RADAR_CLEARAIR_REFLECTIVITY": 42,
+"PRECIPITATION_FALL_SPEED": 43,
+"METAR_U_10_METER_WIND": 44,
+"METAR_V_10_METER_WIND": 45,
+"METAR_TEMPERATURE_2_METER": 46,
+"METAR_SPECIFIC_HUMIDITY_2_METER": 47,
+"METAR_SURFACE_PRESSURE": 48,
+"METAR_POT_TEMP_2_METER": 49,
+"DEWPOINT": 50,
+"DEWPOINT_2_METER": 51,
+"BUOY_DEWPOINT": 52,
+"SHIP_DEWPOINT": 53,
+"SYNOP_DEWPOINT": 54,
+"AIREP_DEWPOINT": 55,
+"AMDAR_DEWPOINT": 56,
+"PILOT_DEWPOINT": 57,
+"BOGUS_DEWPOINT": 58,
+"AIRS_DEWPOINT": 59,
+"METAR_DEWPOINT_2_METER": 60,
+"RADIOSONDE_DEWPOINT": 61,
+"DROPSONDE_DEWPOINT": 62,
+"AIRCRAFT_DEWPOINT": 63,
+"ACARS_DEWPOINT": 64,
+"MARINE_SFC_DEWPOINT": 65,
+"LAND_SFC_DEWPOINT": 66,
+"RADIOSONDE_RELATIVE_HUMIDITY": 67,
+"DROPSONDE_RELATIVE_HUMIDITY": 68,
+"AIRCRAFT_RELATIVE_HUMIDITY": 69,
+"ACARS_RELATIVE_HUMIDITY": 70,
+"MARINE_SFC_RELATIVE_HUMIDITY": 71,
+"LAND_SFC_RELATIVE_HUMIDITY": 72,
+"METAR_RELATIVE_HUMIDITY_2_METER": 73,
+"AIRS_RELATIVE_HUMIDITY": 74,
+"MESONET_RELATIVE_HUMIDITY": 75,
+"RADIOSONDE_SURFACE_ALTIMETER": 76,
+"DROPSONDE_SURFACE_ALTIMETER": 77,
+"MARINE_SFC_ALTIMETER": 78,
+"LAND_SFC_ALTIMETER": 79,
+"METAR_ALTIMETER": 80,
+"MESONET_SURFACE_ALTIMETER": 81,
+"TEMPERATURE": 82,
+"SPECIFIC_HUMIDITY": 83,
+"PRESSURE": 84,
+"GPSRO_REFRACTIVITY": 85,
+"VORTEX_LAT": 86,
+"VORTEX_LON": 87,
+"VORTEX_PMIN": 88,
+"VORTEX_WMAX": 89,
+"BUOY_U_WIND_COMPONENT": 90,
+"BUOY_V_WIND_COMPONENT": 91,
+"BUOY_SURFACE_PRESSURE": 92,
+"BUOY_TEMPERATURE": 93,
+"SHIP_U_WIND_COMPONENT": 94,
+"SHIP_V_WIND_COMPONENT": 95,
+"SHIP_SURFACE_PRESSURE": 96,
+"SHIP_TEMPERATURE": 97,
+"SYNOP_U_WIND_COMPONENT": 98,
+"SYNOP_V_WIND_COMPONENT": 99,
+"SYNOP_SURFACE_PRESSURE": 100,
+"SYNOP_SPECIFIC_HUMIDITY": 101,
+"SYNOP_TEMPERATURE": 102,
+"AIREP_U_WIND_COMPONENT": 103,
+"AIREP_V_WIND_COMPONENT": 104,
+"AIREP_PRESSURE": 105,
+"AIREP_TEMPERATURE": 106,
+"AMDAR_U_WIND_COMPONENT": 107,
+"AMDAR_V_WIND_COMPONENT": 108,
+"AMDAR_PRESSURE": 109,
+"AMDAR_TEMPERATURE": 110,
+"PILOT_U_WIND_COMPONENT": 111,
+"PILOT_V_WIND_COMPONENT": 112,
+"PILOT_PRESSURE": 113,
+"PILOT_TEMPERATURE": 114,
+"BOGUS_U_WIND_COMPONENT": 115,
+"BOGUS_V_WIND_COMPONENT": 116,
+"BOGUS_PRESSURE": 117,
+"BOGUS_TEMPERATURE": 118,
+"PROFILER_U_WIND_COMPONENT": 119,
+"PROFILER_V_WIND_COMPONENT": 120,
+"PROFILER_PRESSURE": 121,
+"SATEM_THICKNESS": 122,
+"NOAA_1_VTPR1_RADIANCE": 123,
+"NOAA_2_VTPR1_RADIANCE": 124,
+"NOAA_3_VTPR1_RADIANCE": 125,
+"NOAA_4_VTPR1_RADIANCE": 126,
+"NOAA_5_HIRS_RADIANCE": 127,
+"NOAA_5_MSU_TB": 128,
+"NOAA_5_AVHRR_RADIANCE": 129,
+"NOAA_6_HIRS_RADIANCE": 130,
+"NOAA_6_MSU_TB": 131,
+"NOAA_6_AVHRR_RADIANCE": 132,
+"NOAA_7_HIRS_RADIANCE": 133,
+"NOAA_7_MSU_TB": 134,
+"NOAA_7_AVHRR_RADIANCE": 135,
+"NOAA_8_HIRS_RADIANCE": 136,
+"NOAA_8_MSU_TB": 137,
+"NOAA_8_AVHRR_RADIANCE": 138,
+"NOAA_9_HIRS_RADIANCE": 139,
+"NOAA_9_MSU_TB": 140,
+"NOAA_9_AVHRR_RADIANCE": 141,
+"NOAA_10_HIRS_RADIANCE": 142,
+"NOAA_10_MSU_TB": 143,
+"NOAA_10_AVHRR_RADIANCE": 144,
+"NOAA_11_HIRS_RADIANCE": 145,
+"NOAA_11_MSU_TB": 146,
+"NOAA_11_AVHRR_RADIANCE": 147,
+"NOAA_12_HIRS_RADIANCE": 148,
+"NOAA_12_MSU_TB": 149,
+"NOAA_12_AVHRR_RADIANCE": 150,
+"NOAA_13_AVHRR_RADIANCE": 151,
+"NOAA_14_HIRS_RADIANCE": 152,
+"NOAA_14_MSU_TB": 153,
+"NOAA_14_AVHRR_RADIANCE": 154,
+"NOAA_15_HIRS_RADIANCE": 155,
+"NOAA_15_AMSUA_TB": 156,
+"NOAA_15_AMSUB_TB": 157,
+"NOAA_15_AVHRR_RADIANCE": 158,
+"NOAA_16_HIRS_RADIANCE": 159,
+"NOAA_16_AMSUA_TB": 160,
+"NOAA_16_AMSUB_TB": 161,
+"NOAA_16_AVHRR_RADIANCE": 162,
+"NOAA_17_HIRS_RADIANCE": 163,
+"NOAA_17_AMSUA_TB": 164,
+"NOAA_17_AMSUB_TB": 165,
+"NOAA_17_AVHRR_RADIANCE": 166,
+"NOAA_18_HIRS_RADIANCE": 167,
+"NOAA_18_AMSUA_TB": 168,
+"NOAA_18_AVHRR_RADIANCE": 169,
+"NOAA_18_MHS_TB": 170,
+"NOAA_19_HIRS_RADIANCE": 171,
+"NOAA_19_AMSUA_TB": 172,
+"NOAA_19_AVHRR_RADIANCE": 173,
+"NOAA_19_MHS_TB": 174,
+"NOAA_20_ATMS_TB": 175,
+"NOAA_20_VIIRS_RADIANCE": 176,
+"DMSP_8_SSMI_TB": 177,
+"DMSP_9_SSMI_TB": 178,
+"DMSP_10_SSMI_TB": 179,
+"DMSP_11_SSMI_TB": 180,
+"DMSP_11_SSMT2_TB": 181,
+"DMSP_12_SSMI_TB": 182,
+"DMSP_12_SSMT2_TB": 183,
+"DMSP_13_SSMI_TB": 184,
+"DMSP_14_SSMI_TB": 185,
+"DMSP_14_SSMT2_TB": 186,
+"DMSP_15_SSMI_TB": 187,
+"DMSP_15_SSMT2_TB": 188,
+"DMSP_16_SSMIS_TB": 189,
+"DMSP_17_SSMIS_TB": 190,
+"DMSP_18_SSMIS_TB": 191,
+"DMSP_19_SSMIS_TB": 192,
+"METEOSAT_1_MVIRI_RADIANCE": 193,
+"METEOSAT_2_MVIRI_RADIANCE": 194,
+"METEOSAT_3_MVIRI_RADIANCE": 195,
+"METEOSAT_4_MVIRI_RADIANCE": 196,
+"METEOSAT_5_MVIRI_RADIANCE": 197,
+"METEOSAT_6_MVIRI_RADIANCE": 198,
+"METEOSAT_7_MVIRI_RADIANCE": 199,
+"GOES_4_SOUNDER_RADIANCE": 200,
+"GOES_5_SOUNDER_RADIANCE": 201,
+"GOES_6_SOUNDER_RADIANCE": 202,
+"GOES_7_SOUNDER_RADIANCE": 203,
+"GOES_8_IMAGER_RADIANCE": 204,
+"GOES_8_SOUNDER_RADIANCE": 205,
+"GOES_9_IMAGER_RADIANCE": 206,
+"GOES_9_SOUNDER_RADIANCE": 207,
+"GOES_10_IMAGER_RADIANCE": 208,
+"GOES_10_SOUNDER_RADIANCE": 209,
+"GOES_11_IMAGER_RADIANCE": 210,
+"GOES_11_SOUNDER_RADIANCE": 211,
+"GOES_12_IMAGER_RADIANCE": 212,
+"GOES_12_SOUNDER_RADIANCE": 213,
+"GOES_13_IMAGER_RADIANCE": 214,
+"GOES_13_SOUNDER_RADIANCE": 215,
+"GOES_14_IMAGER_RADIANCE": 216,
+"GOES_14_SOUNDER_RADIANCE": 217,
+"GOES_15_IMAGER_RADIANCE": 218,
+"GOES_15_SOUNDER_RADIANCE": 219,
+"GOES_16_ABI_RADIANCE": 220,
+"GOES_17_ABI_RADIANCE": 221,
+"GOES_18_ABI_RADIANCE": 222,
+"GOES_19_ABI_RADIANCE": 223,
+"GMS_1_IMAGER_RADIANCE": 224,
+"GMS_2_IMAGER_RADIANCE": 225,
+"GMS_3_IMAGER_RADIANCE": 226,
+"GMS_4_IMAGER_RADIANCE": 227,
+"GMS_5_IMAGER_RADIANCE": 228,
+"FY2_2_VISSR_RADIANCE": 229,
+"FY2_3_VISSR_RADIANCE": 230,
+"FY2_4_VISSR_RADIANCE": 231,
+"FY2_5_VISSR_RADIANCE": 232,
+"FY2_7_VISSR_RADIANCE": 233,
+"TRMM_1_TMI_TB": 234,
+"ERS_1_ATSR_RADIANCE": 235,
+"ERS_1_MWR_TB": 236,
+"ERS_2_ATSR_RADIANCE": 237,
+"ERS_2_MWR_TB": 238,
+"EOS_1_MODIS_RADIANCE": 239,
+"EOS_1_ASTER_RADIANCE": 240,
+"EOS_2_AMSUA_TB": 241,
+"EOS_2_AIRS_RADIANCE": 242,
+"EOS_2_HSB_TB": 243,
+"EOS_2_MODIS_RADIANCE": 244,
+"EOS_2_AMSRE_TB": 245,
+"METOP_1_HIRS_RADIANCE": 246,
+"METOP_1_AMSUA_TB": 247,
+"METOP_1_AVHRR_RADIANCE": 248,
+"METOP_1_MHS_TB": 249,
+"METOP_2_HIRS_RADIANCE": 250,
+"METOP_2_AMSUA_TB": 251,
+"METOP_2_AVHRR_RADIANCE": 252,
+"METOP_2_MHS_TB": 253,
+"METOP_3_AVHRR_RADIANCE": 254,
+"ENVISAT_1_ATSR_RADIANCE": 255,
+"ENVISAT_1_MWR_TB": 256,
+"MSG_1_SEVIRI_RADIANCE": 257,
+"MSG_2_SEVIRI_RADIANCE": 258,
+"MSG_3_SEVIRI_RADIANCE": 259,
+"MSG_4_SEVIRI_RADIANCE": 260,
+"MSG_4_SEVIRI_TB": 261,
+"MSG_4_SEVIRI_BDRF": 262,
+"FY1_3_MVISR_RADIANCE": 263,
+"FY1_4_MVISR_RADIANCE": 264,
+"MTSAT_1_IMAGER_RADIANCE": 265,
+"MTSAT_2_IMAGER_RADIANCE": 266,
+"CORIOLIS_1_WINDSAT_TB": 267,
+"JPSS_0_ATMS_TB": 268,
+"JPSS_0_VIIRS_RADIANCE": 269,
+"SENTINEL3_1_SLSTR_RADIANCE": 270,
+"SENTINEL3_2_SLSTR_RADIANCE": 271,
+"MEGHATR_1_SAPHIR_TB": 272,
+"MEGHATR_1_MADRAS_TB": 273,
+"FY3_1_MWTS_TB": 274,
+"FY3_1_MWHS_TB": 275,
+"FY3_1_IRAS_RADIANCE": 276,
+"FY3_1_MWRI_TB": 277,
+"FY3_2_MWTS_TB": 278,
+"FY3_2_MWHS_TB": 279,
+"FY3_2_MWRI_TB": 280,
+"FY3_3_MWRI_TB": 281,
+"FY3_3_MWTS2_TB": 282,
+"FY3_3_MWHS2_TB": 283,
+"FY3_3_MERSI1_RADIANCE": 284,
+"FY3_4_MWRI_TB": 285,
+"FY3_4_MWTS2_TB": 286,
+"FY3_4_MWHS2_TB": 287,
+"FY3_4_MERSI2_RADIANCE": 288,
+"COMS_1_MI_RADIANCE": 289,
+"METEOR_M_1_MSUMR_RADIANCE": 290,
+"METEOR_M_2_MSUMR_RADIANCE": 291,
+"METEOR_M_2_MTVZAGY_TB": 292,
+"CALIPSO_1_IIR_RADIANCE": 293,
+"GCOM_W_1_AMSR2_TB": 294,
+"NIMBUS_3_MRIR_RADIANCE": 295,
+"NIMBUS_4_THIR_RADIANCE": 296,
+"NIMBUS_5_THIR_RADIANCE": 297,
+"NIMBUS_6_HIRS_RADIANCE": 298,
+"NIMBUS_6_SCAMS_TB": 299,
+"NIMBUS_6_THIR_RADIANCE": 300,
+"NIMBUS_7_SMMR_TB": 301,
+"NIMBUS_7_THIR_RADIANCE": 302,
+"HIMAWARI_8_AHI_RADIANCE": 303,
+"HIMAWARI_9_AHI_RADIANCE": 304,
+"MTG_1_FCI_RADIANCE": 305,
+"SARAL_1_ALTIKA_TB": 306,
+"METOPSG_1_ICI_TB": 307,
+"METOPSG_1_METIMAGE_RADIANCE": 308,
+"METOPSG_1_MWS_TB": 309,
+"METOPSG_1_MWI_TB": 310,
+"LANDSAT_4_TM_RADIANCE": 311,
+"LANDSAT_5_TM_RADIANCE": 312,
+"LANDSAT_7_TM_RADIANCE": 313,
+"LANDSAT_8_TIRS_RADIANCE": 314,
+"JASON_2_AMR_TB": 315,
+"GPM_1_GMI_TB": 316,
+"GPM_1_DPR_TB": 317,
+"INSAT3_4_IMAGER_RADIANCE": 318,
+"INSAT3_4_SOUNDER_RADIANCE": 319,
+"INSAT3_5_IMAGER_RADIANCE": 320,
+"INSAT3_5_SOUNDER_RADIANCE": 321,
+"TICFIRE_1_MBFIRI_RADIANCE": 322,
+"ISS_1_ECOSTRES_RADIANCE": 323,
+"HJ1_2_IRMSS_RADIANCE": 324,
+"GKOMPSAT2_1_AMI_RADIANCE": 325,
+"GCOM_C_1_SGLI_RADIANCE": 326,
+"SMOS_1_MIRAS_TB": 327,
+"ORS_6_COWVR_TB": 328,
+"FY4_1_AGRI_RADIANCE": 329,
+"TROPICS_0_TROPICS_TB": 330,
+"GF5_1_VIMS_RADIANCE": 331,
+"HY2_1_MWRI_TB": 332,
+"CLOUDSAT_1_CPR_TB": 333,
+}
\ No newline at end of file
diff --git a/dartwrf/obsseq.py b/dartwrf/obsseq.py
index 3508941..fc20e51 100755
--- a/dartwrf/obsseq.py
+++ b/dartwrf/obsseq.py
@@ -128,7 +128,7 @@ class ObsRecord(pd.DataFrame):
def determine_nlayers(self):
nlayers = 1 # first guess
- from config.cfg import exp
+ from dartwrf.exp_config import exp
if len(exp.observations) == 1:
# obscfg = exp.observations[0]
diff --git a/dartwrf/obsseq_2dim.py b/dartwrf/obsseq_2dim.py
index ec08e03..c9a647c 100755
--- a/dartwrf/obsseq_2dim.py
+++ b/dartwrf/obsseq_2dim.py
@@ -19,7 +19,7 @@ import time as time_module
import datetime as dt
import numpy as np
-from server_config import cluster
+from dartwrf.server_config import cluster
from dartwrf import utils
from dartwrf import assim_synth_obs as aso
from dartwrf import obsseq
diff --git a/dartwrf/obsseq_to_netcdf.py b/dartwrf/obsseq_to_netcdf.py
index 7bdc670..14b0447 100644
--- a/dartwrf/obsseq_to_netcdf.py
+++ b/dartwrf/obsseq_to_netcdf.py
@@ -1,7 +1,7 @@
import os, sys, glob, warnings
-from exp_config import exp
-from server_config import cluster
+from dartwrf.exp_config import exp
+from dartwrf.server_config import cluster
import dartwrf.run_obs_diag as rod
def listdir_dirs(path):
diff --git a/dartwrf/prep_IC_prior.py b/dartwrf/prep_IC_prior.py
index 9b27d51..8ad84de 100755
--- a/dartwrf/prep_IC_prior.py
+++ b/dartwrf/prep_IC_prior.py
@@ -2,8 +2,8 @@ import os, sys, warnings, glob
import datetime as dt
import numpy as np
-from exp_config import exp
-from server_config import cluster
+from dartwrf.exp_config import exp
+from dartwrf.server_config import cluster
from dartwrf.utils import copy, clean_wrfdir, try_remove
"""
diff --git a/dartwrf/prepare_namelist.py b/dartwrf/prepare_namelist.py
index 293fc23..c3e0e59 100755
--- a/dartwrf/prepare_namelist.py
+++ b/dartwrf/prepare_namelist.py
@@ -12,8 +12,8 @@ import os, sys, shutil, warnings
import datetime as dt
from docopt import docopt
-from exp_config import exp
-from server_config import cluster
+from dartwrf.exp_config import exp
+from dartwrf.server_config import cluster
from dartwrf.utils import sed_inplace, copy, symlink, mkdir
def run(iens, begin, end, hist_interval=5, radt=5, archive=True,
diff --git a/dartwrf/prepare_wrfrundir.py b/dartwrf/prepare_wrfrundir.py
index 5fc2c5c..2d0b141 100755
--- a/dartwrf/prepare_wrfrundir.py
+++ b/dartwrf/prepare_wrfrundir.py
@@ -9,11 +9,11 @@ Returns:
import os, sys, shutil
import datetime as dt
-from exp_config import exp
-from server_config import cluster
+from dartwrf.exp_config import exp
+from dartwrf.server_config import cluster
-from utils import symlink, copy, link_contents
-import prepare_namelist
+from dartwrf.utils import symlink, copy, link_contents
+from dartwrf import prepare_namelist
if __name__ == '__main__':
diff --git a/dartwrf/run_obs_diag.py b/dartwrf/run_obs_diag.py
index 49132b0..fa1e78e 100644
--- a/dartwrf/run_obs_diag.py
+++ b/dartwrf/run_obs_diag.py
@@ -1,7 +1,7 @@
import os, sys, shutil, glob
-from exp_config import exp
-from server_config import cluster
+from dartwrf.exp_config import exp
+from dartwrf.server_config import cluster
from dartwrf.utils import symlink, copy, sed_inplace, append_file, shell
rundir_program = '/home/fs71386/lkugler/data/run_DART/'
diff --git a/dartwrf/server_config.py b/dartwrf/server_config.py
old mode 100644
new mode 100755
index a978a51..bd9c6b1
--- a/dartwrf/server_config.py
+++ b/dartwrf/server_config.py
@@ -1,47 +1,6 @@
-import os, sys
-import datetime as dt
+"""Cluster configuration file, see docstring of ClusterConfig class in dartwrf/utils.py for details"""
from dartwrf import utils
-from cfg import exp
-
-"""Configuration name docs
-
-When coding, use attributes of a dictionary like this:
-$ from cfg import exp, cluster
-$ path = cluster.archivedir
-
-
-attribute name | description
-------------------------------------------------------
-name any string (currently unused)
-
-python path of python version to use
-python_enstools path of python version to use for verification script (not provided)
-ncks path to 'ncks' program; type 'which ncks' to find the path,
- if it doesn't exist, try to load the module first ('module load nco')
-ideal path to WRF's ideal.exe
-wrfexe path to WRF's wrf.exe
-
-wrf_rundir_base path for temporary files for WRF
-dart_rundir_base path for temporary files for DART
-archive_base path for long-time output storage
-
-srcdir path to where WRF has been compiled, including the 'run' folder of WRF, e.g. /home/WRF-4.3/run
-dart_srcdir path to DART compile directory, e.g. /home/DART-9.11.9/models/wrf/work
-rttov_srcdir path to RTTOV compile directory, e.g. /home/RTTOV13/rtcoef_rttov13/
-scriptsdir path where DART-WRF scripts reside, e.g. /home/DART-WRF/scripts
-
-namelist path to a namelist template; strings like <hist_interval>, will be overwritten in scripts/prepare_namelist.py
-run_WRF path to script which runs WRF on a node of the cluster
-obs_impact_filename path to obs_impact_filename (see DART guide; module assim_tools_mod and program obs_impact_tool)
-geo_em path to NetCDF file of WRF domain (see WRF guide)
-
-slurm_cfg python dictionary, containing options of SLURM
- defined in SLURM docs (https://slurm.schedmd.com/sbatch.html)
- this configuration can be overwritten later on, for example:
- 'dict(cluster.slurm_cfg, **cfg_update)' where
- 'cfg_update = {"nodes": "2"}'
-"""
-
+from dartwrf.exp_config import exp
cluster = utils.ClusterConfig(exp)
cluster.name = 'jet'
diff --git a/dartwrf/update_IC.py b/dartwrf/update_IC.py
index 5e74b46..16d856a 100755
--- a/dartwrf/update_IC.py
+++ b/dartwrf/update_IC.py
@@ -2,8 +2,8 @@ import os, sys, warnings
import datetime as dt
import netCDF4 as nc
-from exp_config import exp
-from server_config import cluster
+from dartwrf.exp_config import exp
+from dartwrf.server_config import cluster
def update_initials_in_WRF_rundir(time):
"""Updates wrfrst-files in `/run_WRF/` directory
diff --git a/dartwrf/utils.py b/dartwrf/utils.py
index fb9151d..9c36880 100755
--- a/dartwrf/utils.py
+++ b/dartwrf/utils.py
@@ -3,7 +3,6 @@ import builtins as __builtin__
import subprocess
import datetime as dt
import re, tempfile
-import importlib
class Experiment(object):
"""Collection of variables regarding the experiment configuration"""
diff --git a/dartwrf/workflows.py b/dartwrf/workflows.py
index 45cba00..bbc67b4 100644
--- a/dartwrf/workflows.py
+++ b/dartwrf/workflows.py
@@ -5,9 +5,8 @@ e.g. assimilate() calls dartwrf/assim_synth_obs.py through the shell.
This would not be necessary, but some users might want to use queueing systems (e.g. SLURM) which must call scripts.
"""
-import os, sys, shutil, glob, warnings
+import os, sys, shutil, warnings
import datetime as dt
-import importlib
from dartwrf.utils import script_to_str
@@ -31,7 +30,7 @@ class WorkFlows(object):
exp (obj): experiment configuration as defined in exp_config file
"""
- def copy_dartwrf_to_archive():
+ def _copy_dartwrf_to_archive():
# Copy scripts to self.cluster.archivedir folder
try:
shutil.copytree(self.cluster.dartwrf_dir, self.cluster.archivedir+'/DART-WRF/')
@@ -45,52 +44,6 @@ class WorkFlows(object):
except:
raise
- # def copy_config_to_archive():
- # os.makedirs(self.cluster.scripts_rundir+'/config/', exist_ok=True)
-
- # # later, we can load the exp cfg with `from config.cfg import exp`
- # shutil.copyfile('config/'+exp_config, self.cluster.scripts_rundir+'/config/cfg.py')
-
- # # later, we can load the cluster cfg with `from config.cluster import cluster`
- # shutil.copyfile('config/'+server_config, self.cluster.scripts_rundir+'/config/cluster.py') # whatever server, the config name is always the same!
-
- print('------ start exp from ', exp_config, ' and ', server_config, ' ------')
-
- # experiment starts, we dont know where the code shall run
- # => read the configuration file
-
- # copy the config files to this folder
- this_dir = '/'.join(__file__.split('/')[:-1])
- try:
- shutil.copyfile('config/'+server_config, this_dir+'/server_config.py')
- except shutil.SameFileError:
- pass
- try:
- shutil.copyfile('config/'+exp_config, this_dir+'/exp_config.py')
- except shutil.SameFileError:
- pass
-
- sys.path.append(this_dir)
- from server_config import cluster
- self.cluster = cluster
- from exp_config import exp
- self.exp = exp
-
- copy_dartwrf_to_archive() # includes config files
-
- # we set the path from where python should import dartwrf modules
- self.cluster.python = 'export PYTHONPATH='+self.cluster.scripts_rundir+'; '+self.cluster.python
-
- # Set paths and backup scripts
- self.cluster.log_dir = self.cluster.archivedir+'/logs/'
- print('logging to', self.cluster.log_dir)
-
- if self.cluster.use_slurm:
- self.cluster.slurm_scripts_dir = self.cluster.archivedir+'/slurm-scripts/'
- print('SLURM scripts will be in', self.cluster.slurm_scripts_dir)
-
- # copy obs kind def to config, we will read a table from there
- # file needs to exist within package so sphinx can read it
def _obskind_read():
"""Read dictionary of observation types + ID numbers ("kind")
from DART f90 script and return it as python dictionary
@@ -135,10 +88,45 @@ class WorkFlows(object):
txt += '}'
f.write(txt)
- _dict_to_py(_obskind_read(), self.cluster.scripts_rundir+'/obskind.py')
-
- # probably not needed
- # shutil.copy('config/'+server_config, 'config/cluster.py') # whatever server, the config name is always the same!
+ print('------ start exp from ', exp_config, ' and ', server_config, ' ------')
+
+ # experiment starts, we dont know where the code shall run
+ # => read the configuration file
+
+ # copy the config files to this folder
+ this_dir = '/'.join(__file__.split('/')[:-1])
+ try:
+ shutil.copyfile('config/'+server_config, this_dir+'/server_config.py')
+ except shutil.SameFileError:
+ pass
+ try:
+ shutil.copyfile('config/'+exp_config, this_dir+'/exp_config.py')
+ except shutil.SameFileError:
+ pass
+
+ sys.path.append(this_dir)
+ from server_config import cluster
+ self.cluster = cluster
+ from exp_config import exp
+ self.exp = exp
+
+ # copy obs kind def to config, we will read a table from there
+ # file needs to exist within package so sphinx can read it
+ _dict_to_py(_obskind_read(), this_dir+'/obskind.py')
+
+ _copy_dartwrf_to_archive() # includes config files
+
+ # we set the path from where python should import dartwrf modules
+ self.cluster.python = 'export PYTHONPATH='+self.cluster.scripts_rundir+'; '+self.cluster.python
+
+ # Set paths and backup scripts
+ self.cluster.log_dir = self.cluster.archivedir+'/logs/'
+ print('logging to', self.cluster.log_dir)
+
+ if self.cluster.use_slurm:
+ self.cluster.slurm_scripts_dir = self.cluster.archivedir+'/slurm-scripts/'
+ print('SLURM scripts will be in', self.cluster.slurm_scripts_dir)
+
print('------ dartwrf experiment initialized ------')
print('--------------------------------------------')
diff --git a/dartwrf/wrfinput_add_geo.py b/dartwrf/wrfinput_add_geo.py
index c4317bf..aa1400c 100755
--- a/dartwrf/wrfinput_add_geo.py
+++ b/dartwrf/wrfinput_add_geo.py
@@ -10,9 +10,7 @@ example call:
"""
import os, sys
import netCDF4 as nc
-
-from exp_config import exp
-from server_config import cluster
+from dartwrf.server_config import cluster
def run(geo_data_file, wrfinput_file):
geo_ds = nc.Dataset(geo_data_file, 'r')
diff --git a/dartwrf/wrfout_add_geo.py b/dartwrf/wrfout_add_geo.py
index 48a9b96..8be29aa 100755
--- a/dartwrf/wrfout_add_geo.py
+++ b/dartwrf/wrfout_add_geo.py
@@ -1,8 +1,6 @@
import os, sys
import netCDF4 as nc
-
-from exp_config import exp
-from server_config import cluster
+from dartwrf.server_config import cluster
fields_old = ["XLAT_M", "XLONG_M", "CLAT",
"XLONG_U", "XLONG_V", "XLAT_U", "XLAT_V"]
diff --git a/docs/source/conf.py b/docs/source/conf.py
index cdc7c64..4a482c9 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -11,8 +11,7 @@ author = 'Lukas Kugler'
release = '2023.2.21'
# -- General configuration
-sys.path.insert(0, os.path.abspath('.'))
-sys.path.insert(0, os.path.abspath('../'))
+sys.path.insert(0, os.path.abspath('../../'))
master_doc = 'index'
diff --git a/docs/source/dartwrf.rst b/docs/source/dartwrf.rst
index d358f32..d8bab9e 100644
--- a/docs/source/dartwrf.rst
+++ b/docs/source/dartwrf.rst
@@ -7,20 +7,11 @@ Subpackages
.. toctree::
:maxdepth: 4
- dartwrf.config
dartwrf.obs
Submodules
----------
-dartwrf.workflows module
-------------------------
-
-.. automodule:: dartwrf.workflows
- :members:
- :undoc-members:
- :show-inheritance:
-
dartwrf.assim\_synth\_obs module
--------------------------------
@@ -53,6 +44,22 @@ dartwrf.create\_wbubble\_wrfinput module
:undoc-members:
:show-inheritance:
+dartwrf.dart\_nml module
+------------------------
+
+.. automodule:: dartwrf.dart_nml
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+dartwrf.evaluate\_obs\_space module
+-----------------------------------
+
+.. automodule:: dartwrf.evaluate_obs_space
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
dartwrf.evaluate\_posterior module
----------------------------------
@@ -69,10 +76,18 @@ dartwrf.evaluate\_prior module
:undoc-members:
:show-inheritance:
-dartwrf.link\_dart\_rttov module
---------------------------------
+dartwrf.exp\_config module
+--------------------------
+
+.. automodule:: dartwrf.exp_config
+ :members:
+ :undoc-members:
+ :show-inheritance:
-.. automodule:: dartwrf.link_dart_rttov
+dartwrf.obskind module
+----------------------
+
+.. automodule:: dartwrf.obskind
:members:
:undoc-members:
:show-inheritance:
@@ -133,6 +148,14 @@ dartwrf.run\_obs\_diag module
:undoc-members:
:show-inheritance:
+dartwrf.server\_config module
+-----------------------------
+
+.. automodule:: dartwrf.server_config
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
dartwrf.update\_IC module
-------------------------
@@ -149,6 +172,14 @@ dartwrf.utils module
:undoc-members:
:show-inheritance:
+dartwrf.workflows module
+------------------------
+
+.. automodule:: dartwrf.workflows
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
dartwrf.wrfinput\_add\_geo module
---------------------------------
diff --git a/tests/test_assim.py b/tests/test_assim.py
index aecc515..d53b53b 100644
--- a/tests/test_assim.py
+++ b/tests/test_assim.py
@@ -2,7 +2,7 @@ import os, shutil
import datetime as dt
from dartwrf import obsseq, assim_synth_obs
-from config.cfg import cluster
+from dartwrf.server_config import cluster
class ExperimentConfiguration(object):
def __init__(self):
diff --git a/tests/test_dart-rttov.py b/tests/test_dart-rttov.py
index 4d502b3..ada56bf 100644
--- a/tests/test_dart-rttov.py
+++ b/tests/test_dart-rttov.py
@@ -3,7 +3,6 @@ import numpy as np
import datetime as dt
import pandas as pd
-from config.cfg import exp, cluster
from dartwrf import obsseq
import dartwrf.create_obsseq as osq
import dartwrf.assim_synth_obs as aso
diff --git a/tests/test_obsseq.py b/tests/test_obsseq.py
index 96d7dbe..215df54 100644
--- a/tests/test_obsseq.py
+++ b/tests/test_obsseq.py
@@ -1,7 +1,7 @@
import os, filecmp, shutil
import numpy as np
-from config.cfg import exp, cluster
+from dartwrf.server_config import cluster
from dartwrf import obsseq
--
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