standardised import statements in inputs, run_scripts, and data_assim…

…ilation #25

untested, may contain typos

docs/source/apis/inputs.rising_bubble.rst

@@ -13,8 +13,6 @@
 
    .. autosummary::
 
-      hydrostatic_state
-      set_explicit_boundary_data
       sol_init
 
 

docs/source/apis/run_scripts.test_suite.rst

@@ -13,12 +13,6 @@
 
 
 
-   .. rubric:: Classes
-
-   .. autosummary::
-
-      compare_sol
-
 
 
 

docs/source/apis/src.data_assimilation.blending.rst

@@ -15,18 +15,12 @@
 
       blending_after_timestep
       blending_before_timestep
-      colored
-      compressibility
-      deepcopy
       do_comp_to_psinc_conv
       do_hydro_to_nonhydro_conv
       do_lake_to_swe_conv
       do_nonhydro_to_hydro_conv
       do_psinc_to_comp_conv
       do_swe_to_lake_conv
-      is_compressible
-      is_nonhydrostatic
-      nonhydrostasy
 
 
 

docs/source/apis/src.data_assimilation.letkf.rst

@@ -14,15 +14,9 @@
    .. autosummary::
 
       bin_func
-      convolve2d
       da_interface
-      deepcopy
-      interpn
       interpolation_func
-      map_coordinates
       none_func
-      sliding_window_view
-      spsolve
 
 
 
@@ -32,8 +26,6 @@
 
    .. autosummary::
 
-      BdryType
-      ProgressBar
       analysis
       prepare_rloc
 

docs/source/apis/src.data_assimilation.localisation.rst

@@ -20,12 +20,6 @@
 
 
 
-   .. rubric:: Classes
-
-   .. autosummary::
-
-      BdryType
-
 
 
 

docs/source/apis/src.data_assimilation.params.rst

@@ -9,13 +9,6 @@
 
 
 
-   .. rubric:: Functions
-
-   .. autosummary::
-
-      set_explicit_boundary_data
-      set_ghostnodes_p2
-
 
 
 

docs/source/apis/src.data_assimilation.utils.rst

@@ -16,7 +16,6 @@
       HSprojector_2t3D
       HSprojector_3t2D
       boundary_mask
-      deepcopy
       ensemble_inflation
       obs_noiser
       set_p2_nodes
@@ -32,7 +31,6 @@
 
    .. autosummary::
 
-      BdryType
       ensemble
 
 

docs/source/apis/src.dycore.discretisation.time_update.rst

@@ -18,14 +18,14 @@
       colored
       data_init
       deepcopy
+      do
       dynamic_timestep
       euler_backward_non_advective_expl_part
       euler_backward_non_advective_impl_part
       euler_forward_non_advective
       is_nonhydrostatic
       nonhydrostasy
       recompute_advective_fluxes
-      time_update
 
 
 

inputs/rising_bubble.py

@@ -1,6 +1,6 @@
 import numpy as np
-from dycore.physics.hydrostatics import hydrostatic_state
-from dycore.utils.boundary import set_explicit_boundary_data
+import dycore.physics.hydrostatics as hydro
+import dycore.utils.boundary as bdry
 
 class UserData(object):
     # Nsq_ref = grav * 1.3e-05
@@ -51,7 +51,7 @@ def sol_init(Sol, mpv, elem, node, th, ud, seed=None):
     g = ud.gravity_strength[1]
     # print(ud.rho_ref)
 
-    hydrostatic_state(mpv, elem, node, th, ud)
+    hydro.hydrostatic_state(mpv, elem, node, th, ud)
 
     x = elem.x
     y = elem.y
@@ -94,6 +94,6 @@ def sol_init(Sol, mpv, elem, node, th, ud, seed=None):
     rhoY = mpv.HydroState_n.rhoY0[0]
     mpv.p2_nodes[...] = (p - mpv.HydroState_n.p0[0]) / rhoY / ud.Msq
 
-    set_explicit_boundary_data(Sol,elem,ud,th,mpv)
+    bdry.set_explicit_boundary_data(Sol,elem,ud,th,mpv)
 
     return Sol

run_scripts/test_suite.py

@@ -1,16 +1,16 @@
 # %%
 from run import run_params as rp
-from pybella.tests.diagnostics import compare_sol
+import pybella.tests.diagnostics as td
 import json
 
 # The first run MUST have gen_targets = True
 # This is to generate the target outputs
 # so that a comparison can be made
-gen_targets = True
+gen_targets = False
 
 # Only set this to True if the diagnostic targets
 # are to be updated. Required for the first run.
-updt_targets = True
+updt_targets = False
 
 # define run instance
 rp = rp()
@@ -39,7 +39,7 @@
     rp.queue_run()
 
 if updt_targets:
-    diag = compare_sol("gen_target")
+    diag = td.compare_sol("gen_target")
     diag.update_targets()
 
 

src/data_assimilation/blending.py

@@ -1,17 +1,11 @@
 import numpy as np
 from scipy import signal
-import scipy.sparse.linalg as la
-
-from dycore.physics.gas_dynamics.eos import (
-    nonhydrostasy,
-    compressibility,
-    is_compressible,
-    is_nonhydrostatic,
-)
-import logging
 
-from termcolor import colored
-from copy import deepcopy
+import dycore.physics.gas_dynamics as eos
+
+import logging
+import termcolor
+import copy
 
 
 class Blend(object):
@@ -112,7 +106,7 @@ def update_p2n(self, Sol, mpv, node, th, ud):
 
 
 def do_comp_to_psinc_conv(Sol, mpv, bld, elem, node, th, ud, label, writer):
-    logging.info(colored("Converting COMP to PSINC", "blue"))
+    logging.info(termcolor.colored("Converting COMP to PSINC", "blue"))
     dp2n = mpv.p2_nodes
     bld.convert_p2n(dp2n)
     bld.update_Sol(Sol, elem, node, th, ud, mpv, "bef", label=label, writer=writer)
@@ -126,9 +120,9 @@ def do_psinc_to_comp_conv(
 ):
     from dycore.discretisation import time_update
 
-    logging.info(colored("Blending... step = %i" % step, "blue"))
-    Sol_freeze = deepcopy(Sol)
-    mpv_freeze = deepcopy(mpv)
+    logging.info(termcolor.colored("Blending... step = %i" % step, "blue"))
+    Sol_freeze = copy.deepcopy(Sol)
+    mpv_freeze = copy.deepcopy(mpv)
 
     ret = time_update.time_update(
         Sol,
@@ -169,7 +163,7 @@ def do_psinc_to_comp_conv(
 
     if writer != None:
         writer.populate(str(label) + "_after_full_step", "dp2n", dp2n)
-    logging.info(colored("Converting PSINC to COMP", "blue"))
+    logging.info(termcolor.colored("Converting PSINC to COMP", "blue"))
     bld.convert_p2n(dp2n)
     bld.update_Sol(Sol, elem, node, th, ud, mpv, "aft", label=label, writer=writer)
     bld.update_p2n(Sol, mpv, node, th, ud)
@@ -183,7 +177,7 @@ def do_psinc_to_comp_conv(
 
 
 def do_swe_to_lake_conv(Sol, mpv, elem, node, ud, th, writer, label, debug):
-    logging.info(colored("swe to lake conversion...", "blue"))
+    logging.info(termcolor.colored("swe to lake conversion...", "blue"))
 
     H1 = Sol.rho[
         :,
@@ -227,10 +221,10 @@ def do_lake_to_swe_conv(
     if debug == True:
         writer.write_all(Sol, mpv, elem, node, th, str(label) + "_after_lake_time_step")
 
-    Sol_freeze = deepcopy(Sol)
-    mpv_freeze = deepcopy(mpv)
+    Sol_freeze = copy.deepcopy(Sol)
+    mpv_freeze = copy.deepcopy(mpv)
 
-    logging.info(colored("doing lake-to-swe time-update...", "blue"))
+    logging.info(termcolor.colored("doing lake-to-swe time-update...", "blue"))
     ret = time_update.time_update(
         Sol,
         flux,
@@ -260,13 +254,13 @@ def do_lake_to_swe_conv(
     else:
         assert 0, "incorrect ud.blending_type"
 
-    Sol = deepcopy(Sol_freeze)
-    mpv = deepcopy(mpv_freeze)
+    Sol = copy.deepcopy(Sol_freeze)
+    mpv = copy.deepcopy(mpv_freeze)
 
     mpv.p2_nodes[...] = dp2n
 
     H10 = mpv.p2_nodes[:, 2:-2, :].mean(axis=1)
-    logging.info(colored("lake to swe conversion...", "blue"))
+    logging.info(termcolor.colored("lake to swe conversion...", "blue"))
     H10 -= H10.mean()
 
     # define 2D kernel
@@ -301,7 +295,7 @@ def do_nonhydro_to_hydro_conv(
     Sol, flux, mpv, bld, elem, node, th, ud, label, writer, step, window_step, t, dt
 ):
 
-    logging.info(colored("nonhydrostatic to hydrostatic conversion...", "blue"))
+    logging.info(termcolor.colored("nonhydrostatic to hydrostatic conversion...", "blue"))
     # bld.convert_p2n(mpv.p2_nodes)
     # bld.update_Sol(Sol,elem,node,th,ud,mpv,'bef',label=label,writer=writer)
     # Sol.rhov = Sol.rhov_half
@@ -331,8 +325,8 @@ def do_hydro_to_nonhydro_conv(
     Sol, flux, mpv, bld, elem, node, th, ud, label, writer, step, window_step, t, dt
 ):
 
-    logging.info(colored("hydrostatic to nonhydrostatic conversion...", "blue"))
-    logging.info(colored("Blending... step = %i" % step, "blue"))
+    logging.info(termcolor.colored("hydrostatic to nonhydrostatic conversion...", "blue"))
+    logging.info(termcolor.colored("Blending... step = %i" % step, "blue"))
 
     # Sol_tmp = deepcopy(Sol)
     # flux_tmp = deepcopy(flux)
@@ -542,10 +536,10 @@ def blending_before_timestep(
             ud.is_nonhydrostatic = 1
             ud.nonhydrostasy = 1.0
     else:
-        ud.is_compressible = is_compressible(ud, window_step)
-        ud.compressibility = compressibility(ud, t, window_step)
-        ud.is_nonhydrostatic = is_nonhydrostatic(ud, window_step)
-        ud.nonhydrostasy = nonhydrostasy(ud, t, window_step)
+        ud.is_compressible = eos.is_compressible(ud, window_step)
+        ud.compressibility = eos.compressibility(ud, t, window_step)
+        ud.is_nonhydrostatic = eos.is_nonhydrostatic(ud, window_step)
+        ud.nonhydrostasy = eos.nonhydrostasy(ud, t, window_step)
 
     return swe_to_lake, Sol, mpv, t
 

src/data_assimilation/etpf.py

@@ -1,5 +1,4 @@
 import numpy as np
-
 import logging
 
 def da_interface(results, obs, obs_attributes, delta, times, tout, N, loc=0):
@@ -11,7 +10,6 @@ def da_interface(results, obs, obs_attributes, delta, times, tout, N, loc=0):
     # local_ens = np.array([mem[inner] for mem in local_ens])
     # local_ens = analysis(local_ens,attr)
     # print(results[:,0,...][0].rho)
-
     attributes = ['rho','rhou','rhov','rhow','rhoY','rhoX']
     # attributes = ['rho', 'rhou', 'rhov']
     tmp = np.array([getattr(results[:,loc,...][n],obs_attributes[0])[inner] for n in range(N)])