Refactored until second_project.explicit_forward_non_advective

.coveragerc

@@ -1,9 +1,9 @@
 [run]
 source = src
 omit = 
-    src/data_assimilation/*
-    src/inputs/*
-    src/utils/debug_helpers.py
+    src/pybella/data_assimilation/*
+    src/pybella/inputs/*
+    src/pybella/utils/debug_helpers.py
     */tests/*
     */test_*
     setup.py

README.md

@@ -8,8 +8,8 @@
 
 
 <p align="center">
-<a href="https://github.com/ray-chew/pyBELLA/actions/workflows/documentation.yml">
-<img alt="GitHub Actions: docs" src=https://img.shields.io/github/actions/workflow/status/ray-chew/pyBELLA/documentation.yml?logo=github&label=docs>
+<a href="https://github.com/ray-chew/pyBELLA/actions/workflows/deploy.yml">
+<img alt="GitHub Actions: docs" src=https://img.shields.io/github/actions/workflow/status/ray-chew/pyBELLA/deploy.yml?logo=github&label=docs>
 </a>
 <a href="https://github.com/ray-chew/pyBELLA/issues">
 <img alt="open issues" src=https://img.shields.io/github/issues/ray-chew/pyBELLA>

run_scripts/test_suite.py

@@ -43,7 +43,6 @@
         diag = td.compare_sol("gen_target")
         diag.update_targets()
 
-
     ud["output_type"] = "test"
     # Do diagnostics
     ud["diag"] = True

src/pybella/__main__.py

@@ -4,6 +4,8 @@
 
 import numpy as np
 
+from .flow_solver.utils import prepare
+
 # dependencies of the atmospheric flow solver
 from .flow_solver.discretisation import time_update as dis_time_update
 
@@ -16,7 +18,7 @@
 from .data_assimilation import prepare as da_prepare, analysis as da_analysis
 
 # package imports
-from .utils import prepare, io, sim_params as params
+from .utils import io, sim_params as params
 
 
 ##########################################################
@@ -67,23 +69,21 @@ def main():
             debug_writer = io.create_debug_writer(params.debug, writer, mem)
 
             logging.info("For ensemble member = %i..." % cnt)
-            mem = dis_time_update.do(
-                sst,
-                mem,
-                tout,
-                blend,
-                step_writer,
-                debug_writer
-            )
+            mem = dis_time_update.do(mem, sst.ud, tout, blend, step_writer, debug_writer)
 
             if sst.ud.diag:
                 if sst.ud.diag_updt_targets:
-                    strip_target.do(step_writer.OUTPUT_FILENAME + step_writer.BASE_NAME + step_writer.SUFFIX + '.h5', sst.ud, time_increment=sst.diag_comparison.time_increment)
+                    strip_target.do(
+                        step_writer.OUTPUT_FILENAME
+                        + step_writer.BASE_NAME
+                        + step_writer.SUFFIX
+                        + ".h5",
+                        sst.ud,
+                        time_increment=sst.diag_comparison.time_increment,
+                    )
                     sst.diag_comparison.update_targets()
                 else:
-                    sst.diag_comparison.test_do(
-                        mem, sst.ud
-                    )
+                    sst.diag_comparison.test_do(mem, sst.ud)
 
             futures.append(mem)
 

src/pybella/data_assimilation/analysis.py

@@ -120,7 +120,7 @@ def do_for_window(tout, outer_step, results, sst, writer):
     # Update ensemble with analysis
     ######################################################
     for mem in results:
-        elem, node, Sol, _, mpv, th, _ = mem
+        elem, node, Sol, _, mpv, th, _, _ = mem
         bdry.set_explicit_boundary_data(Sol, elem, sst.ud, th, mpv)
         p2_nodes = mpv.p2_nodes
         bdry.set_ghostnodes_p2(p2_nodes, node, sst.ud)

src/pybella/data_assimilation/letkf.py

@@ -11,7 +11,7 @@
 
 import matplotlib.pyplot as plt
 
-from ..flow_solver.utils import options as opts
+from ..utils import options as opts
 from . import utils
 
 debug_cnt = 0

src/pybella/data_assimilation/utils.py

@@ -5,7 +5,9 @@
 
 import matplotlib.pyplot as plt
 
-from ..flow_solver.utils import options as opts, boundary as bdry
+from ..utils import options as opts
+
+from ..flow_solver.utils import boundary as bdry
 
 
 class ensemble(object):

src/pybella/flow_solver/discretisation/grid.py

@@ -1,6 +1,6 @@
 import numpy as np
 
-from ..utils import options as opts
+from ...utils import options as opts
 
 
 def grid_init(ud):