Merge pull request #519 from firedrakeproject/TBendall/GreatReorganis…

…ation

Restructure codebase

LICENSE

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2016 Firedrake
+Copyright (c) 2016 Gusto
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

examples/shallow_water/moist_thermal_williamson5.py

@@ -4,7 +4,7 @@
 """
 from gusto import *
 from firedrake import (IcosahedralSphereMesh, SpatialCoordinate,
-                       as_vector, pi, sqrt, min_value, exp, cos)
+                       as_vector, pi, sqrt, min_value, exp, cos, sin)
 import sys
 
 # ----------------------------------------------------------------- #

gusto/__init__.py

@@ -1,29 +1,15 @@
 
 # Start logging first, incase anything goes wrong
-from gusto.logging import *                          # noqa
+from gusto.core.logging import *                     # noqa
 set_log_handler()
 
-from gusto.active_tracers import *                   # noqa
-from gusto.common_forms import *                     # noqa
-from gusto.configuration import *                    # noqa
-from gusto.coord_transforms import *                 # noqa
-from gusto.domain import *                           # noqa
+from gusto.core import *                             # noqa
 from gusto.diagnostics import *                      # noqa
-from gusto.diffusion_methods import *                # noqa
 from gusto.equations import *                        # noqa
-from gusto.forcing import *                          # noqa
-from gusto.initialisation_tools import *             # noqa
-from gusto.io import *                               # noqa
-from gusto.labels import *                           # noqa
-from gusto.limiters import *                         # noqa
-from gusto.linear_solvers import *                   # noqa
-from gusto.meshes import *                           # noqa
-from gusto.numerical_integrator import *             # noqa
+from gusto.initialisation import *                   # noqa
 from gusto.physics import *                          # noqa
-from gusto.preconditioners import *                  # noqa
 from gusto.recovery import *                         # noqa
+from gusto.solvers import *                          # noqa
 from gusto.spatial_methods import *                  # noqa
 from gusto.time_discretisation import *              # noqa
-from gusto.timeloop import *                         # noqa
-from gusto.transport_methods import *                # noqa
-from gusto.wrappers import *                         # noqa
+from gusto.timestepping import *                     # noqa

gusto/core/__init__.py

@@ -0,0 +1,11 @@
+from gusto.core.configuration import *           # noqa
+from gusto.core.coordinates import *             # noqa
+from gusto.core.coord_transforms import *        # noqa
+from gusto.core.domain import *                  # noqa
+from gusto.core.fields import *                  # noqa
+from gusto.core.function_spaces import *         # noqa
+from gusto.core.io import *                      # noqa
+from gusto.core.kernels import *                 # noqa
+from gusto.core.labels import *                  # noqa
+from gusto.core.logging import *                 # noqa
+from gusto.core.meshes import *                  # noqa

gusto/coordinates.py → gusto/core/coordinates.py

@@ -3,8 +3,8 @@
 Coordinate fields are stored in specified VectorFunctionSpaces.
 """
 
-from gusto.coord_transforms import lonlatr_from_xyz, rotated_lonlatr_coords
-from gusto.logging import logger
+from gusto.core.coord_transforms import lonlatr_from_xyz, rotated_lonlatr_coords
+from gusto.core.logging import logger
 from firedrake import SpatialCoordinate, Function
 import numpy as np
 import pandas as pd

gusto/domain.py → gusto/core/domain.py

@@ -4,8 +4,8 @@
 model's time interval.
 """
 
-from gusto.coordinates import Coordinates
-from gusto.function_spaces import Spaces, check_degree_args
+from gusto.core.coordinates import Coordinates
+from gusto.core.function_spaces import Spaces, check_degree_args
 from firedrake import (Constant, SpatialCoordinate, sqrt, CellNormal, cross,
                        inner, grad, VectorFunctionSpace, Function, FunctionSpace,
                        perp)

gusto/function_spaces.py → gusto/core/function_spaces.py

@@ -3,7 +3,7 @@
 used by the model.
 """
 
-from gusto import logger
+from gusto.core.logging import logger
 from firedrake import (HCurl, HDiv, FunctionSpace, FiniteElement,
                        TensorProductElement, interval)
 

gusto/io.py → gusto/core/io.py

@@ -6,13 +6,13 @@
 import sys
 import time
 from gusto.diagnostics import Diagnostics, CourantNumber
-from gusto.meshes import get_flat_latlon_mesh
+from gusto.core.meshes import get_flat_latlon_mesh
 from firedrake import (Function, functionspaceimpl, Constant,
                        DumbCheckpoint, FILE_CREATE, FILE_READ, CheckpointFile)
 from firedrake.output import VTKFile
 from pyop2.mpi import MPI
 import numpy as np
-from gusto.logging import logger, update_logfile_location
+from gusto.core.logging import logger, update_logfile_location
 
 __all__ = ["pick_up_mesh", "IO"]
 

gusto/labels.py → gusto/core/labels.py

@@ -3,7 +3,7 @@
 import ufl
 from firedrake import Function
 from firedrake.fml import Term, Label, LabelledForm
-from gusto.configuration import IntegrateByParts, TransportEquationType
+from gusto.core.configuration import IntegrateByParts, TransportEquationType
 from types import MethodType
 
 dynamics_label = Label("dynamics", validator=lambda value: type(value) is str)

gusto/logging.py → gusto/core/logging.py

@@ -1,7 +1,7 @@
 """Gusto Logging Module
 
 All logging functionality for Gusto is controlled from
-``gusto.logging``. A logger object ``logging.getLogger("gusto")`` is
+``gusto.core.logging``. A logger object ``logging.getLogger("gusto")`` is
 created internally.
 
 The primary means of configuration is via environment variables, the