add init and package structure

pyproject.toml

@@ -1,5 +1,5 @@
 [project]
-name = "KNP-EMI-DG"
+name = "knpemidg"
 version = "0.0.1"
 requires-python = ">=3.8"
 
@@ -15,5 +15,5 @@ dependencies = [
     'numpy',
     'numba',
     'matplotlib',
-    'git+https://github.com/MiroK/ulfy.git'
+    'ulfy@git+https://github.com/MiroK/ulfy.git'
 ]

src/knpemidg/__init__.py

@@ -0,0 +1,16 @@
+from knpemidg.dlt_dof_extraction import get_indices
+from knpemidg.dlt_dof_extraction import is_dlt_scalar
+from knpemidg.dlt_dof_extraction import get_values
+from knpemidg.dlt_dof_extraction import set_values
+from knpemidg.membrane import MembraneModel
+from knpemidg.utils import subdomain_marking_foo
+from knpemidg.utils import interface_normal
+from knpemidg.utils import plus
+from knpemidg.utils import minus
+from knpemidg.utils import pcws_constant_project
+from knpemidg.utils import CellCenterDistance
+from knpemidg.solver import Solver
+
+__all__ = ["Solver", "MembraneModel", "subdomain_marking_foo",
+        "interface_normal", "plus", "minus", "pcws_constant_project",
+        "CellCenterDistance"]

src/KNP-EMI-DG/membrane.py → src/knpemidg/membrane.py

@@ -1,4 +1,4 @@
-import dlt_dof_extraction as dlt
+import knpemidg.dlt_dof_extraction as dlt
 import dolfin as df
 import numpy as np
 

src/KNP-EMI-DG/solver.py → src/knpemidg/solver.py

@@ -5,11 +5,10 @@
 import time
 from petsc4py import PETSc
 
-from utils import pcws_constant_project
-from utils import interface_normal, plus, minus
-from utils import CellCenterDistance
-
-from membrane import MembraneModel
+from knpemidg.utils import pcws_constant_project
+from knpemidg.utils import interface_normal, plus, minus
+from knpemidg.utils import CellCenterDistance
+from knpemidg.membrane import MembraneModel
 
 # define jump across the membrane (interface gamma)
 JUMP = lambda f, n: minus(f, n) - plus(f, n)

tests/run_MMS_space.py

@@ -9,7 +9,7 @@
 
 if __name__ == '__main__':
     from mms_space import setup_mms
-    from solver import Solver
+    from knpemidg import Solver
     from collections import namedtuple
     from itertools import chain