Remove 'src' prefix from imports - standardize package structure

.github/workflows/tests.yaml

@@ -3,8 +3,6 @@ name: Run Python Tests
 on:
   workflow_dispatch:
   push:
-    branches: [ main megha]
-  pull_request:
     branches: [ main ]
 
 jobs:

Tests/test_cell.py

@@ -2,7 +2,7 @@
 
 from Tests.test_geo import check_if_cells_are_the_same
 from Tests.tests import Tests, load_data
-from src.pyVertexModel.geometry.cell import Cell
+from pyVertexModel.geometry.cell import Cell
 
 class TestCell(Tests):
     def test_compute_cell_area(self):

Tests/test_degreesOfFreedom.py

@@ -2,7 +2,7 @@
 
 from Tests import test_kg
 from Tests.tests import Tests
-from src.pyVertexModel.geometry.degreesOfFreedom import DegreesOfFreedom
+from pyVertexModel.geometry.degreesOfFreedom import DegreesOfFreedom
 
 
 class TestDofs(Tests):

Tests/test_face.py

@@ -1,7 +1,7 @@
 import numpy as np
 
 from Tests.tests import Tests, load_data, assert_matrix
-from src.pyVertexModel.geometry.face import get_key, Face
+from pyVertexModel.geometry.face import get_key, Face
 
 
 class TestFace(Tests):

Tests/test_flip.py

@@ -3,9 +3,9 @@
 
 from Tests.test_geo import check_if_cells_are_the_same
 from Tests.tests import Tests, load_data, assert_array1D
-from src.pyVertexModel.geometry.degreesOfFreedom import DegreesOfFreedom
-from src.pyVertexModel.geometry.geo import Geo
-from src.pyVertexModel.mesh_remodelling.flip import y_flip_nm, y_flip_nm_recursive, post_flip
+from pyVertexModel.geometry.degreesOfFreedom import DegreesOfFreedom
+from pyVertexModel.geometry.geo import Geo
+from pyVertexModel.mesh_remodelling.flip import y_flip_nm, y_flip_nm_recursive, post_flip
 
 
 class TestFlip(Tests):

Tests/test_geo.py

@@ -1,10 +1,10 @@
 import numpy as np
 
 from Tests.tests import Tests, load_data, assert_matrix, assert_array1D
-from src.pyVertexModel.algorithm.vertexModelBubbles import extrapolate_ys_faces_ellipsoid
-from src.pyVertexModel.algorithm.vertexModelVoronoiFromTimeImage import VertexModelVoronoiFromTimeImage
-from src.pyVertexModel.geometry.geo import Geo, get_node_neighbours_per_domain
-from src.pyVertexModel.util.utils import load_state, ismember_rows
+from pyVertexModel.algorithm.vertexModelBubbles import extrapolate_ys_faces_ellipsoid
+from pyVertexModel.algorithm.vertexModelVoronoiFromTimeImage import VertexModelVoronoiFromTimeImage
+from pyVertexModel.geometry.geo import Geo, get_node_neighbours_per_domain
+from pyVertexModel.util.utils import load_state, ismember_rows
 from Tests.tests import Tests, load_data, assert_matrix
 
 

Tests/test_kg.py

@@ -1,16 +1,16 @@
 import numpy as np
 
 from Tests.tests import Tests, load_data, assert_array1D, assert_matrix
-from src.pyVertexModel.Kg import kg_functions
-from src.pyVertexModel.Kg.kgContractility import KgContractility
-from src.pyVertexModel.Kg.kgSubstrate import KgSubstrate
-from src.pyVertexModel.Kg.kgSurfaceCellBasedAdhesion import KgSurfaceCellBasedAdhesion
-from src.pyVertexModel.Kg.kgTriAREnergyBarrier import KgTriAREnergyBarrier
-from src.pyVertexModel.Kg.kgTriEnergyBarrier import KgTriEnergyBarrier
-from src.pyVertexModel.Kg.kgViscosity import KgViscosity
-from src.pyVertexModel.Kg.kgVolume import KgVolume
-from src.pyVertexModel.algorithm.newtonRaphson import KgGlobal
-from src.pyVertexModel.geometry.geo import Geo
+from pyVertexModel.Kg import kg_functions
+from pyVertexModel.Kg.kgContractility import KgContractility
+from pyVertexModel.Kg.kgSubstrate import KgSubstrate
+from pyVertexModel.Kg.kgSurfaceCellBasedAdhesion import KgSurfaceCellBasedAdhesion
+from pyVertexModel.Kg.kgTriAREnergyBarrier import KgTriAREnergyBarrier
+from pyVertexModel.Kg.kgTriEnergyBarrier import KgTriEnergyBarrier
+from pyVertexModel.Kg.kgViscosity import KgViscosity
+from pyVertexModel.Kg.kgVolume import KgVolume
+from pyVertexModel.algorithm.newtonRaphson import KgGlobal
+from pyVertexModel.geometry.geo import Geo
 
 
 def test_kg_global_filename(filename):

Tests/test_newtonRaphson.py

@@ -2,11 +2,11 @@
 
 from Tests.test_geo import check_if_cells_are_the_same
 from Tests.tests import load_data, Tests, assert_array1D, assert_matrix
-from src.pyVertexModel.algorithm.newtonRaphson import line_search, newton_raphson, newton_raphson_iteration, ml_divide, \
+from pyVertexModel.algorithm.newtonRaphson import line_search, newton_raphson, newton_raphson_iteration, ml_divide, \
     solve_remodeling_step
-from src.pyVertexModel.geometry.degreesOfFreedom import DegreesOfFreedom
-from src.pyVertexModel.geometry.geo import Geo
-from src.pyVertexModel.parameters.set import Set
+from pyVertexModel.geometry.degreesOfFreedom import DegreesOfFreedom
+from pyVertexModel.geometry.geo import Geo
+from pyVertexModel.parameters.set import Set
 
 
 class TestNewtonRaphson(Tests):

Tests/test_remodelling.py

@@ -2,9 +2,9 @@
 
 from Tests.test_geo import check_if_cells_are_the_same
 from Tests.tests import Tests, load_data, assert_matrix
-from src.pyVertexModel.geometry.degreesOfFreedom import DegreesOfFreedom
-from src.pyVertexModel.geometry.geo import Geo
-from src.pyVertexModel.mesh_remodelling.remodelling import Remodelling
+from pyVertexModel.geometry.degreesOfFreedom import DegreesOfFreedom
+from pyVertexModel.geometry.geo import Geo
+from pyVertexModel.mesh_remodelling.remodelling import Remodelling
 
 
 class TestRemodelling(Tests):

Tests/test_tris.py

@@ -1,7 +1,7 @@
 import numpy as np
 
 from Tests.tests import load_data, Tests, assert_array1D
-from src.pyVertexModel.geometry.tris import Tris
+from pyVertexModel.geometry.tris import Tris
 
 
 class TestTris(Tests):

Tests/test_utils.py

@@ -2,12 +2,12 @@
 
 from Tests.test_geo import check_if_cells_are_the_same
 from Tests.tests import Tests
-from src.pyVertexModel.geometry.cell import Cell
-from src.pyVertexModel.geometry.degreesOfFreedom import DegreesOfFreedom
-from src.pyVertexModel.geometry.face import Face
-from src.pyVertexModel.geometry.geo import Geo
-from src.pyVertexModel.geometry.tris import Tris
-from src.pyVertexModel.util.utils import save_backup_vars, load_backup_vars
+from pyVertexModel.geometry.cell import Cell
+from pyVertexModel.geometry.degreesOfFreedom import DegreesOfFreedom
+from pyVertexModel.geometry.face import Face
+from pyVertexModel.geometry.geo import Geo
+from pyVertexModel.geometry.tris import Tris
+from pyVertexModel.util.utils import save_backup_vars, load_backup_vars
 
 
 class TestUtils(Tests):

Tests/test_vertexModel.py

@@ -7,16 +7,16 @@
 from Tests import TEST_DIRECTORY
 from Tests.test_geo import check_if_cells_are_the_same
 from Tests.tests import Tests, assert_matrix, load_data, assert_array1D
-from src.pyVertexModel.algorithm import newtonRaphson
-from src.pyVertexModel.algorithm.newtonRaphson import newton_raphson
-from src.pyVertexModel.algorithm.vertexModel import create_tetrahedra
-from src.pyVertexModel.algorithm.vertexModelBubbles import build_topo, SeedWithBoundingBox, generate_first_ghost_nodes, \
+from pyVertexModel.algorithm import newtonRaphson
+from pyVertexModel.algorithm.newtonRaphson import newton_raphson
+from pyVertexModel.algorithm.vertexModel import create_tetrahedra
+from pyVertexModel.algorithm.vertexModelBubbles import build_topo, SeedWithBoundingBox, generate_first_ghost_nodes, \
     delaunay_compute_entities, VertexModelBubbles
-from src.pyVertexModel.algorithm.vertexModelVoronoiFromTimeImage import build_triplets_of_neighs, \
+from pyVertexModel.algorithm.vertexModelVoronoiFromTimeImage import build_triplets_of_neighs, \
     VertexModelVoronoiFromTimeImage, add_tetrahedral_intercalations, \
     get_four_fold_vertices, divide_quartets_neighbours, process_image
-from src.pyVertexModel.geometry.degreesOfFreedom import DegreesOfFreedom
-from src.pyVertexModel.util.utils import save_backup_vars
+from pyVertexModel.geometry.degreesOfFreedom import DegreesOfFreedom
+from pyVertexModel.util.utils import save_backup_vars
 
 
 class TestVertexModel(Tests):
@@ -502,7 +502,7 @@ def test_initialize_cells_with_numpy_array(self):
         :return:
         """
         import scipy.io
-        from src.pyVertexModel.parameters.set import Set
+        from pyVertexModel.parameters.set import Set
 
         # Load an existing image as a numpy array
         mat_data = scipy.io.loadmat('resources/LblImg_imageSequence.mat')
@@ -553,7 +553,7 @@ def test_initialize_with_numpy_array(self):
         :return:
         """
         import scipy.io
-        from src.pyVertexModel.parameters.set import Set
+        from pyVertexModel.parameters.set import Set
 
         # Load an existing image as a numpy array
         mat_data = scipy.io.loadmat('resources/LblImg_imageSequence.mat')

Tests/tests.py

@@ -3,9 +3,9 @@
 import numpy as np
 from os.path import exists, abspath
 
-from src.pyVertexModel.geometry.geo import Geo
-from src.pyVertexModel.parameters.set import Set
-from src.pyVertexModel.Kg import kg_functions
+from pyVertexModel.geometry.geo import Geo
+from pyVertexModel.parameters.set import Set
+from pyVertexModel.Kg import kg_functions
 
 def load_data(file_name, return_geo=True):
     test_dir = abspath('Tests/data/%s' % file_name)

setup.py

@@ -1,13 +1,14 @@
 import numpy as np
 from Cython.Build import cythonize
-from setuptools import Extension, setup
+from setuptools import Extension, setup, find_packages
 
 ext_options = {"compiler_directives": {"profile": True}, "annotate": True}
-extensions = [Extension("src.pyVertexModel.Kg.kg_functions", ["src/pyVertexModel/Kg/kg_functions.pyx"])]
+extensions = [Extension("pyVertexModel.Kg.kg_functions", ["src/pyVertexModel/Kg/kg_functions.pyx"])]
 
 setup(
     name='pyVertexModel',
-    packages=['src', 'src.pyVertexModel', 'src.pyVertexModel.Kg', 'pyVertexModel'],
+    packages=find_packages(where='src'),
+    package_dir={'': 'src'},
     ext_modules=cythonize(extensions, **ext_options),
     include_dirs=[np.get_include()],
     zip_safe=False,

src/pyVertexModel/Kg/kgContractility.py

@@ -2,8 +2,8 @@
 
 import numpy as np
 
-from src.pyVertexModel.Kg.kg import Kg
-from src.pyVertexModel.util.utils import get_interface
+from pyVertexModel.Kg.kg import Kg
+from pyVertexModel.util.utils import get_interface
 
 
 def get_intensity_based_contractility(c_set, current_face, intensity_images=True):

src/pyVertexModel/Kg/kgContractility_external.py

@@ -3,8 +3,8 @@
 
 import numpy as np
 
-from src.pyVertexModel.Kg.kgContractility import KgContractility, compute_energy_contractility
-from src.pyVertexModel.util.utils import get_interface
+from pyVertexModel.Kg.kgContractility import KgContractility, compute_energy_contractility
+from pyVertexModel.util.utils import get_interface
 
 
 class KgContractilityExternal(KgContractility):

src/pyVertexModel/Kg/kgSubstrate.py

@@ -2,8 +2,8 @@
 
 import numpy as np
 
-from src.pyVertexModel.Kg.kg import Kg
-from src.pyVertexModel.util.utils import get_interface
+from pyVertexModel.Kg.kg import Kg
+from pyVertexModel.util.utils import get_interface
 
 
 class KgSubstrate(Kg):

src/pyVertexModel/Kg/kgSurfaceCellBasedAdhesion.py

@@ -2,9 +2,9 @@
 
 import numpy as np
 
-from src.pyVertexModel.Kg import kg_functions
-from src.pyVertexModel.Kg.kg import Kg
-from src.pyVertexModel.util.utils import get_interface
+from pyVertexModel.Kg import kg_functions
+from pyVertexModel.Kg.kg import Kg
+from pyVertexModel.util.utils import get_interface
 
 
 def get_lambda(c_cell, face, Set, Geo):

src/pyVertexModel/Kg/kgTriAREnergyBarrier.py

@@ -2,8 +2,8 @@
 
 import numpy as np
 
-from src.pyVertexModel.Kg.kg import Kg
-from src.pyVertexModel.util.utils import get_interface
+from pyVertexModel.Kg.kg import Kg
+from pyVertexModel.util.utils import get_interface
 
 
 class KgTriAREnergyBarrier(Kg):

src/pyVertexModel/Kg/kgTriEnergyBarrier.py

@@ -2,9 +2,9 @@
 
 import numpy as np
 
-from src.pyVertexModel.Kg import kg_functions
-from src.pyVertexModel.Kg.kg import Kg
-from src.pyVertexModel.util.utils import get_interface
+from pyVertexModel.Kg import kg_functions
+from pyVertexModel.Kg.kg import Kg
+from pyVertexModel.util.utils import get_interface
 
 
 class KgTriEnergyBarrier(Kg):

src/pyVertexModel/Kg/kgViscosity.py

@@ -2,7 +2,7 @@
 
 import numpy as np
 
-from src.pyVertexModel.Kg.kg import Kg
+from pyVertexModel.Kg.kg import Kg
 
 
 class KgViscosity(Kg):

src/pyVertexModel/Kg/kgVolume.py

@@ -2,8 +2,8 @@
 
 import numpy as np
 
-from src.pyVertexModel.Kg import kg_functions
-from src.pyVertexModel.Kg.kg import Kg
+from pyVertexModel.Kg import kg_functions
+from pyVertexModel.Kg.kg import Kg
 
 
 def compute_final_k_volume(ge, K, Vol, Vol0, n):