migrate to 'src' directory structure

whitews · Sep 27, 2023 · f376eac · f376eac
1 parent 23162d1
commit f376eac
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Showing 24 changed files with 16 additions and 15 deletions.
diff --git a/run_tests.py b/run_tests.py
@@ -1,4 +1,4 @@
 import unittest
 
 
-unittest.main('flowutils.tests')
+unittest.main('tests')
diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 import numpy as np  # NumPy is needed to build C extensions
 
 # read in version string
-VERSION_FILE = 'flowutils/_version.py'
+VERSION_FILE = 'src/flowutils/_version.py'
 __version__ = None  # to avoid inspection warning and check if __version__ was loaded
 exec(open(VERSION_FILE).read())
 
@@ -18,27 +18,28 @@
 logicle_extension = Extension(
     'flowutils.logicle_c',
     sources=[
-        'flowutils/logicle_c_ext/_logicle.c',
-        'flowutils/logicle_c_ext/logicle.c'
+        'src/flowutils/logicle_c_ext/_logicle.c',
+        'src/flowutils/logicle_c_ext/logicle.c'
     ],
-    include_dirs=[np.get_include(), 'flowutils/logicle_c_ext'],
+    include_dirs=[np.get_include(), 'src/flowutils/logicle_c_ext'],
     extra_compile_args=['-std=c99']
 )
 
 gating_extension = Extension(
     'flowutils.gating_c',
     sources=[
-        'flowutils/gating_c_ext/_gate_helpers.c',
-        'flowutils/gating_c_ext/gate_helpers.c'
+        'src/flowutils/gating_c_ext/_gate_helpers.c',
+        'src/flowutils/gating_c_ext/gate_helpers.c'
     ],
-    include_dirs=[np.get_include(), 'flowutils/gating_c_ext'],
+    include_dirs=[np.get_include(), 'src/flowutils/gating_c_ext'],
     extra_compile_args=['-std=c99']
 )
 
 setup(
     name='FlowUtils',
     version=__version__,  # noqa PyTypeChecker
     packages=['flowutils'],
+    package_dir={'': "src"},
     package_data={'': []},
     description='Flow Cytometry Standard Utilities',
     long_description=long_description,

diff --git a/flowutils/__init__.py → src/flowutils/__init__.py b/flowutils/__init__.py → src/flowutils/__init__.py
diff --git a/flowutils/_version.py → src/flowutils/_version.py b/flowutils/_version.py → src/flowutils/_version.py
diff --git a/flowutils/compensate.py → src/flowutils/compensate.py b/flowutils/compensate.py → src/flowutils/compensate.py
diff --git a/flowutils/gating.py → src/flowutils/gating.py b/flowutils/gating.py → src/flowutils/gating.py
diff --git a/flowutils/gating_c_ext/_gate_helpers.c → src/flowutils/gating_c_ext/_gate_helpers.c b/flowutils/gating_c_ext/_gate_helpers.c → src/flowutils/gating_c_ext/_gate_helpers.c
diff --git a/flowutils/gating_c_ext/gate_helpers.c → src/flowutils/gating_c_ext/gate_helpers.c b/flowutils/gating_c_ext/gate_helpers.c → src/flowutils/gating_c_ext/gate_helpers.c
diff --git a/flowutils/gating_c_ext/gate_helpers.h → src/flowutils/gating_c_ext/gate_helpers.h b/flowutils/gating_c_ext/gate_helpers.h → src/flowutils/gating_c_ext/gate_helpers.h
diff --git a/flowutils/logicle_c_ext/_logicle.c → src/flowutils/logicle_c_ext/_logicle.c b/flowutils/logicle_c_ext/_logicle.c → src/flowutils/logicle_c_ext/_logicle.c
diff --git a/flowutils/logicle_c_ext/logicle.c → src/flowutils/logicle_c_ext/logicle.c b/flowutils/logicle_c_ext/logicle.c → src/flowutils/logicle_c_ext/logicle.c
diff --git a/flowutils/logicle_c_ext/logicle.h → src/flowutils/logicle_c_ext/logicle.h b/flowutils/logicle_c_ext/logicle.h → src/flowutils/logicle_c_ext/logicle.h
diff --git a/flowutils/transforms.py → src/flowutils/transforms.py b/flowutils/transforms.py → src/flowutils/transforms.py
diff --git a/flowutils/tests/__init__.py → tests/__init__.py b/flowutils/tests/__init__.py → tests/__init__.py
diff --git a/flowutils/tests/compensation_tests.py → tests/compensation_tests.py b/flowutils/tests/compensation_tests.py → tests/compensation_tests.py
@@ -39,8 +39,8 @@
     'G560-A'
 ]
 
-test_data_npy_path = "flowutils/tests/test_data/test_comp_event_data.npy"
-test_comp_csv_path = "flowutils/tests/test_data/test_comp_matrix.csv"
+test_data_npy_path = "tests/test_data/test_comp_event_data.npy"
+test_comp_csv_path = "tests/test_data/test_comp_matrix.csv"
 test_data_channels = [
     'FSC-A', 'FSC-W', 'SSC-A',
     'Ax488-A', 'PE-A', 'PE-TR-A',
@@ -108,7 +108,7 @@ def test_parse_compensation_matrix_from_path(self):
         self.assertIsInstance(matrix_array, np.ndarray)
 
     def test_parse_compensation_matrix_missing_row(self):
-        comp_path = pathlib.Path("flowutils/tests/test_data/test_comp_matrix_missing_row.csv")
+        comp_path = pathlib.Path("tests/test_data/test_comp_matrix_missing_row.csv")
 
         self.assertRaises(
             ValueError,

diff --git a/flowutils/tests/gating_tests.py → tests/gating_tests.py b/flowutils/tests/gating_tests.py → tests/gating_tests.py
@@ -14,10 +14,10 @@ def test_points_in_ellipse():
         coords = [12.99701, 16.22941]
         distance_square = 1.0
 
-        npy_file_path = "flowutils/tests/test_data/event_data_for_ellipse_test.npy"
+        npy_file_path = "tests/test_data/event_data_for_ellipse_test.npy"
         event_data = np.load(npy_file_path)
 
-        truth_path = 'flowutils/tests/test_data/truth/Results_Ellipse1.txt'
+        truth_path = 'tests/test_data/truth/Results_Ellipse1.txt'
         truth = np.genfromtxt(truth_path, delimiter=',').astype('bool')
 
         result = gating.points_in_ellipsoid(
@@ -39,10 +39,10 @@ def test_points_in_polygon():
             ]
         )
 
-        npy_file_path = "flowutils/tests/test_data/event_data_for_poly_test.npy"
+        npy_file_path = "tests/test_data/event_data_for_poly_test.npy"
         event_data = np.load(npy_file_path)
 
-        truth_path = 'flowutils/tests/test_data/truth/Results_Polygon4.txt'
+        truth_path = 'tests/test_data/truth/Results_Polygon4.txt'
         truth = np.genfromtxt(truth_path, delimiter=',').astype('bool')
 
         result = gating.points_in_polygon(poly_vertices, event_data)

diff --git a/...test_data/event_data_for_ellipse_test.npy → ...test_data/event_data_for_ellipse_test.npy b/...test_data/event_data_for_ellipse_test.npy → ...test_data/event_data_for_ellipse_test.npy
diff --git a/...ts/test_data/event_data_for_poly_test.npy → tests/test_data/event_data_for_poly_test.npy b/...ts/test_data/event_data_for_poly_test.npy → tests/test_data/event_data_for_poly_test.npy
diff --git a/.../tests/test_data/test_comp_event_data.npy → tests/test_data/test_comp_event_data.npy b/.../tests/test_data/test_comp_event_data.npy → tests/test_data/test_comp_event_data.npy
diff --git a/...tils/tests/test_data/test_comp_matrix.csv → tests/test_data/test_comp_matrix.csv b/...tils/tests/test_data/test_comp_matrix.csv → tests/test_data/test_comp_matrix.csv
diff --git a/...est_data/test_comp_matrix_missing_row.csv → ...est_data/test_comp_matrix_missing_row.csv b/...est_data/test_comp_matrix_missing_row.csv → ...est_data/test_comp_matrix_missing_row.csv
diff --git a/...ests/test_data/truth/Results_Ellipse1.txt → tests/test_data/truth/Results_Ellipse1.txt b/...ests/test_data/truth/Results_Ellipse1.txt → tests/test_data/truth/Results_Ellipse1.txt
diff --git a/...ests/test_data/truth/Results_Polygon4.txt → tests/test_data/truth/Results_Polygon4.txt b/...ests/test_data/truth/Results_Polygon4.txt → tests/test_data/truth/Results_Polygon4.txt
diff --git a/flowutils/tests/transform_tests.py → tests/transform_tests.py b/flowutils/tests/transform_tests.py → tests/transform_tests.py