move to 'src' structure & migrate to pyproject.toml

Author: whitews

pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ['setuptools>=61.0']
+build-backend   = 'setuptools.build_meta'

run_tests.py

@@ -1,4 +1,4 @@
 import unittest
 
 if __name__ == '__main__':
-    unittest.main('flowkit.tests')
+    unittest.main('tests')

setup.py

@@ -4,7 +4,7 @@
 from setuptools import setup, find_packages
 
 # read in version string
-VERSION_FILE = 'flowkit/_version.py'
+VERSION_FILE = 'src/flowkit/_version.py'
 __version__ = None  # to avoid inspection warning and check if __version__ was loaded
 exec(open(VERSION_FILE).read())
 
@@ -31,7 +31,8 @@
 setup(
     name='FlowKit',
     version=__version__,  # noqa PyTypeChecker
-    packages=find_packages(exclude=["flowkit/tests/"]),
+    packages=['flowkit'],
+    package_dir={'': 'src'},
     package_data={'': ['_resources/*.xsd']},
     include_package_data=True,
     description='Flow Cytometry Toolkit',

flowkit/__init__.py src/flowkit/__init__.py

@@ -2,16 +2,12 @@
 Tests for exporting to GatingML
 """
 import unittest
-import sys
-import os
 import glob
 import re
 from io import BytesIO
 import numpy as np
 import pandas as pd
 
-sys.path.append(os.path.abspath('../..'))
-
 from flowkit import Sample, Session
 
 data1_fcs_path = 'data/gate_ref/data1.fcs'

flowkit/_conf.py src/flowkit/_conf.py

@@ -2,13 +2,9 @@
 Tests for custom gates in the GatingStrategy Class
 """
 import copy
-import os
-import sys
 import unittest
 import flowkit as fk
 
-sys.path.append(os.path.abspath('../..'))
-
 
 class GatingStrategyCustomGatesTestCase(unittest.TestCase):
     def setUp(self):

flowkit/_models/__init__.py src/flowkit/_models/__init__.py

@@ -3,13 +3,9 @@
 """
 import copy
 import unittest
-import sys
-import os
 import numpy as np
 import pandas as pd
 
-sys.path.append(os.path.abspath('../..'))
-
 import flowkit as fk
 
 data1_fcs_path = 'data/gate_ref/data1.fcs'

flowkit/_models/dimension.py src/flowkit/_models/dimension.py

@@ -1,14 +1,10 @@
 import unittest
-import sys
-import os
 import glob
 import re
 import numpy as np
 import pandas as pd
 
-sys.path.append(os.path.abspath('../..'))
-
-from flowkit import Sample, GatingStrategy, Session, gates, parse_gating_xml
+from flowkit import Sample, GatingStrategy, Session, parse_gating_xml
 
 data1_fcs_path = 'data/gate_ref/data1.fcs'
 data1_sample = Sample(data1_fcs_path)

flowkit/_models/gate_node.py src/flowkit/_models/gate_node.py

@@ -3,16 +3,12 @@
 """
 import copy
 import unittest
-import sys
-import os
 from pathlib import Path
 import numpy as np
 import pandas as pd
 import flowio
 import warnings
 
-sys.path.append(os.path.abspath('../..'))
-
 from flowkit import Sample, transforms, read_multi_dataset_fcs
 from flowkit.exceptions import DataOffsetDiscrepancyError
 

flowkit/_models/gates/__init__.py src/flowkit/_models/gates/__init__.py

@@ -3,13 +3,9 @@
 """
 import copy
 import unittest
-import sys
-import os
 import numpy as np
 import pandas as pd
 
-sys.path.append(os.path.abspath('../..'))
-
 from flowkit import Session, Sample, Matrix, Dimension, gates, transforms, load_samples
 from .gating_strategy_prog_gate_tests import data1_sample, poly1_gate, poly1_vertices, comp_matrix_01, asinh_xform1