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

whitews · Mar 28, 2024 · 44be3c0 · 44be3c0
1 parent 64e086d
commit 44be3c0
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Showing 56 changed files with 8 additions and 28 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,3 @@
+[build-system]
+requires = ['setuptools>=61.0']
+build-backend   = 'setuptools.build_meta'
diff --git a/run_tests.py b/run_tests.py
@@ -1,4 +1,4 @@
 import unittest
 
 if __name__ == '__main__':
-    unittest.main('flowkit.tests')
+    unittest.main('tests')
diff --git a/setup.py b/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',

diff --git a/flowkit/__init__.py → src/flowkit/__init__.py b/flowkit/__init__.py → src/flowkit/__init__.py
diff --git a/flowkit/_conf.py → src/flowkit/_conf.py b/flowkit/_conf.py → src/flowkit/_conf.py
diff --git a/flowkit/_models/__init__.py → src/flowkit/_models/__init__.py b/flowkit/_models/__init__.py → src/flowkit/_models/__init__.py
diff --git a/flowkit/_models/dimension.py → src/flowkit/_models/dimension.py b/flowkit/_models/dimension.py → src/flowkit/_models/dimension.py
diff --git a/flowkit/_models/gate_node.py → src/flowkit/_models/gate_node.py b/flowkit/_models/gate_node.py → src/flowkit/_models/gate_node.py
diff --git a/flowkit/_models/gates/__init__.py → src/flowkit/_models/gates/__init__.py b/flowkit/_models/gates/__init__.py → src/flowkit/_models/gates/__init__.py
diff --git a/flowkit/_models/gates/_base_gate.py → src/flowkit/_models/gates/_base_gate.py b/flowkit/_models/gates/_base_gate.py → src/flowkit/_models/gates/_base_gate.py
diff --git a/flowkit/_models/gates/_gates.py → src/flowkit/_models/gates/_gates.py b/flowkit/_models/gates/_gates.py → src/flowkit/_models/gates/_gates.py
diff --git a/flowkit/_models/gates/_gml_gates.py → src/flowkit/_models/gates/_gml_gates.py b/flowkit/_models/gates/_gml_gates.py → src/flowkit/_models/gates/_gml_gates.py
diff --git a/flowkit/_models/gates/_wsp_gates.py → src/flowkit/_models/gates/_wsp_gates.py b/flowkit/_models/gates/_wsp_gates.py → src/flowkit/_models/gates/_wsp_gates.py
diff --git a/flowkit/_models/gating_results.py → src/flowkit/_models/gating_results.py b/flowkit/_models/gating_results.py → src/flowkit/_models/gating_results.py
diff --git a/flowkit/_models/gating_strategy.py → src/flowkit/_models/gating_strategy.py b/flowkit/_models/gating_strategy.py → src/flowkit/_models/gating_strategy.py
diff --git a/flowkit/_models/sample.py → src/flowkit/_models/sample.py b/flowkit/_models/sample.py → src/flowkit/_models/sample.py
diff --git a/flowkit/_models/session.py → src/flowkit/_models/session.py b/flowkit/_models/session.py → src/flowkit/_models/session.py
diff --git a/flowkit/_models/transforms/__init__.py → src/flowkit/_models/transforms/__init__.py b/flowkit/_models/transforms/__init__.py → src/flowkit/_models/transforms/__init__.py
diff --git a/...kit/_models/transforms/_base_transform.py → ...kit/_models/transforms/_base_transform.py b/...kit/_models/transforms/_base_transform.py → ...kit/_models/transforms/_base_transform.py
diff --git a/flowkit/_models/transforms/_matrix.py → src/flowkit/_models/transforms/_matrix.py b/flowkit/_models/transforms/_matrix.py → src/flowkit/_models/transforms/_matrix.py
diff --git a/flowkit/_models/transforms/_transforms.py → ...flowkit/_models/transforms/_transforms.py b/flowkit/_models/transforms/_transforms.py → ...flowkit/_models/transforms/_transforms.py
diff --git a/...kit/_models/transforms/_wsp_transforms.py → ...kit/_models/transforms/_wsp_transforms.py b/...kit/_models/transforms/_wsp_transforms.py → ...kit/_models/transforms/_wsp_transforms.py
diff --git a/flowkit/_models/workspace.py → src/flowkit/_models/workspace.py b/flowkit/_models/workspace.py → src/flowkit/_models/workspace.py
diff --git a/flowkit/_resources/DataTypes.v2.0.xsd → src/flowkit/_resources/DataTypes.v2.0.xsd b/flowkit/_resources/DataTypes.v2.0.xsd → src/flowkit/_resources/DataTypes.v2.0.xsd
diff --git a/flowkit/_resources/Gating-ML.v2.0.xsd → src/flowkit/_resources/Gating-ML.v2.0.xsd b/flowkit/_resources/Gating-ML.v2.0.xsd → src/flowkit/_resources/Gating-ML.v2.0.xsd
diff --git a/flowkit/_resources/Transformations.v2.0.xsd → ...owkit/_resources/Transformations.v2.0.xsd b/flowkit/_resources/Transformations.v2.0.xsd → ...owkit/_resources/Transformations.v2.0.xsd
diff --git a/flowkit/_resources/__init__.py → src/flowkit/_resources/__init__.py b/flowkit/_resources/__init__.py → src/flowkit/_resources/__init__.py
diff --git a/flowkit/_utils/__init__.py → src/flowkit/_utils/__init__.py b/flowkit/_utils/__init__.py → src/flowkit/_utils/__init__.py
diff --git a/flowkit/_utils/gating_utils.py → src/flowkit/_utils/gating_utils.py b/flowkit/_utils/gating_utils.py → src/flowkit/_utils/gating_utils.py
diff --git a/flowkit/_utils/gml_write.py → src/flowkit/_utils/gml_write.py b/flowkit/_utils/gml_write.py → src/flowkit/_utils/gml_write.py
diff --git a/flowkit/_utils/plot_utils.py → src/flowkit/_utils/plot_utils.py b/flowkit/_utils/plot_utils.py → src/flowkit/_utils/plot_utils.py
diff --git a/flowkit/_utils/sample_utils.py → src/flowkit/_utils/sample_utils.py b/flowkit/_utils/sample_utils.py → src/flowkit/_utils/sample_utils.py
diff --git a/flowkit/_utils/wsp_utils.py → src/flowkit/_utils/wsp_utils.py b/flowkit/_utils/wsp_utils.py → src/flowkit/_utils/wsp_utils.py
diff --git a/flowkit/_utils/xml_common.py → src/flowkit/_utils/xml_common.py b/flowkit/_utils/xml_common.py → src/flowkit/_utils/xml_common.py
diff --git a/flowkit/_utils/xml_utils.py → src/flowkit/_utils/xml_utils.py b/flowkit/_utils/xml_utils.py → src/flowkit/_utils/xml_utils.py
diff --git a/flowkit/_version.py → src/flowkit/_version.py b/flowkit/_version.py → src/flowkit/_version.py
diff --git a/flowkit/exceptions.py → src/flowkit/exceptions.py b/flowkit/exceptions.py → src/flowkit/exceptions.py
diff --git a/flowkit/tests/__init__.py → tests/__init__.py b/flowkit/tests/__init__.py → tests/__init__.py
diff --git a/flowkit/tests/export_gml_tests.py → tests/export_gml_tests.py b/flowkit/tests/export_gml_tests.py → tests/export_gml_tests.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'

diff --git a/flowkit/tests/gate_tests.py → tests/gate_tests.py b/flowkit/tests/gate_tests.py → tests/gate_tests.py
diff --git a/flowkit/tests/gating_results_tests.py → tests/gating_results_tests.py b/flowkit/tests/gating_results_tests.py → tests/gating_results_tests.py
diff --git a/...sts/gating_strategy_custom_gates_tests.py → tests/gating_strategy_custom_gates_tests.py b/...sts/gating_strategy_custom_gates_tests.py → tests/gating_strategy_custom_gates_tests.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):

diff --git a/.../tests/gating_strategy_prog_gate_tests.py → tests/gating_strategy_prog_gate_tests.py b/.../tests/gating_strategy_prog_gate_tests.py → tests/gating_strategy_prog_gate_tests.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'

diff --git a/...sts/gating_strategy_remove_gates_tests.py → tests/gating_strategy_remove_gates_tests.py b/...sts/gating_strategy_remove_gates_tests.py → tests/gating_strategy_remove_gates_tests.py
diff --git a/...sts/gating_strategy_reused_gates_tests.py → tests/gating_strategy_reused_gates_tests.py b/...sts/gating_strategy_reused_gates_tests.py → tests/gating_strategy_reused_gates_tests.py
diff --git a/flowkit/tests/gating_strategy_tests.py → tests/gating_strategy_tests.py b/flowkit/tests/gating_strategy_tests.py → tests/gating_strategy_tests.py
diff --git a/flowkit/tests/gatingml_tests.py → tests/gatingml_tests.py b/flowkit/tests/gatingml_tests.py → tests/gatingml_tests.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)

diff --git a/flowkit/tests/matrix_tests.py → tests/matrix_tests.py b/flowkit/tests/matrix_tests.py → tests/matrix_tests.py
diff --git a/flowkit/tests/plot_tests.py → tests/plot_tests.py b/flowkit/tests/plot_tests.py → tests/plot_tests.py
diff --git a/flowkit/tests/sample_export_tests.py → tests/sample_export_tests.py b/flowkit/tests/sample_export_tests.py → tests/sample_export_tests.py
diff --git a/flowkit/tests/sample_tests.py → tests/sample_tests.py b/flowkit/tests/sample_tests.py → tests/sample_tests.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
 

diff --git a/flowkit/tests/session_export_tests.py → tests/session_export_tests.py b/flowkit/tests/session_export_tests.py → tests/session_export_tests.py
diff --git a/flowkit/tests/session_tests.py → tests/session_tests.py b/flowkit/tests/session_tests.py → tests/session_tests.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
 

diff --git a/flowkit/tests/string_repr_tests.py → tests/string_repr_tests.py b/flowkit/tests/string_repr_tests.py → tests/string_repr_tests.py
diff --git a/flowkit/tests/transform_tests.py → tests/transform_tests.py b/flowkit/tests/transform_tests.py → tests/transform_tests.py
diff --git a/flowkit/tests/workspace_tests.py → tests/workspace_tests.py b/flowkit/tests/workspace_tests.py → tests/workspace_tests.py