update manifest

MANIFEST.in

@@ -1,2 +1,8 @@
 include LICENSE
-include Readme.md
+include Readme.md
+include vital_sqi/resource/sqi_dict.json
+include vital_sqi/resource/rule_dict.json
+include tests/test_data/sqi_dict.json
+include tests/test_data/rule_dict.json
+include vital_sqi/resource/peak_dectector_list.txt
+include vital_sqi/resource/citations.bib

setup.py

@@ -39,6 +39,10 @@
                         'dateparser>=1.0.0',
                         'pyflowchart>=0.1.3'],
     python_requires = '>=3.7',
+    include_package_data=True,
+    package_data={
+        "vital_sqi": ["resource/*.json"],
+    },
     zip_safe = False,
     url = 'https://github.com/meta00/vital_sqi',
     license = 'MIT',

vital_sqi/pipeline/pipeline_highlevel.py

@@ -394,41 +394,41 @@ def get_qualified_ecg(
 
     return signal_obj
 
-import tempfile
-
-if __name__ == "__main__":
-    # Example-based input files and parameters
-    file_in = os.path.abspath("tests/test_data/ppg_smartcare.csv")
-    # file_in = os.path.abspath("tests/test_data/example.edf")
-    sqi_dict = os.path.abspath("tests/test_data/sqi_dict.json")
-    rule_dict_filename = os.path.abspath("tests/test_data/rule_dict_test.json")
-    ruleset_order = {2: "skewness_1", 1: "perfusion"}
-    # output_dir = tempfile.gettempdir()
-    output_dir = "D:\Workspace\Oucru\\vital_sqi\outdir"
-
-    # Call the function under test
-    # signal_obj = get_qualified_ecg(
-    #     file_name=file_in,
-    #     sqi_dict_filename=sqi_dict,
-    #     # signal_idx=6,
-    #     # timestamp_idx=0,
-    #     file_type="edf",  # File type explicitly defined as in the example
-    #     duration=30,  # Duration parameter passed
-    #     rule_dict_filename=rule_dict_filename,
-    #     ruleset_order=ruleset_order,
-    #     output_dir=output_dir,
-    # )
-
-    signal_obj = get_qualified_ppg(
-            file_name=file_in,
-            sqi_dict_filename=sqi_dict,
-            signal_idx=6,
-            timestamp_idx=0,
-            # file_type="edf",  # File type explicitly defined as in the example
-            duration=30,      # Duration parameter passed
-            rule_dict_filename=rule_dict_filename,
-            ruleset_order=ruleset_order,
-            output_dir=output_dir,
-    )
-
-    print(signal_obj.signals[0:100])
+# import tempfile
+
+# if __name__ == "__main__":
+#     # Example-based input files and parameters
+#     file_in = os.path.abspath("tests/test_data/ppg_smartcare.csv")
+#     # file_in = os.path.abspath("tests/test_data/example.edf")
+#     sqi_dict = os.path.abspath("tests/test_data/sqi_dict.json")
+#     rule_dict_filename = os.path.abspath("tests/test_data/rule_dict_test.json")
+#     ruleset_order = {2: "skewness_1", 1: "perfusion"}
+#     # output_dir = tempfile.gettempdir()
+#     output_dir = "D:\Workspace\Oucru\\vital_sqi\outdir"
+
+#     # Call the function under test
+#     # signal_obj = get_qualified_ecg(
+#     #     file_name=file_in,
+#     #     sqi_dict_filename=sqi_dict,
+#     #     # signal_idx=6,
+#     #     # timestamp_idx=0,
+#     #     file_type="edf",  # File type explicitly defined as in the example
+#     #     duration=30,  # Duration parameter passed
+#     #     rule_dict_filename=rule_dict_filename,
+#     #     ruleset_order=ruleset_order,
+#     #     output_dir=output_dir,
+#     # )
+
+#     signal_obj = get_qualified_ppg(
+#             file_name=file_in,
+#             sqi_dict_filename=sqi_dict,
+#             signal_idx=6,
+#             timestamp_idx=0,
+#             # file_type="edf",  # File type explicitly defined as in the example
+#             duration=30,      # Duration parameter passed
+#             rule_dict_filename=rule_dict_filename,
+#             ruleset_order=ruleset_order,
+#             output_dir=output_dir,
+#     )
+
+#     print(signal_obj.signals[0:100])