merge

setup.cfg

@@ -53,7 +53,7 @@ where = src
 
 [options.entry_points]
 console_scripts =
-    poretitioner = poretitioner:main
+    poretitioner = poretitioner:__main__
 
 [options.extras_require]
 pdf = ReportLab>=1.2; RXP

src/poretitioner/__main__.py

@@ -1,3 +1,3 @@
-from poretitioner import main
+from .poretitioner import main
 
 main()

src/poretitioner/poretitioner.py

@@ -5,10 +5,10 @@
 
 import numpy as np
 
-import logger
+from . import logger
 from .getargs import ARG, COMMAND, get_args
 from .utils import segment
-from .utils.configuration import CONFIG, readconfig, SegmentConfiguration, GeneralConfiguration
+from .utils.configuration import CONFIG, readconfig, SegmentConfiguration, GeneralConfiguration, FilterConfiguration
 from .utils.filtering import (
     get_plugins,
     LengthFilter,
@@ -20,33 +20,6 @@
     StandardDeviationFilter,
 )
 
-class Poretitoner:
-    general_config: GeneralConfiguration
-    segment_config: SegmentConfiguration
-
-    def __init__(self, config):
-        pass
-
-    def segment(self):
-        pass
-
-    def filter(self):
-        pass
-
-    def classify(self):
-        pass
-
-    def quantify(self):
-        pass
-
-
-from poretitioner import Poretitoner
-
-porty = Poretitoner("../path/tpo/config.toml")
-
-porty.segment()
-
-
 def run(args):
     # Configures the root application logger.
     # After these line, it's safe to log using src.poretitioner.logger.getLogger() throughout the application.
@@ -71,13 +44,13 @@ def run(args):
         bulk_f5_filepath = Path(command_line_args[ARG.BULK_FAST5]).resolve()
 
         seg_config = configuration[CONFIG.SEGMENTATION]
-        filter_config = configuration[CONFIG.FILTER]
+        filter_config: FilterConfiguration = configuration[CONFIG.FILTER]
         config = configuration[CONFIG.GENERAL]
 
-        filters = get_plugins(filter_configs)
+        filters = get_plugins(filter_config)
 
         save_location = Path(getattr(args, ARG.CAPTURE_DIRECTORY)).resolve()
-        
+
         segmentation_config_str = pprint.pformat(seg_config.__dict__)
         general_config_str = pprint.pformat(config.__dict__)
         log.warning(f"bulk_f5_filepath: {bulk_f5_filepath}")
@@ -135,6 +108,3 @@ def main():
         args = get_args()
     # test_fast5()
     run(args)
-
-if __name__ == "__main__":
-    main()

src/poretitioner/utils/configuration.py

@@ -226,6 +226,12 @@ def from_json(cls, json_dict: Dict):
         }
         return cls.__new__(filters)
 
+    def __setitem__(self, name, my_filter):
+          self.filters[name] = my_filter
+
+    def __getitem__(self, name):
+          return self.filters[name]
+
 
 @dataclass(frozen=True)
 class GeneralConfiguration(BaseConfiguration):

src/tests/test_segment.py

@@ -611,6 +611,7 @@ def prep_capture_windows_test():
         assert count_by_channel[channel_number] == 4
 
 
+@pytest.mark.xfail(reason="Need to implement config (filters currently in progress).")
 class TestParallelFindCaptures:
     def parallel_find_captures_test(self):
         bulk_f5_fname = "src/tests/data/bulk_fast5_dummy.fast5"