change utils module io to io_utils to not clash with core io model

VERSION

@@ -1 +1,2 @@
-0.1.1
+0.1.0
+

cobrawap/__main__.py

@@ -14,17 +14,17 @@
 from pprint import pformat
 from pathlib import Path
 import inspect
-sys.path.append(str(Path(inspect.getfile(lambda: None)).parent))
+# sys.path.append(str(Path(inspect.getfile(lambda: None)).parent))
 sys.path.append(str(Path(inspect.getfile(lambda: None)).parent / 'pipeline'))
-from cmd_utils import get_setting, set_setting, get_initial_available_stages
-from cmd_utils import is_profile_name_valid, create_new_configfile 
-from cmd_utils import input_profile, get_profile, setup_entry_stage 
-from cmd_utils import working_directory, load_config_file, get_config
-from cmd_utils import locate_str_in_list, read_stage_output
+from .cmd_utils import get_setting, set_setting, get_initial_available_stages
+from .cmd_utils import is_profile_name_valid, create_new_configfile 
+from .cmd_utils import input_profile, get_profile, setup_entry_stage 
+from .cmd_utils import working_directory, load_config_file, get_config
+from .cmd_utils import locate_str_in_list, read_stage_output
 log = logging.getLogger()
 logging.basicConfig(level=logging.INFO)
 
-# requires hardcoded location where to lookup all defined paths
+
 try:
     STAGES = get_setting('stages')
 except Exception as e:

cobrawap/cmd_utils.py

@@ -6,10 +6,10 @@
 from string import ascii_lowercase
 import contextlib
 from pathlib import Path
-sys.path.append(str(Path(__file__).parent / 'pipeline' / 'utils'))
-from snakefile import update_configfile, get_setting, set_setting
-from snakefile import load_config_file, locate_str_in_list, get_config
-from snakefile import read_stage_output
+# sys.path.append(str(Path(__file__).parent / 'pipeline' / 'utils'))
+from .pipeline.utils.snakefile import  get_setting, set_setting, get_config
+from .pipeline.utils.snakefile import load_config_file, locate_str_in_list
+from .pipeline.utils.snakefile import read_stage_output, update_configfile
 log = logging.getLogger()
 logging.basicConfig(level=logging.INFO)
 

cobrawap/pipeline/stage01_data_entry/scripts/check_input.py

@@ -7,7 +7,7 @@
 import numpy as np
 import argparse
 from pathlib import Path
-from utils.io import load_neo
+from utils.io_utils import load_neo
 from utils.neo_utils import analogsignal_to_imagesequence, imagesequence_to_analogsignal
 
 CLI = argparse.ArgumentParser()

cobrawap/pipeline/stage01_data_entry/scripts/enter_data_template.py

@@ -9,7 +9,7 @@
 from utils.parse import parse_string2dict, none_or_float, none_or_int, none_or_str
 from utils.neo_utils import imagesequence_to_analogsignal, merge_analogsignals
 from utils.neo_utils import flip_image, rotate_image, time_slice
-from utils.io import load_neo, write_neo
+from utils.io_utils import load_neo, write_neo
 
 
 CLI = argparse.ArgumentParser()

cobrawap/pipeline/stage01_data_entry/scripts/plot_traces.py

@@ -7,7 +7,7 @@
 from pathlib import Path
 import matplotlib.pyplot as plt
 import seaborn as sns
-from utils.io import load_neo, save_plot
+from utils.io_utils import load_neo, save_plot
 from utils.neo_utils import time_slice
 from utils.parse import parse_plot_channels, none_or_int
 

cobrawap/pipeline/stage02_processing/scripts/background_subtraction.py

@@ -7,7 +7,7 @@
 import argparse
 from pathlib import Path
 import os
-from utils.io import load_neo, write_neo, save_plot
+from utils.io_utils import load_neo, write_neo, save_plot
 from utils.parse import none_or_str
 
 CLI = argparse.ArgumentParser()

cobrawap/pipeline/stage02_processing/scripts/check_input.py

@@ -7,7 +7,7 @@
 import numpy as np
 import argparse
 import quantities as pq
-from utils.io import load_neo
+from utils.io_utils import load_neo
 
 CLI = argparse.ArgumentParser()
 CLI.add_argument("--data", nargs='?', type=str, required=True,

cobrawap/pipeline/stage02_processing/scripts/detrending.py

@@ -8,7 +8,7 @@
 import argparse
 import os
 import warnings
-from utils.io import load_neo, write_neo, save_plot
+from utils.io_utils import load_neo, write_neo, save_plot
 from utils.parse import none_or_int
 
 CLI = argparse.ArgumentParser()

cobrawap/pipeline/stage02_processing/scripts/frequency_filter.py

@@ -6,7 +6,7 @@
 import quantities as pq
 import os
 from elephant.signal_processing import butter
-from utils.io import load_neo, write_neo
+from utils.io_utils import load_neo, write_neo
 from utils.parse import none_or_float
 
 CLI = argparse.ArgumentParser()

cobrawap/pipeline/stage02_processing/scripts/logMUA_estimation.py

@@ -13,7 +13,7 @@
 import argparse
 import os
 from pathlib import Path
-from utils.io import load_neo, write_neo, save_plot
+from utils.io_utils import load_neo, write_neo, save_plot
 from utils.parse import none_or_float, none_or_int
 from utils.neo_utils import time_slice
 

cobrawap/pipeline/stage02_processing/scripts/normalization.py

@@ -8,7 +8,7 @@
 import quantities as pq
 import os
 import sys
-from utils.io import write_neo, load_neo
+from utils.io_utils import write_neo, load_neo
 
 CLI = argparse.ArgumentParser()
 CLI.add_argument("--data",    nargs='?', type=str, required=True,

cobrawap/pipeline/stage02_processing/scripts/phase_transform.py

@@ -6,7 +6,7 @@
 from elephant.signal_processing import hilbert
 import argparse
 import os
-from utils.io import load_neo, write_neo
+from utils.io_utils import load_neo, write_neo
 
 CLI = argparse.ArgumentParser()
 CLI.add_argument("--data", nargs='?', type=str, required=True,

cobrawap/pipeline/stage02_processing/scripts/plot_power_spectrum.py

@@ -8,7 +8,7 @@
 import matplotlib.pyplot as plt
 import seaborn as sns
 from elephant.spectral import welch_psd
-from utils.io import load_neo, save_plot
+from utils.io_utils import load_neo, save_plot
 from utils.parse import none_or_float
 
 CLI = argparse.ArgumentParser()

cobrawap/pipeline/stage02_processing/scripts/plot_processed_trace.py

@@ -6,7 +6,7 @@
 import seaborn as sns
 import argparse
 import os
-from utils.io import load_neo, save_plot
+from utils.io_utils import load_neo, save_plot
 from utils.neo_utils import time_slice
 
 CLI = argparse.ArgumentParser()

cobrawap/pipeline/stage02_processing/scripts/roi_selection.py

@@ -9,7 +9,7 @@
 import argparse
 import neo
 import os
-from utils.io import load_neo, write_neo, save_plot
+from utils.io_utils import load_neo, write_neo, save_plot
 from utils.parse import none_or_str
 from utils.neo_utils import analogsignal_to_imagesequence, imagesequence_to_analogsignal
 

cobrawap/pipeline/stage02_processing/scripts/spatial_downsampling.py

@@ -8,7 +8,7 @@
 import os
 import neo
 from skimage import measure
-from utils.io import load_neo, write_neo, save_plot
+from utils.io_utils import load_neo, write_neo, save_plot
 from utils.parse import none_or_str
 from utils.neo_utils import analogsignal_to_imagesequence, imagesequence_to_analogsignal
 

cobrawap/pipeline/stage02_processing/scripts/subsampling.py

@@ -6,7 +6,7 @@
 import quantities as pq
 import numpy as np
 from pathlib import Path
-from utils.io import load_neo, write_neo
+from utils.io_utils import load_neo, write_neo
 
 CLI = argparse.ArgumentParser()
 CLI.add_argument("--data", nargs='?', type=str, required=True,

cobrawap/pipeline/stage02_processing/scripts/z_score.py

@@ -5,7 +5,7 @@
 import argparse
 from pathlib import Path
 from elephant.signal_processing import zscore
-from utils.io import load_neo, write_neo
+from utils.io_utils import load_neo, write_neo
 
 CLI = argparse.ArgumentParser()
 CLI.add_argument("--data", nargs='?', type=Path, required=True,

cobrawap/pipeline/stage03_trigger_detection/scripts/calc_thresholds_fitted.py

@@ -10,7 +10,7 @@
 import warnings
 from scipy.optimize import OptimizeWarning
 import matplotlib.pyplot as plt
-from utils.io import load_neo, save_plot
+from utils.io_utils import load_neo, save_plot
 from utils.parse import none_or_int
 
 CLI = argparse.ArgumentParser()

cobrawap/pipeline/stage03_trigger_detection/scripts/calc_thresholds_fixed.py

@@ -4,7 +4,7 @@
 
 import numpy as np
 import argparse
-from utils.io import load_neo
+from utils.io_utils import load_neo
 
 CLI = argparse.ArgumentParser()
 CLI.add_argument("--data", nargs='?', type=str, required=True,

cobrawap/pipeline/stage03_trigger_detection/scripts/check_input.py

@@ -7,7 +7,7 @@
 import numpy as np
 import argparse
 import quantities as pq
-from utils.io import load_neo
+from utils.io_utils import load_neo
 
 CLI = argparse.ArgumentParser()
 CLI.add_argument("--data",    nargs='?', type=str, required=True,

cobrawap/pipeline/stage03_trigger_detection/scripts/hilbert_phase.py

@@ -11,7 +11,7 @@
 from scipy.stats import zscore
 import matplotlib.pyplot as plt
 import seaborn as sns
-from utils.io import load_neo, write_neo, save_plot
+from utils.io_utils import load_neo, write_neo, save_plot
 from utils.neo_utils import time_slice, remove_annotations
 from utils.parse import none_or_int, none_or_float
 from pathlib import Path

cobrawap/pipeline/stage03_trigger_detection/scripts/minima.py

@@ -8,7 +8,7 @@
 import quantities as pq
 from scipy.signal import find_peaks
 import argparse
-from utils.io import load_neo, write_neo, save_plot
+from utils.io_utils import load_neo, write_neo, save_plot
 from utils.neo_utils import remove_annotations, time_slice
 from utils.parse import none_or_int, none_or_float, none_or_str
 import seaborn as sns

cobrawap/pipeline/stage03_trigger_detection/scripts/plot_trigger_times.py

@@ -6,7 +6,7 @@
 import seaborn as sns
 import argparse
 import os
-from utils.io import load_neo, save_plot
+from utils.io_utils import load_neo, save_plot
 from utils.parse import none_or_int, none_or_float
 from utils.neo_utils import time_slice
 

cobrawap/pipeline/stage03_trigger_detection/scripts/remove_short_states.py

@@ -8,7 +8,7 @@
 import argparse
 import quantities as pq
 from distutils.util import strtobool
-from utils.io import load_neo, write_neo
+from utils.io_utils import load_neo, write_neo
 
 CLI = argparse.ArgumentParser()
 CLI.add_argument("--data", nargs='?', type=str, required=True,

cobrawap/pipeline/stage03_trigger_detection/scripts/threshold.py

@@ -6,7 +6,7 @@
 import neo
 import numpy as np
 import argparse
-from utils.io import load_neo, write_neo
+from utils.io_utils import load_neo, write_neo
 from utils.neo_utils import remove_annotations
 
 CLI = argparse.ArgumentParser()

cobrawap/pipeline/stage04_wave_detection/scripts/check_input.py

@@ -7,7 +7,7 @@
 import numpy as np
 import argparse
 import quantities as pq
-from utils.io import load_neo
+from utils.io_utils import load_neo
 from snakemake.logging import logger
 
 CLI = argparse.ArgumentParser()

cobrawap/pipeline/stage04_wave_detection/scripts/critical_points.py

@@ -8,7 +8,7 @@
 import neo
 import matplotlib.pyplot as plt
 from shapely.geometry import LineString
-from utils.io import load_neo, write_neo, save_plot
+from utils.io_utils import load_neo, write_neo, save_plot
 from utils.neo_utils import analogsignal_to_imagesequence
 
 CLI = argparse.ArgumentParser()

cobrawap/pipeline/stage04_wave_detection/scripts/merge_wave_definitions.py

@@ -5,7 +5,7 @@
 
 import argparse
 from pathlib import Path
-from utils.io import load_neo, write_neo
+from utils.io_utils import load_neo, write_neo
 
 CLI = argparse.ArgumentParser()
 CLI.add_argument("--data", nargs='?', type=Path, required=True,

cobrawap/pipeline/stage04_wave_detection/scripts/optical_flow.py

@@ -11,7 +11,7 @@
 from copy import copy
 import matplotlib.pyplot as plt
 from distutils.util import strtobool
-from utils.io import load_neo, write_neo, save_plot
+from utils.io_utils import load_neo, write_neo, save_plot
 from utils.parse import none_or_str
 from utils.neo_utils import imagesequence_to_analogsignal, analogsignal_to_imagesequence
 from utils.convolve import phase_conv2d, get_kernel, conv, norm_angle

cobrawap/pipeline/stage04_wave_detection/scripts/plot_clustering.py

@@ -11,7 +11,7 @@
 import seaborn as sns
 import random
 import warnings
-from utils.io import load_neo, save_plot
+from utils.io_utils import load_neo, save_plot
 from utils.parse import none_or_float
 from utils.neo_utils import time_slice
 

cobrawap/pipeline/stage04_wave_detection/scripts/plot_critical_points.py

@@ -6,7 +6,7 @@
 import numpy as np
 from copy import copy
 import matplotlib.pyplot as plt
-from utils.io import load_neo, save_plot
+from utils.io_utils import load_neo, save_plot
 from utils.neo_utils import analogsignal_to_imagesequence
 
 CLI = argparse.ArgumentParser()

cobrawap/pipeline/stage04_wave_detection/scripts/plot_movie_frames.py

@@ -7,7 +7,7 @@
 import argparse
 import matplotlib.pyplot as plt
 import numpy as np
-from utils.io import load_neo, save_plot
+from utils.io_utils import load_neo, save_plot
 from utils.neo_utils import analogsignal_to_imagesequence
 from utils.parse import none_or_str, none_or_float
 

cobrawap/pipeline/stage04_wave_detection/scripts/plot_waves.py

@@ -7,7 +7,7 @@
 import quantities as pq
 import argparse
 import matplotlib.pyplot as plt
-from utils.io import load_neo, save_plot
+from utils.io_utils import load_neo, save_plot
 from utils.neo_utils import analogsignal_to_imagesequence
 
 CLI = argparse.ArgumentParser()

cobrawap/pipeline/stage04_wave_detection/scripts/time_slice.py

@@ -4,7 +4,7 @@
 
 import argparse
 import quantities as pq
-from utils.io import load_neo, write_neo
+from utils.io_utils import load_neo, write_neo
 from utils.neo_utils import time_slice
 
 CLI = argparse.ArgumentParser()

cobrawap/pipeline/stage04_wave_detection/scripts/trigger_clustering.py

@@ -7,7 +7,7 @@
 import quantities as pq
 import argparse
 from sklearn.cluster import DBSCAN
-from utils.io import load_neo, write_neo
+from utils.io_utils import load_neo, write_neo
 from utils.neo_utils import remove_annotations
 
 CLI = argparse.ArgumentParser()

cobrawap/pipeline/stage04_wave_detection/scripts/wave_mode_clustering.py

@@ -17,7 +17,7 @@
 from scipy.spatial.distance import cdist
 import matplotlib as mpl
 import matplotlib.pyplot as plt
-from utils.io import load_neo, write_neo, save_plot
+from utils.io_utils import load_neo, write_neo, save_plot
 from utils.parse import none_or_str, none_or_int
 from utils.neo_utils import analogsignal_to_imagesequence, remove_annotations
 

cobrawap/pipeline/stage05_channel_wave_characterization/scripts/annotations.py

@@ -8,7 +8,7 @@
 import pandas as pd
 import quantities as pq
 import re
-from utils.io import load_neo, save_plot
+from utils.io_utils import load_neo, save_plot
 from utils.parse import none_or_str
 from utils.neo_utils import remove_annotations
 

cobrawap/pipeline/stage05_channel_wave_characterization/scripts/check_input.py

@@ -9,7 +9,7 @@
 import quantities as pq
 import warnings
 import re
-from utils.io import load_neo
+from utils.io_utils import load_neo
 from utils.parse import none_or_str
 
 CLI = argparse.ArgumentParser()

cobrawap/pipeline/stage05_channel_wave_characterization/scripts/direction_local.py

@@ -7,7 +7,7 @@
 import numpy as np
 import pandas as pd
 import matplotlib.pyplot as plt
-from utils.io import load_neo, save_plot
+from utils.io_utils import load_neo, save_plot
 from utils.parse import none_or_str
 
 CLI = argparse.ArgumentParser()

cobrawap/pipeline/stage05_channel_wave_characterization/scripts/flow_direction_local.py

@@ -7,7 +7,7 @@
 import numpy as np
 import pandas as pd
 import matplotlib.pyplot as plt
-from utils.io import load_neo, save_plot
+from utils.io_utils import load_neo, save_plot
 from utils.parse import none_or_str
 
 CLI = argparse.ArgumentParser()