Explicit package references and rename process

Author: MaxvandenBoom

erdetect/__init__.py

@@ -1,10 +1,10 @@
 import logging
 import sys
 from erdetect.utils.misc import CustomLoggingFormatter
-from version import __version__
-from erdetect._erdetect import process_subset
+from erdetect.version import __version__
+from erdetect._erdetect import process
 from erdetect.views.gui import open_gui
-__all__ = ['process_subset', 'open_gui', '__version__']
+__all__ = ['process', 'open_gui', '__version__']
 
 #
 # logging

erdetect/_erdetect.py

@@ -4,16 +4,16 @@
 import numpy as np
 import scipy.io as sio
 
-from core.config import write_config, get as cfg, get_config_dict, OUTPUT_IMAGE_SIZE, LOGGING_CAPTION_INDENT_LENGTH
-from core.detection import ieeg_detect_er
-from views.output_images import calc_sizes_and_fonts, calc_matrix_image_size, gen_amplitude_matrix, gen_latency_matrix
-from utils.bids import load_channel_info, load_event_info, load_ieeg_sidecar, load_data_epochs_averages, RerefStruct
-from utils.misc import print_progressbar, is_number, multi_line_list, create_figure
+from erdetect.core.config import write_config, get as cfg, get_config_dict, OUTPUT_IMAGE_SIZE, LOGGING_CAPTION_INDENT_LENGTH
+from erdetect.core.detection import ieeg_detect_er
+from erdetect.views.output_images import calc_sizes_and_fonts, calc_matrix_image_size, gen_amplitude_matrix, gen_latency_matrix
+from erdetect.utils.bids import load_channel_info, load_event_info, load_ieeg_sidecar, load_data_epochs_averages, RerefStruct
+from erdetect.utils.misc import print_progressbar, is_number, multi_line_list, create_figure
 from erdetect.core.metrics.metric_cross_proj import metric_cross_proj
 from erdetect.core.metrics.metric_waveform import metric_waveform
 
 
-def process_subset(bids_subset_data_path, output_dir, preproc_prioritize_speed=False):
+def process(bids_subset_data_path, output_dir, preproc_prioritize_speed=False):
     """
     Process a BIDS subset, perform pre-processing, evoked response detection and produce output
 

erdetect/main_cli.py

@@ -13,20 +13,19 @@
 warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
 You should have received a copy of the GNU General Public License along with this program.  If not, see <https://www.gnu.org/licenses/>.
 """
-import sys
 import argparse
 import os
 import logging
 from glob import glob
 
-from version import __version__
+from erdetect.version import __version__
 from bids_validator import BIDSValidator
-from core.config import load_config, get as cfg, set as cfg_set, rem as cfg_rem,\
+from erdetect.core.config import load_config, get as cfg, set as cfg_set, rem as cfg_rem,\
     LOGGING_CAPTION_INDENT_LENGTH, CONFIG_DETECTION_STD_BASE_BASELINE_EPOCH_DEFAULT, \
     CONFIG_DETECTION_STD_BASE_BASELINE_THRESHOLD_FACTOR, CONFIG_DETECTION_CROSS_PROJ_THRESHOLD, CONFIG_DETECTION_WAVEFORM_PROJ_THRESHOLD
-from _erdetect import process_subset
-from utils.IeegDataReader import VALID_FORMAT_EXTENSIONS
-from utils.misc import is_number, CustomLoggingFormatter, multi_line_list
+from erdetect._erdetect import process
+from erdetect.utils.IeegDataReader import VALID_FORMAT_EXTENSIONS
+from erdetect.utils.misc import is_number, multi_line_list
 from erdetect._erdetect import log_indented_line