Address PR issues

README.md

@@ -2,6 +2,7 @@
 
 
 [![BciPy](https://github.com/CAMBI-tech/BciPy/actions/workflows/main.yml/badge.svg)](https://github.com/CAMBI-tech/BciPy/actions/workflows/main.yml)
+[![Codacy Badge](https://app.codacy.com/project/badge/Grade/96e31da4b0554dae9db7a1356556b0d5)](https://app.codacy.com/gh/CAMBI-tech/BciPy/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade)
 [![contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg)](https://github.com/CAMBI-tech/BciPy/fork)
 [![Follow on Twitter](https://img.shields.io/twitter/follow/cambi_tech?label=Follow&style=social)](https://twitter.com/cambi_tech)
 
@@ -18,7 +19,7 @@ Memmott, T., Koçanaoğulları, A., Lawhead, M., Klee, D., Dudy, S., Fried-Oken,
 
 ## Dependencies
 ---------------
-This project requires Python 3.8, 3.9 or 3.10. Please see notes below for additional OS specific dependencies before installation can be completed and reference our documentation/FAQs for more information: https://bcipy.github.io/hardware-os-config/
+This project requires Python 3.8, 3.9 or 3.10. Please see notes below for additional OS specific dependencies before installation. See our documentation/FAQs for more information [here](https://bcipy.github.io/hardware-os-config/).
 
 ### Linux
 
@@ -46,8 +47,8 @@ In order to run BciPy on your computer, after following the dependencies above,
 To install for use locally and use of the GUI:
 1. Git clone https://github.com/BciPy/BciPy.git
 2. Change directory in your terminal to the repo directory.
-4. [Optional] Install the kenlm language model package. `pip install kenlm==0.1 --global-option="--max_order=12"`.
-5. Install BciPy in development mode. `pip install -e .`
+3. [Optional] Install the kenlm language model package. `pip install kenlm==0.1 --global-option="--max_order=12"`.
+4. Install BciPy in development mode. `pip install -e .`
 
 
 If wanting the latest version from PyPi and to build using modules:

bcipy/core/session.py

@@ -5,7 +5,6 @@
 import json
 import os
 import sqlite3
-import subprocess
 from dataclasses import dataclass, fields
 from typing import Any, Dict, List, Optional
 
@@ -17,12 +16,10 @@
 BLACK = COLOR_INDEX[0]
 WHITE = COLOR_INDEX[1]
 YELLOW = COLOR_INDEX[5]
-from bcipy.config import (BCIPY_ROOT, DEFAULT_ENCODING,
-                          DEFAULT_PARAMETERS_FILENAME, EXPERIMENT_DATA_FILENAME,
+from bcipy.config import (DEFAULT_ENCODING,
+                          DEFAULT_PARAMETERS_FILENAME,
                           SESSION_DATA_FILENAME, SESSION_SUMMARY_FILENAME)
-from bcipy.io.load import (load_experiment_fields, load_experiments,
-                           load_json_parameters)
-from bcipy.helpers.validate import validate_field_data_written
+from bcipy.io.load import load_json_parameters
 from bcipy.task.data import Session
 
 
@@ -46,21 +43,6 @@ def session_data(data_dir: str) -> Dict:
     return data
 
 
-def collect_experiment_field_data(experiment_name: str,
-                                  save_path: str,
-                                  file_name: str = EXPERIMENT_DATA_FILENAME) -> None:
-    experiment = load_experiments()[experiment_name]
-    experiment_fields = load_experiment_fields(experiment)
-
-    if experiment_fields:
-        cmd = (f'python {BCIPY_ROOT}/gui/experiments/ExperimentField.py -e'
-               f' "{experiment_name}" -p "{save_path}" -f "{file_name}"')
-        subprocess.check_call(cmd, shell=True)
-        # verify data was written before moving on
-        if not validate_field_data_written(save_path, file_name):
-            raise Exception('Field data not collected!')
-
-
 @dataclass(frozen=True)
 class EvidenceRecord:
     """Record summarizing Inquiry evidence."""

bcipy/helpers/offset.py

@@ -111,6 +111,7 @@ def calculate_latency(raw_data: RawData,
         if value < 1 and diode_enc:
             diode_enc = False
 
+    trigger_diodes_timestamps = []
     # Plot triggers.txt data if present; vertical line for each value.
     if triggers:
         trigger_diodes_timestamps = [

bcipy/task/demo/control/demo_handler.py

@@ -39,8 +39,6 @@ def _demo_decision_maker():
 
     conjugator = EvidenceFusion(evidence_names, len_dist=len_alp)
     decision_maker = DecisionMaker(
-        min_num_inq=1,
-        max_num_inq=10,
         state='',
         alphabet=alp)
 

pyproject.toml

@@ -26,8 +26,8 @@ classifiers = [
 dependencies = [
     "attrdict3==2.0.2",
     "EDFlib-Python==1.0.8",
-    "transformers==4.26.0",
-    "torch==2.0.0",
+    "transformers==4.36.0",
+    "torch==2.2.0",
     "construct==2.8.14",
     "mne==1.6.1",
     "mne-bids==0.14.0",
@@ -46,7 +46,7 @@ dependencies = [
     "pylsl==1.16.2",
     "pandas==2.0.3",
     "psutil==5.7.2",
-    "Pillow==9.4.0",
+    "Pillow==10.2.0",
     "py-cpuinfo==9.0.0",
     "pyopengl==3.1.7",
     "PyQt6==6.7.1",