ci: update Python to 3.8, update wxPython

.github/workflows/docs.yml

@@ -8,7 +8,7 @@ on:
 
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python
@@ -22,7 +22,7 @@ jobs:
 
         # Install wxPython wheels since they are distribution-specific and therefore not on PyPI
         # See: https://wxpython.org/pages/downloads/index.html
-        pip install -U -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-20.04 wxPython
+        pip install -U -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-22.04 wxPython
 
         pip install .
     - name: Build docs

.github/workflows/test.yml

@@ -13,30 +13,34 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest, macOS-latest]
-        python_version: [3.7]
+        os: ['ubuntu-22.04', windows-latest, macOS-latest]
+        python_version: ['3.8']
         include:
-          - os: ubuntu-latest
-            python_version: 3.8
           # Experimental: Python 3.9
           # Works fine, commented out because mostly covered (at least installing/building deps) by the typecheck job
           # See issue: https://github.com/NeuroTechX/eeg-notebooks/issues/50
           #- os: ubuntu-latest
           #  python_version: 3.9
 
+          # Check 3.10 for future-proofing
+          - os: ubuntu-22.04
+            python_version: '3.10'
+
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python_version }}
+
     # Not needed if pywinhook is installed from wheels
     #- name: Install swig
     #  if: "startsWith(runner.os, 'windows')"
     #  run: |
     #    (New-Object System.Net.WebClient).DownloadFile("http://prdownloads.sourceforge.net/swig/swigwin-4.0.1.zip","swigwin-4.0.1.zip");
     #    Expand-Archive .\swigwin-4.0.1.zip .;
     #    echo "$((Get-Item .).FullName)/swigwin-4.0.1" | Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append
+
     - name: Install APT dependencies
       if: "startsWith(runner.os, 'Linux')"
       run: |
@@ -53,9 +57,10 @@ jobs:
 
         # Install wxPython wheels since they are distribution-specific and therefore not on PyPI
         # See: https://wxpython.org/pages/downloads/index.html
-        pip install -U -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-18.04 wxPython
+        pip install -U -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-22.04 wxPython
 
         pip install .
+
     - name: Install MacOS/Windows dependencies
       run: |
         python -m pip install --upgrade pip wheel
@@ -85,7 +90,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest]
+        os: ['ubuntu-22.04']
         python_version: [3.9]
 
     steps:
@@ -110,7 +115,7 @@ jobs:
 
         # Install wxPython wheels since they are distribution-specific and therefore not on PyPI
         # See: https://wxpython.org/pages/downloads/index.html
-        pip install -U -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-18.04 wxPython
+        pip install -U -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-22.04 wxPython
 
         pip install .
     - name: Install MacOS/Windows dependencies

eegnb/cli/__main__.py

@@ -12,6 +12,7 @@
 from eegnb.devices.eeg import EEG
 from eegnb.analysis.utils import check_report
 from eegnb.analysis.pipelines import load_eeg_data, make_erp_plot, analysis_report, example_analysis_report
+from typing import Optional
 
 
 @click.group(name="eegnb")
@@ -31,10 +32,10 @@ def main():
 )
 def runexp(
     experiment: str,
-    eegdevice: str = None,
-    macaddr: str = None,
-    recdur: float = None,
-    outfname: str = None,
+    eegdevice: Optional[str] = None,
+    macaddr: Optional[str] = None,
+    recdur: Optional[float] = None,
+    outfname: Optional[str] = None,
     prompt: bool = False,
     dosigqualcheck = True,
     generatereport = True
@@ -107,11 +108,11 @@ def askforreportcheck():
 )
 def create_analysis_report(
     experiment: str,
-    eegdevice: str = None,
-    subject: str = None, 
-    session: str = None,
-    site: str = None,
-    filepath:str = None,
+    eegdevice: Optional[str] = None,
+    subject: Optional[str] = None, 
+    session: Optional[str] = None,
+    site: Optional[str] = None,
+    filepath: Optional[str] = None,
     prompt: bool = False,
 ):
     """

eegnb/cli/utils.py

@@ -15,6 +15,7 @@
 from eegnb.experiments.visual_codeprose import codeprose
 from eegnb.experiments.auditory_oddball import diaconescu
 from eegnb.experiments.auditory_ssaep import ssaep, ssaep_onefreq
+from typing import Optional
 
 
 # New Experiment Class structure has a different initilization, to be noted
@@ -40,7 +41,7 @@ def get_exp_desc(exp: str):
 
 
 def run_experiment(
-    experiment: str, eeg_device: EEG, record_duration: float = None, save_fn=None
+    experiment: str, eeg_device: EEG, record_duration: Optional[float] = None, save_fn=None
 ):
     if experiment in experiments:
         module = experiments[experiment]

eegnb/experiments/auditory_oddball/aMMN.py

@@ -9,10 +9,11 @@
 from psychopy import visual, core, event, sound
 
 from eegnb import generate_save_fn
+from typing import Optional
 
 
 def present(
-    save_fn: str = None,
+    save_fn: Optional[str] = None,
     duration=120,
     stim_types=None,
     itis=None,

eegnb/experiments/auditory_oddball/aob.py

@@ -5,11 +5,12 @@
 from time import time
 from eegnb.devices.eeg import EEG
 from eegnb.experiments import Experiment
+from typing import Optional
 
 
 class AuditoryOddball(Experiment.BaseExperiment):
 
-    def __init__(self, duration=120, eeg: EEG=None, save_fn=None, n_trials = 2010, iti = 0.3, soa = 0.2, jitter = 0.2, secs=0.2, volume=0.8, random_state=42, s1_freq="C", s2_freq="D", s1_octave=5, s2_octave=6):
+    def __init__(self, duration=120, eeg: Optional[EEG]=None, save_fn=None, n_trials = 2010, iti = 0.3, soa = 0.2, jitter = 0.2, secs=0.2, volume=0.8, random_state=42, s1_freq="C", s2_freq="D", s1_octave=5, s2_octave=6):
         """
 
         Auditory Oddball Experiment

eegnb/experiments/auditory_oddball/auditory_erp_arrayin.py

@@ -16,10 +16,12 @@
 
 from eegnb import generate_save_fn
 from eegnb.devices.eeg import EEG
+from typing import Optional
+
 #from eegnb.stimuli import FACE_HOUSE
 
 
-def present(eeg: EEG=None, save_fn=None,
+def present(eeg: Optional[EEG]=None, save_fn=None,
             stim_types=None, itis=None, additional_labels={},
             secs=0.07, volume=0.8,tone1_hz =440, tone2_hz = 528,
             do_fixation=True):

eegnb/experiments/visual_codeprose/codeprose.py

@@ -9,7 +9,7 @@
 
 # TODO: Switch to using time_ns when Python 3.7 is the minimum version for eegnb
 from time import time, strftime, gmtime
-from typing import List
+from typing import Optional, List
 from pathlib import Path
 from dataclasses import dataclass, field
 from ...devices.eeg import EEG
@@ -167,7 +167,7 @@ def run(window: visual.Window) -> pd.DataFrame:
     return pd.DataFrame(responses)
 
 
-def fixate(window: visual.Window, text: str = None):
+def fixate(window: visual.Window, text: Optional[str] = None):
     visual.TextStim(
         win=window,
         text=text,

eegnb/experiments/visual_n170/n170.py

@@ -19,11 +19,12 @@
 from eegnb.devices.eeg import EEG
 from eegnb.stimuli import FACE_HOUSE
 from eegnb.experiments import Experiment
+from typing import Optional
 
 
 class VisualN170(Experiment.BaseExperiment):
 
-    def __init__(self, duration=120, eeg: EEG=None, save_fn=None,
+    def __init__(self, duration=120, eeg: Optional[EEG]=None, save_fn=None,
             n_trials = 2010, iti = 0.4, soa = 0.3, jitter = 0.2):
 
         # Set experiment name        

eegnb/experiments/visual_p300/p300.py

@@ -15,10 +15,11 @@
 from eegnb.stimuli import CAT_DOG
 from eegnb.experiments import Experiment
 from eegnb.devices.eeg import EEG
+from typing import Optional
 
 class VisualP300(Experiment.BaseExperiment):
 
-    def __init__(self, duration=120, eeg: EEG=None, save_fn=None,
+    def __init__(self, duration=120, eeg: Optional[EEG]=None, save_fn=None,
             n_trials = 2010, iti = 0.4, soa = 0.3, jitter = 0.2):
 
         exp_name = "Visual P300"

eegnb/experiments/visual_ssvep/ssvep.py

@@ -12,11 +12,12 @@
 
 from eegnb.devices.eeg import EEG
 from eegnb import generate_save_fn
+from typing import Optional
 
 
 class VisualSSVEP(Experiment.BaseExperiment):
 
-    def __init__(self, duration=120, eeg: EEG=None, save_fn=None, n_trials = 2010, iti = 0.5, soa = 3.0, jitter = 0.2):
+    def __init__(self, duration=120, eeg: Optional[EEG]=None, save_fn=None, n_trials = 2010, iti = 0.5, soa = 3.0, jitter = 0.2):
 
         exp_name = "Visual SSVEP"
         super().__init__(exp_name, duration, eeg, save_fn, n_trials, iti, soa, jitter)

eegnb/experiments/visual_vep/vep.py

@@ -1,11 +1,12 @@
 from time import time, strftime, gmtime
 from pylsl import StreamInfo, StreamOutlet
 from eegnb.experiments.Experiment import Experiment
+from typing import Optional
 
 
 class VisualVEP(Experiment):
 
-    def __init__(self, duration=120, eeg: EEG=None, save_fn=None,
+    def __init__(self, duration=120, eeg: Optional[EEG]=None, save_fn=None,
             n_trials = 2000, iti = 0.2, soa = 0.2, jitter = 0.1):
 
         exp_name = "Visual VEP"

requirements.txt

@@ -1,9 +1,9 @@
 # Main repo requirements
-psychopy==2022.2.4
+psychopy==2023.1.0
 psychtoolbox
 scikit-learn>=0.23.2
 pandas>=1.1.4
-numpy>=1.19.4
+numpy>=1.19.4,<1.24  # due to outdated libs not changing the names after: https://github.com/numpy/numpy/pull/22607
 mne>=0.20.8
 seaborn>=0.9.0
 pyriemann>=0.2.7