Merge pull request #167 from NeuroTechX/fix-ci

Author: ErikBjare

.github/workflows/docs.yml

@@ -8,7 +8,7 @@ on:
 
 jobs:
   build:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python
@@ -17,16 +17,14 @@ jobs:
         python-version: 3.8
     - name: Install dependencies
       run: |
+        make install-deps-apt
         python -m pip install --upgrade pip wheel
 
-        # 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
-
+        make install-deps-wxpython
         pip install .
     - name: Build docs
       run: |
-        cd doc && make html
+        make docs
     - name: Deploy Docs
       uses: peaceiris/actions-gh-pages@v3
       if: github.ref == 'refs/heads/master'

.github/workflows/test.yml

@@ -8,16 +8,18 @@ on:
 
 jobs:
   test:
-    name: ${{ matrix.os }}, py-${{ matrix.python_version }}
+    name: test (${{ matrix.os }}, py-${{ matrix.python_version }})
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macOS-latest]
-        python_version: [3.7]
+        python_version: [3.8]
         include:
           - os: ubuntu-latest
-            python_version: 3.8
+            python_version: 3.9
+          #- os: macOS-latest
+          #  python_version: 3.9
           # Experimental: Python 3.9
           # See issue: https://github.com/NeuroTechX/eeg-notebooks/issues/50
           #- os: ubuntu-18.04
@@ -39,33 +41,22 @@ jobs:
     - name: Install APT dependencies
       if: "startsWith(runner.os, 'Linux')"
       run: |
-        # update archive links
-        sudo apt-get update
-        # xvfb is a dependency to create a virtual display
-        # libgtk-3-dev is a requirement for wxPython
-        # freeglut3-dev is a requirement for a wxPython dependency
-        sudo apt-get -y install xvfb libgtk-3-dev freeglut3-dev
+        make install-deps-apt
+    - name: Upgrade pip
+      run: |
+        python -m pip install --upgrade pip wheel
     - name: Install Linux dependencies
       if: "startsWith(runner.os, 'Linux')"
       run: |
-        python -m pip install --upgrade pip wheel
-
-        # Install wxPython wheels since they are distribution-specific and therefore not on PyPI
-        # See: https://wxpython.org/pages/downloads/index.html
-        pip install -U -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-18.04 wxPython
-
-        pip install .
-    - name: Install MacOS/Windows dependencies
+        make install-deps-wxpython
+    - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip wheel
-        pip install .
+        make build
     - name: Run eegnb install test
       shell: bash  
-        pip install -U psychtoolbox # JG_ADD
       run: |
         if [ "$RUNNER_OS" == "Linux" ]; then
           Xvfb :0 -screen 0 1024x768x24 -ac +extension GLX +render -noreset &> xvfb.log &
-          /
           export DISPLAY=:0
         fi
         eegnb --help
@@ -77,9 +68,10 @@ jobs:
           Xvfb :0 -screen 0 1024x768x24 -ac +extension GLX +render -noreset &> xvfb.log &
           export DISPLAY=:0
         fi
-        pytest
+        make test
 
   typecheck:
+    name: typecheck (${{ matrix.os }}, py-${{ matrix.python_version }})
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -96,27 +88,17 @@ jobs:
     - name: Install APT dependencies
       if: "startsWith(runner.os, 'Linux')"
       run: |
-        # update archive links
-        sudo apt-get update
-        # xvfb is a dependency to create a virtual display
-        # libgtk-3-dev is a requirement for wxPython
-        # freeglut3-dev is a requirement for a wxPython dependency
-        sudo apt-get -y install xvfb libgtk-3-dev freeglut3-dev
+        make install-deps-apt
+    - name: Upgrade pip
+      run: |
+        python -m pip install --upgrade pip wheel
     - name: Install Linux dependencies
       if: "startsWith(runner.os, 'Linux')"
       run: |
-        python -m pip install --upgrade pip wheel
-
-        # 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 .
-    - name: Install MacOS/Windows dependencies
+        make install-deps-wxpython
+    - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip wheel
-        pip install .
+        make build
     - name: Typecheck
       run: |
-        # Exclude visual_cueing due to errors
-        python -m mypy --exclude 'examples/visual_cueing'
+        make typecheck

Makefile

@@ -0,0 +1,32 @@
+build:
+	pip install .
+
+test:
+	pytest
+
+typecheck:
+	# Exclude visual_cueing due to errors
+	python -m mypy --exclude 'examples/visual_cueing'
+
+docs:
+	cd doc && make html
+
+clean:
+	cd doc && make clean
+
+install-deps-apt:
+	sudo apt-get update  # update archive links
+
+	# xvfb is a dependency to create a virtual display
+	# libgtk-3-dev is a requirement for wxPython
+	# freeglut3-dev is a requirement for a wxPython dependency
+	# portaudio19-dev *might* be required to import psychopy on Ubuntu
+	# pulseaudio *might* be required to actually run the tests (on PsychoPy import)
+	# libpulse-dev required to build pocketsphinx (speech recognition dependency of psychopy)
+	# libsdl2-dev required by psychopy
+	sudo apt-get -y install xvfb libgtk-3-dev freeglut3-dev portaudio19-dev libpulse-dev pulseaudio libsdl2-dev
+
+install-deps-wxpython:
+	# 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

doc/conf.py

@@ -263,7 +263,7 @@ def setup(app):
                        'backreferences_dir': 'generated',   # Where to drop linking files between examples & API
                        'doc_module': ('eeg-notebooks'),
                        'reference_url': {'eeg-notebooks': None},
-                       'remove_conffig_comments': True}
+                       'remove_config_comments': True}
 
 """
 sphinx_gallery_conf = {
@@ -284,7 +284,7 @@ def setup(app):
     'backreferences_dir': 'generated',   # Where to drop linking files between examples & API
     'doc_module': ('eeg-notebooks',),
     'reference_url': {'eeg-notebooksS': None},
-    'remove_conffig_comments': True,
+    'remove_config_comments': True,
 }
 
 """

eegnb/analysis/utils.py

@@ -2,11 +2,11 @@
 from copy import deepcopy
 import math
 import logging
+import sys
 from collections import OrderedDict
 from glob import glob
-from typing import Union, List, Dict
+from typing import Union, List
 from time import sleep, time
-from numpy.core.fromnumeric import std
 
 import pandas as pd
 import numpy as np
@@ -16,13 +16,13 @@
 from mne.channels import make_standard_montage
 from mne.filter import create_filter
 from matplotlib import pyplot as plt
+from scipy import stats
 from scipy.signal import lfilter, lfilter_zi
 
 from eegnb import _get_recording_dir
 from eegnb.devices.eeg import EEG
 from eegnb.devices.utils import EEG_INDICES, SAMPLE_FREQS
 
-                        
 
 # this should probably not be done here
 sns.set_context("talk")
@@ -32,6 +32,33 @@
 logger = logging.getLogger(__name__)
 
 
+def _bootstrap(data, n_boot: int, ci: float):
+    """From: https://stackoverflow.com/a/47582329/965332"""
+    boot_dist = []
+    for i in range(int(n_boot)):
+        resampler = np.random.randint(0, data.shape[0], data.shape[0])
+        sample = data.take(resampler, axis=0)
+        boot_dist.append(np.mean(sample, axis=0))
+    b = np.array(boot_dist)
+    s1 = np.apply_along_axis(stats.scoreatpercentile, 0, b, 50 - ci / 2)
+    s2 = np.apply_along_axis(stats.scoreatpercentile, 0, b, 50 + ci / 2)
+    return (s1, s2)
+
+
+def _tsplotboot(ax, data, time: list, n_boot: int, ci: float, color):
+    """From: https://stackoverflow.com/a/47582329/965332"""
+    # Time forms the xaxis of the plot
+    if time is None:
+        x = np.arange(data.shape[1])
+    else:
+        x = np.asarray(time)
+    est = np.mean(data, axis=0)
+    cis = _bootstrap(data, n_boot, ci)
+    ax.fill_between(x, cis[0], cis[1], alpha=0.2, color=color)
+    ax.plot(x, est, color=color)
+    ax.margins(x=0)
+
+
 def load_csv_as_raw(
     fnames: List[str],
     sfreq: float,
@@ -152,7 +179,9 @@ def load_data(
         site = "*"
 
     data_path = (
-        _get_recording_dir(device_name, experiment, subject_str, session_str, site, data_dir)
+        _get_recording_dir(
+            device_name, experiment, subject_str, session_str, site, data_dir
+        )
         / "*.csv"
     )
     fnames = glob(str(data_path))
@@ -193,7 +222,8 @@ def plot_conditions(
     ylim=(-6, 6),
     diff_waveform=(1, 2),
     channel_count=4,
-    channel_order=None):
+    channel_order=None,
+):
     """Plot ERP conditions.
     Args:
         epochs (mne.epochs): EEG epochs
@@ -219,10 +249,9 @@ def plot_conditions(
     """
 
     if channel_order:
-      channel_order = np.array(channel_order)
+        channel_order = np.array(channel_order)
     else:
-      channel_order = np.array(range(channel_count))
-
+        channel_order = np.array(range(channel_count))
 
     if isinstance(conditions, dict):
         conditions = OrderedDict(conditions)
@@ -232,7 +261,7 @@ def plot_conditions(
 
     X = epochs.get_data() * 1e6
 
-    X = X[:,channel_order]
+    X = X[:, channel_order]
 
     times = epochs.times
     y = pd.Series(epochs.events[:, -1])
@@ -249,13 +278,15 @@ def plot_conditions(
 
     for ch in range(channel_count):
         for cond, color in zip(conditions.values(), palette):
-            sns.tsplot(
-                X[y.isin(cond), ch],
+            y_cond = y.isin(cond)
+            X_cond = X[y_cond, ch]
+            _tsplotboot(
+                ax=axes[ch],
+                data=X_cond,
                 time=times,
                 color=color,
                 n_boot=n_boot,
                 ci=ci,
-                ax=axes[ch],
             )
 
         if diff_waveform: