Revert PR #167: "ci: fix broken CI" (#169)

NeuroTechX · Mar 27, 2022 · 2d74871 · 2d74871
1 parent d358d5e
commit 2d74871
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Showing 10 changed files with 391 additions and 133 deletions.
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -8,7 +8,7 @@ on:
 
 jobs:
   build:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-18.04
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python
@@ -17,14 +17,16 @@ jobs:
         python-version: 3.8
     - name: Install dependencies
       run: |
-        make install-deps-apt
         python -m pip install --upgrade pip wheel
 
-        make 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
+
         pip install .
     - name: Build docs
       run: |
-        make docs
+        cd doc && make html
     - name: Deploy Docs
       uses: peaceiris/actions-gh-pages@v3
       if: github.ref == 'refs/heads/master'

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -8,14 +8,16 @@ on:
 
 jobs:
   test:
-    name: test (${{ matrix.os }}, py-${{ matrix.python_version }})
+    name: ${{ matrix.os }}, py-${{ matrix.python_version }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macOS-latest]
-        python_version: [3.8]
-        #include:
+        python_version: [3.7]
+        include:
+          - os: ubuntu-latest
+            python_version: 3.8
           # Experimental: Python 3.9
           # Works fine, commented out because mostly covered (at least installing/building deps) by the typecheck job
           # See issue: https://github.com/NeuroTechX/eeg-notebooks/issues/50
@@ -38,22 +40,33 @@ jobs:
     - name: Install APT dependencies
       if: "startsWith(runner.os, 'Linux')"
       run: |
-        make install-deps-apt
-    - name: Upgrade pip
-      run: |
-        python -m pip install --upgrade pip wheel
+        # update archive links
+        sudo apt-get update
+        # xvfb is a dependency to create a virtual display
+        # libgtk-3-dev is a requirement for wxPython
+        # freeglut3-dev is a requirement for a wxPython dependency
+        sudo apt-get -y install xvfb libgtk-3-dev freeglut3-dev
     - name: Install Linux dependencies
       if: "startsWith(runner.os, 'Linux')"
       run: |
-        make install-deps-wxpython
-    - name: Install dependencies
+        python -m pip install --upgrade pip wheel
+
+        # Install wxPython wheels since they are distribution-specific and therefore not on PyPI
+        # See: https://wxpython.org/pages/downloads/index.html
+        pip install -U -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-18.04 wxPython
+
+        pip install .
+    - name: Install MacOS/Windows dependencies
       run: |
-        make build
+        python -m pip install --upgrade pip wheel
+        pip install .
     - name: Run eegnb install test
       shell: bash  
+        pip install -U psychtoolbox # JG_ADD
       run: |
         if [ "$RUNNER_OS" == "Linux" ]; then
           Xvfb :0 -screen 0 1024x768x24 -ac +extension GLX +render -noreset &> xvfb.log &
+          /
           export DISPLAY=:0
         fi
         eegnb --help
@@ -65,10 +78,9 @@ jobs:
           Xvfb :0 -screen 0 1024x768x24 -ac +extension GLX +render -noreset &> xvfb.log &
           export DISPLAY=:0
         fi
-        make test
+        pytest
 
   typecheck:
-    name: typecheck (${{ matrix.os }}, py-${{ matrix.python_version }})
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -85,17 +97,27 @@ jobs:
     - name: Install APT dependencies
       if: "startsWith(runner.os, 'Linux')"
       run: |
-        make install-deps-apt
-    - name: Upgrade pip
-      run: |
-        python -m pip install --upgrade pip wheel
+        # 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
     - name: Install Linux dependencies
       if: "startsWith(runner.os, 'Linux')"
       run: |
-        make install-deps-wxpython
-    - name: Install dependencies
+        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
       run: |
-        make build
+        python -m pip install --upgrade pip wheel
+        pip install .
     - name: Typecheck
       run: |
-        make typecheck
+        # Exclude visual_cueing due to errors
+        python -m mypy --exclude 'examples/visual_cueing'
diff --git a/Makefile b/Makefile
diff --git a/doc/conf.py b/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_config_comments': True}
+                       'remove_conffig_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_config_comments': True,
+    'remove_conffig_comments': True,
 }
 
 """
diff --git a/eegnb/analysis/utils.py b/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
+from typing import Union, List, Dict
 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")
@@ -32,33 +32,6 @@
 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,
@@ -179,9 +152,7 @@ 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))
@@ -222,8 +193,7 @@ 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
@@ -249,9 +219,10 @@ 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)
@@ -261,7 +232,7 @@ 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])
@@ -278,15 +249,13 @@ def plot_conditions(
 
     for ch in range(channel_count):
         for cond, color in zip(conditions.values(), palette):
-            y_cond = y.isin(cond)
-            X_cond = X[y_cond, ch]
-            _tsplotboot(
-                ax=axes[ch],
-                data=X_cond,
+            sns.tsplot(
+                X[y.isin(cond), ch],
                 time=times,
                 color=color,
                 n_boot=n_boot,
                 ci=ci,
+                ax=axes[ch],
             )
 
         if diff_waveform: