Get CI test builds working again! (#170)

* Revert "Revert PR #167: "ci: fix broken CI" (#169)" This reverts commit 2d74871. * Update Makefile * fix: Update vep.py import * Update Makefile * Update vep.py * fix: typo in makefile * fix: update BaseExperiment class reference * Update Makefile * Update vep.py * Update 01r__n170_viz.py * makefile: install libnotify4 --------- Co-authored-by: Ore O <[email protected]>
NeuroTechX · Apr 27, 2023 · 7be54d6 · 7be54d6
1 parent 81dd244
commit 7be54d6
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diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -17,17 +17,18 @@ jobs:
         python-version: 3.8
     - name: Install dependencies
       run: |
+        make install-deps-apt
         python -m pip install --upgrade pip wheel
         python -m pip install attrdict
 
-        # 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-22.04 wxPython
+        make install-deps-wxpython
+    - name: Build project
+      run: |
+        make build
 
-        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'  # TODO: Deploy seperate develop-version of docs?

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -8,7 +8,7 @@ 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
@@ -44,29 +44,17 @@ 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-22.04 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 .
-        pip install -U psychtoolbox  # JG_ADD
-                                     # EB: needed?
+        make build
     - name: Run eegnb install test
       shell: bash
       run: |
@@ -83,9 +71,10 @@ 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
@@ -102,27 +91,17 @@ 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-22.04 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
diff --git a/Makefile b/Makefile
@@ -0,0 +1,39 @@
+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
+	# libnotify4 is so we can have the libnotify.so module used in wxPython working
+	sudo apt-get -y install xvfb libgtk-3-dev freeglut3-dev portaudio19-dev libpulse-dev pulseaudio libsdl2-dev libnotify4
+
+	# configure dynamic links
+	sudo ldconfig
+
+	UPDATED_LIBPATH=$(sudo find / -name libnotify.so)
+	LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$UPDATED_LIBPATH
+
+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-22.04 wxPython
diff --git a/doc/conf.py b/doc/conf.py
@@ -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,
 }
 
 """
diff --git a/eegnb/analysis/utils.py b/eegnb/analysis/utils.py
@@ -2,6 +2,7 @@
 from copy import deepcopy
 import math
 import logging
+import sys
 from collections import OrderedDict
 from glob import glob
 from typing import Union, List#, Dict
@@ -20,6 +21,7 @@
 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
@@ -221,7 +223,8 @@ 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
@@ -247,10 +250,9 @@ 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)
@@ -260,7 +262,7 @@ 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])