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ErikBjareoreHGA
ErikBjare
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oreHGA
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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]>
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‎.github/workflows/docs.yml

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@@ -17,17 +17,18 @@ jobs:
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python-version: 3.8
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- name: Install dependencies
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run: |
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make install-deps-apt
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python -m pip install --upgrade pip wheel
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python -m pip install attrdict
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# Install wxPython wheels since they are distribution-specific and therefore not on PyPI
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# See: https://wxpython.org/pages/downloads/index.html
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pip install -U -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-22.04 wxPython
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make install-deps-wxpython
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- name: Build project
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run: |
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make build
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pip install .
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- name: Build docs
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run: |
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cd doc && make html
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make docs
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- name: Deploy Docs
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uses: peaceiris/actions-gh-pages@v3
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if: github.ref == 'refs/heads/master' # TODO: Deploy seperate develop-version of docs?

‎.github/workflows/test.yml

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@@ -8,7 +8,7 @@ on:
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jobs:
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test:
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name: ${{ matrix.os }}, py-${{ matrix.python_version }}
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name: test (${{ matrix.os }}, py-${{ matrix.python_version }})
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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- name: Install APT dependencies
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if: "startsWith(runner.os, 'Linux')"
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run: |
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# update archive links
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sudo apt-get update
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# xvfb is a dependency to create a virtual display
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# libgtk-3-dev is a requirement for wxPython
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# freeglut3-dev is a requirement for a wxPython dependency
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sudo apt-get -y install xvfb libgtk-3-dev freeglut3-dev
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make install-deps-apt
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- name: Upgrade pip
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run: |
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python -m pip install --upgrade pip wheel
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- name: Install Linux dependencies
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if: "startsWith(runner.os, 'Linux')"
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run: |
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python -m pip install --upgrade pip wheel
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# Install wxPython wheels since they are distribution-specific and therefore not on PyPI
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# See: https://wxpython.org/pages/downloads/index.html
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pip install -U -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-22.04 wxPython
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pip install .
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- name: Install MacOS/Windows dependencies
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make install-deps-wxpython
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip wheel
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pip install .
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pip install -U psychtoolbox # JG_ADD
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# EB: needed?
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make build
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- name: Run eegnb install test
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shell: bash
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run: |
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Xvfb :0 -screen 0 1024x768x24 -ac +extension GLX +render -noreset &> xvfb.log &
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export DISPLAY=:0
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fi
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pytest
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make test
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typecheck:
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name: typecheck (${{ matrix.os }}, py-${{ matrix.python_version }})
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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- name: Install APT dependencies
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if: "startsWith(runner.os, 'Linux')"
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run: |
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# update archive links
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sudo apt-get update
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# xvfb is a dependency to create a virtual display
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# libgtk-3-dev is a requirement for wxPython
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# freeglut3-dev is a requirement for a wxPython dependency
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sudo apt-get -y install xvfb libgtk-3-dev freeglut3-dev
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make install-deps-apt
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- name: Upgrade pip
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run: |
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python -m pip install --upgrade pip wheel
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- name: Install Linux dependencies
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if: "startsWith(runner.os, 'Linux')"
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run: |
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python -m pip install --upgrade pip wheel
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# Install wxPython wheels since they are distribution-specific and therefore not on PyPI
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# See: https://wxpython.org/pages/downloads/index.html
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pip install -U -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-22.04 wxPython
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pip install .
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- name: Install MacOS/Windows dependencies
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make install-deps-wxpython
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip wheel
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pip install .
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make build
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- name: Typecheck
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run: |
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# Exclude visual_cueing due to errors
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python -m mypy --exclude 'examples/visual_cueing'
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make typecheck

‎Makefile

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build:
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pip install .
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test:
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pytest
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typecheck:
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# Exclude visual_cueing due to errors
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python -m mypy --exclude 'examples/visual_cueing'
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docs:
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cd doc && make html
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clean:
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cd doc && make clean
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install-deps-apt:
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sudo apt-get update # update archive links
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# xvfb is a dependency to create a virtual display
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# libgtk-3-dev is a requirement for wxPython
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# freeglut3-dev is a requirement for a wxPython dependency
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# portaudio19-dev *might* be required to import psychopy on Ubuntu
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# pulseaudio *might* be required to actually run the tests (on PsychoPy import)
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# libpulse-dev required to build pocketsphinx (speech recognition dependency of psychopy)
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# libsdl2-dev required by psychopy
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# libnotify4 is so we can have the libnotify.so module used in wxPython working
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sudo apt-get -y install xvfb libgtk-3-dev freeglut3-dev portaudio19-dev libpulse-dev pulseaudio libsdl2-dev libnotify4
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# configure dynamic links
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sudo ldconfig
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UPDATED_LIBPATH=$(sudo find / -name libnotify.so)
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LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$UPDATED_LIBPATH
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install-deps-wxpython:
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# Install wxPython wheels since they are distribution-specific and therefore not on PyPI
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# See: https://wxpython.org/pages/downloads/index.html
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pip install -U -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-22.04 wxPython

‎doc/conf.py

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

‎eegnb/analysis/utils.py

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from copy import deepcopy
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import math
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import logging
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import sys
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from collections import OrderedDict
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from glob import glob
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from typing import Union, List#, Dict
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from mne.channels import make_standard_montage
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from mne.filter import create_filter
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from matplotlib import pyplot as plt
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from scipy import stats
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from scipy.signal import lfilter, lfilter_zi
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from eegnb import _get_recording_dir
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ylim=(-6, 6),
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diff_waveform=(1, 2),
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channel_count=4,
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channel_order=None):
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channel_order=None,
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):
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"""Plot ERP conditions.
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Args:
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epochs (mne.epochs): EEG epochs
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"""
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if channel_order:
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channel_order = np.array(channel_order)
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channel_order = np.array(channel_order)
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else:
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channel_order = np.array(range(channel_count))
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channel_order = np.array(range(channel_count))
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if isinstance(conditions, dict):
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conditions = OrderedDict(conditions)
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X = epochs.get_data() * 1e6
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X = X[:,channel_order]
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X = X[:, channel_order]
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times = epochs.times
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y = pd.Series(epochs.events[:, -1])

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