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Complete Phase 5 & 6: Docs Fixes, CI/CD, and Examples Restructure
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‎.github/workflows/publish.yml‎

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name: Upload Python Package
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on:
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release:
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types: [published]
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permissions:
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contents: read
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jobs:
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deploy:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: "3.10"
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -U uv
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- name: Build package
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run: uv build
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- name: Publish to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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user: __token__
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password: ${{ secrets.PYPI_API_TOKEN }}

‎.github/workflows/test.yml‎

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name: Tests
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on:
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push:
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branches: [ main, dev ]
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pull_request:
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branches: [ main, dev ]
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jobs:
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test:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.10"]
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install .[ml,gui]
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pip install pytest pytest-cov
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- name: Run tests
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run: |
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pytest tests/

‎README.md‎

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# Python Open-Ephys
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# Python OEphys
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A comprehensive Python toolkit for working with Open Ephys devices, featuring signal processing, machine learning, and real-time visualization tools. This package seamlessly integrates with the Open Ephys GUI via ZMQ.
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## Examples
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Check the `examples/` directory for complete scripts:
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- `examples/ml/train_cnn_lstm.py`: Train a gesture classifier.
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- `examples/integration/sync_multimodal_data.py`: Align EMG with 3D hand landmarks.
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- `examples/processing/run_channel_qc.py`: Run quality control checks.
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- `examples/gesture_classifier/2v2_train_model.py`: Train a gesture classifier.
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- `examples/synchronization/sync_multimodal_data.py`: Align EMG with 3D hand landmarks.
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- `examples/analysis/run_channel_qc.py`: Run quality control checks.
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- `examples/interface/zmq_client.py`: Real-time ZMQ client example.
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- `examples/read_files/example_load_oebin_file.py`: Load Open Ephys data.
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## License
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MIT License. See [LICENSE](LICENSE) for details.

‎docs/source/conf.py‎

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# Configuration file for the Sphinx documentation builder.
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import os
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import sys
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sys.path.insert(0, os.path.abspath('../../src'))
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project = 'python-oephys'
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copyright = '2025, Jonathan Shulgach'
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author = 'Jonathan Shulgach'
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release = '0.0.1'
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extensions = [
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'sphinx.ext.autodoc',
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'sphinx.ext.napoleon',
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'sphinx.ext.viewcode',
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'sphinx_autodoc_typehints',
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'myst_parser',
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]
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autodoc_mock_imports = [
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'open_ephys',
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'pylsl',
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'PyQt5',
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'pyqtgraph',
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'zmq'
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]
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templates_path = ['_templates']
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exclude_patterns = []
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html_theme = 'alabaster'
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html_static_path = ['_static']
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autodoc_member_order = 'bysource'

‎docs/source/index.rst‎

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Welcome to python-oephys's documentation!
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=========================================
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**python-oephys** is a comprehensive Python toolkit for working with Open Ephys devices, featuring signal processing, machine learning, and real-time visualization tools.
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.. toctree::
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:maxdepth: 2
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:caption: Contents:
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modules
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Indices and tables
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==================
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* :ref:`genindex`
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* :ref:`modindex`
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* :ref:`search`

‎docs/source/modules.rst‎

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pyoephys
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========
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.. toctree::
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:maxdepth: 4
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pyoephys

‎docs/source/pyoephys.applications.rst‎

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pyoephys.applications package
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=============================
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.. automodule:: pyoephys.applications
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:members:
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:undoc-members:
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:show-inheritance:

‎docs/source/pyoephys.interface.rst‎

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pyoephys.interface package
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==========================
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.. automodule:: pyoephys.interface
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:members:
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:undoc-members:
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:show-inheritance:

‎docs/source/pyoephys.io.rst‎

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pyoephys.io package
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===================
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.. automodule:: pyoephys.io
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:members:
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:undoc-members:
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:show-inheritance:

‎docs/source/pyoephys.ml.rst‎

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pyoephys.ml package
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===================
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.. automodule:: pyoephys.ml
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:members:
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:undoc-members:
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:show-inheritance:

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