meeg-utils 0.1.0__tar.gz

meeg_utils-0.1.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main, master, develop]
+  pull_request:
+    branches: [main, master, develop]
+  workflow_dispatch:
+
+env:
+  CACHE_NUMBER: 0  # Increase to reset cache manually
+
+jobs:
+  # Code quality checks
+  lint:
+    name: Lint & Format Check
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+
+      - name: Install dependencies
+        run: |
+          uv sync --all-extras --dev
+
+      - name: Run ruff linter
+        run: |
+          uv run ruff check src/ tests/
+
+
+  # Type checking
+  type-check:
+    name: Type Check
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+
+      - name: Install dependencies
+        run: |
+          uv sync --all-extras --dev
+
+      - name: Run mypy
+        run: |
+          uv run mypy src/
+
+  # Security checks
+  security:
+    name: Security Check
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+
+      - name: Install dependencies
+        run: |
+          uv sync --all-extras --dev
+
+      - name: Run bandit
+        run: |
+          uv run bandit -r src/ -c pyproject.toml
+
+  # Test suite
+  test:
+    name: Test Python ${{ matrix.python-version }} on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+
+      - name: Install dependencies
+        run: |
+          uv sync --all-extras --dev
+
+      - name: Run tests
+        run: |
+          uv run pytest tests/ -v --cov=src/meeg_utils --cov-report=xml --cov-report=term
+
+      - name: Upload coverage to Codecov
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11'
+        uses: codecov/codecov-action@v4
+        with:
+          file: ./coverage.xml
+          flags: unittests
+          name: codecov-umbrella
+          fail_ci_if_error: false
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+  # Documentation build check
+  docs:
+    name: Documentation Build
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+
+      - name: Install dependencies
+        run: |
+          uv sync --all-extras --dev
+
+      - name: Check docstring coverage
+        run: |
+          uv run interrogate src/ --config pyproject.toml
+
+  # All checks passed
+  all-checks:
+    name: All Checks Passed
+    if: always()
+    needs: [lint, type-check, security, test, docs]
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check all job results
+        run: |
+          if [ "${{ needs.lint.result }}" != "success" ] || \
+             [ "${{ needs.type-check.result }}" != "success" ] || \
+             [ "${{ needs.security.result }}" != "success" ] || \
+             [ "${{ needs.test.result }}" != "success" ] || \
+             [ "${{ needs.docs.result }}" != "success" ]; then
+            echo "One or more checks failed"
+            exit 1
+          fi
+          echo "All checks passed successfully!"

meeg_utils-0.1.0/.github/workflows/docs.yml

@@ -0,0 +1,59 @@
+name: Documentation
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+
+      - name: Install dependencies
+        run: |
+          uv sync --all-extras --dev
+
+      - name: Build documentation
+        run: |
+          cd docs
+          uv run make html
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/build/html
+
+  deploy:
+    if: github.event_name == 'push' && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master')
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

meeg_utils-0.1.0/.github/workflows/release.yml

@@ -0,0 +1,95 @@
+name: Release
+
+on:
+  push:
+    tags:
+      - "v*.*.*"
+  workflow_dispatch:
+    inputs:
+      version:
+        description: "Version to release (e.g., 0.1.0)"
+        required: true
+        type: string
+
+permissions:
+  contents: write
+
+jobs:
+  build:
+    name: Build Distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Build package
+        run: |
+          uv build
+
+      - name: Store the distribution packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+  publish-pypi:
+    name: Publish to PyPI
+    if: startsWith(github.ref, 'refs/tags/')
+    needs: [build]
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/meeg-utils
+
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}
+
+  github-release:
+    name: Create GitHub Release
+    needs: [publish-pypi]
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      id-token: write
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Create GitHub Release
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        run: >-
+          gh release create
+          '${{ github.ref_name }}'
+          --repo '${{ github.repository }}'
+          --notes "Release ${{ github.ref_name }}"
+
+      - name: Upload artifact signatures to GitHub Release
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        run: >-
+          gh release upload
+          '${{ github.ref_name }}' dist/**
+          --repo '${{ github.repository }}'

meeg_utils-0.1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# IDEs
+.idea/
+.vscode/
+*.swp
+*.swo
+*~
+.DS_Store
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# ruff
+.ruff_cache/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# Project specific
+.claude
+derivatives/
+*.fif
+*.vhdr
+*.vmrk
+*.edf
+*.bdf
+*.sqd
+*.con
+*.raw
+*.ave
+*.cov
+*.trans
+*.fwd
+*.inv
+data/
+results/
+outputs/
+*.h5
+*.hdf5

meeg_utils-0.1.0/.pre-commit-config.yaml

@@ -0,0 +1,30 @@
+# Pre-commit hooks configuration
+# See https://pre-commit.com for more information
+
+repos:
+  # General file checks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+        args: [--markdown-linebreak-ext=md]
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-toml
+      - id: check-json
+      - id: check-added-large-files
+        args: [--maxkb=1000]
+      - id: check-merge-conflict
+      - id: check-case-conflict
+      - id: mixed-line-ending
+        args: [--fix=lf]
+
+  # Python code formatting with ruff
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.8.4
+    hooks:
+      # Run the linter
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+      # Run the formatter
+      - id: ruff-format

meeg_utils-0.1.0/.python-version

@@ -0,0 +1 @@
+3.11

meeg_utils-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 meeg-utils contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

meeg_utils-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: meeg-utils
+Version: 0.1.0
+Summary: A Python-based MEEG processing toolkit primarily based on MNE-Python.
+Author-email: Your Name <your.email@example.com>
+License: MIT
+License-File: LICENSE
+Keywords: EEG,MEEG,MEG,MNE-Python,neuroscience,preprocessing
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.11
+Requires-Dist: loguru>=0.7.3
+Requires-Dist: meegkit>=0.1.9
+Requires-Dist: mne-bids>=0.18.0
+Requires-Dist: mne-icalabel>=0.8.1
+Requires-Dist: mne>=1.11.0
+Requires-Dist: onnxruntime>=1.24.2
+Requires-Dist: pyprep>=0.6.0
+Description-Content-Type: text/markdown
+
+# meeg-utils
+
+[![CI](https://github.com/colehank/meeg-utils/workflows/CI/badge.svg)](https://github.com/colehank/meeg-utils/actions)
+[![Documentation](https://github.com/colehank/meeg-utils/workflows/Documentation/badge.svg)](https://colehank.github.io/meeg-utils/)
+[![codecov](https://codecov.io/gh/colehank/meeg-utils/branch/main/graph/badge.svg)](https://codecov.io/gh/colehank/meeg-utils)
+[![PyPI version](https://badge.fury.io/py/meeg-utils.svg)](https://badge.fury.io/py/meeg-utils)
+[![Python 3.11+](https://img.shields.io/badge/python-3.11+-blue.svg)](https://www.python.org/downloads/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Code style: ruff](https://img.shields.io/badge/code%20style-ruff-000000.svg)](https://github.com/astral-sh/ruff)
+
+> A Python-based MEG/EEG processing toolkit built on MNE-Python, providing a high-level, user-friendly API for processing MEG/EEG data.
+
+## Features
+### Preprocessing
+*Epoching In Progress*
+- High-level `PreprocessingPipeline` class for streamlined MEG/EEG preprocessing.
+![Pipeline Diagram](resources/preprocessing_pipeline.png)
+
+### Feature Extraction
+*In Progress*
+- Common MEG/EEG features (e.g., power spectral density, connectivity metrics).
+
+## 📦 Installation
+
+```bash
+pip install meeg-utils
+```
+
+## 🚀 Quick Start
+
+```python
+from meeg_utils.preprocessing import PreprocessingPipeline
+from mne_bids import BIDSPath
+
+# Create pipeline
+pipeline = PreprocessingPipeline(
+    input_path=BIDSPath(
+        subject="01", session="01", task="rest",
+        datatype="eeg", root="/data/bids"
+    ),
+    output_dir="/data/output"
+)
+
+# Run preprocessing
+result = pipeline.run(
+    filter_params={"highpass": 0.1, "lowpass": 100.0, "sfreq": 250.0},
+    detect_bad_channels=True,
+    remove_line_noise=True,
+    apply_ica=True
+)
+
+# Save results
+pipeline.save()
+```
+
+**Batch processing:**
+
+```python
+from meeg_utils.preprocessing import BatchPreprocessingPipeline
+
+# Process multiple subjects in parallel
+batch = BatchPreprocessingPipeline(
+    input_paths=bids_paths,  # List of BIDSPaths
+    output_dir="/data/output",
+    n_jobs=4  # Use 4 parallel workers
+)
+
+batch.run(detect_bad_channels=True, remove_line_noise=True, apply_ica=True)
+```
+
+## 📚 Documentation
+
+**Full documentation:** https://colehank.github.io/meeg-utils/
+
+- [Installation Guide](https://colehank.github.io/meeg-utils/user_guide/installation.html)
+- [Quick Start](https://colehank.github.io/meeg-utils/user_guide/quickstart.html)
+- [Preprocessing Guide](https://colehank.github.io/meeg-utils/user_guide/preprocessing.html)
+- [Batch Processing](https://colehank.github.io/meeg-utils/user_guide/batch_processing.html)
+- [API Reference](https://colehank.github.io/meeg-utils/api/preprocessing.html)
+- [Contributing Guide](https://colehank.github.io/meeg-utils/developer/contributing.html)
+
+## 🛠️ Development
+
+```bash
+# Clone and setup
+git clone https://github.com/colehank/meeg-utils.git
+cd meeg-utils
+uv sync --dev
+uv run pre-commit install
+
+# Run tests
+uv run pytest
+
+# Build docs
+cd docs && uv run make html
+```
+
+See the [Contributing Guide](https://colehank.github.io/meeg-utils/developer/contributing.html) for detailed development instructions.
+
+## 📄 License
+
+MIT License - see [LICENSE](LICENSE) file for details.
+
+## 🙏 Acknowledgments
+
+Built on the excellent [MNE-Python](https://mne.tools/) ecosystem.
+
+## 📞 Support
+
+- 📖 [Documentation](https://colehank.github.io/meeg-utils/)
+- 🐛 [Issue Tracker](https://github.com/colehank/meeg-utils/issues)
+- 💬 [Discussions](https://github.com/colehank/meeg-utils/discussions)