Initial commit

.github/workflows/lint_and_format.yml

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+name: lint_and_format
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+
+on:
+  push:
+    branches:
+      - '*'
+  pull_request:
+    branches:
+      - '*'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10"]
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+
+    - name: Lint with isort
+      run: |
+        pip install isort
+        isort $(git ls-files '*.py') --verbose
+
+    - name: Format with black
+      run: |
+        pip install black
+        black . --verbose
+
+    - name: Lint the code with pylint
+      run: |
+        pip install pylint
+        pylint --rcfile pylintrc $(git ls-files '*.py')

.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/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Visual Studio Code
+.vscode
+
+# PyCharm
+.idea
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/

LICENSE

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+MIT License
+
+Copyright (c) [2021-2022] [authors of PTE Decode]
+
+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.

README.md

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+[![Homepage][homepage-shield]][homepage-url]
+[![License][license-shield]][license-url]
+[![Contributors][contributors-shield]][contributors-url]
+[![Code Style][codestyle-shield]][codestyle-url]
+
+
+# PTE Decode - Python tools for electrophysiology
+
+PTE Decode is an open-source software package for neural decoding.
+
+It builds upon [PTE](https://github.com/richardkoehler/pte) and aims at decoding intracranial EEG (iEEG) signals such as local field potentials (LFP) electrocorticography (ECoG).
+
+PTE Decode implements sample-wise decoding and lets you define epochs based on specific events to avoid circular training.
+
+## Installing PTE Decode
+
+First, get the current development version of PTE using [git](https://git-scm.com/). Then type the following command into a terminal:
+
+```bash
+git clone https://github.com/richardkoehler/pte-decode
+```
+
+Use the package manager [conda](https://docs.conda.io/projects/conda/en/latest/index.html) to set up a new working environment. To do so, use ``cd`` in your terminal to navigate to the PTE root directory and type:
+
+```bash
+conda env create -f env.yml
+```
+
+This will set up a new conda environment called ``pte-decode``.
+
+To activate the environment then type:
+
+```bash
+conda activate pte-decode
+```
+
+Finally, to install PTE Decode in an editable development version inside your conda environment type the following inside the PTE Decode root directory:
+
+```bash
+conda develop .
+```
+
+## Usage
+
+```python
+import pte_decode
+
+# Examples
+```
+
+## Contributing
+Please feel free to contribute. 
+
+For any minor additions or bugfixes, you may simply create a **pull request**. 
+
+For any major changes, make sure to open an **issue** first. When you then create a pull request, be sure to **link the pull request** to the open issue in order to close the issue automatically after merging.
+
+To contribute, consider installing the full conda development environment to include such tools as black, pylint and isort:
+
+```bash
+conda env create -f env_dev.yml
+conda activate pte-decode-dev
+```
+
+Continuous Integration (CI) including automated testing are set up.
+
+## License
+PTE is licensed under the [MIT license](license-url).
+
+<!-- MARKDOWN LINKS & IMAGES -->
+<!-- https://www.markdownguide.org/basic-syntax/#reference-style-links -->
+[homepage-shield]: https://img.shields.io/static/v1?label=Homepage&message=ICN&logoColor=black&labelColor=grey&logoWidth=20&color=9cf&style=for-the-badge
+[homepage-url]: https://www.icneuromodulation.org/
+[contributors-shield]: https://img.shields.io/github/contributors/richardkoehler/pte.svg?style=for-the-badge
+[contributors-url]: https://github.com/richardkoehler/pte/graphs/contributors
+[license-shield]: https://img.shields.io/static/v1?label=License&message=MIT&logoColor=black&labelColor=grey&logoWidth=20&color=yellow&style=for-the-badge
+[license-url]: https://github.com/richardkoehler/pte/blob/main/LICENSE/
+[codestyle-shield]: https://img.shields.io/static/v1?label=CodeStyle&message=black&logoColor=black&labelColor=grey&logoWidth=20&color=black&style=for-the-badge
+[codestyle-url]: https://github.com/psf/black

env.yml

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+name: pte-decode
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  # basic dependencies
+  - bayesian-optimization
+  - catboost
+  - imbalanced-learn
+  - matplotlib
+  - mne-bids
+  - numba
+  - numpy
+  - pandas
+  - pip
+  - python >= 3.9
+  - scikit-learn
+  - scipy
+  - seaborn
+  - xgboost
+  - pip:
+    - pte-stats
+    - statannotations

env_dev.yml

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+name: pte-decode-dev
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  # basic dependencies
+  - bayesian-optimization
+  - catboost
+  - imbalanced-learn
+  - matplotlib
+  - mne-bids
+  - numba
+  - numpy
+  - pandas
+  - pip
+  - python >= 3.9
+  - scikit-learn
+  - scipy
+  - seaborn
+  - xgboost
+  - pip:
+    - pte-stats
+    - statannotations 
+  # development dependencies
+  - black
+  - isort
+  - pylint
+  - pytest